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Results for “insertion, inversion”

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PubMed2003

Local side effects observed among long-term users of norplant contraceptive implants.

The prevalence of local signs and symptoms related to the site of insertion of implants, and the association of these signs and symptoms with time of use, skin color and body mass index (BMI) was evaluated among users of the Norplant implant system. Three hundred and three Norplant users attending at the reproductive health clinic of PROFAMILIA in Santo Domingo, Dominican Republic, were asked if they had ever had any discomfort at the site/arm of implant insertion and the implant insertion area was examined and hyperpigmentation and hollowing of the surface was recorded. Half of the subjects reported either pain or paresthesia or both, in almost equal numbers, some time since insertion. Hyperpigmentation was observed in 35.6% and hollowing in 22.4% of the subjects. Report of pain and paresthesia was inversely associated to time of use and to BMI. Hyperpigmentation was directly associated to time of use and darker skin, and hollowing of the arm surface in the implants area with time of use and BMI. Local signs and symptoms were more frequent than previously reported, although they were of mild nature and appeared not to worry most of the users.

Adult↗

PubMed1999

A Novel Dimeric Ni-Substituted beta-Keggin Silicotungstate: Structure and Magnetic Properties of K(12)[{beta-SiNi(2)W(10)O(36)(OH)(2)(H(2)O)}(2)].20H(2)O.

The novel dimeric polyoxometalate [{beta-SiNi(2)W(10)O(36)(OH)(2)(H(2)O)}(2)](12)(-) (1) has been synthesized and characterized by IR spectroscopy, polarography, elemental analysis, thermogravimetric analysis, and magnetic measurements. An X-ray single-crystal analysis was carried out on K(12)[{beta-SiNi(2)W(10)O(36)(OH)(2)(H(2)O)}(2)].20H(2)O, which crystallizes in the monoclinic system, space group P2(1)/n, with a = 13.701(4) Å, b = 24.448(11) Å, c = 13.995(5) Å, beta = 99.62(3) degrees, and Z = 4. The anion consists of two [beta-SiNi(2)W(10)O(36)(OH)(2)(H(2)O)] Keggin moieties linked via two OH bridging groups, leading to a planar Ni(2)(OH)(2) unit. The two half-units are related by an inversion center and each contain one Ni atom in the rotated triad. The formation of the new anion involves insertion, isomerization, and dimerization. Magnetic measurements show that the central Ni(4) unit exhibits ferromagnetic (J' = 4.14 cm(-)(1)) as well as weak antiferromagnetic (J = -0.65 cm(-)(1)) Ni-Ni exchange interactions.

Journal Article↗

PubMed2004

Novel long-circulating lipid nanocapsules.

PURPOSE: To develop and evaluate novel long-circulating lipid nanocapsules (LN) designed for tumor delivery of lipophilic drugs. METHODS: Nanocapsules were produced by a solvent-free phase inversion process and were coated with polyethylene glycoldistearoylphosphatidylethanolamine conjugate (DSPE-PEG) during preparation or by a post-insertion step. In vivo studies were conducted in rats to assess LN pharmacokinetics and biodistribution. RESULTS: Post-insertion of DSPE-PEG appeared to be a convenient and effective method of obtaining LN of controlled sizes with high PEG density at their surface. After intravenous injection to rats, PEGylated lipid nanocapsules obtained by the post-insertion method exhibited long-circulating properties. Up to 50% of the injected dose was still present in the blood 8 h after administration for LN containing 6 mol% PEG 5000 or 10 mol% PEG 2000. This represented an area under the blood concentration-time curve of almost 70% that of liposomes used in the Doxil formulation. CONCLUSION: With a simple solvent free-process, it was possible to produce long-circulating LN of controlled sizes. Such LN could prove useful for the passive delivery of lipophilic anticancer drugs to solid tumors.

Algorithms↗

PubMed1976

Characterization of 2-mum DNA of Saccharomyces cerevisiae by restriction fragment analysis and integration in an Escherichia coli plasmid.

Electrophoretic analysis of EcoRI and HindIII restriction fragments of 2-mum supercoiled DNA of Saccharomyces cerevisiae indicated that this class of DNA is heterogeneous and probably consists of two types of molecules. Integration of the 2-mum yeast DNA in E. coli plasmid pCR1 directly showed that existence of two types of molecules as each of these could be individually inserted into separate bacterial plasmids. The difference between the two types of 2-mum circles is due to an inversion of about 1.6 X 10(6) daltons. The inversion is flanked by a reversed duplicated sequence of 0.45 X 10(6) daltons. Possible implications of this structure are dicussed.

Chromosome Mapping↗

PubMed2004

Effective reduction of critical current for current-induced magnetization switching by a Ru layer insertion in an exchange-biased spin valve.

Recently, it has been predicted that a spin-polarized electrical current perpendicular to plane directly flowing through a magnetic element can induce magnetization switching through spin-momentum transfer. In this Letter, the first observation of current-induced magnetization switching (CIMS) in exchange-biased spin valves (ESPVs) at room temperature is reported. The ESPVs show the CIMS behavior under a sweeping dc current with a very high critical current density. It is demonstrated that a thin ruthenium (Ru) layer inserted between a free layer and a top electrode effectively reduces the critical current densities for the CIMS. An "inverse" CIMS behavior is also observed when the thickness of the free layer increases.

Journal Article↗

PubMed1990

Recombination resulting in unusual features in the polyomavirus genome isolated from a murine tumor cell line.

Polyomavirus-induced tumor formation in the adult natural mouse host has been investigated. Tumors were produced in nude mice with the transformation-defective mutant strain NG18 after a long latency period by apparent activation of a cryptic endogenous transforming viral function. A tumor cell line, designated ScB, was established and characterized. Cells from this morphologically distinct line were unusual in that they grew in soft agar but did not form foci. They were highly tumorigenic. They had a 3.1-kilobase major viral transcript that hybridized to probes derived from regions encoding both the T antigens and the structural proteins. ScB cells expressed polyomavirus small T antigen, a slightly altered middle T antigen, and a truncated large T antigen but no capsid proteins. Middle T antigen preserved its interactions with host proteins of 60 and 37 kilodaltons and with c-src. Analysis of cDNA and genomic clones indicated that the stable viral insert in the ScB genome contained multiple copies of the viral B-enhancer. The genome contained two intragenic inversions which created novel early- to late-strand switches. A simple model for the generation of one inversion is proposed that involves the juxtaposition of two stem-loop structures at an illegitimate recombination site; the location of the inverted segment within the integrated sequence permits use of the viral late polyadenylation signal in early-region transcripts, as confirmed by DNA sequence. A repetitive sequence may facilitate recombination at the other inversion site. Both the biological consequences of the observed rearrangements and the structure of the integrated viral DNA suggest that the recombination events are nonrandom.

Animals↗

PubMed2004

A novel cis-acting element facilitates minus-strand DNA synthesis during reverse transcription of the hepatitis B virus genome.

Hepadnaviruses replicate through reverse transcription of an RNA pregenome, resulting in a relaxed circular DNA genome. The first 3 or 4 nucleotides (nt) of minus-strand DNA are synthesized by the use of a bulge in a stem-loop structure near the 5' end of the pregenome as a template. This primer is then transferred to a complementary UUCA motif, termed an acceptor, within DR1* near the 3' end of the viral pregenome via 4-nt homology, and it resumes minus-strand DNA synthesis: this process is termed minus-strand transfer or primer translocation. Aside from the sequence identity of the donor and acceptor, little is known about the sequence elements contributing to minus-strand transfer. Here we report a novel cis-acting element, termed the beta5 region (28 nt in length), located 20 nt upstream of DR1*, that facilitates minus-strand DNA synthesis. The deletion or inversion of the sequence including the beta5 region diminished minus-strand DNA synthesis initiated at DR1*. Furthermore, the insertion of the beta5 region into its own position in a mutant in which the sequences including the beta5 region were replaced restored minus-strand DNA synthesis at DR1*. We speculate that the beta5 region facilitates minus-strand transfer, possibly by bringing the acceptor site in proximity to the donor site via base pairing or by interacting with protein factors involved in this process.

Cell Line, Tumor↗

PubMed2006

[Progress of the PCR amplification techniques for chromosome walking].

Various PCR-based methods are available for chromosome walking from a known sequence to an unknown region. It is promising in genome-related research for the following experiments: promoter cloning, obtaining non-conservative parts of genes in new species, identification of T-DNA or transposon insertion sites and filling in gaps or unknown chromosome regions in genome sequencing. These methods consisted of three types: inverse PCR, ligation-mediated PCR and specific primer PCR. In this review, we illustrated and compared the current techniques.

Animals↗

PubMed1990

Growth depression of Serratia marcescens by plasmids that belong to incompatibility group P.

The IncP plasmids R702, RP4 and derivative plasmids including RP4::Mu cts were studied in two pigmented strains of Serratia marcescens. Maintenance of these plasmids resulted in reduced pigmentation and the growth rate of colonies was slower than the plasmid-free parent organisms. DNA inserts and deletions in RP4 altered both the pigmentation phenotype and growth rate of S. marcescens transconjugants and was inversely related to the change in molecular weight. The unrelated plasmids R446b and R46, although of comparable size to RP4, produced neither effect and Rts1, more than three times larger than RP4, produced no visible change in pigmentation phenotype and only a minimal decrease in growth rate. Integration of RP4::Mu cts into the Serratia genome restored pigmentation and growth rate to the same level as the plasmid-free parent. Partial induction at 43 degrees C restored the plasmid to a cytoplasmic state in a proportion of surviving colonies which were typically pale and slow growing.

Conjugation, Genetic↗

PubMed2006

Structural divergence between the human and chimpanzee genomes.

The structural microheterogeneity evident between the human and chimpanzee genomes is quite considerable and includes inversions and duplications as well as deletions, ranging in size from a few base-pairs up to several megabases (Mb). Insertions and deletions have together given rise to at least 150 Mb of genomic DNA sequence that is either present or absent in humans as compared to chimpanzees. Such regions often contain paralogous sequences and members of multigene families thereby ensuring that the human and chimpanzee genomes differ by a significant fraction of their gene content. There is as yet no evidence to suggest that the large chromosomal rearrangements which serve to distinguish the human and chimpanzee karyotypes have influenced either speciation or the evolution of lineage-specific traits. However, the myriad submicroscopic rearrangements in both genomes, particularly those involving copy number variation, are unlikely to represent exclusively neutral changes and hence promise to facilitate the identification of genes that have been important for human-specific evolution.

Animals↗

PubMed1993

Transposon-induced inversion in Antirrhinum modifies nivea gene expression to give a novel flower color pattern under the control of cycloidearadialis.

The nivea (niv) gene of Antirrhinum majus encodes chalcone synthase, an enzyme involved in synthesis of anthocyanin pigments. The nivrec:98 allele contains a single copy of the transposon Tam3 inserted at the niv locus. A large chromosomal rearrangement derived from this mutant has been shown to be flanked by two copies of Tam3. In this study, we compared sequences involved in this rearrangement with their progenitor sequences and concluded that the rearrangement is an inversion resulting from an aberrant transposition occurring shortly after replication of Tam3 that left both copies of Tam3 active after the rearrangement. Excision of Tam3 from its position adjacent to the niv coding region resulted in a novel distribution of anthocyanin pigment in the flower tube, caused by the interaction of the new sequences with the remnant of the niv promoter. The new sequences upstream of niv serve both to enhance niv transcription and to redirect the pattern of gene expression, placing niv under the control of the gene cycloidearadialis, which determines the morphogenetic polarity of the flower.

Alleles↗

PubMed2003

Rubisco activase is required for optimal photosynthesis in the green alga Chlamydomonas reinhardtii in a low-CO(2) atmosphere.

This report describes a Chlamydomonas reinhardtii mutant that lacks Rubisco activase (Rca). Using the BleR (bleomycin resistance) gene as a positive selectable marker for nuclear transformation, an insertional mutagenesis screen was performed to select for cells that required a high-CO2 atmosphere for optimal growth. The DNA flanking the BleR insert of one of the high-CO2-requiring strains was cloned using thermal asymmetric interlaced-polymerase chain reaction and inverse polymerase chain reaction and sequenced. The flanking sequence matched the C. reinhardtii Rca cDNA sequence previously deposited in the National Center for Biotechnology Information database. The loss of a functional Rca in the strain was confirmed by the absence of Rca mRNA and protein. The open reading frame for Rca was cloned and expressed in pSL18, a C. reinhardtii expression vector conferring paromomycin resistance. This construct partially complemented the mutant phenotype, supporting the hypothesis that the loss of Rca was the reason the mutant grew poorly in a low-CO2 atmosphere. Sequencing of the C. reinhardtii Rca gene revealed that it contains 10 exons ranging in size from 18 to 470 bp. Low-CO2-grown rca1 cultures had a growth rate and maximum rate of photosynthesis 60% of wild-type cells. Results obtained from experiments on a cia5 rca1 double mutant also suggest that the CO2-concentrating mechanism partially compensates for the absence of an active Rca in the green alga C. reinhardtii.

Animals↗

PubMed2002

A 10-Mb paracentric inversion of chromosome arm 2p inactivates MSH2 and is responsible for hereditary nonpolyposis colorectal cancer in a North-American kindred.

Genomic deletions of the MSH2 gene are a frequent cause of hereditary nonpolyposis colorectal cancer (HNPCC), a common hereditary predisposition to the development of tumors in several organs including the gastrointestinal and urinary tracts and endometrium. The mutation spectrum at the MSH2 gene is extremely heterogeneous because it includes nonsense and missense point mutations, small insertions and deletions leading to frameshifts, and larger genomic deletions, the latter representing approximately 25% of the total mutation burden. Here, we report the identification and molecular characterization of the first paracentric inversion of the MSH2 locus known to cause HNPCC. Southern blot analysis and inverse PCR showed that the centromeric and telomeric breakpoints of the paracentric inversion map within intron 7 and to a contig 10 Mb 3' of MSH2, respectively. Pathogenicity of the paracentric inversion was demonstrated by conversion analysis. The patient's lymphocytes were employed to generate somatic cell hybrids to analyze the expression of the inverted MSH2 allele in an Msh2-deficient rodent cellular background. The inversion was shown to abolish MSH2 expression by both northern and western analysis. This study confirms that Southern blot analysis still represents a useful and informative tool to screen for and identify complex genomic rearrangements in HNPCC. Moreover, monoallelic expression analysis represents an attractive approach to demonstrate pathogenicity of unusual mutations in autosomal dominant hereditary conditions.

Adenosine Triphosphatases↗

PubMed1978

Instability of plasmid DNA sequences: macro and micro evolution of the antibiotic resistance plasmid R6-5.

Detailed examination of the structure of cloned DNA fragments of the R6-5 antibiotic resistance plasmid has revealed a substantial degree of polynucleotide sequence heterogeneity and indicates that sequence rearrangements in plasmids and possible other replicons occur more frequently than has hitherto been appreciated. The sequences changes in cloned R6-5 fragments were shown in some instances to have occurred prior to cloning, i.e. existing in the original population of R6-5 molecules that was obtained from a single bacterial clone and by several different criteria judged to be homogeneous, and in others to have occurred either during the cloning procedure or during subsequent propagation of hybrid molecules. The molecular changes that are described involved insertion/deletion of the previously characterized IS2 insertion element, formation of a new inverted repeat structure probably by duplication of a preexisting R6-5 DNA sequence, sequence inversion, and loss and gain of restriction endonuclease cleavage sites.

Anti-Bacterial Agents↗

PubMed1975

Structural X-chromosome abnormality in a female with gonadal dysgenesis.

A patient with gonadal dysgenesis and 46 chromosomes is described. In the inactive X chromosome there seems to be a deletion of the short arms and an insertion of heterochromatin in the long arms. The most probable mechanism to explain this structurally abnormal X is a pericentric inversion, with breakage and union having occurred in the centromeric heterochromatin of the short arm and in band q23 of the long arm. An amplification of the centromeric heterochromatin left in the short arm is also supposed.

Adult↗

PubMed1996

Failure of embryonic hematopoiesis and lethal hemorrhages in mouse embryos heterozygous for a knocked-in leukemia gene CBFB-MYH11.

The fusion oncogene CBFB-MYH11 is generated by a chromosome 16 inversion in human acute myeloid leukemia subtype M4Eo. Mouse embryonic stem (ES) cells heterozygous for this oncogene were generated by inserting part of the human MYH11 cDNA into the mouse Cbfb gene through homologous recombination (knock-in). Chimeric mice were leukemia free, but the ES cells with the knocked-in Cbfb-MYH11 gene did not contribute to their hematopoietic tissues. Mouse embryos heterozygous for Cbfb-MYH11 lacked definitive hematopoiesis and developed multiple fatal hemorrhages around embryonic day 12.5. This phenotype is very similar to that resulting from homozygous deletions of either Cbfb or Cbfa2 (AML1), consistent with a dominant negative function of the Cbfb-MYH11 fusion oncogene. An impairment of primitive hematopoiesis was also observed, however, suggesting a possible additional function of Cbfb-MYH11.

Amino Acid Sequence↗

PubMed1992

Analysis of the Fis-dependent and Fis-independent transcription activation mechanisms of the Escherichia coli ribosomal RNA P1 promoter.

The role of the curved DNA sequence upstream to the Escherichia coli ribosomal RNA P1 promoter in transcription activation was studied. This sequence region had been shown to activate transcription from P1 in vivo and in vitro and to harbor binding sites for the trans-activating protein Fis. We have constructed a series of linker scanning mutants spanning the region -104 to -47, relative to the transcription start site. DNA fragments carrying the mutations show altered gel electrophoretic mobilities, consistent with reduced DNA bending angles compared to the wild-type sequence. Using gel retardation assays, qualitative as well as quantitative differences in the binding of the trans-activating protein Fis to the mutant DNA fragments could be observed. The effects of the mutations on rrnB P1 promoter activation were studied in vivo in fis+ and fis- backgrounds. A reduction in the promoter strength for some of the linker mutants correlates with altered Fis binding to two of the known Fis binding sites. Shifting the Fis binding region by half a helical turn, relative to the promoter core sequence, abolishes Fis-mediated activation almost totally, whereas activation is partly restored by a shift of a complete helical turn. For one mutant, which does not show alterations in Fis binding, a decrease in the promoter strength was observed in a fis- strain. From the results, we conclude that two upstream activating mechanisms, one Fis-dependent and one Fis-independent, influence the rrnB P1 promoter strength. Sequence determinants for the Fis-independent mechanism are closer to the promoter core region than the Fis binding sites. In addition, the study demonstrates that both the helical geometry and the absolute distance of the UAS region relative to the promoter are crucial for transcription activation.

Base Sequence↗

PubMed2001

Characterisation of IS153, an IS3-family insertion sequence isolated from Lactobacillus sanfranciscensis and its use for strain differentiation.

An insertion sequence has been identified in the genome of Lactobacillus sanfranciscensis DSM 20451T as segment of 1351 nucleotides containing 37-bp imperfect terminal inverted repeats. The sequence of this element encodes two out of phase, overlapping open reading frames, orfA and orfB, from which three putative proteins are produced. OrfAB is a transframe protein produced by -1 translational frame shifting between orf A and orf B that is presumed to be the transposase. The large orfAB of this element encodes a 342 amino acid protein that displays similarities with transposases encoded by bacterial insertion sequences belonging to the IS3 family. In L. sanfranciscensis type strain DSM 20451T multiple truncated IS elements were identified. Inverse PCR was used to analyze target sites of four of these elements, but except of their highly AT rich character not any sequence specificity was identified so far. Moreover, no flanking direct repeats were identified. Multiple copies of IS153 were detected by hybridization in other strains of L. sanfranciscensis. Resulting hybridization patterns were shown to differentiate between organisms at strain level rather than a probe targeted against the 16S rDNA. With a PCR based approach IS153 or highly similar sequences were detected in L. acidophilus, L. casei, L. malefermentans, L. plantarum, L. hilgardii, L. collinoides L. farciminis L. sakei and L. salivarius, L. reuteri as well as in Enterococcus faecium, Pediococcus acidilactici and P. pentosaceus.

Amino Acid Sequence↗