Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Base Composition”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed1994

Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 degrees C.

Using high-precision densitometric and ultrasonic measurements, we have determined, at 25 degrees C, the apparent molar volumes, phi V, and the apparent molar compressibilities, phi KS, of five natural and three synthetic B-form DNA duplexes with varying base compositions and base sequences. We find that phi V ranges from 152.0 to 186.6 cm3 mol-1, while phi KS ranges from -73.0 x 10(-4) to -32.6 x 10(-4) cm3 mol-1 bar-1. We interpret these data in terms of DNA hydration which, by the definition employed in this work, refers to those water molecules whose density and compressibility differ from those of bulk water due to interactions with the DNA solute. This definition implies that hydration depends not just on the quantity but also on the quality of the solvent molecules perturbed by the solute. In fact, we find that the number of water molecules perturbed by the DNA duplexes (the quantity of water in their hydration shells) is approximately the same for all of the B-form double helixes studied, while the quality of this water differs as measured by its density and compressibility, thereby yielding differences in the overall hydration properties. Specifically, we find a linear relationship between the density and the coefficient of adiabatic compressibility, beta Sh, of water in the hydration shell of the DNA duplexes, with the range of values for beta Sh being only 65-80% of the value of bulk water.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗
PubMed1990

[Mechanical properties and curing depth of urethane tetramethacrylate-based composite resins].

Mechanical properties and curing depth of light-cured composite resins based on five types of urethane tetramethacrylate (UTeMA; IP-4 M, XY-4 M, MC-4 M, HM-4 M and TM-4 M) were investigated, and compared them with those of UDMA-based composite resins. Composites based on UTeMA monomers containing an aromatic or cyclohexane ring in their chemical structure (IP-4 M, XY-4 M and MC-4 M) showed a relatively rigid properties than those based on aliphatic UTeMA (HM-4 M and TM-4 M). The composite resins based on XY-4 M monomer showed a curing depth and transmission coefficient superior to the other composite resins. UTeMA-based composites showed a significantly higher rigid properties than UDMA-based composites, while their rigidity did not improve the flexural strength.

Composite Resins↗
PubMed1997

Bacterial features in the genome of Methanococcus jannaschii in terms of gene composition and biased base composition in ORFs and their surrounding regions.

As a result of genome projects, the complete nucleotide sequence of the entire genome of an archaeon, Methanococcus jannaschii, was recently determined as well as other complete sequences of bacterial and eucaryal genomes. When all the 1680 predicted protein-coding [corrected] genes of M. jannaschii were classified on the basis of sequence similarity, it was found that this archaeon had a chimeric set of 1016 bacterial-type, 471 eucaryal-type and 193 species- or archaebacteria-specific genes. However, most of the genes predicted to be involved in translation and transcription pathways including RNA genes were of the eucaryal-type with only a few exceptions such as 16S ribosomal RNA and some translation factor-like genes. This appeared curious since previous studies indicated that methanogens have bacterial features in gene organization and expression. To understand the apparent inconsistency between physiological observations and the result of the classification of genes for transcription and translation, we examined the structural relatedness of the genome of M. jannaschii to those of other species. In practice, we compared base compositional patterns in ORFs and their surrounding regions. This made it possible to reveal the relationships among the translation- and transcription-related structures in genomes. In this study, we conducted a statistical test called 'G-test' to evaluate the base biases around the boundaries of ORFs. We then found that M. jannaschii possesses more bacterial features in base biases than eucaryal ones, e.g. strong G biases at the positions corresponding to the Shine-Dalgarno site. This indicates that the few exceptional bacterial genes for translation, such as 16S ribosomal RNA and translation factor-like genes, play crucial roles in the translation pathway in M. jannaschii. The possibility that the genome structure in the last common ancestor of all present species was bacterial is discussed.

Base Composition↗
PubMed2007

Application of CE for determination of DNA base composition.

DNA base composition expressed as mol% of guanine plus cytosine (% GC) or GC content is a key parameter of bacterial taxonomy and genomic analyses. Direct chemical determination methods such as HPLC as well as indirect methods based on physical properties of deoxyribonucleic acid (DNA), melting point (T(m)), and buoyant density (B(d)) have been conventionally applied to determine the GC content. However, these methods require relatively large amounts of sample DNA, time, and labor. We have developed a protocol to determine the GC content by fine separation of nucleosides with CZE. Genomic DNAs with known GC content from 23 bacterial strains were determined by CE at the optimized conditions of 27 degrees C, 20 kV in 50 mM of NaHCO(3) (pH 9.0) and 70 mM SDS added. Nucleosides from <1 microg of DNA hydrolyzed with nuclease-P1 and bacterial alkaline phosphatase were separated in a 75 microm wide and 80 cm long silica capillary. The nucleoside peak areas were determined at 254 nm in less than 12 min. The CE-based determination of GC content requires only small amounts of DNA, and thus should be applicable to environmental genomics (metagenomics), as >90% of environmental micro-organisms are nonculturable and produce only small amounts of genomic DNA.

Base Composition↗
PubMed1998

[The biomedical efficacy of 2 variants of polyacrylamide gel- and hydroxyapatite-based composite materials in the plastic repair of bone defects (experimental morphological research)].

Tissue status at the site of experimental bone defects filled by two compositions based on polyacrylamide gel and hydroxyapatite with (experimental group) and without (controls) lysozyme was studied in rats by the histomorphological method. "Negative" symptoms, such as inflammation, formation of osteocyte-free bone at the interface of the defect, and reduction of red bone marrow were more manifest in the controls than in animals treated with lysozyme. In the test group substitution of composite material for connective tissue structures and bone reparation were much more active and rapid than in the controls. Inflammation and dystrophic changes at the interface of defects were less pronounced and gradually resolved.

Acrylic Resins↗
PubMed1992

Development of a degradable composite for orthopaedic use: in vivo biomechanical and histological evaluation of two bioactive degradable composites based on the polyhydroxybutyrate polymer.

As a direct method for the evaluation of tissue bonding to two polyhydroxybutyrate (PHB) based composites, a mechanical push-out test was performed on implants in the femur of mature Japanese White rabbits. Three composites were tested. The first, a hydroxyapatite/PHB (HA/PHB) composite showed an increase in interfacial shear strength (ISS) up to 8 wk, after which the ISS decreased due to degradation of the implant. The second composite was an HA/glass/PHB (HGP) composite and this gave lower values for the ISS attributed to ion release from the glass causing a soft tissue reaction at the interface. The third composite was a carbon fibre reinforced polysulfone (CFRP) and this showed high interfacial shear strength values, which continued to increase with time. These conclusions were supported by contact microradiography (CMR) and histology which showed enhanced endosteal bone growth for the HA/PHB but for the HGP, no periosteal or endosteal activity was detected. Interposed soft tissue for the HGP composite was difficult to discern, histologically, but it was proposed that this was the reason for the low ISS values. It was concluded that the high ISS values for the carbon fibre control were due to surface morphology allowing deep ingrowth of soft tissue and this was confirmed by SEM.

Animals↗
PubMed1995

Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome.

Nucleotide sequence from a region of the chloroplast genome is presented for 12 species spanning four subfamilies of the grass family. The region contains the coding sequence for the rbcL gene and the intergenic spacer between the gene coding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and the photosystem I gene psaI. This intergenic spacer contains a pseudogene for rpl23 as well as two noncoding segments with different A+T contents. Using the sequence of rbcL a chloroplast phylogeny of this family was constructed by parsimony. Variable sites of the two noncoding segments were traced onto the phylogeny to study the dynamics of base substitution. This was also performed for the fourfold-degenerate sites of the rbcL gene. A wide variation in transversion/transition is observed between the two noncoding segments and between the noncoding DNA and the fourfold-degenerate sites of rbcL. This variation is correlated with regional A+T content. As regional A+T content decreases, the ratio of transversions to transitions also decreases. Substitutions were then scored in relation to neighboring base composition. The composition of the two bases immediately flanking each substitution is highly correlated with the transversion/transition bias. When both the 5' and 3' flanking bases are an A or a T, transversions are observed 2.2 times as frequently as transitions. When either or both neighbors are a C or a G, the opposite trend is found; transitions are observed 1.5 times more frequently than transversions.

Bacterial Proteins↗
PubMed2005

Hierarchical structure analysis describing abnormal base composition of genomes.

Abnormal base compositional patterns of genomic DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed turbulence [She and Lévêque, Phys. Rev. Lett. 72, 336 (1994)]. The HS similarity law is verified over scales between 10(3)bp and 10(5)bp, and the HS parameter beta is proposed to describe the degree of heterogeneity in the base composition patterns. More than one hundred bacteria, archaea, virus, yeast, and human genome sequences have been analyzed and the results show that the HS analysis efficiently captures abnormal base composition patterns, and the parameter beta is a characteristic measure of the genome. Detailed examination of the values of beta reveals an intriguing link to the evolutionary events of genetic material transfer. Finally, a sequence complexity (S) measure is proposed to characterize gradual increase of organizational complexity of the genome during the evolution. The present study raises several interesting issues in the evolutionary history of genomes.

Animals↗
PubMed1990

[Mechanical properties and cure depth of UDMA-based composite resins].

Mechanical properties and cure depth of visible light-cured composite resins based on six types of UDMA (IP-HEMA, IP-HPMA, XY-HPMA, MC-HPMA, UEDMA and UPDMA) monomers were investigated. Under wet conditions, the mechanical properties of the composite resins based on aliphatic UDMA (UEDMA and UPDMA) monomers were inferior to those based on the other UDMA monomers containing aromatic or cyclohexane rings in their chemical structures. The cure depth for these UDMA-based composite resins increased with increasing irradiation time. The composite resin based on the XY-HPMA monomer showed a cure depth and transmission coefficient superior to the other composite resins.

Absorption↗
PubMed1998

Effect of composite basing on the resistance to bulk fracture of industrial porcelain inlays.

OBJECTIVES: Bases are used in restorative dentistry for several reasons (i.e. isolation, elimination of undercuts, etc). Glass ionomers are the standard materials used as bases for porcelain inlays, despite the disadvantages of their mechanical properties. An alternative basing material is composite: a generous layer of posterior composite is cured and shaped in the cavity before an impression is taken. The composite basing technique has several clinical advantages. The aim of this study was to investigate the effect of the thickness of a composite base on the bulk fracture resistance of industrial porcelain, and to describe the procedure. METHODS: Fifteen porcelain (P) and 15 composite (C) bars, 1-, 2-, and 3-mm thick were joined to form 15 C/P bars, all 4-mm thick. Three groups were created: C 1 mm/P 3 mm (group 1), C 2 mm/P 2 mm (group 2), and C 3 mm/P 1 mm (group 3). The pairs were joined using Twinlook cement, subjected to a three-point bending test and loaded to fracture. The beam theory was used to support and explain the results. RESULTS: The fracture load means were: group 1, 197.7 +/- 18.7 N; group 2, 234.3 +/- 63.3 N, group 3, 336.3 +/- 31.3 N. Group 3 was significantly stronger than group 1 (P = 0.01) and group 2 (P = 0.03). Groups 1 and 2 were not statistically different. CONCLUSION: Composite basing is a tissue conserving method which may significantly increase the resistance to bulk fracture of adhesive porcelain inlays.

Acid Etching, Dental↗
PubMed2003

Two-year clinical evaluation of a packable resin-based composite.

BACKGROUND: Packable resin-based composites were introduced in 1998, but few clinical studies have been conducted to evaluate them. The authors conducted a clinical study to determine the two-year performance of SureFil (Dentsply DeTrey GmbH, Konstanz, Germany) packable posterior resin-based composite in Class I and II restorations. METHODS: An operator (L.S.T.) restored 55 cavities in 36 patients (16 Class I restorations and 39 Class II restorations). After cavity preparation, she etched the enamel with 34 percent phosphoric acid, applied Prime & Bond NT (Dentsply DeTrey GmbH) to dentin and etched enamel for 20 seconds and then cured it for 20 seconds. She restored the cavity using 3- to 5-millimeter increments of SureFil. Independent examiners assessed the restorations after placement and at six months, one year and two years for color matching, marginal discoloration, marginal adaptation, secondary caries, surface texture, anatomical form and postoperative sensitivity, using the Ryge criteria. RESULTS: The authors assessed the changes in the parameters during the two-year period using a software program with Friedman test analysis with a Bonferroni adjustment at significant level of P = .05. At baseline, 31 restorations were graded as Bravo for color match. At the six-month and one-year recall periods (n = 55), 53 restorations remained unchanged. Two restorations from the same patient fell out after one month. After two years (n = 50), there were five Bravos for surface staining and three for marginal adaptation (P < .05). CONCLUSION: After two years of clinical service, SureFil packable resin-based composite had a success rate of 96 percent, and the authors considered it successful in Class I and II restorations. CLINICAL IMPLICATIONS: SureFil packable resin-based composite can be successful in clinical situations with limited-sized cavities and proper application of restorative techniques.

Acid Etching, Dental↗
PubMed2000

The evolution of base composition and phylogenetic inference.

Base composition varies at all levels of the phylogenetic hierarchy and throughout the genome, and can be caused by active selection or passive mutation pressure. This variation can make reconstructing trees difficult. However, recent tree-based analyses have shed light on the forces responsible for the evolution of base composition, forces that might be very general. More explicit tree-based work is encouraged.

Journal Article↗
PubMedDate not supplied

The use of resin-based composite in children.

Resin-based composites are an integral component of contemporary pediatric restorative dentistry. They can be utilized effectively for preventive resin restorations, moderate Class II restorations, Class III restorations, Class IV restorations, Class V restorations and strip crowns. Tooth isolation to prevent contamination is a critical factor, and high-risk children may not be ideal candidates for resin-based composite restorations. Important factors to consider during composite placement are isolation, polymerization shrinkage and extent of restoration. When utilized correctly, resin-based composites can provide excellent restorations in the primary and permanent dentition.

Child↗
PubMed2000

Resin-based composites and compomers in primary molars.

Resin-based composite resins and polyacid-modified resin-based composites (compomers) have become popular for the restoration of primary anterior and posterior teeth. In some European countries, resin-based composites or glass-ionomers are the materials of choice for primary teeth because of the controversy over dental amalgam and its alleged adverse health effects resulting from the release of mercury, although a clear correlation between amalgam restorations and health has not been determined. Another reason for the worldwide increased use of resin-based composites and glass-ionomers in pediatric dentistry could be attributed to the growing demand from parents to provide esthetic restorations to their children. More conservative preparations can be performed maintaining more tooth structure because of the adhesive properties of the composites and compomers. The most conservative treatment planning and meticulous care in the placement of the resin-based composites and compomers would produce long-term satisfactory results. These restorations should be placed in patients with low-to-moderate caries risk, and after placement the restorations should be monitored carefully to avoid complications mainly produced by recurrent caries and wear.

Adhesives↗
PubMed1992

Base compositional structure of genomes.

We model the base compositional structure of the human and Escherichia coli genomes. Three particular properties are first quantified: (1) There is a significant tendency for any region of either genome to have a strand-symmetric base composition. (2) The variation in base composition from region to region, within each genome, is very much larger than expected from common homogeneous stochastic models. (3) A given local base composition tends to persist over a scale of at least kilobases (E. coli) or tens of kilobases (human). Multidomain stochastic models from the literature are reviewed and sharpened. In particular, quantitative measurements of the third property lead us to suggest a significant shift in the style of domain models, in which the variation of A+T content with position is modeled by a random walk with frequent small steps rather than with large quantum jumps. As an application, we suggest a way to reduce the amount of computation in the assembly of large sequences from sequences of randomly chosen fragments.

Escherichia coli↗
PubMed1999

Microleakage of resin-based composite restorations using different solvent-based bonding agents and methods of drying acid-etched dentin.

PURPOSE: To evaluate the effect of a wet, conventionally dried, and dry bonding technique on microleakage of Class V resin-based composite (RBC) restorations bonded with three different solvent-based adhesive agents. MATERIALS AND METHODS: Forty five extracted human premolars and molars were randomly assigned to nine groups for bonding with Syntac original, Syntac Single Component, or Syntac Sprint (all by Ivoclar/Vivadent). Cavities were cut in both the buccal and lingual surfaces. Half of each preparation was in enamel and the other was in cementum/dentin. The cavities were restored with RBC after the applications of dentin bonding agents to acid-conditioned cavities using a wet, conventionally dried, and a dry technique for each material. The teeth were thermocycled and the restorations examined microscopically for leakage using Procion Brilliant Red as a marker. SEM microphotographs were prepared from dye-labeled and non dye-labeled areas. RESULTS: All groups showed microleakage at the gingival margins with no significant difference between the groups irrespective of the bonding material or the method of drying acid-etched dentin [Kruskal-Wallis: (ANOVA) P = 0.1858]. Neither was there a significant difference between the groups irrespective of bonding material or drying method at the enamel margin [Kruskal-Wallis: (ANOVA) P = 0.3434). SEM showed that in dye-labeled areas debonding was predominantly cohesive in resin.

Acetone↗
PubMed1980

Deoxyribonucleic acid base composition of bacteria.

As the base composition of deoxyribonucleic acid has become a highly significant parameter in the taxonomy of bacteria, a reference list for the known deoxyribonucleic acid base composition (G + C) values of bacteria is given which compiles the data published between 1972 and 1978.

Bacteria↗
PubMed2000

The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes.

Asymmetries in base composition between the leading and the lagging strands have been observed previously in many prokaryotic genomes. Since a majority of genes is encoded on the leading strand in these genomes, previous analyses have not been able to determine the relative contribution to the base composition skews of replication processes and transcriptional and/or translational forces. Using qualitative graphical presentations and quantitative statistical analyses (analysis of variance), we have found that a significant proportion of the GC and AT skews can be attributed to replication orientation, i.e., the sequence of a gene is influenced by whether it is encoded on the leading or lagging strand. This effect of replication orientation on skews is independent of, and can be opposite in sign to, the effects of transcriptional or translational processes, such as selection for codon usage, amino acid preferences, expression levels (inferred from codon adaptation index), or potential short signal sequences (e.g., chi sequences). Mutational differences between the leading and the lagging strands are the most likely explanation for a significant proportion of the base composition skew in these bacterial genomes. The finding that base composition skews due to replication orientation are independent of those due to selection for function of the encoded protein may complicate the interpretation of phylogenetic relationships, conserved positions in nucleotide or amino acid sequence alignments, and codon usage patterns.

Analysis of Variance↗