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PubMed1998

Organization of the human RH50A gene (RHAG) and evolution of base composition of the RH gene family.

Human Rh (rhesus) antigens are expressed in the red cell membrane as a multi-subunit complex, the central core of which is presumably composed of a tetramer made of two Rh and two Rh50 protein subunits. The interaction between Rh and Rh50 polypeptides is thought to be crucial to the correct assembly and transport of the complex to the cell surface. Here, we show that the human RH50A gene (RHAG) is composed of 10 exons whose size and exon/intron junctions are well conserved compared to those of the RH genes. We have also analyzed the RH50A 5' flanking region where the transcription initiation site has been identified. These results conclusively establish that the RH50A and RH genes do belong to the same gene family. Moreover, we show that the RH50A and RH genes are embedded in different compositional genomic contexts (i.e., different isochores) that are likely to drive the evolution of these genes, the base compositions (G + C content) of which differ drastically. Finally, we propose a scenario in which an RH50-like gene is likely to have played a founding role in the evolution of the RH gene family.

Animals↗
PubMed2002

Searching for RNA genes using base-composition statistics.

The hypothesis that genomic regions rich in non-protein-coding RNAs (ncRNAs) can be identified using local variations in single-base and dinucleotide statistics has been investigated. (G+C)%, (G-C)% difference, (A-T)% difference and dinucleotide-frequency statistics were compared among seven classes of ncRNAs and three genomes. Significant variations were observed in (G+C)% and, in Methanococcus jannaschii, in the frequency of the dinucleotide 'CG'. Screening programs based on these two base-composition statistics were developed. With (G+C)% screening alone, a 1% fraction of the M.jannaschii genome containing all 44 known transfer RNAs, ribosomal RNAs and signal recognition particle RNAs could be identified. When (G+C)% combined with CG dinucleotide-frequency screening was used, 43 of the 44 known M.jannaschii structural ncRNAs were again identified, while the number of presumably false hits overlapping a known or putative protein-coding gene was reduced from 15 to 6. In addition, 19 candidate ncRNAs were identified including one with significant homology to several known archaeal RNaseP RNAs.

Animals↗
PubMed2006

A prospective randomised clinical trial of one bis-GMA-based and two ormocer-based composite restorative systems in class II cavities: three-year results.

OBJECTIVES: Ormocer composites, consisting of a silicon-based polymer, have been developed recently as a tooth-coloured restorative material. The purpose of this prospective randomised clinical trial was to evaluate the performance of two small-particle hybrid ormocer-based restorative systems (AD, Admira/Admira Bond, VOCO; DE, Definite/Etch & Prime 3.0, Dentsply) and one small-particle hybrid bis-GMA-based composite restorative system (TC, Tetric-Ceram/Syntac, Ivoclar-Vivadent) in occlusal stress-bearing restorations. METHODS: One hundred and twenty-eight occlusal-proximal restorations (44 AD, 43 DE and 41 TC) were placed according to the manufacturer's instructions in thirty-two adult patients. Their clinical performance was scored according to the USPHS criteria and evaluation of bite-wing radiographs. RESULTS: After 3 years, four AD, five DE and four TC restorations had failed due to fracture or marginal gap formation. Surface roughness improved significantly when compared to the baseline in AD and TC (Friedman test, p<0.05) during the first year but returned to baseline values after 3 years. DE had a significant tendency towards discolouration (p<0.05). Bite-wing radiographs showed two AD and one TC restorations with internal porosities. ANOVA showed that larger restorations (> or = 3 surfaces) showed significantly more degradation than smaller ones. CONCLUSIONS: In a group of class II restorations, there was no significant difference in failures after 3 years between ormocer-based and bis-GMA-based restorative systems.

Acrylates↗
PubMed2003

Intimate evolution of proteins. Proteome atomic content correlates with genome base composition.

Discerning the significant relations that exist within and among genome sequences is a major step toward the modeling of biopolymer evolution. Here we report the systematic analysis of the atomic composition of proteins encoded by organisms representative of each kingdoms. Protein atomic contents are shown to vary largely among species, the larger variations being observed for the main architectural component of proteins, the carbon atom. These variations apply to the bulk proteins as well as to subsets of ortholog proteins. A pronounced correlation between proteome carbon content and genome base composition is further evidenced, with high G+C genome content being related to low protein carbon content. The generation of random proteomes and the examination of the canonical genetic code provide arguments for the hypothesis that natural selection might have driven genome base composition.

Animals↗
PubMed2004

In vivo versus in vitro microtensile bond strength of axial versus gingival cavity preparation walls in Class II resin-based composite restorations.

BACKGROUND: Gingival margins in Class II composite restorations are a site of frequent failure. The purpose of the authors' study was to compare the microtensile dentin bond strength of gingival and axial restored cavity preparation walls of Class II composite restorations under in vivo and in vitro conditions. METHODS: After obtaining informed consent, the authors placed Class II resin-based composite restorations in 14 premolar teeth from five patients, under in vivo or in vitro conditions. The teeth were sectioned to obtain rectangular specimens from axial and gingival walls with a surface area of approximately 0.5 square millimeter. The authors tested 85 microtensile adhesive samples from the 14 teeth on a testing instrument (Universal Instron, Model 125, Instron, Canton, Mass.) until failure. RESULTS: The mean (+/- standard deviation) mircotensile dentin bond strengths in mega-pascals were as follows: in vivo axial, 36.5 (14.9); in vivo gingival, 17.6 (11.6); in vitro axial, 49.5 (13.9); in vitro gingival, 34.0 (13.1). A two-way analysis of variance found a statistically significant difference between in vitro and in vivo conditions and between the axial and gingival walls (P < or = .001). Eighty-eight percent of the fractured samples involved the adhesive layer as observed under scanning electron microscopy up to x2,500. Seventeen of the gingival samples and two of the axial samples debonded during the preparation phase and could not be tested. CONCLUSION: The dentinal microtensile strength of adhesive/resin-based composite bonded to the gingival wall was significantly weaker than the bond to the axial wall, and in vivo conditions produced significantly weaker bond strengths than did in vitro conditions. CLINICAL IMPLICATIONS: The dentinal adhesive bond of resin-based composite to gingival walls is significantly weaker and thus more subject to failure than the bond to axial walls. In vitro bond strength studies may overestimate the bond strength of adhesives in in vivo applications.

Adolescent↗
PubMed2002

Base composition at mtDNA boundaries suggests a DNA triple helix model for human mitochondrial DNA large-scale rearrangements.

Different mechanisms have been proposed to account for mitochondrial DNA (mtDNA) instability based on the presence of short homologous sequences (direct repeats, DR) at the potential boundaries of mtDNA rearrangements. Among them, slippage-mispairing of the replication complex during the asymmetric replication cycle of the mammalian mitochondrial DNA has been proposed to account for the preferential localization of deletions. This mechanism involves a transfer of the replication complex from the first neo-synthesized heavy (H) strand of the DR1, to the DR2, thus bypassing the intervening sequence and producing a deleted molecule. Nevertheless, the nature of the bonds between the DNA strands remains unknown as the forward sequence of DR2, beyond the replication complex, stays double-stranded. Here, we have analyzed the base composition of the DR at the boundaries of mtDNA deletions and duplications and found a skewed pyrimidine content of about 75% in the light-strand DNA template. This suggests the possible building of a DNA triple helix between the G-rich neo-synthesized DR1 and the base-paired homologous G.C-rich DR2. In vitro experiments with the purified human DNA polymerase gamma subunits enabled us to show that the third DNA strand may be used as a primer for DNA replication, using a template with the direct repeat forming a hairpin, with which the primer could initiate DNA replication. These data suggest a novel molecular basis for mitochondrial DNA rearrangements through the distributive nature of the DNA polymerase gamma, at the level of the direct repeats. A general model accounting for large-scale mitochondrial DNA deletion and duplication is proposed. These experiments extend to a DNA polymerase from an eucaryote source the use of a DNA triple helix strand as a primer, like other DNA polymerases from phage and bacterial origins.

Base Composition↗
PubMed2004

Color and opacity variations in three different resin-based composite products after water aging.

OBJECTIVES: Correct shade selection and clinical procedures may be invalidated as a result of intrinsic color shifting with time. The aim of this study was to test the influence of exposure to water on the color stability of three structurally different resin-based composites. METHODS: Six comparable Vita shades of three different resin-based composite systems were selected. For each product at each shade, three disks were made, 1 mm in thickness and 15 mm in diameter. The samples were studied with a spectrophotometer equipped with an integrating sphere. For color determinations, a 50% gray card was used as background, and the data were recorded in the CIE L*a*b* system. Opacity was calculated as the ratio of the reflectance of a specimen disk when backed by a black standard that when backed by a white standard. After the initial measurements, the samples were stored for 30 days in a 60 degrees C water bath and then measured again under the same conditions. The color shifts were calculated using the formula: delta E = [(L1 - L2)2 + (a1 - a2)2 + (b1 - b2)2]1/2. RESULTS: If the standard of delta E < 3.3 as clinically acceptable was taken into consideration, one of the three materials involved in the study showed an unacceptable color shift for all shades. Only one of the three materials remained completely within an acceptable shade shift (delta E < 3.3) after aging. The difference in the color stability between products was significant (p < 0.001). The differences may be due to the different nature of the matrix and could also be correlated with filler particles dimensions. With reference to opacity; the results showed a similar pattern as that of the color and the statistical analysis also correlated. SIGNIFICANCE: From this work, it can be concluded that for some products, aging of composites in water leads to color instability and opacity variation.

Analysis of Variance↗
PubMed1975

Studies on the species, amount and base composition of nucleic acids in psoriatic scales and normal horny layer.

The amount of RNA as well as DNA is considerably increased in psoriatic scales as compared with normal horny layer; RNA was characterized as a low-molecular tRNA; as concerns the base composition of DNA, no particularities in comparison with other DNA species were found, and the base composition of tRNA revealed that cytosine and guanosine are in excess; pseudouridine could not be detected in psoriatic tRNA.

Adolescent↗
PubMed2001

The A--B transition: temperature and base composition effects on hydration of DNA.

Natural DNAs and some polynucleotides organised in fiber present the A--B form transition at a relative humidity (r.h.) which depends on the temperature. A shift of the midpoint of that helix--helix transition to higher r.h. values is observed when the temperature is risen. It is shown that the average number of water molecules associated to a nucleotide pair is the relevant parameter for the A-B transition and that this parameter can be given a precise value by a combination of different r.h. and temperature values. The minimum number of water molecules necessary to get the B form depends on the base composition of the DNA. It is observed that AT base pairs have a higher affinity toward water molecules than GC base pairs. In the B form there are 27 water molecules per GC nucleotide pair and 44 per AT pair. Moreover, we noted that the fraction of nucleotides in the B form as a function of the average number of water molecules associated per base pair does not depend on the temperature. The A helical form is obtained with about 11 water molecules per nucleotide pair and this number is not very sensitive to the base composition of DNA.

Base Pairing↗
PubMed1987

Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence.

Heteroduplexes with single base pair mismatches of known sequence were prepared by annealing separated strands of bacteriophage lambda DNA and used to transfect Escherichia coli. A series of transition (G:T and A:C) and transversion (G:A and C:T) mismatches located throughout most of the bacteriophage lambda cI gene has been examined. The results suggest that the transition mismatches are generally better repaired than the transversion mismatches and that, at least for the transversion mismatches studied, repair efficiency increases with increasing G:C content in the neighboring nucleotide sequence. This specificity of the E. coli mismatch repair system can account, in part, for the similar frequencies of base substitution mutations throughout the E. coli genome.

Bacteriophage lambda↗
PubMed1971

Quantitative aspects of deoxyribonucleic acid renaturation: base composition, state of chromosome replication, and polynucleotide homologies.

The base composition of a deoxyribonucleic acid (DNA) sample affects its intrinsic rate of renaturation. In agreement with the information of Wetmur and Davidson, it was established that high guanosine plus cytosine (GC) DNA renatures faster than expected from analytical measurement of its molecular weight. A calculated correction factor of 1.8% of the observed C(0)t(.5) is required for every mole per cent GC difference from 51% GC. The correction factor is now established in the range of 32 to 65% GC. Renaturation of DNA mixtures prepared from pairs of organisms has been studied. When no similarity existed between the two organisms, the observed C(0)t(.5) of the mixture was the sum of the independently determined C(0)t(.5) values. Lack of additivity was correlated with similarities in polynucleotide sequence of the reassociating DNA molecules. A quantitative relationship was formulated to relate C(0)t(.5) values of renatured DNA mixtures to per cent binding ("homology"). Finally, it was demonstrated that DNA prepared from log-phase cells renatures faster than stationary-phase DNA and also departs from theoretical second-order kinetics.

Autoradiography↗
PubMed1998

Oxazole yellow dye interactions with short DNA oligomers of homogeneous base composition and their hybrids.

Interactions between short single-stranded DNA oligomers of homogeneous base composition and the fluorescent probes oxazole yellow (YO) and its homodimer YOYO are described. The oligomers included 15-mers and 30-mers of polydA, polydT, polydG, and polydC. Interactions between the dyes and DNA hybrids formed from complementary homogeneous strands of equal length were also investigated. No interactions were observed between the dyes and the monomeric monophosphate nucleosides A, G, T, or C. The dyes were found to interact much more strongly with the purine oligomers polydA and polydG than with the pyrimidine oligomers polydT and polydC. PolydA of both lengths has strong interactions with YOYO, whereas the polydG 30-mer interacts strongly with monomeric YO. The 15-mers of polydG and polydC of both lengths show little interaction with either dye. Interactions of the dyes with the polydA/polydT and polydG/polydC hybrids tend to be dominated by interactions with polydA and polydG, respectively. Although dye interactions generally were facilitated by hybridization, particularly for polydA/polydT, the interactions were similar to those with the single strands and different from those that have been observed in long double-stranded DNA.

Base Composition↗
PubMed1991

Numerical analysis and DNA base compositions of some thermophilic Bacillus species.

Morphological, physiological, and biochemical characteristics and the DNA base compositions of 133 thermophilic Bacillus strains were determined. A total of 54 of these strains were received as identified species (mainly Bacillus stearothermophilus, Bacillus coagulans, Bacillus brevis, and Bacillus licheniformis) from international culture collections, and 79 newly isolated strains, which were isolated mainly from sugar diffusion juices of Italian plants, were also examined. Numerical taxonomy techniques (simple matching coefficient and unweight pair grouping using the mathematical average) and DNA G + C values showed that the strains aggregated into nine clusters. Both B. licheniformis and B. brevis were well separated from the other organisms. B. stearothermophilus and B. coagulans were confirmed as separate clusters and exhibited greater heterogeneity than previously shown. The B. stearothermophilus strains clustered into four groups, three of which have been recognized previously by other authors; the members of the fourth group had distinctive characteristics, including considerable biochemical inertness, an inability to grow at temperatures greater than 60 degrees C, and a high G + C content. Within the B. coagulans cluster the strains with characteristics very similar to those of the new species Bacillus smithii clustered together. However, the remaining strains were still clearly separated into two groups; one of these groups was considered B. coagulans sensu stricto, and the other was distinguished by morphological and biochemical criteria, such as spores which do not swell the sporangia, utilization of citrate, a higher proteolytic activity, and acidification of some carbohydrates. Our results were confirmed by comparing them with distinctive characteristics of recently described thermophilic Bacillus species.

Aerobiosis↗
PubMedDate not supplied

Restoring coronal contours of retained infraoccluded primary second molars using bonded resin-based composite.

The purpose of this case report is to describe a step-by-step method of restoring function (and esthetics) to infraoccluded second primary molars using a crown-form crown, in a case of bilateral congenital missing premolars. This technique restores form and function, with a minimal reduction to the tooth. It also conserves tooth material and permits good bonding of the resin-based composite to the enamel. The crown-form resin-based composite restoration is an easy and inexpensive solution in cases of infraoccluded teeth. Yet, patients must be warned about the possible failure of the crown and the need of periodic follow-up appointments.

Adolescent↗