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PubMed1997

In vitro marginal leakage around Class II resin composite restorations with glass-ceramic inserts.

The aim of the study was to evaluate in vitro the marginal seal in Class II resin composite restorations reinforced with glass-ceramic inserts. Forty Class II cavities, with the gingival margins located at the cementoenamel junction, were restored with Palfique Estelite light-cured resin composite and one of two different bonding agents, All Bond 2 and Tokuso Light Bond, with or without the inclusion of glass-ceramic inserts. The extent of dye penetration along the tooth-restoration interface was measured under an optical microscope. The marginal seal of composite restorations placed with All Bond 2 was significantly better than that of restorations placed with Tokuso Light Bond. There was significantly less microleakage in All Bond 2 restorations without glass-ceramic inserts than in All Bond 2 restorations containing glass-ceramic inserts. No significant difference in marginal seal was demonstrated between Tokuso Light Bond restorations with glass-ceramic inserts and those without inserts.

Bicuspid↗
PubMed1997

X-linked retinitis pigmentosa associated with a 2-base pair insertion in codon 99 of the RP3 gene RPGR.

BACKGROUND: Mutations in the RPGR gene at the RP3 locus have been found to cause x-linked retinitis pigmentosa in some families. OBJECTIVES: To identify a previously undescribed 2-base pair insertion in codon 99 of the RPGR gene and to describe the phenotype in a well-characterized family with X-linked retinitis pigmentosa. DESIGN: Case reports with clinical features, fluorescein angiography, kinetic perimetry, electrophysiological studies, and molecular genetics. SETTING: University medical centers. PATIENTS: Eight members of the family were screened for the codon 99 insertion in the RPGR gene. RESULTS: Three affected males were found to be hemizygous for the 2-base pair insertion; 2 carriers were heterozygous. This insertion creates a frameshift that would be expected to cause a premature arrest of translation after only 132 amino acids (683 amino acids less than the normal protein). The affected males had typical retinitis pigmentosa with visual field contraction and abnormal findings on electroretinograms with little to no rod activity, profoundly subnormal residual cone responses to single flash and 30-Hz flicker stimuli, and prolonged b-wave implicit times. The electroretinogram of a 49-year-old carrier showed amplitudes that were roughly half of normal. Carrier women did not show a tapetallike fundus reflex but showed asymmetrical patchy pigmentary disturbances consistent with lyonization. CONCLUSION: A frameshifting 2-base pair insertion at codon 99 of the RPGR gene produced typical retinitis pigmentosa and carrier findings (but no tapetallike reflex) in this family.

Adolescent↗
PubMed2006

dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans.

Retrotransposons constitute over 40% of the human genome and play important roles in the evolution of the genome. Since certain types of retrotransposons, particularly members of the Alu, L1, and SVA families, are still active, their recent and ongoing propagation generates a unique and important class of human genomic diversity/polymorphism (for the presence and absence of an insertion) with some elements known to cause genetic diseases. So far, over 2,300, 500, and 80 Alu, L1, and SVA insertions, respectively, have been reported to be polymorphic and many more are yet to be discovered. We present here the Database of Retrotransposon Insertion Polymorphisms (dbRIP; http://falcon.roswellpark.org:9090), a highly integrated and interactive database of human retrotransposon insertion polymorphisms (RIPs). dbRIP currently contains a nonredundant list of 1,625, 407, and 63 polymorphic Alu, L1, and SVA elements, respectively, or a total of 2,095 RIPs. In dbRIP, we deploy the utilities and annotated data of the genome browser developed at the University of California at Santa Cruz (UCSC) for user-friendly queries and integrative browsing of RIPs along with all other genome annotation information. Users can query the database by a variety of means and have access to the detailed information related to a RIP, including detailed insertion sequences and genotype data. dbRIP represents the first database providing comprehensive, integrative, and interactive compilation of RIP data, and it will be a useful resource for researchers working in the area of human genetics.

Databases, Genetic↗
PubMed2003

Screening and characterization of transposon-insertion mutants in a pseudohyphal strain of Saccharomyces cerevisiae.

Strains of Saccharomyces cerevisiae with sigma1278b background are widely used for elucidation of pseudohyphal differentiation and signal transduction. However, information and resources on the strains are limited compared to the S288C strains. To facilitate functional analysis of strains with sigma1278b background, mutant strains were generated by using a mini-transposon3-3 x HA/LacZ (mTn3)-mutagenized library. Mutants with mTn3 insertions were screened for expression of beta-galactosidase activity under nitrogen starvation and the insertion sites were identified. One hundred and five heterozygous diploid strains were selected and subjected to tetrad analysis. Insertion of mTn3 in 11 genes was lethal in the strain, including three genes, HAC1, TPS1 and UME6, which are non-essential genes according to the Saccharomyces Genome Database. Viable haploid strains with mTn3 insertions were examined for invasive growth, which is a differentiation process in haploid strains including agar penetration on rich medium, and cell morphology during invasive growth. We also examined homozygous diploid strains with mTn3-insertions for filamentous growth and sporulation.

DNA Transposable Elements↗
PubMed1994

Linker insertion mutagenesis of Drosophila topoisomerase II. Probing the structure of eukaryotic topoisomerase II.

The sequences of all type II DNA topoisomerases, and possibly some of their key structural features, are conserved. The N-terminal and middle regions of the eukaryotic DNA topoisomerase II are homologous to the bacterial gyrase subunits B and A, respectively, and the hydrophilic C-terminal region is more divergent among these enzymes. To gain further insights into the structure of eukaryotic topoisomerase II, we constructed 23 linker insertion mutants of Drosophila DNA topoisomerase II. These mutant proteins were expressed in a heterologous yeast system, in which we have previously demonstrated that Drosophila DNA topoisomerase II could be functionally expressed and complement yeast top2 mutations. The linker insertion mutants were characterized genetically by testing for complementation of yeast top2ts mutation at the non-permissive temperature and complementation of yeast top2 null mutation using a color sector assay. We also partially purified the mutant proteins and examined their enzymatic activity by unknotting the P4 knotted DNA. There appears to be a good correlation between the in vivo and in vitro activities. There are nine fully active, six partially active, and eight negative linker insertion mutants. All five linker insertion mutants in the C-terminal region are active and two linker insertion mutants located in the junction of the two regions homologous to gyrB/gyrA subunits are also active. In addition, we also mapped the trypsin-sensitive sites in Drosophila DNA topoisomerase II. The C-terminal region is extremely sensitive to trypsin digestion. Another major trypsin-sensitive site is located between Lys406 and Thr407, which is near the protease sites also observed in the bacterial gyrB subunit and yeast topoisomerase II. We discuss the possible structural and functional implications of these results.

Amino Acid Sequence↗
PubMed2001

Structural rearrangements and insertions of dispersed elements in pericentromeric alpha satellites occur preferably at kinkable DNA sites.

Centromeric region of human chromosome 21 comprises two long alphoid DNA arrays: the well homogenized and CENP-B box-rich alpha21-I and the alpha21-II, containing a set of less homogenized and CENP-B box-poor subfamilies located closer to the short arm of the chromosome. Continuous alphoid fragment of 100 monomers bordering the non-satellite sequences in human chromosome 21 was mapped to the pericentromeric short arm region by fluorescence in situ hybridization (alpha21-II locus). The alphoid sequence contained several rearrangements including five large deletions within monomers and insertions of three truncated L1 elements. No binding sites for centromeric protein CENP-B were found. We analyzed sequences with alphoid/non-alphoid junctions selectively screened from current databases and revealed various rearrangements disrupting the regular tandem alphoid structure, namely, deletions, duplications, inversions, expansions of short oligonucleotide motifs and insertions of different dispersed elements. The detailed analysis of more than 1100 alphoid monomers from junction regions showed that the vast majority of structural alterations and joinings with non-alphoid DNAs occur in alpha satellite families lacking CENP-B boxes. Most analyzed events were found in sequences located toward the edges of the centromeric alphoid arrays. Different dispersed elements were inserted into alphoid DNA at kinkable dinucleotides (TG, CA or TA) situated between pyrimidine/purine tracks. DNA rearrangements resulting from different processes such as recombination and replication occur at kinkable DNA sites alike insertions but irrespectively of the occurrence of pyrimidine/purine tracks. It seems that kinkable dinucleotides TG, CA and TA are part of recognition signals for many proteins involved in recombination, replication, and insertional events. Alphoid DNA is a good model for studying these processes.

Alu Elements↗
PubMed1994

Nucleotide sequence of the Pseudomonas aeruginosa insertion sequence IS222: another member of the IS3 family.

Sequence analysis of the Pseudomonas aeruginosa insertion sequence element IS222 revealed it to be 1234 bp in size with 23 bp imperfect terminal inverted repeats. Insertion caused a 5-bp duplication of the insertion site. Two ORFs were identified, one of which, ORFA, could encode a basic (pI 10.5) polypeptide with a mass of 11,709. This sequence bears strong homology to the putative ORFA product from the Shigella dysenteriae insertion sequence element IS911, which is a member of the IS3 family of insertion elements. As with other members of this group the nucleotide sequence contains a "frameshift window" (AAAAAAG; M. Chandler and O. Fayet (1993). Mol. Microbiol. 7, 497-503) at which ribosome slippage can result in a fusion protein (ORFAB).

Amino Acid Sequence↗
PubMed2002

Influence of Tn917 insertion on transcription of the icaADBC operon in six biofilm-negative transposon mutants of Staphylococcus epidermidis.

Insertion of Tn917 into the icaADBC operon determines a biofilm-negative phenotype in biofilm-producing Staphylococcus epidermidis due to the inactivation of the genes responsible for the synthesis of the polysaccharide intercellular adhesin. We previously characterized six isogenic biofilm-negative transposon mutants of S. epidermidis 1457 with Tn917 insertions in either icaA or icaC. Northern blot analysis using ica- and Tn917-specific probes revealed that ica sequences located upstream and downstream of the transposon insertion site were still transcribed in five mutants in which Tn917 was inserted in the same transcriptional orientation. Outward-directed transcription initiating from within the transposon resulted in the complete expression of individual ica genes. Our results indicate that not only the inactivation of the entire operon but the isolated interruption of individual icaA and icaC genes led to a biofilm-negative phenotype in S. epidermidis. Tn917 mutagenesis may also result in the activation of genes located downstream of the insertion site.

Amino Acid Sequence↗
PubMed1997

Identification of a MMTV insertion mutation within the coding region of the Fgf-3 protooncogene.

The Fgf-3 protooncogene (previously called int-2) is a target of proviral insertion mutations in mammary tumors induced by the mouse mammary tumor virus (MMTV). These insertion mutations result in the transcriptional activation of Fgf-3, which is not normally expressed in the adult mammary gland. Previous mapping studies of numerous Fgf-3 insertion mutations have failed to reveal any provirus integrations within the gene coding region. This finding is consistent with the hypothesis that oncogenesis occurs in this system as a consequence of up-regulation of Fgf-3 transcription, rather than from alterations of the gene product. During an analysis of a new cohort of tumors from the WXG-2 mouse strain, a breast tumor was identified which had a MMTV provirus integrated 24 bp upstream of the Fgf-3 stop codon. This insertion mutation generated a fusion transcript which was readily detectable in tumor RNA by RT-PCR. The predicted protein product of this fusion transcript is missing 8 aa of native sequence and contains an additional 8 aa of cryptic MMTV-encoded sequence. These data document the first exception to the generalization that the Fgf-3 coding region is not disrupted by MMTV insertion mutation.

Amino Acid Sequence↗
PubMed1991

Effects of Tnt1 tobacco retrotransposon insertion on target gene transcription.

The effects of Tnt1 retrotransposon insertion on nitrate reductase (NR) gene transcription have been analyzed in three NR-deficient insertional, mutants of Nicotiana tabacum. In the three mutants, named h9-Nia4, h9-Nia5 and h9-Nia6, Tnt1 was inserted into exon 3, exon 2 and exon 1 of the nia2 NR alloallelle, respectively. The mutants h9-Nia4 and h9-Nia6, which contained Tnt1 insertions that were oriented opposite to the direction of nia2 gene transcription, expressed chimaeric nia2-Tnt1 RNAs, respectively 12 kb and 10 kb long. The size observed in h9-Nia6 was close to the expected size for a full-length hybrid transcript starting and ending under the control of nia2 signals (about 9 kb). The larger transcript found in h9-Nia4 was shown to be due to a failure to splice the nia2 intron 2. The mutant h9-Nia5, which contained a Tnt1 insertion oriented in parallel with the direction of nia2 transcription expressed two truncated nia2-Tnt1 RNAs, 2 kb and 6.7 kb long. These transcripts arose from termination in the long terminal repeats (LTRs) of Tnt1. Since no full-length hybrid RNA was detected, we suggest that Tnt1 carries efficient termination signals, which are more efficiently recognized in the 3' LTR than in the 5' LTR.

Base Sequence↗
PubMed1987

Insertional DNA and spontaneous mutation at the white locus in Drosophila simulans.

A large body of data on molecular analyses of several multiallelic loci in Drosophila melanogaster has demonstrated a high incidence of mobile DNA element insertions among spontaneous mutations. In the sibling species D. simulans, the dispersed, middle repetitive, nomadic sequences are reduced to about one-seventh that of its sibling species (Dowsett and Young 1982). Does this reduced amount of middle repetitive DNA (or mobile DNA sequences) mean that in D. simulans the occurrence of insertion mutants will be rare compared with that of D. melanogaster? To test this possibility, we collected seven different spontaneous white mutants of D. simulans and studied their molecular gene structures. Five out of seven mutants had insertion sequences which varied in length from 0.4 kb to 16 kb. One bore a deletion spanning the w region and another showed no gross structural alteration. Thus the proportion of insertional mutations at the white locus in D. simulans is equivalent to that observed in D. melanogaster. Among the five insertional mutants, one, wmky, showed genetic instability; the other four were stable. wmky was found to mutate at a frequency of 2.1 x 10(-5) in meiotic cells and may also be unstable in somatic cells.

ATP-Binding Cassette Transporters↗
PubMed1994

Insertion mutations of the RIIA Na+ channel reveal novel features of voltage gating and protein kinase A modulation.

A linker insertion mutagenesis strategy was developed to probe functional subdomains of the RIIA Na+ channel alpha-subunit. We describe mutations within the first two repeat domains that provide new functional information for three segments of the channel structure. 1. The insertion of two alanine residues within the short peptide segment joining helices S4 and S5 in domain II had two effects: a depolarizing shift of steady-state activation and reduced single-channel currents. These results suggest that the peptide segment following the S4 voltage sensor is involved in the activation process and is facing the ion pore. 2. An insertion immediately N-terminal to the proposed transmembrane helix S1 in domain II shifted the steady-state activation in the depolarizing direction, suggesting a functional role in channel gating. 3. Insertions in the large, cytoplasmic loop between domains I and II affect two channel functions: inactivation and protein kinase A modulation. These results demonstrate that the linker insertion approach can provide novel insights into the structure-function relationships of large, multi-domain ion channel proteins.

Amino Acid Sequence↗
PubMed1995

Insertion mutations at the maize Opaque2 locus induced by transposable element families Ac, En/Spm and Bg.

Eight independently isolated unstable alleles of the Opaque2 (O2) locus were analysed genetically and at the DNA level. The whole series of mutations was isolated from a maize strain carrying a wild-type O2 allele and the transposable element Activator (Ac) at the wx-m7 allele. Previous work with another unstable allele of the same series has shown that it was indeed caused by the insertion of an Ac element. Unexpectedly, the remaining eight mutations were not caused by the designated Ac element, but by other insertions that are structurally similar or identical to one of two different autonomous transposable elements. Six mutations were caused by the insertion of a transposable element of the Enhancer/Suppressor-Mutator (En/Spm) family. Two mutations were the result of the insertion of a transposable element of the Bergamo (Bg) family. Genetic tests carried out with plants carrying the unstable mutations demonstrated that all were caused by the insertion of an autonomous transposable element.

Alleles↗
PubMed1999

Promoter-tagged restriction enzyme-mediated insertion (PT-REMI) mutagenesis in Aspergillus niger.

Promoter-tagged restriction enzyme-mediated insertion (PT-REMI) mutagenesis was performed in the fungus Aspergillus niger, using a plasmid containing a strong transcriptional promoter. Two DNA-tagged mutants were analyzed in detail. A white-spored mutant was shown to contain a plasmid insertion that disrupted a gene that shows a high degree of homology to the polyketide synthase gene wA of A. nidulans. A morphological mutant was shown to contain a plasmid insertion in the 5' upstream region of a gene that strongly resembles COX5, which encodes the cytochrome c oxidase subunit V. Insertion of the plasmid resulted in enhanced expression of the COX5 RNA, demonstrating that the combination of REMI with a promoter-containing insert can be used to activate gene transcription.

Amino Acid Sequence↗
PubMed2004

High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.

A high-oleate trait in the cultivated peanut ( Arachis hypogaea L.) was reported to rely on the allelic composition of the two homeologous, microsomal oleoyl-PC desaturase genes ( ahFAD2A or ahFAD2B). The enzyme activity of either ahFAD2A or ahFAD2B is sufficient for a normal oleate phenotype, and a significant reduction in the levels of ahFAD2B and a mutation in ahFAD2A were reported to be responsible for the high-oleate phenotype in one chemically induced mutant (M2-225) and one derived from a naturally occurring (8-2122) mutant. Here, we report an insertion of the same miniature inverted-repeat transposable element (MITE) in the ahFAD2B gene in another chemically induced mutant (Mycogen-Flavo) and the previously characterized M2-225 mutant. In both cases, this MITE insertion in ahFAD2B causes a frameshift, resulting in a putatively truncated protein sequence in both mutants. The insertion of this MITE in ahFAD2B, in addition to the point mutation in ahFAD2A, appears to be the cause of the high-oleate phenotype in Mycogen-Flavo and M2-225 mutants. Utilizing sequences of the MITE, we developed a DNA marker strategy to differentiate the two insertion-containing mutants from the normal oleate peanut variety (AT-108) and the naturally occurring, high-oleate mutant 8-2122. Reverse transcript-PCR/differential digestion results reveal the expression of both ahFAD2A and ahFAD2B genes in Mycogen-Flavo mutant. This result is in contrast to the observation that ahFAD2B transcripts are greatly reduced in the M2-225 mutant having the MITE insertion further 3' in ahFAD2B gene.

Amino Acid Sequence↗
PubMed2006

Structure and transcriptional impact of divergent repetitive elements inserted within Phanerochaete chrysosporium strain RP-78 genes.

We describe the structure, organization, and transcriptional impact of repetitive elements within the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Searches of the P. chrysosporium genome revealed five copies of pce1, a ~1,750-nt non-autonomous, class II element. Alleles encoding a putative glucosyltransferase and a cytochrome P450 harbor pce insertions and produce incomplete transcripts. Class I elements included pcret1, an intact 8.14-kb gypsy-like retrotransposon inserted within a member of the multicopper oxidase gene family. Additionally, we describe a complex insertion of nested transposons within another putative cytochrome P450 gene. The disrupted allele lies within a cluster of >14 genes, all of which encode family 64 cytochrome P450s. Components of the insertion include a disjoint copia-like element, pcret3, the pol domain of a second retroelement, pcret2, and a duplication of an extended ORF of unknown function. As in the case of the pce elements, pcret1 and pcret2/3 insertions are confined to single alleles, transcripts of which are truncated. The corresponding wild-type alleles are apparently unaffected. In aggregate, P. chrysosporium harbors a complex array of repetitive elements, at least five of which directly influence expression of genes within families of structurally related sequences.

Alleles↗
PubMed1993

Immediate postplacental insertion and fixation of the CuFix postpartum implant system.

Since promising results were obtained with the CuFix interval implant system in international clinical trials conducted worldwide, a modification of the device adapting it for immediate postplacental insertion and fixation (IPPIF) seemed a logical approach to solve the expulsion problem of IUDs inserted at that particular time. Seventy-three insertions were performed at three university centers, during 1990 and 1991, both by skilled and unskilled investigators. The results of this multicenter study show the excellent retainability of the modified IUD supporting the validity of the anchoring principle. The insertion procedure is easy, requiring minimal training, and the insertion technique appeared to be safe.

Equipment Design↗
PubMed1992

Insertional mutations in mammals and mammalian cells.

The retroposon sequences, their mechanisms of transposition and the occurrence of insertional mutation in the mammalian genome are reviewed. Insertional mutations fall into two broad categories: those due to the disruption of a gene following the physical integration of a foreign DNA sequence result in loss of gene product and would be expected to be associated with a recessive mutation. A second class of insertional mutation is well documented in which upon integration the promoter/enhancer activities inherent in the retroposon genome exert their influence on neighboring genes. This promoter/enhancer activity of integrated retroposons may have effects over relatively long distances and thus limit the possibilities of establishing an association between retroposon integration and mutation. It is emphasized that a systematic search for insertional mutations in the mammalian genome involves an extensive two-dimensional array of possible retroposon sequences and mutant alleles. Present results represent only a small portion of the total array. Future studies promise to be fruitful in efforts to isolate genes through insertional tagging, to characterize the mechanisms of retroposon transposition, as well as to study the stability of the mammalian genome.

Animals↗