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PubMed2004

[Study on polysiloxane resin-based composites for bone surgery application].

The study aimed at determination of mechanical and biological properties of three types of carbon fibers-based composites differing in matrix as potential materials for bone surgery. Three types of polymethylphenyl siloxane resins (produced by Lucebni zavody, Kolin, Czech Republic) differing with Si/C ratio were used as matrix. Carbon fibers T-300 (Torayca) were used as the reinforcement. The composite samples were manufactured by liquid impregnation of carbon roving followed by thermal curing. The resins were characterized by means of infrared spectroscopy. The strength and Young's modulus of the composite samples were determined in three-point bending test. The MTT tests were led in the presence of line KMA human macrophages and line hFOB 1.19 human osteoblasts. The results presented in this work indicate that mechanical properties of the composites are adequate from viewpoint of bone surgery requirement for load-bearing implants. The viability of macrophages cultures in contact with all examined samples was higher than 85%. The highest viability of human osteoblasts was obtained for composites based on L 901 and L 4102 resins-above 60%. The results suggest that the investigated polysiloxane-based composites are biocompatible, however their possible use as implants needs further study.

Cell Line↗
PubMed2006

A composition-based cartilage model for the assessment of compositional changes during cartilage damage and adaptation.

OBJECTIVE: The composition of articular cartilage changes with progression of osteoarthritis. Since compositional changes are associated with changes in the mechanical properties of the tissue, they are relevant for understanding how mechanical loading induces progression. The objective of this study is to present a computational model of articular cartilage which enables to study the interaction between composition and mechanics. METHODS: Our previously developed fibril-reinforced poroviscoelastic swelling model for articular cartilage was combined with our tissue composition-based model. In the combined model both the depth- and strain-dependencies of the permeability are governed by tissue composition. All local mechanical properties in the combined model are directly related to the local composition of the tissue, i.e., to the local amounts of proteoglycans and collagens and to tissue anisotropy. RESULTS: Solely based on the composition of the cartilage, we were able to predict the equilibrium and transient response of articular cartilage during confined compression, unconfined compression, indentation and two different 1D-swelling tests, simultaneously. CONCLUSION: Since both the static and the time-dependent mechanical properties have now become fully dependent on tissue composition, the model allows assessing the mechanical consequences of compositional changes seen during osteoarthritis without further assumptions. This is a major step forward in quantitative evaluations of osteoarthritis progression.

Adaptation, Physiological↗
PubMed1978

A critical examination of possible fractionations of human DNA according to base composition.

Human DNA has been fractionated according to base composition by sedimentation equilibrium in an HgCl2/Cs2SO4 density gradient, followed by sedimentation equilibrium in an actinomycin/cesium formate density gradient. The fractions of different base composition resulting from this procedure were subsequently analyzed by sedimentation equilibrium in CsCl, DNA renaturation kinetics, and electron microscopy. All fractions contain similar kinetic classes of repeated DNA sequences as judged by renaturation studies. Short (300 nucleotides) interspersed repeated sequences are found in all fractions with no noticeable enrichment for these sequences in any fraction. Repeated sequences from fractions of different base composition are partially able to cross-hybridize, demonstrating that nearly identical repeated sequences occur in molecules of different base composition. These findings are critically compared to reports of successful density gradient fractionations of different human DNA sequence classes.

Centrifugation, Density Gradient↗
PubMed2003

The leakage of Class II cavities restored with packable resin-based composites.

Recently, new resin-based composites, called "packable" or "condensable" resin composites, are being promoted as amalgam alternatives. The purpose of this study was to evaluate leakage in Class II cavities restored with the five packable resin-based composites. On 45 freshly extracted human molars, cavities were prepared following a standardized pattern in which the Class II cavity had a length of 3.0 mm, width of 2.0 mm, and depth of 1.5 mm occlusally. The proximal box had an axial depth of 1.5 mm and a buccolingual width of 4.0 mm. The cervical margin was located 1.0 mm below the cement enamel junction (CEJ). The teeth were randomly divided into five groups of 8 each. The cavity surface was conditioned with 36% phosphoric acid, rinsed, excess water removed, and a dental bonding adhesive (Prime&Bond NT) was used for all the cavities. The teeth were then restored according to the manufacturer's instructions: Group 1, Surefil; Group 2, Solitaire; Group 3, Alert; Group 4, Filtek P60; and Group 5, Prodigy Condensable. After the restorations were completed, the specimens were finished and polished with an aluminum-oxide-coated disc, thermocycled, stained, sectioned, and viewed under a stereomicroscope for leakage at occlusal/enamel and gingival/dentin margins. All test groups showed that leakage of gingival/dentin margins were greater when compared with leakage of occlusal/enamel margins. At the occlusal/enamel margins, there were no significant differences between the materials; however, at gingival/dentin margins, Filtek P60 and Prodigy Condensable demonstrated less leakage, while Solitaire demonstrated greater leakage.

Composite Resins↗
PubMed2006

Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome.

Fluctuations in base composition appear to be prevalent in Drosophila and mammal genome evolution, but their timescale, genomic breadth, and causes remain obscure. Here, we study base composition evolution within the X chromosomes of Drosophila melanogaster and five of its close relatives. Substitutions were inferred on six extant and two ancestral lineages for 14 near-telomeric and 9 nontelomeric genes. GC content evolution is highly variable both within the genome and within the phylogenetic tree. In the lineages leading to D. yakuba and D. orena, GC content at silent sites has increased rapidly near telomeres, but has decreased in more proximal (nontelomeric) regions. D. orena shows a 17-fold excess of GC-increasing vs. AT-increasing synonymous changes within a small (approximately 130-kb) region close to the telomeric end. Base composition changes within introns are consistent with changes in mutation patterns, but stronger GC elevation at synonymous sites suggests contributions of natural selection or biased gene conversion. The Drosophila yakuba lineage shows a less extreme elevation of GC content distributed over a wider genetic region (approximately 1.2 Mb). A lack of change in GC content for most introns within this region suggests a role of natural selection in localized base composition fluctuations.

Animals↗
PubMed2003

Depth of cure and microleakage with high-intensity and ramped resin-based composite curing lights.

BACKGROUND: The authors conducted a study to determine whether high-intensity curing lights in high and ramped intensity modes affect microleakage of resin-based composite restorations and whether different types of resin-based composites meet American National Standards Institute/American Dental Association Specification no. 27 (1993): 7.7 for depth of cure when polymerized using these lights. METHODS: The authors compared five high-intensity lights, three plasma arc lights and two quartz-tungsten-halogen lights in their regular and ramped intensity modes with a quartz-tungsten-halogen 40-second light. The parameters tested were microleakage one month after bonding and curing depth for different resin-based composite types. The authors measured curing depth using a scratch test. RESULTS: Light curing with Optilux 501 (Kerr/Demetron, Orange, Calif.) for 10 seconds and ADT Power PAC (American Dental Technologies, Corpus Christi, Texas) for 10 seconds resulted in higher microleakage values than light curing with other lights (P < .05). The microhybrid resin-based composite was the only material that met the specification when light cured with all of the lights tested. The flowable resin-based composite did not meet the specification when light cured with all lights tested. Microhybrid resin-based composite had the greatest depth of cure, and flowable resin-based composite had the least depth of cure. CONCLUSIONS: Microhybrid resin-based composite microleakage is affected by some light-curing modes. Different categories of resin-based composites are cured to different depths using high-intensity lights. CLINICAL IMPLICATIONS: Light curing with some high-intensity lights compared with halogen lights may result in higher microleakage values. Use caution when light curing flowable resin-based composite with the high-intensity lights. Place increments less than 2 millimeters in depth when using this material.

Analysis of Variance↗
PubMed1987

High-performance liquid chromatographic analysis of oligodeoxyribonucleotide base composition.

A significantly improved method for base composition analysis of synthetic oligodeoxyribonucleotides is presented. This highly accurate and sensitive method used enzymatic digestion followed by high-resolution HPLC of the nucleosides to determine the empirical base composition of the parent compound. The enzymatic digestion reaction is quantitative and is not blocked by modified bases, thus allowing the degree of base deprotection and chemical modification to be assessed. Digestion data are presented for oligodeoxyribonucleotides which range from 18 to 150 bases in length with excellent agreement of experimental and theoretical composition. The method is also applicable to high-molecular-weight genomic DNA.

Alkaline Phosphatase↗
PubMed2001

Evolution of base composition and codon usage bias in the genus Flavivirus.

The extent to which base composition and codon usage vary among RNA viruses, and the possible causes of this bias, is undetermined in most cases. A maximum-likelihood statistical method was used to test whether base composition and codon usage bias covary with arthropod association in the genus Flavivirus, a major source of disease in humans and animals. Flaviviruses are transmitted by mosquitoes, by ticks, or directly between vertebrate hosts. Those viruses associated with ticks were found to have a significantly lower G+C content than non-vector-borne flaviviruses and this difference was present throughout the genome at all amino acids and codon positions. In contrast, mosquito-borne viruses had an intermediate G+C content which was not significantly different from those of the other two groups. In addition, biases in dinucleotide and codon usage that were independent of base composition were detected in all flaviviruses, but these did not covary with arthropod association. However, the overall effect of these biases was slight, suggesting only weak selection at synonymous sites. A preliminary analysis of base composition, codon usage, and vector specificity in other RNA virus families also revealed a possible association between base composition and vector specificity, although with biases different from those seen in the Flavivirus genus.

Amino Acids↗
PubMed2004

Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.

The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (AT-->GC vs. GC-->AT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 AT-->GC:GC-->AT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of AT-->GC and GC-->AT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N(e) in the molecular evolution of bacterial endosymbionts.

Animals↗
PubMed2003

Clinical evaluation of packable and conventional hybrid resin-based composites for posterior restorations in permanent teeth: results at 12 months.

BACKGROUND: Packable resin-based composites and simplified resin bonding systems are marketed to offer many advantages over conventional posterior hybrid composites and total-etch bonding systems. The authors conducted a study to evaluate the initial clinical performances of a packable and a conventional hybrid resin-based composite used with a simplified bonding system. METHODS: A total of 57 Class I and 45 Class II restorations were placed in the permanent teeth of 65 adult patients. The carious lesions were restored with either packable resin-based composite (SureFil, Dentsply DeTrey GmbH, Konstanz, Germany) or conventional hybrid resin-based composite (SpectrumTPH, Dentsply DeTrey GmbH), using a resin adhesive (Non-Rinse Conditioner and Prime & Bond NT, both manufactured by Dentsply DeTrey GmbH). The authors evaluated the restorations using U.S. Public Health Service-Ryge modified criteria (in which Alfa is the highest rating) and by using color transparencies and die stone replicas. RESULTS: Three SureFil restorations failed before their baseline evaluation. There were no failures among the 78 SpectrumTPH restorations evaluated at 12 months. For both resin-based composites, Alfa ratings were 90 percent or higher for marginal discoloration, anatomical form, surface texture and surface staining. Lower percentages of restorations were rated Alfa for color match, marginal integrity and gingival health. Occasional mild postoperative sensitivity was reported for four SureFil restorations and one SpectrumTPH restoration. The mean occlusal wear rate was 38 micrometers for the larger SureFil restorations and 25 microm for the smaller SpectrumTPH restorations. CONCLUSIONS: The 12-month clinical performances of the two restorative materials were satisfactory and not significantly different for each of the parameters evaluated. CLINICAL IMPLICATIONS: A packable and a conventional hybrid resin-based composite placed with a simplified bonding system in posterior permanent teeth showed satisfactory and similar results after 12 months.

Adolescent↗
PubMed2003

Estimation of the optimal electrophoretic temperature of DNA single-strand conformation polymorphism by DNA base composition.

To explore the relation between DNA base composition and the optimal single-strand conformation polymorphism (SSCP) electrophoretic temperature (T(s)), we analyzed DNA base composition and T(s) of 24 DNA fragments from different genes and found that T(s) was positively correlative with the ratio of base C/base A. T(s) could be estimated by the formula T(s) = [80 x C/(A+1)]/[2.71 + [C/(A+1)]]. T(s) could be increased dramatically by the complementary sequences in both 5'-and 3'-ends of a DNA single-strand.

Base Composition↗
PubMed2002

Hydroxyapatite-based composite for dental implants: an in vivo removal torque experiment.

Screw-shaped dental implants were fabricated from commercially pure Ti (c.p. Ti) and HA-based composites. The HA-based composites were fabricated by mixing HA with Al(2)O(3)-coated ZrO(2) powders. The mechanical properties of these composites were enhanced by a factor of 3. These were implanted into the rabbit tibiae and the removal torque to loosen the implants in vivo was measured in order to investigate the osteointegration. After a healing period of 6 weeks, the implants were retrieved with a torque gauge instrument. The HA-based composite implants showed an almost 2-times-higher removal torque when compared to the Ti implants (ANOVA, p < 0.05), indicating excellent biocompatibility to bone. Thus, HA-based composites had not only better mechanical properties but also similar bioactivity as HA itself. It is believed that a HA-based composite is suitable for artificial dental implants.

Aluminum Oxide↗
PubMed1998

Base compositional bias and phylogenetic analyses: a test of the "flying DNA" hypothesis.

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along different lineages. Pettigrew (1994, Curr. Biol. 4:277-280) has suggested that base composition bias is responsible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from several different nuclear and mitochondrial genes. Pettigrew's "flying DNA" hypothesis makes several predictions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and microbats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from several nuclear and mitochondrial genes, and (3) that phylogenetic analysis using pairwise distances corrected for compositional bias should eliminate the support for bat monophyly. We tested these predictions by analyzing DNA sequences from two nuclear and three mitochondrial genes. The predicted base compositional bias does not appear to exist in some of the genes, and in other genes the differences in AT content are very small. Analyses under a wide diversity of criteria and models of evolution, including analyses that take base composition into account (using log-determinant distances), all strongly support bat monophyly. Moreover, simulation analyses indicate that even extreme bias toward AT-base composition in bats would be insufficient to explain the observed levels of support for bat monophyly. These analyses provide no support for the "flying DNA" hypothesis, whereas the monophyly of bats appears to be well supported by the DNA sequence data.

Animals↗
PubMed2006

Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST.

BACKGROUND: TBLASTN is a mode of operation for BLAST that aligns protein sequences to a nucleotide database translated in all six frames. We present the first description of the modern implementation of TBLASTN, focusing on new techniques that were used to implement composition-based statistics for translated nucleotide searches. Composition-based statistics use the composition of the sequences being aligned to generate more accurate E-values, which allows for a more accurate distinction between true and false matches. Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server. RESULTS: We evaluate the statistical and retrieval accuracy of the E-values reported by a baseline version of TBLASTN and by two variants that use different types of composition-based statistics. To test the statistical accuracy of TBLASTN, we ran 1000 searches using scrambled proteins from the mouse genome and a database of human chromosomes. To test retrieval accuracy, we modernize and adapt to translated searches a test set previously used to evaluate the retrieval accuracy of protein-protein searches. We show that composition-based statistics greatly improve the statistical accuracy of TBLASTN, at a small cost to the retrieval accuracy. CONCLUSION: TBLASTN is widely used, as it is common to wish to compare proteins to chromosomes or to libraries of mRNAs. Composition-based statistics improve the statistical accuracy, and therefore the reliability, of TBLASTN results. The algorithms used by TBLASTN are not widely known, and some of the most important are reported here. The data used to test TBLASTN are available for download and may be useful in other studies of translated search algorithms.

Algorithms↗
PubMed1977

The structure of animal mitochondrial DNA (base composition, pyrimidine clusters, character of methylation).

Base composition, content of pyrimidine isopliths and the degree of methylation of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) from various vertebrates and protozoon Crithidia oncopelti have been studied. MtDNAs from mammals (ox, rat) do not differ in fact in the GC content from the respective nDNA. The GC content in mtDNA from fishes (sheat fish) and birds (duck, chicken) is 1.5-2.5 mole % higher than in the respective nDNA. Kinetoplast DNA (kDNA) from Crithidia oncopelti (GC = 42.9 mole %) differs significantly in base composition from nDNA (GC = 51.3 mole %). All the mtDNA and kDNA studied differ from the respective nDNA by a lower degree of pyrimidine clustering. The amount of mono and dipyrimidine fragments in mtDNA is more than 30 mole %, whereas in nDNA it does not exceed 23 mole %. The quantity of long pyrimidine clusters (hexa and others) is 2-4 times lower in mtDNA than in nDNA. The lower degree of clustering of pyrimidine nucleotides seems to be a specific feature of all the mtDNA studied. This may be indicative of common traits in the organization and origin of mtDNA. All mtDNA of vertebrates contain 5-methylcytosine as a 'minor' base (1.5- 3.15 mole %) and surpass by 1.5-2 times the respective nDNA in the methylation degree. It has been found that in animals mtDNA is species specific as far as the 5-methyl-cytosine content is concerned. In mitochondria and nuclei of rat liver certain DNA methylase activity has been detected, which provides in vitro the methylation of cytosine residues both in homologous DNA and various heterologous DNAs. The specificity of methylation in vitro of cytosine residues in the same heterologous DNA from E. coli B varies with the source of enzymes. The mitochondrial enzyme methylates cytosine as the lone monopyrimidine residue, whereas the nuclear enzyme methylase cytosine in the di- and tripyrimidine fragments.

Animals↗
PubMed1977

Structure of animal mitochondrial DNA (base composition, pyrimidine clusters, character of methylation).

Base composition, content of pyrimidine isopliths and methylation degree of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) from various vertebrates and protozoon Crithidia oncopelti have been studied. mtDNAs from mammals (ox, rat) do not differ in fact in the G + C content from the respective nDNA. The G + C content in mtDNA from fishes (sheat-fish) and birds (duck, chicken) is 1.5--2.5 mol % higher than in the respective nDNA. Kinetoplast DNA (kDNA) from Crithidia oncopelti (G + C = 42.9 mol %) differs significantly in base composition from nDNA (G + C 51.3 mol%). All the mtDNA and kDNA studied differ from the respective nDNA by a lower degree of pyrimidine clustering. The amount of mono- and dipyrimidine fragments in mtDNA is more than 30 mol %, whereas in nDNA it does not exceed 23 mol %. The quantity of long pyrimidine clusters (hexa- and others) is 2--4 times lower in mtDNA than in nDNA. The lower degree of clustering of pyrimidine nucleotides seems to be a specific feature of all the mtDNA studied. This may be indicative of common traits in the organization and origin of mtDNA. All mtDNA of vertebrates contain 5-methylcytosine as "minor" base (1.5--3.15 mol %) and surpass by 1.5--2 times the respective nDNA in the methylation degree. It has been found that in animals mtDNA is species specific as far as the 5-methylcytosine content is concerned. mtDNA of beef heart differs significantly from nDNA in the mode of 5-methylcytosine distribution in pyrimidine isopliths, which may indicate that methylation specificity of nuclear and mitochondrial DNA is not the same. In mitochondria and nuclei of rat liver certain DNA-methylase activity has been detected, which provides in vitro the methylation of cytosine residues both in homologbous DNA and various heterologous DNAs. Specificity of methylation in vitro of cytosine residues in one and the same heterologous DNA from Escherichia coli B with nuclear and mitochondrial enzymes is different. Mitochondrial enzyme methylates cytosine residues chiefly in mono-, whereas nuclear enzyme, in di- and tripyrimidine fragments.

Animals↗
PubMedDate not supplied

Posterior resin-based composite: review of the literature.

The use of direct posterior resin-based composite has increased primarily due to patient esthetic desires and product improvements. Other factors (substantiated or not) contributing to increased use of resin-based composite are environmental and health concerns with dental amalgam. New visible light cured resin-based composite products are introduced yearly, as manufacturers continue to improve this tooth-colored restorative material. This paper will characterize current posterior resin-based composite materials (hybrid, microfill, flowable, and packable), review recent in vitro and clinical research, and recommend indications for these materials. In addition, the literature on compomers will be reviewed and recommendation made for their use. The data indicates that composite resin is a technique sensitive restorative material that can be used in large preparations if proper manipulation and isolation can be maintained. Compomers may also be used as an esthetic posterior restorative if proper isolation is provided.

Bicuspid↗
PubMed1976

A chemical and physical method for determining the complete base composition of plant DNA.

Two physical methods are routinely used to determine the base composition of DNA. One measures the temperature corresponding to the midpoint of the absorbance rise (TM) and relates it to base composition with the equation, TM = 41 (dG + dC) + 69, the other measures buoyant density (rho) and relates it to base composition rho = 0.098(dG + dC) + 1.6535. The base composition of DNA from various sources was first determined by a chemical method and these values compared to those determined by the physical methods. Higher plants contained up to 7 mol% 5-methyldeoxycytidine in their DNA and in all cases tested deoxyguanosine = deoxycytidine + 5-methyldeoxycytidine. After determining that TM was unaffected by the amount of 5-methyldeoxycytidine in DNA, the mol% of dA, dT, dG, and the total of dC plus 5-methyldeoxycytidine for any DNA could be calculated. Buoyant density on the other hand, was lowered 0.004 g . cm-3 for every 6.3 mol% 5-methyldeoxycytidine. Therefore, both physical parameters were related to the mole fraction of 5-methyldeoxycytidine by the following equation: (see article). With a value of r 5-methyldeoxycytidine an estimation of deoxycytidine was made. The resultant values agreed with the chromatographic determinations.

Deoxyribonucleosides↗