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PubMed2004

A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods.

Phylogenetic analysis of mammalian species using mitochondrial protein genes has proved to be problematic in many previous studies. The high mutation rate of mitochondrial DNA and unusual base composition of several species has prompted us to conduct a detailed study of the composition of 69 mammalian mitochondrial genomes. Most major changes in base composition between lineages can be attributed to shifts between the proportions of C and T on the L-strand. These changes are significant at all codon positions and are shown to affect amino acid composition. Correlated changes in the base composition of the RNA loops and stems are also observed. Following up from previous studies, we investigate changes in the base composition of all 12 H-strand proteins and find that variability in proportions of C and T is correlated with location on the genome. Variation in base composition across genes and species is known to adversely affect the performance of phylogenetic inference methods. We have, therefore, developed a customized three-state general time-reversible DNA substitution model, implemented in the PHASE phylogenetic inference package, which lumps C and T into a composite pyrimidine state. We compare the phylogenetic tree obtained using the new three-state model with that obtained using a standard four-state model. Results using the three-state model are more congruent with recent studies using large sets of nuclear genes and help resolve some of the apparent conflicts between studies using nuclear and mitochondrial proteins.

Animals↗
PubMed2001

Statistical measures of DNA sequence dissimilarity under Markov chain models of base composition.

In molecular biology, the issue of quantifying the similarity between two biological sequences is very important. Past research has shown that word-based search tools are computationally efficient and can find some new functional similarities or dissimilarities invisible to other algorithms like FASTA. Recently, under the independent model of base composition, Wu, Burke, and Davison (1997, Biometrics 53, 1431 1439) characterized a family of word-based dissimilarity measures that defined distance between two sequences by simultaneously comparing the frequencies of all subsequences of n adjacent letters (i.e., n-words) in the two sequences. Specifically, they introduced the use of Mahalanobis distance and standardized Euclidean distance into the study of DNA sequence dissimilarity. They showed that both distances had better sensitivity and selectivity than the commonly used Euclidean distance. The purpose of this article is to extend Mahalanobis and standardized Euclidean distances to Markov chain models of base composition. In addition, a new dissimilarity measure based on Kullback-Leibler discrepancy between frequencies of all n-words in the two sequences is introduced. Applications to real data demonstrate that Kullback-Leibler discrepancy gives a better performance than Euclidean distance. Moreover, under a Markov chain model of order kQ for base composition, where kQ is the estimated order based on the query sequence, standardized Euclidean distance performs very well. Under such a model, it performs as well as Mahalanobis distance and better than Kullback-Leibler discrepancy and Euclidean distance. Since standardized Euclidean distance is drastically faster to compute than Mahalanobis distance, in a usual workstation/PC computing environment, the use of standardized Euclidean distance under the Markov chain model of order kQ of base composition is generally recommended. However, if the user is very concerned with computational efficiency, then the use of Kullback-Leibler discrepancy, which can be computed as fast as Euclidean distance, is recommended. This can significantly enhance the current technology in comparing large datasets of DNA sequences.

Algorithms↗
PubMed2002

Curing-light intensity and depth of cure of resin-based composites tested according to international standards.

BACKGROUND: Several factors control the light curing of a resin-based composite: the composition of the composite, the shade of the composite, the wavelength and bandwidth of the curing light, the distance of the light from the composite, the intensity of the curing light and the irradiation time. The authors investigated the depth of cure of several shades of five brands of resin-based composites when irradiated via light in the 400- to 515-nanometer wavelength bandwidth at the International Organization for Standardization, or ISO, recommended intensity of 300 milliwatts per square centimeter. The resin-based composites were irradiated for the times recommended by the products' manufacturers. METHODS: The authors used a curing light adjusted to emit 300 mW/cm2 in the 400-nm to 515-nm wavelength bandwidth to polymerize five samples of each composite brand type and shade. They measured depth of cure using a scraping method described in the ISO standard for resin-based composites. Depth of cure was defined as 50 percent of the length of the composite specimen after uncured material was removed by manual scraping. The authors determined a mean from the five samples of each composite brand and shade. RESULTS: Thirteen (62 percent) of 21 composite materials met the ISO standard depth-of-cure requirement of 1.5 millimeters. Six of the eight remaining materials met the depth-of-cure requirement when the authors doubled the irradiation time recommended by the product manufacturers. CONCLUSIONS AND CLINICAL IMPLICATIONS: Curing lights with an intensity of 300 mW/cm2 appear to effectively cure most resin-based composite materials when appropriate curing times are used, which, in some cases, are longer than those recommended by the manufacturers. Dentists should verify the depth of cure of a composite material as a baseline measure, and then check depth of cure periodically to confirm light and material performance. The ISO depth-of-cure measurement method can be used for this purpose.

Composite Resins↗
PubMed1985

Spectral analysis for base composition of DNA undergoing melting.

A microcomputer-controlled spectrophotometer is described for obtaining the base composition of melting domains in DNA from derivative melting curves. Values have been determined for the differential molar extinction coefficients for the A-T and G-C base pair at the three wavelengths most useful for spectral analysis of base composition, 260, 270 and 282 nm. The average RMS error for these values was 29 l(mol X cm)-1 for the melting of 14 DNA specimens ranging in base composition from 0-0.72 F(G + C). A precision of approximately 1% in base composition of domains is possible. Such analysis is useful for confirming or establishing assignments of domains to particular subtransitional features in high resolution melting curves.

Base Composition↗
PubMed1976

Mechanisms of chromosome banding. IX. Are variations in DNA base composition adequate to account for quinacrine, Hoechst 33258 and daunomycin banding?

Prior studies on subfractions of mouse and Kangaroo rat DNA have suggested that variations in base concentration within a given genome may not be great enough to account for Q-banding. To examine this with another species, calf DNA was subfractionated by CsCl ultracentrifugation into GC-rich satellites and the main band DNA was further fractionated into AT-rich, intermediate and GC-rich portions. The effect of varying concentrations of these DNAs on quinacrine and Hoechst 33258 fluorescence was examined. Although with both compounds there was less fluorescence in the presence of the GC-rich satellites than main band fractions, these results per se did not answer the question of whether the variation in base composition alone was adequate to account for chromosome banding. To answer this the fluorescence observed in the presence of DNA of a given base composition was related to the fluorescence observed in the presence of DNA of 40% GC content (F/F40). This allowed the derivation of a term B which indicated the relative change in fluorescence per 1% change in base composition of DNA. To determine the percent change in fluorescence observed in Q-banding, the photoelectric recordings of Caspersson et al. (1971) were used. From these data we conclude: 1. Quinacrine is twice as sensitive to changes in base composition as Hoechst 33258. 2. Variation in the base content of DNA along the base content of DNA along the chromosome is sufficient to account for most Q-banding, except possibly for some of the extremes of quinacrine fluorescence. This was further examined with daunomycin. Even though daunomycin gives good fluorescent banding, DNAs varying in base composition from 100 to 40% GC content all resulted in the same relative fluorescence of 0.03. However, in the presence of poly (dA-dT) the relative fluorescence was 0.85, indicating a great sensitivity to very AT-rich DNA. This suggests that with daunomycin and possibly other fluorochromes, stretches of very AT-rich DNA may be more important in fluorescent banding than simple variation in mean base composition.

Adenine Nucleotides↗
PubMed2004

Effect of two different restorative techniques using resin-based composites on microleakage.

PURPOSE: To evaluate in vitro the extent of microleakage of Class II cavities restored with two different brands of resin-based composite, one hybrid (Tetric Ceram) and the other "packable" (Surefil) taking into account two variables: the localization of the margins and the insertion technique. METHODS: 100 bovine teeth, recently extracted, had standardized Class II slot cavities prepared on the mesial and distal surfaces with the gingival floor located on enamel or dentin, for a total 200 cavities. The teeth were randomly divided into eight groups of 25 teeth each (25 restorations in each group): (1) margin on dentin, restored with Surefil, bulk insertion; (2) margin on dentin, restored with Tetric Ceram, bulk insertion; (3) Margin on enamel, restored with Surefil, incremental technique; (4) margin on enamel, restored with Tetric Ceram, incremental technique; (5) margin on enamel, restored with Surefil, bulk insertion; (6) margin on enamel, restored with Tetric Ceram, bulk insertion; (7) margin on dentin, restored with Surefil, incremental technique; (8) margin on dentin, restored with Tetric Ceram, incremental technique. After this procedure, the teeth were subjected to 1000 thermocycles, stained with 2% methylene blue solution, and then sectioned in the mesiodistal direction. Dye penetration at tooth/restoration interface was scored based upon the extent of the dye using a light stereoscope x 35. RESULTS: All groups showed considerable levels of microleakage at both dentin and enamel margins (P < 0.05). Restorations with margins in enamel using the hybrid resin-based composite with the incremental technique did not show statistically significant differences when compared to bulk placement. However, restorations with hybrid resin-based composite have significantly less microleakage than either bulk or incremental technique for the "packable" resin-based composite Surefil. As for the margins in dentin, Tetric Ceram in bulk placement did not differ from the incremental technique and Tetric in bulk placement had significantly less microleakage than Surefil either bulk or incremental technique. The hybrid resin-based composite with margins in dentin and incremental technique showed less microleakage than the "packable" resin in bulk placement. CLINICAL SIGNIFICANCE: The two types of resin-based composites, hybrid and "packable" were unable to completely prevent microleakage. The study demonstrated the difficulty in sealing a proximal margin.

Animals↗
PubMed1964

Base composition of deoxyribonucleic acid of sulfate-reducing bacteria deduced from buoyant density measurements in cesium chloride.

Saunders, Grady F. (University of Illinois, Urbana), L. Leon Campbell, and John R. Postgate. Base composition of deoxyribonucleic acid of sulfate-reducing bacteria deduced from buoyant density measurements in cesium chloride. J. Bacteriol. 87:1073-1078. 1964.-The base composition of the deoxyribonucleic acid (DNA) of sulfate-reducing bacteria was calculated from buoyant density measurements in CsCl. The sporulating sulfate-reducing bacteria fell into two groups: Desulfovibrio orientis with a DNA base composition of 42% guanine plus cytosine (G + C), and Clostridium nigrificans with a DNA base composition of 45% G + C. The mesophilic relative of C. nigrificans had a DNA base composition of 46% G + C. Thirty strains of nonsporulating sulfate-reducing bacteria called D. desulfuricans were studied. They fell into three groups as judged by DNA base composition: group I (11 strains), 60 to 62% G + C; group II (13 strains), 54 to 56% G + C; and group III (6 strains), 46 to 47% G + C. These data underline the need for a taxonomic revision of this group of microorganisms.

Bacteria↗
PubMed2003

Comparison of responses by bacteriophages and bacteria to pressures on the base composition of open reading frames.

Differences in the base composition of genomes can occur because of GC pressure, purine-loading pressure (AG pressure) and RNY pressure, for which there are possible functional explanations, and because of the more abstract pressures exerted by individual bases. The graphical approach of Muto and Osawa was used to analyse how bacteriophages and bacteria balance potentially conflicting pressures on their genomes. Phages generally respond to AG pressure by increasing A while keeping T constant, and by decreasing C while keeping G constant. In contrast, bacteria generally increase both A and T, the former more so, and decrease both G and C, the latter more so. These differences largely occur at third codon positions, which are more responsive than first and second codon positions to AG pressure and GC pressure. Phages respond to AG pressure more in the third codon position than bacteria, whereas bacteria respond more in the first codon position than phages. Conversely, bacteria respond to GC pressure more in the third codon position than phages, whereas phages respond more in the first codon position than bacteria. As GC pressure increases, A is traded for C and AG pressure decreases; first and second codon positions, having more A than T, are most responsive to this negative effect of increased GC pressure; third positions either do not respond (phages) or respond weakly (bacteria). In a set of 48 phage-host pairs, degrees of purine loading were less correlated between phage and host than were GC percentages. These results suggest that pressures on conventional and genome phenotypes operate differentially in phages and bacteria, generating both general differences in base composition and specific differences characteristic of particular phage-host pairs. The reciprocal relationship between GC pressure and AG pressure implies that effects attributed to GC pressure may actually be due to AG pressure, and vice versa.

Bacteria↗
PubMed2006

Light-emitting diode curing light irradiance and polymerization of resin-based composite.

BACKGROUND: Light-emitting diode (LED) curing lights are becoming popular; however, questions about their efficiency remain. The authors performed a comprehensive analysis of the properties of resin-based composites cured with LED lights. METHODS: The authors evaluated seven LED lights and one quartz-tungsten-halogen light (control). They measured intensity, depth of cure (DOC), degree of conversion (DC), hardness and temperature rise. They used three shades of a hybrid resin-based composite and a microfill composite, as well as one shade of another hybrid composite. RESULTS: Two LED lights required additional cure time to reach a DOC similar to that of the control light. DC at the top of the samples was independent of the light used. At 2.0 millimeters, the DC for several LED lights was significantly lower than that for the control light and was correlated strongly to the light's intensity. The bottom-to-top ratio for hardness of resin-based composites cured by all but one light was greater than 0.80. All LED lights except one had smaller temperature rise than did the control light. CONCLUSIONS: Six of the seven LED curing lights performed similarly to a quartz-tungsten-halogen curing light in curing resin-based composites. Clinical Implications. While LED curing lights and a quartz-tungsten-halogen light could cure resin-based composites, some resin-based composites cured with LED lights may require additional curing time or smaller increments of thickness.

Composite Resins↗
PubMed1999

Sorting out the confusing array of resin-based composites in dentistry.

Several categories of useful restorative resin-based composites have evolved over the past 40 years. Some of them are indispensable; others are clearly not as necessary. It is possible that dental practitioners could practice successfully with only one type of resin-based composite: hybrid. But each type added to a clinical armamentarium provides possibilities for better esthetic results, easier and better clinical placement, or better long-term function. Undoubtedly, even more categories of restorative resin-based composite will evolve in the future. Dentists are advised to observe them carefully before buying to see if they satisfy any additional needs.

Composite Resins↗
PubMed1977

Intramolecular base composition heterogeneity of human DNA.

The intramolecular base composition heterogeneity of human DNA has been investigated by electron microscopic observations of partially denatured structures and by equilibrium solution thermal denaturation techniques. DNA sequences having an average length of less than 2000 base pairs are found to be heterogeneous in base composition. These heterogeneous sequences occupy a minimum of 67 to 81% of the human genome.

Base Sequence↗
PubMed1999

Pulse activation: reducing resin-based composite contraction stresses at the enamel cavosurface margins.

PURPOSE: To evaluate the effect of pulse activation light-curing of resin-based composites on the stress reduction at the enamel surface. MATERIALS AND METHODS: The rate of polymerization of a resin-based composite known to be accompanied by high contraction stress was examined by its surface hardness. The effects of polymerization stresses were examined with the use of dye penetration along enamel margins in cavities with a C-factor of 5. The occlusal-most layer of resin-based composite was polymerized at different power densities and time intervals; 40 s@600 mW/cm2, 40 s@100 mW/cm2 and pulse activation; 2 s@300-350 mW/cm2, followed by additional exposure of 10 s@600 mW/cm2. Diametral tensile strengths were measured for each parameter. RESULTS: The surface hardnesses of both the 40 s@600 mW/cm2 group and the 40 s@100 mW/cm2 group developed at nearly the same rate. The surface hardness of the pulse activated group developed appreciably slower. The diametral tensile strengths of all three groups were not significantly different. There was significantly less dye penetration with the use of the lower power density but there was very little leakage noted with the pulse-activated group. It is believed that this is the result of a prolonged gel state, which allowed flow to occur in the resin-based composite. There is significant clinical potential for the use of pulse activation of light-cured resin-based composite materials.

Composite Resins↗
PubMed1997

Length and base composition of PCR-amplified nucleic acids using mass measurements from electrospray ionization mass spectrometry.

A generally applicable algorithm has been developed to allow base composition of polymerase chain reaction (PCR) products to be determined from mass spectrometrically measured molecular weights and the complementary nature of DNA. Mass measurements of arbitrary precision for single-stranded DNA species are compatible with an increasingly large number of possible base compositions as molecular weight increases. For example, the number of base compositions that are consistent with a molecular weight of 35,000 is approximately 6000, based on a mass measurement precision of 0.01%. However, given the low misincorporation rate of standard DNA polymerases, mass measurement of both of the complementary single strands produced in the PCR reduces the number of possibilities to less than 100 at 0.01% mass precision, and base composition is uniquely defined at 0.001% mass precision. Taking into account the low misincorporation rate of standard DNA polymerases and the fact that the final PCR product also contains primers of known sequence (generally 15-20-mer in size, which flank the targeted region), this reduces the number of possible base combinations to only approximately 3 at MW = 35,000. In addition, the number of base pairs (i.e., length of the DNA molecule) is uniquely defined. We show that the use of modified bases in PCR or post-PCR modification chemistry allows unique solutions for the base composition of the PCR product with only modest mass measurement precision.

Algorithms↗
PubMed2001

The effect of a dental unit waterline treatment regimen on the shear bond strength of resin-based composite.

BACKGROUND: Numerous methods of disinfecting dental waterlines have been suggested. This study evaluates the effects of one disinfecting technique on the strength of resin-based composite's bond to enamel and to dentin. METHODS: The authors bonded resin-based composite cylinders to enamel and dentin surfaces similarly mounted and prepared using three irrigation solutions. After undergoing acid etching, the tooth surface was rinsed with either distilled water, water from a municipal water source or a mixture of distilled water and mouthwash concentrate. The authors shear-tested the samples and analyzed the data statistically. RESULTS: The group rinsed with distilled water mixed with mouthwash exhibited the lowest shear bond strengths. However, a one-way ANOVA indicated no statistically significant differences in the mean values among the treatment groups for either enamel (P = .295) or dentin (P = .393). Specimens bonded to enamel demonstrated primarily adhesive fracture at the tooth/composite interface. Those bonded to dentin showed a similar pattern, with some sites of cohesive fracture in the resin-based composite. CONCLUSIONS: There was no significant difference in shear bond strengths of resin-based composite to tooth structure when rinsed with distilled water mixed with mouthwash, distilled water or water from a municipal source. CLINICAL IMPLICATIONS: Dental unit waterlines disinfected using a diluted mouthwash solution may be used while bonding resin-based composite to either enamel or dentin.

Acid Etching, Dental↗
PubMed1994

Skewed base compositions, asymmetric transition matrices, and phylogenetic invariants.

Evolutionary inference methods that assume equal DNA base compositions and symmetric nucleotide substitution matrices, where these assumptions do not hold, are likely to group species on the basis of similar base compositions rather than true phylogenetic relationships. We propose an invariants-based method for dealing with this problem. An invariant QT of a tree T under a k-state Markov model, where a generalized time parameter is identified with the E edges of T, allows us to recognize whether data on N observed species can be associated with the N terminal vertices of T in the sense of having been generated on T rather than on any other tree with N terminals. The form of the generalized time parameter is a positive determinant matrix in some semigroup S of stochastic matrices. The invariance is with respect to the choice of the set of E matrices in S, one associated with each of the E edges of T. We apply a general "empirical" method of finding invariants of a parametrized functional form. It involves calculating the probability f of all KN data possibilities for each of m sets of E matrices in S to associate with the edges of T, then solving for the parameters using the m equations of form Q(f) = 0. We discuss the problems of finding asymmetric models satisfying the property of semigroup closure, of finding asymmetric models that admit invariants at all, and of the computational complexity of the method. We propose a class of semigroups Sc containing matrices of form [formula: see text] to account for A+T versus G+C asymmetries in DNA base composition. Quadratic invariants are obtained for rooted trees with three and with four terminals. In the latter case the smallest set of algebraically independent invariants is sought. These invariants are applied to data pertaining the fungal evolution and to the origin of mitochondria as bacterial endosymbionts.

Algorithms↗
PubMed2000

The physical properties of packable and conventional posterior resin-based composites: a comparison.

BACKGROUND: The authors compared the physical properties of three packable hybrid resin-based composites with those of a conventional hybrid and a microfill composite material advocated for use as posterior restorative materials. They evaluated diametral tensile strength, or DTS; compressive strength, or CS; flexural strength, or FS; and depth of cure, or DC. METHODS: The authors studied the following resin-based restorative materials: three packable composites, Alert Condensable Composite (Jeneric Pentron), SureFil High Density Posterior Restorative (Dentsply Caulk) and Solitaire (Heraeus Kulzer); one conventional hybrid composite, TPH Spectrum (Dentsply Caulk); and one microfill, Heliomolar Radiopaque (Ivoclar-Vivadent). The authors evaluated DTS, CS, FS and DC, according to American National Standards Institute criteria. They made scanning electron micrographs of the packable resin-based composites. RESULTS: Results demonstrated that the conventional hybrid, TPH Spectrum, had significantly greater DTS and FS than other resin-based composites. Alert and SureFil had comparable DTS and FS, which were significantly greater than Heliomolar's DTS and FS. Solitaire had significantly lower DTS and FS than all other resin-based composites. SureFil had the highest CS, followed by TPH Spectrum, Solitaire and Alert, which were comparable and had significantly greater CS than Heliomolar. TPH Spectrum and Alert had significantly greater DC than all other resin-based composites, followed in decreasing order by SureFil, Solitaire and Heliomolar. CONCLUSION: While the packable composites tested in this study had physical properties superior to those of the microfill composite, they were no better suited for use as a posterior restorative material than was the conventional hybrid resin-based composite. CLINICAL IMPLICATIONS: Packable composites may be easier for clinicians to handle than conventional resin-based composites; however, their physical properties were not superior to those of the conventional small-particle hybrid resin-based composite. In addition, these materials may have the clinical drawback of increased wear and surface roughness that was seen with early, large-particle composite restorative materials.

Acrylic Resins↗
PubMed1981

Marginal adaptation of BIS-GMA-based composites containing various diluents.

The aim of this study was to determine how otherwise acceptable diluent monomers affect the marginal adaptation of BIS-GMA-based composites. Based on the results of the investigation, the following conclusions can be drawn: 1. Addition to dimethacrylate diluents containing (CH2) recurring units generally yields composites having better marginal adaptation than do those containing (CH2 CH2 O) groups. Best marginal adaptation for a single diluent is obtained for compositions using 1, 4 and 1, 10-polymethylene glycol dimethacrylate as diluent. 2. Marginal adaptation is improved on lowering the diluent concentration. Optimum adaptation will be obtained for a formulation containing a minimum percentage of diluent with clinically acceptable working properties. 3. Volume changes on temperature cycling resulting from differences in thermal expansion coefficients of composites do not effect the marginal integrity as much as does curing shrinkage.

Acrylates↗
PubMed2000

Physicochemical evaluation of bioactive polymeric composites based on hybrid amorphous calcium phosphates.

Amorphous calcium phosphate (ACP)-filled methacrylate composites were recently found to effectively remineralize in vitro caries-like enamel lesions. Their inferior mechanical properties compared to glass-filled composites, however, limit their use as a dental restorative material. In this study, the feasibility of introducing glass-forming elements (tetraethoxysilane or zirconyl chloride) during the low-temperature synthesis of ACP was investigated. Composites based on such hybrid fillers (mass fraction, 40%) were evaluated to establish whether hybridization strengthened the composites via improved interfacial interactions with the polymer phase without compromising the release of the mineral ions. Two types of visible-light cured resins were prepared: BTHZ resin from 2, 2-bis[p-(2'-hydroxy-3'-methacryloxypropoxy)phenyl]propane (BisGMA), triethylene glycol dimethacrylate (TEGDMA), 2-hydroxyethyl methacrylate (HEMA) and zirconyl methacrylate (ZrM), and TP resin from TEGDMA and pyromellitic glycerol dimethacrylate (PMGDM). Hybridized fillers and BTHZ- and TP-based composites were characterized by the IR spectroscopy, X-ray diffraction, dissolution/transformation kinetic studies, and biaxial flexure strength (BFS) testing before and after immersion in buffered saline solutions. The feasibility of improving the BFS via hybridization, while retaining, if not enhancing the remineralizing potential was demonstrated for BTHZ-based composites. Both BFS and remineralizing ability of the TP-composites, however, deteriorated upon their exposure to an aqueous environment. Therefore, hybridized ACP-filled BTHZ composites have a potential for utilization in more demanding restorative, sealant, and adhesive applications.

Calcium Phosphates↗