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PubMed1994

Development and validation of a method for routine base composition analysis of phosphorothioate oligonucleotides.

A method for routine base composition determination of phosphorothioate oligonucleotides containing as many as 21 nucleobases has been developed and systematically evaluated in terms of factors contributing to assay precision and accuracy. Phosphorothioate internucleotide linkages were oxidized with a mixture of tetrahydrofuran-water-methylimidazole (16:4:1, v/v/v) which has been shown to be 97.3% effective. This step was followed by enzymolysis and HPLC quantitation of individual nucleobases. RSD for inter-day base composition analysis ranged from 1.1 to 1.3%, and inter-lot variation was 0.6-2.0%. Accuracy of the determined nucleobase ratio was independently confirmed through sequencing of the oxidized oligomer by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS).

Base Composition↗
PubMed1999

Bond strength of a resin-based composite to leucite-reinforced ceramic and dentin.

PURPOSE: To compare the in vitro tensile bond strengths of resin-based composite bonded to dentin and to a leucite-reinforced ceramic in an as-received condition (pre-silanated) or re-etched, re-silanated condition. MATERIALS AND METHODS: Caries-free human molars were ground to expose occlusal, superficial dentin. Dentin surfaces were etched with 37% phosphoric acid and rinsed, leaving a moist dentin surface. Leucite-reinforced ceramic inserts (SONICsys) also were tested as received (pre-etched, pre-silanated) or retreated with hydrofluoric acid and silane. Bonding agent (Syntac Single-Component) was applied in two layers and light cured. An all-purpose resin-based composite (Tetric Ceram) was used to prepare tensile bond strength specimens for the dentin and two ceramic groups. Fourteen specimens were prepared for each group. After 24 hours in distilled water, tensile bond strength (MPa) was measured using a testing machine. Analysis of variance was used to evaluate data. RESULTS: Bond strengths obtained were 10.2 MPa for composite bonded to dentin, 10.5 MPa for composite bonded to as-received ceramic inserts, and 9.6 MPa for composite bonded to retreated ceramic inserts, with no statistical difference between the three groups. Re-treatment of leucite-reinforced inserts did not increase or decrease bond strength to resin-based composite. Also, the bond strength of resin-based composite to dentin was similar to that of the ceramic to composite.

Aluminum Silicates↗
PubMed1999

Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA.

It has been suggested that mutation bias is the major determinant of base composition bias at synonymous, intron, and flanking DNA sites in mammals. Here I test this hypothesis using population genetic data from the major histocompatibility genes of several mammalian species. The results of two tests are inconsistent with the mutation hypothesis in coding, noncoding, CpG-island, and non-CpG-island DNA, but are consistent with selection or biased gene conversion. It is argued that biased gene conversion is unlikely to affect silent site base composition in mammals. The results therefore suggest that selection is acting upon silent site G + C content. This may have broad implications, since silent site base composition reflects large-scale variation in G + C content along mammalian chromosomes. The results therefore suggest that selection may be acting upon the base composition of isochores and large sections of junk DNA.

Alleles↗
PubMedDate not supplied

Base composition of dromedary thymus DNA.

The base composition of dromedary thymus DNA was determined by reversed-phase HPLC determination of the four major deoxyribonucleosides. No significant differences were found between dromedary and calf thymus DNA. The elution system used (different from that suggested in the literature) was ammonium phosphate buffer/acetonitrile.

Animals↗
PubMed1962

Deoxyribonucleic acid base composition of Proteus and Providence organisms.

Falkow, Stanley (Walter Reed Army Institute of Research, Washington D.C.), I. R. Ryman, and O. Washington. Deoxyribonucleic acid base composition of Proteus and Providence organisms. J. Bacteriol. 83:1318-1321. 1962.-Deoxyribonucleic acids (DNA) from various species of Proteus and of Providence bacteria have been examined for their guanine + cytosine (GC) content. P. vulgaris, P. mirabilis, and P. rettgeri possess essentially identical mean GC contents of 39%, and Providence DNA has a GC content of 41.5%. In marked contrast, P. morganii DNA was found to contain 50% GC. The base composition of P. morganii is only slightly lower than those observed for representatives of the Escherichia, Shigella, and Salmonella groups. Aerobacter and Serratia differ significantly from the other members of the family by their relatively high GC content. Since a minimal requirement for genetic compatibility among different species appears to be similarity of their DNA base composition, it is suggested that P. morganii is distinct genetically from the other species of Proteus as well as Providence strains. The determination of the DNA base composition of microorganisms is important for its predictive information. This information should prove of considerable value in investigating genetic and taxonomic relationships among bacteria.

Bacteria↗
PubMed1975

DNA base composition of species of the genus Saccharomyces.

DNA base compositions (GC content) of Saccharomyces species are reported and discussed. Several amendments of the four groups given by van der Walt are suggested, viz. the transfer of S. kluyveri to group 1, and of S. eupagycus, S. cidri, S. montanus, S. microellipsodes and S. florentinus to group 2. The synonomy of S. amurcae and S. cidri is suggested. The DNA base compositions revealed two possible pairs of sibling species: S. elegans and S. bailii, with a difference in GC content of 4.1%; S. dairensis and S. servazzii with a difference in GC content of ca. 3%. S. mrakii had a GC content of 47.3-48.5% the highest encountered in this genus and similar to that of Kluyveromyces thermotolerans.

Cytidine↗
PubMed1981

Base composition of RNA obtained from motor neurons in amyotrophic lateral sclerosis.

The base composition of RNA obtained from the large motor neurons of the cervical and lumbar swelling was examined in amyotrophic lateral sclerosis (ALS) patients and a similar number of age-matched controls. Spinal cords were obtained at autopsy and immediately fixed in buffered formalin. The single cell technique of Edström was employed to extract, hydrolyze, and electrophoresis the RNA. The base composition obtained for the controls was 17.47% adenine, 28.88% guanine, 28.50% cytidylic acid, and 25.14% uridylic acid. The cervical intumescence revealed higher levels of uridylic acid than the lumbar, 27.23% in the cervical and 23.31% in the lumbar intumescence. The motor neuron cell bodies isolated from patients having had ALS revealed a lower percentage of adenine in both the cervical (13%) and lumbar (10%) intumescences. When the data for these areas were combined, the percentage of adenine was 15.52, compared to 17.47% in the controls (p less than 0.01). The A/U ratio was also significantly reduced in the ALS group. The composition of the remaining bases in ALS appeared to be similar to the controls. The significant change in adenine, coupled with the quantitative reduction in total neuronal RNA, suggests that a disorder of nucleic acid metabolism may relate to the pathogenesis of ALS.

Adult↗
PubMed2004

Prevalence of cusp fractures in teeth restored with amalgam and with resin-based composite.

BACKGROUND: Complete cusp fracture in restored teeth is a common problem observed in general dental practice. Many dentists believe that teeth restored with amalgam are more likely to be associated with cusp fractures than are those restored with resin-based composite. METHODS. The authors noted the condition of 10,869 posterior teeth with amalgam or resin-based composite restorations with at least one cusp present, unrestored or missing in 1,902 consecutively seen adult patients in a private general dental practice. For each patient, the authors recorded age, type of restorations, number of surfaces of each restoration, and presence or absence of a complete cusp fracture and of caries. RESULTS: There was a lower percentage of cusp fractures in younger subjects than in older subjects and in teeth with a single restored surface than in those with more than one restored surface. There was no significant difference in the prevalence of cusp fracture rates in amalgam-restored teeth versus composite-restored teeth in subjects aged 18 through 54 years. In subjects aged 55 through 96 years, there was a marginally significantly greater cusp fracture rate in composite-restored teeth than in those restored with amalgam. Overall, there was no significant difference in the prevalence of cusp fracture in teeth restored with amalgam (1.88 percent) versus composite-restored teeth (2.29 percent). CONCLUSIONS: The prevalence of cusp fractures in amalgam-restored teeth and resin-based composite-restored teeth is not significantly different. Teeth with more than one surface restored with either resin-based composite or amalgam and teeth in older subjects were more likely to suffer a cusp fracture. CLINICAL IMPLICATIONS: Teeth restored with amalgam and with resin-based composite exhibited equally low cusp fracture prevalence. When choosing between amalgam and resin-based composite in consideration of the likelihood of a future cusp fracture, either restorative material is acceptable.

Adolescent↗
PubMed1992

Compliance of genetic code with base-composition deflecting pressure.

Gene DNAs of different organisms show a wide variation in their G+C content as much as 20% to 80%. This variation has been regarded as the result of the compliance of the genetic code with the base-composition-deflecting mutational pressure. To make possible a quantitative discussion of this genetic code's elasticity, we made a statistical study of the G+C frequency at the 1st, 2nd, and 3rd positions of codons: 4.5 x 10(6) codons in 11,981 protein coding regions in the DNA data base were analyzed. The data were examined quantitatively by using a species-independent universal equation which describes the base frequencies at the three codon sites in terms of the constraint parameters characteristic of the sites and an intersite interaction. By a best fitting procedure between theoretical curves and data points, the constraint parameters and the characteristic G+C contents to which the 1st and the 2nd site base compositions are bound were determined. The base substituting mutation of the coding sequence under the base-composition-deflecting pressure is divided into following three stages of the different compliance from the elastic one to the rigid: 1) the 3rd position of codons change by synonymous substitution; 2) the 1st and then 2nd positions change accompanying amino acid replacement; and 3) in the organisms exposed under an extremely high base composition deflecting pressure, the codon table is forced to be altered. The compliance parameters were derived quantitatively for the first two stages. In conclusion, a simultaneous analysis of data from organisms as divers as virus and man discovered that there is a set of constraints common to species, which governs the frequency of codon bases, and it can be described by a universal equation.

Animals↗
PubMed2002

DNA base composition of planktonic species of Anabaena (Cyanobacteria) and its taxonomic value.

Fifty axenic strains of planktonic Anabaena, including 24 strains of the straight form and 26 strains of the coiled form, were examined for their DNA base composition (GC content). The taxonomic value of their GC content at species level was evaluated by comparing their morphological, physiological and biochemical properties. The DNA base composition determined for all fifty strains ranged from 35.9 to 56.4 mol% GC. The straight-form strains were in the range of 35.9-56.4 mol% GC, while coiled forms were in the range of 38.1-50.3 mol% GC. In general, strains assigned to the same species showed similar DNA base composition. However, of three strains of A. affinis Lemmermann that were separated into two categories, two had 40.6-40.9 mol% GC, and the third strain 45.6 mol% GC. It is noteworthy that the DNA base composition of the newly established species A. eucompacta Li et Watanabe was 45.5 mol% GC, which differed from 39.5 mol% GC of the morphologically close species, A. compacta (Nygarrd) Hickel.

Anabaena↗
PubMed1964

ADANSONIAN ANALYSIS AND DEOXYRIBONUCLEIC ACID BASE COMPOSITION OF SOME GRAM-NEGATIVE BACTERIA.

Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of some gram-negative bacteria. J. Bacteriol. 87:1412-1422. 1964.-The deoxyribonucleic acid (DNA) base compositions and S values for a minimum of 134 coded properties were determined for representative cultures of the genera Pseudomonas, Xanthomonas, Aeromonas, Vibrio, Aerobacter, Escherichia, Alcaligenes, and Flavobacterium. Those cultures having a high degree of similarity by the criterion of numerical taxonomy were found to have similar DNA base compositions. The relative affinities of clusters of cultures suggest taxonomic relations. Eleven species of Xanthomonas might be a single species, and V. metschnikovii was shown to be more closely related to enteric bacteria than to other vibrios which, in turn, were found to be like pseudomonads. Aeromonas was found to be intermediate in similarity to enterics and pseudomonads and divisible into at least two, but possibly three, species. F. aquatile was unlike any of the other organisms studied, and its DNA also differed greatly in composition from other representatives of the genus.

Aeromonas↗
PubMed1980

Purine base composition analysis of normal and tumor rat DNA.

Chemical and viral induced rat tumors were analyzed for their purine base composition and compared to normal tissue DNA'S. The tumors were induced by 7,12-dimethylbenz[a]anthracene (DMBA), 20-methylcholanthrene (MC), 3,4-benzopyrene (BP), 1,2-dimethylhydrazine (DMH) and Rous sarcoma virus (RSV). Normal DNAs were extracted from colon, caecum, liver, spleen and embryo and used as reference standards for base composition of normal rat DNA. The composition of purines was obtained by spectrophotometric estimation of the total adenine and guanine (A/G) contents after depurination of the DNA with 66% formic acid at 30 degrees C for 18 h and passage over a cationic exchange resin. Statistical comparison of the A/G molar ratios in normal rat DNAs (1.271) to those of chemical-induced primary tumors (1.342) has shown a highly significant increase. No significant differences could be detected when the base composition of the normals were compared to transplanted tumors, whether chemically or virally induced. Possible explanations from a mutational point of view are discussed.

Animals↗
PubMed1995

Inferring phylogenies from DNA sequences of unequal base compositions.

A new method for computing evolutionary distances between DNA sequences is proposed. Contrasting with classical methods, the underlying model does not assume that sequence base compositions (A, C, G, and T contents) are at equilibrium, thus allowing unequal base compositions among compared sequences. This makes the method more efficient than the usual ones in recovering phylogenetic trees from sequence data when base composition is heterogeneous within the data set, as we show by using both simulated and empirical data. When applied to small-subunit ribosomal RNA sequences from several prokaryotic or eukaryotic organisms, this method provides evidence for an early divergence of the microsporidian Vairimorpha necatrix in the eukaryotic lineage.

Algorithms↗
PubMed2003

Effect of low-viscosity resin-based composite on the microleakage of cervical restorations.

PURPOSE: To investigate the effect of a low-viscosity resin-based composite (LVC) liner on the microleakage of cervical resin-based composites bonded with new adhesive systems. METHODS: 180 wedge-shaped cervical cavities on bovine incisors were treated with AQ Bond (all-in-one), ABF (experimental two-step self-etching primer containing antibacterial monomer) or Clearfil SE Bond (two-step self-etching primer) systems according to the manufacturers' instructions. Half of the treated cavities in each adhesive system were lined with an LVC (Protect Liner F) and filled with a hybrid resin-based composite (Clearfil AP-X). Ten specimens from each group were immersed in 0.5% basic fuchsin solution immediately after finishing the restorations. The specimens to be subjected to thermocycling (5-60 degrees C, 15 seconds dwell time, 5,000 cycles) or to flexural load cycling (approximately 0.5 mm labio-lingual displacement at the incisal edge, 10,000 cycles, 1 Hz) prior to immersion in the dye solution were also prepared. The teeth were sectioned through the center of the restorations and the degrees of dye penetration were scored. The data were analyzed with the Mann-Whitney U-test or the Kruskal-Wallis test (P < 0.05). RESULTS: The use of the LVC liner significantly improved marginal sealing of AQ Bond. However, the LVC liner could not prevent the deterioration in the marginal integrity caused by thermocycling or flexural load cycling. In the case of ABF, the use of the LVC liner showed a trend toward less microleakage. For Clearfil SE Bond, the LVC liner prevented the deterioration in the marginal seal caused by thermocycling.

Animals↗
PubMed1996

Mitochondrial COI sequences in mites: evidence for variations in base composition.

Studies of mitochondrial DNA sequences in a variety of animals have shown important differences between phyla, including differences in the genetic codes used, and varying constraints on base composition. In that respect, little is known of mites, an important and diversified group. We sequenced a portion (340 nt) of the cytochrome oxidase subunit I (COI) encoding gene in twenty species of phytophagous mites belonging to nine genera of the two families Tetranychidae and Tenuipalpidae. The mitochondrial genetic code used in mites appeared to be the same as in insects. As is generally also the case in insects, the mite sequences were very rich in A + T (75% on average), especially at the third codon position (94%). However, important variations of base composition were observed among mite species, one of them showing as little as 69% A + T. Variations of base composition occur mostly through synonymous transitions, and do not have detectable effects on polypeptide evolution in this group.

Animals↗
PubMedDate not supplied

Placement and replacement of resin-based composite restorations in Italy.

The use of resin-based composite restorations, the reasons for failure, and the longevity of these restorations have been surveyed in 62 Italian private practices. Almost two-thirds of the 1025 restorations inserted were class 3 and 5 restorations, while 18% were class 1 and 2 restorations. Secondary caries was the most common reason reported for replacement of resin-based composite restorations (44%), followed by discoloration (21%), and bulk and margin fracture (14%). The age of restorations needing replacement was reported for 53% of the sample. The median longevity in this sample was calculated to be 3.3 years.

Composite Resins↗
PubMed2005

Amino acids as placeholders: base-composition pressures on protein length in malaria parasites and prokaryotes.

BACKGROUND: The composition and sequence of amino acids in a protein may serve the underlying needs of the nucleic acids that encode the protein (the genome phenotype). In extreme form, amino acids become mere placeholders inserted between functional segments or domains, and--apart from increasing protein length--playing no role in the specific function or structure of a protein (the conventional phenotype). METHODS: We studied the genomes of two malarial parasites and 521 prokaryotes (144 complete) that differ widely in GC% and optimum growth temperature, comparing the base compositions of the protein coding regions and corresponding lengths (kilobases). RESULTS: Malarial parasites show distinctive responses to base-compositional pressures that increase as protein lengths increase. A low-GC% species (Plasmodium falciparum) is likely to have more placeholder amino acids than an intermediate-GC% species (P. vivax), so that homologous proteins are longer. In prokaryotes, GC% is generally greater and AG% is generally less in open reading frames (ORFs) encoding long proteins. The increased GC% in long ORFs increases as species' GC% increases, and decreases as species' AG% increases. In low- and intermediate-GC% prokaryotic species, increases in ORF GC% as encoded proteins increase in length are largely accounted for by the base compositions of first and second (amino acid-determining) codon positions. In high-GC% prokaryotic species, first and third (non-amino acid-determining) codon positions play this role. CONCLUSION: In low- and intermediate-GC% prokaryotes, placeholder amino acids are likely to be well defined, corresponding to codons enriched in G and/or C at first and second positions. In high-GC% prokaryotes, placeholder amino acids are likely to be less well defined. Increases in ORF GC% as encoded proteins increase in length are greater in mesophiles than in thermophiles, which are constrained from increasing protein lengths in response to base-composition pressures.

Amino Acid Sequence↗
PubMed2004

Physical and mechanical properties of an experimental dental composite based on a new monomer.

OBJECTIVE: The purpose of this study was to investigate the physical and mechanical properties of a dental composite based on BTDMA, a new dimethacrylate monomer based on BTDA (3,3',4,4'-benzophenone tetracarboxylic dianhydride), and to compare these with the properties of a composite based on commonly used Bis-GMA monomer. METHODS: Experimental composites were prepared by mixing the silane-treated filler with the monomers. The prepared pastes were inserted into the test molds and heat-cured. Light-cured composites were also prepared using camphorquinone and amine as photoinitiator system. Degree of conversion of the light-cured and heat-cured composites was measured using FTIR spectroscopy. The flexural strength, flexural modulus, diametral tensile strength (DTS), water sorption, water contact angle, microhardness and thermal expansion coefficient of the prepared composites were measured and compared. Water uptake of the monomers was also measured. RESULTS: The results showed that the mechanical properties of the new composite are comparable with the properties of the Bis-GMA-based composite but its water sorption is higher. BTDMA as a monomer containing aromatic rings and carboxylic acid groups in its structure gives a composite with good mechanical properties. There is a close relation between the contact angle, water sorption of the cured composite and water uptake of their monomers. SIGNIFICANCE: Finding new monomers as alternatives for Bis-GMA have been a challenge in the field of dental materials and any investigation into the properties of new composites would be beneficial in the development of dental materials.

Analysis of Variance↗