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PubMed1973

Size and base composition of RNA in supercoiled plasmid DNA.

The average size and base composition of the covalently integrated RNA segment in supercoiled ColE(1) DNA synthesized in Escherichia coli in the presence of chloramphenicol (CM-ColE(1) DNA) have been determined by two independent methods. The two approaches yielded similar results, indicating that the RNA segment in CM-ColE(1) DNA contains GMP at the 5' end and comprises on the average 25 to 26 ribonucleotides with a base composition of 10-11 G, 3 A, 5-6 C, and 6-7 U.

Adenosine Monophosphate↗

PubMed1986

Differences in the long chain (sphingoid) base composition of sphingomyelin from rats bearing Morris hepatoma 7777.

The long chain bases of sphingomyelin from Morris hepatoma 7777 and host and control livers were analyzed by capillary gas liquid chromatography. Sphingosine (18:1) was the major long chain base of control livers (66.5%) and hepatomas (65.6%), but hepatomas also had a high percentage (9.3 vs 4.4) of the 16:1 homolog. Host liver had the most unusual long chain base composition, with ca. equal 16:1 (24.4%) and 18:1 (21.4%) and high amounts of 20-carbon bases (9.2% 20:0 and 15.3% 20:1). These differences may be related to the aberrant fatty acid metabolism known to occur in tumor-bearing animals. Such large perturbations in the long chain base composition of hepatic sphingomyelin are unprecedented and could have a major impact on the properties of host membranes.

Animals↗

PubMed2003

Effect of high intensity vs. soft-start halogen irradiation on light-cured resin-based composites. Part I. Temperature rise and polymerization shrinkage.

PURPOSE: To determine polymerization shrinkage kinetics and temperature rise of light-cured resin-based composites after high intensity vs. soft-start quartz tungsten halogen irradiation. METHODS: Shrinkage kinetics was evaluated using the "deflecting disk technique", modified for simultaneous measurement of temperature within the resin-based composite using a thermocouple. Additional irradiations after 60 and 65 minutes allowed the determination of temperature rises caused by radiation or by reaction heat. Four hybrids (Filtek Z250, Herculite, Solitaire 2, Tetric Ceram), an inhomogeneously filled hybrid (InTen-S) and a microfill (Filtek A110, formerly Silux Plus) were cured using the quartz tungsten halogen units Astralis 10 and Optilux 501 in the high intensity (A10 HiPo: 10 seconds at 1300 mW/cm2; OL Boost: 10 seconds at 1140 mW/cm2) or soft-start modes (A10 Pulse: increase to 700 mW/cm2 within 10 seconds, three periods of 2 seconds at 1300 mW/cm2 alternating with two periods of 2 seconds at 700 mW/cm2; OL Ramp: exponential increase within 10 seconds, followed by 10 seconds at 1140 mW/cm2). RESULTS: The soft-start protocols produced less contraction, and polymerization shrinkage started later and progressed slower (or: more slowly), compared to high intensity irradiation [correction]. The lowest shrinkage was observed for InTen-S, followed by Filtek Z250 and A110, whereas Solitaire 2, Herculite and Tetric Ceram scored highest for this parameter. Temperature rise was caused more or less equally by radiation and by reaction heat and reached values of up to 28.9 degrees C relative to a baseline of 37 degrees C. For some combinations of curing modes and resin-based composites, less heat was generated by the soft-start protocols and by Optilux 501.

Analysis of Variance↗

PubMed1995

Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions.

The correspondence between the transversion/transition ratio and the neighboring base composition in chloroplast DNA is examined. For 18 noncoding regions of the chloroplast genome, alignments between rice (Oryza sativa) and maize (Zea mays) were generated by two different methods. Difficulties of aligning noncoding DNA are discussed, and the alignments are analyzed in a manner that reduces alignment artifacts. Sequence divergence is < 10%, so multiple substitutions at a site are assumed to be rare. Observed substitutions were analyzed with respect to the A+T content of the two immediately flanking bases. It is shown that as this content increases, the proportion of transversions also increases. When both the 5'- and 3'-flanking nucleotides are G or C (A+T content of 0), only 25% of the observed substitutions are transversions. However, when both the 5'- and 3'-flanking nucleotides are A or T (A+T content of 2), 57% of the observed substitutions are transversions. Therefore, the influence of flanking base composition on substitutions, previously reported for a single noncoding region, is a general feature of the chloroplast genome.

Algorithms↗

PubMed2006

A clinical evaluation of resin-based composite and glass ionomer cement restorations placed in primary teeth using the ART approach: results at 24 months.

BACKGROUND: The authors evaluated the 24-month performance of a packable resin-based composite/dentin bonding system and a high-viscosity glass ionomer cement (GIC) in restorations placed in primary molars with the atraumatic restorative treatment (ART) approach. METHODS: Three dentists placed 419 restorations in 219 children aged 6 through 10 years who had bilateral matched pairs of carious posterior Class I and II primary teeth. They used a split-mouth design to place the two materials, which were assigned randomly to contralateral sides. The authors evaluated the restorations according to U.S. Public Health Service Ryge criteria. RESULTS: After 24 months, 96.7 percent of the Class I GIC restorations and 91 percent of the resin-based composite restorations survived, while the success rates for the Class II restorations were 76.1 percent and 82 percent for the GIC and resin-based composite restorations, respectively. The survival rate of the Class II resin-based composite restorations was 5.9 percent higher than that of the GIC restorations at the 24-month evaluation, but this difference was not statistically significant. However, the study results showed a statistically significant difference in survival rates between Class I and II restorations for both materials. CONCLUSION AND CLINICAL IMPLICATIONS: The two-year clinical performance of both materials was satisfactory for the restoration of Class I and II primary molars using the ART approach.

Acrylic Resins↗

PubMed2004

Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana.

BACKGROUND: Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, however, heterozygosity is expected to be strongly reduced and recombination will be much less effective, so that its influence on genome organization should be greatly reduced. RESULTS: Here we investigated theoretically the joint effects of recombination and self-fertilization on base composition, and tested the predictions with genomic data from the complete A. thaliana genome. We show that, in this species, both codon-usage bias and GC content do not correlate with the local rates of crossing over, in agreement with our theoretical results. CONCLUSIONS: We conclude that levels of inbreeding modulate the effect of recombination on base composition, and possibly other genomic features (for example, transposable element dynamics). We argue that inbreeding should be considered when interpreting patterns of molecular evolution.

Arabidopsis↗

PubMed1993

Base composition analysis of oligonucleotides containing apurinic sites.

Upon base composition analysis, oligonucleotides which are labeled at the 3'-terminus with fluorescein or biotin generate an additional, late eluting peak in the HPLC chromatogram. Investigation of this effect revealed the haptens acted as apurinic sites, and phosphodiesterase cleavage of the phosphate bond between the upstream nucleotide and apurinic site is inhibited. Extension of this work with a base-stable apurinic site inserted into all possible junctures of 5'-TGAC-3' tetramers showed this to be a general effect. As a consequence of this work, acid-catalyzed depurination resulting in apurinic sites can be monitored in oligonucleotide synthesis.

Apurinic Acid↗

PubMed2004

DNAskew: statistical analysis of base compositional asymmetry and prediction of replication boundaries in the genome sequences.

Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

Algorithms↗

PubMed1969

Deoxyribonucleic acid base composition in yeasts.

The deoxyribonucleic acid base composition of 15 species of yeasts was determined to obtain further clues to or supporting evidence for their taxonomic position. Species examined belonged to the genera Saccharomyces, Debaryomyces, Lodderomyces, Metschnikowia, and Candida. The range of moles per cent guanine plus cytosine (GC content) for all yeasts examined extended from 34.9 to 48.3%. The sporogenous species and the asporogenous yeasts spanned the range with 36.6 to 48.3% GC and 34.9 to 48% GC, respectively. Three Saccharomyces species (S. rosei and related species) exhibited significantly higher GC contents than S. cerevisiae, whereas the fermentative species D. globosus revealed a%GC more aligned to the S. rosei group than to the nonfermentative D. hansenii. Similar GC contents were demonstrated by L. elongasporus and its proposed imperfect form C. parapsilosis. The range of GC contents of various strains of three Metschnikowia species studied was 6.1%, with the type strain of M. pulcherrima having the highest GC content (48.3%) of all of the yeasts examined.

Candida↗

PubMed1999

Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant.

The evolution of DNA base composition evolution is simplified to a six-parameter model when there are no strand biases for mutation and selection. We analyzed the dynamics of this model with special attention to the influence of a change in substitution rates. The G + C content of the DNA sequence tends to an equilibrium value that is controlled by four parameters of the model. When the substitution rates are not constant, the G + C equilibrium position is not constant. The DNA sequence base frequencies always tend to a state in which A = T and G = C within a strand, regardless of substitution rates. This is true even when the substitution rates are not constant over time. This provides a simple way of rejecting the model from inspection of present-day DNA base composition.

Base Composition↗

PubMed1980

Base composition of rubella virus RNA. Brief report.

The base composition of 32P-labelled RNA of rubella virus was shown to be; Gp:31.1, Ap:21.9, Cp:34.3 and Up:12.8 per 100 nucleotides. The result demonstrates that the virus is distinct from other members of family Togaviridae in that it possesses RNA with relatively high contents of Gp and Cp, and low content of Up. Viral RNA adsorbed to oligo (dT)-cellulose column was shown to be infectious, whereas no infectivity of RNA appearing in the void volume was found. This may indicate that viral RNA needs to carry a minimal length of poly(A) to be infectious.

Base Composition↗

PubMed2003

The disinfection of water by microalloyed aluminium-based composite.

In the submitted paper the water disinfection capacity of the microalloyed aluminium based composite (MABC) was studied. MABC is material in the form of steel wire, plated with microalloyed aluminium. The effects of the composite are based on the very negative stationary potential of microalloyed aluminium, and its spontaneous dissolution in water with generation of AI(III) ions, and reduction of water with the generation of H2 and OH ions. As a final product of these reactions, a voluminous Al(OH)3 precipitate is formed. Having in mind its great efficacy in purification of different waters from many chemical pollutants we made the following hypothesis: reduction characteristics of the MABC surface, presence of Al(III) and OH ions, and coprecipitation on Al(OH)3, can be also toxic and destructive for bacteria in water. The experiments were carried out with the water model solutions (WMS) based on adapted natural surface water (NSW), inoculated with the Escherichia coli. All treatments were performed in the original semi-flow system (SFS), in which convection increases efficacy. The results show that approximately every 10 min the number of viable bacteria was reduced for about one log10 count, with the complete disinfected water phase as the outcome of the treatment. At the end of the treatment, the Al(OH)3 precipitate still contained a low amount of coprecipitated viable bacteria, which died within a relatively short period.

Aluminum↗

PubMed2000

Pulp capping with adhesive resin-based composite vs. calcium hydroxide: a review.

The results of some short-term experiments suggest that direct capping of a vital pulp with the modern resin-based composite systems may be as effective as capping with calcium hydroxide. Total cavity etching with 10% phosphoric acid seems to be safe for the exposed pulp, but unless annulled by calcium hydroxide 35% phosphoric acid may be disastrous. For hemostasis and cleaning of the pulp wound both sodium hypochlorite and saline seem suitable, whereas the effectiveness of a 2% chlorhexidine solution is questionable. Although hard-setting calcium hydroxide cements may induce the formation of dentin bridges, they appear not to provide an effective long-term seal against bacterial factors. Within a few years, the majority of mechanically exposed and capped pulps show infection and necrosis due to microleakage of such capping materials and tunnel defects in the dentin bridges. It is unknown whether newer types of resin containing calcium-hydroxide-products will act as a permanent barrier. The cytotoxicity of the resin-based composites and the temperature rise during polymerisation may not be of concern, but microleakage, sensitisation and allergic reactions may pose problems. Based on available data, pulp capping with resin-based composites may be said to be promising, but more and long-term research is mandatory before the method can be recommended.

Acid Etching, Dental↗

PubMed1978

Base composition studies on transfer RNA from normal and regenerating rat liver.

The base composition of bulk tRNA isolated from regenerating rat liver, 12, 18, 24 and 30 h after partial hepatectomy, was determined by a 3H derivative method. Only a few minor statistically significant changes (2--11%), as compared to sham-operated liver, were found at 18, 24 and 30 h after hepatectomy. These included a reduction in the amounts of adenosine and 3-(3-amino-3-carboxypropyl)-uridine, and an increase in the amounts of 1-methyl-adenosine, 1-methylguanosine, 3-methylcytidine and pseudouridine. Similarly, when the base composition of tRNA fractions from control and 24-h regenerating rat liver, partially purified by one-dimensional polyacrylamide gel electrophoresis, was determined, no gross differences were observed. These results suggest that the process of liver regeneration is not accompanied by a gross alteration of the modification pattern of tRNA.

Animals↗

PubMedDate not supplied

Influence of curing methods and matrix type on the marginal seal of class II resin-based composite restorations in vitro.

This study determined the influence of light curing protocols and matrix type on the margin quality and marginal seal of Class II resin-based composite restorations. In extracted human molars, box-shaped MOD cavities with 1 mm wide interproximal bevels were prepared with cervical margins located at least 1 mm coronal to the cemento-enamel junction. The prepared teeth were mounted in a jig featuring artificial training teeth that served as adjacent teeth. A contoured sectional metal matrix band was placed in one interproximal area, and a section of a contoured transparent matrix band was placed in the opposite interproximal area. Both were kept in position using wooden wedges. After etching (35% H3PO4 gel) and the application of a three-step etch & rinse dentin adhesive (Optibond FL, Kerr), a thin layer of flowable resin-based composite (Revolution, Kerr) was applied to the interproximal margins. The cavities were restored by placing one horizontal and two oblique increments of a fine hybrid resin-based composite (Herculite XRV, Kerr). The curing protocols included one standard halogen protocol (Elipar Trilight, 3M ESPE, 40 seconds @ 800 mW/cm2), 3 halogen soft-start protocols (Step: Elipar HiLight, 3M ESPE; 10 seconds @ 150 mW/cm2, 30 seconds @ 850 mW/cm2; Ramp: Elipar TriLight, 3M ESPE, 5 seconds @ 100 mW/cm2, exponential increase for 10 seconds, 25 seconds @ 800 mW/cm2; Pulse delay: VIP Light, BISCO, cervical increment: 10 seconds @ 500 mW/cm2, occlusal increments: 3 seconds @ 200 mW/cm2, final irradiation after a 5 minute interval: 30 seconds @ mW/cm2) and 2 plasma arc high intensity protocols (PAC: Lightning Cure, ADT, 10 seconds @ 1400 mW/cm2; APO: Apollo 95E, DMDS, 2 x 3 seconds @ 1570 mW/cm2). The restored teeth were stored in 0.9% saline at 37 degrees C for 4 weeks and submitted to thermal cycling [TC] with 2500 cycles between 5 degrees C and 55 degrees C after 2 weeks. The margin quality before and after TC was analyzed in SEM using the replica technique, and the marginal seal was determined using the dye penetration test (50% AgNO3, 2 hours) at the end of the study. The matrix type did not significantly influence the quality and seal of the respective margins. For the complete restoration margin, one of the high intensity protocols (APO) produced a higher percentage of "continuous margin" compared to pulse delay irradiation after TC and lower percentages of "marginal opening" compared to halogen standard irradiation before and after TC. Halogen step irradiation produced a superior marginal seal compared to pulse delay curing at the occlusal margins; equivalent results were observed for all curing modes at the cervical margins. Neither a general advantage of soft-start irradiation nor a general disadvantage of high intensity curing was confirmed.

Acid Etching, Dental↗

PubMed1975

Effect of DNA base composition on the intercalation of proflavine. A kinetic study.

The effect of DNA base composition on the kinetics of the association between DNA and proflavine has been investigated using the temperature jump relaxation method. It is found that, regardless of the G + C base composition the results fit a two step mechanism, the second of which exhibits characteristics of intercalation of proflavine into DNA. However, they two equilibrium constants corresponding to these steps, KI and KII, depend on the nature of the DNAs. The constant KI is found to be an order of magnitude greater for M. lysodeikticus DNA (72% G + C) than for calf thymus DNA (48% G + C). Increasing G-C content thus appears to favor the intermediate non-intercalated complex of proflavine with DNA. Methylation of M. lysodeikticus DNA with dimethyl sulfate, preferentially yielding N7 methyl guanine as the modified base, again leads to an apparent two step mechanism, with the value of KI unchanged with respect to untreated DNA, while the affinity of proflavine for the intercalated complex measured by the value of KII increases for methylated DNA.

Acridines↗

PubMed2005

Effect of LED and halogen light curing on polymerization of resin-based composites.

The clinical performance of light polymerized resin-based composites (RBCs) is greatly influenced by the quality of the light curing unit (LCU). A commonly used unit for polymerization of RBC material is the halogen LCUs. However, they have some drawbacks. Development of new blue superbright light emitting diodes (LED LCU) of 470 nm wavelengths with high light irradiance offers an alternative to standard halogen LCU. The aim of this study is compared the effectiveness of LED LCU and halogen LCU on the degree of conversion (DC) of different resin composites [two hybrid (Esthet-X, Filtek Z 250), four packable (Filtek P60, Prodigy Condensable, Surefil, Solitaire), one ormocer-based resin composite (Admira)]. The DC values of RBCs polymerized by LED LCU and halogen LCU ranged approximately from 61.1 +/- 0.4 to 50.6 +/- 0.6% and from 55.6 +/- 0.7 to 47.4 +/- 0.5%, respectively. Significantly higher DC of RBCs except Surefil and Filtek Z 250 was obtained for LED LCU compared with halogen LCU (P < 0.05). Surefil and Filtek Z 250 exhibited no statistically significant difference values between LED LCU and halogen LCU (P > 0.05). As a result, it was observed that the performance of LED LCU used in the study was satisfactory clinically and had sufficient irradiance to polymerize RBCs (hybrid, packable and ormocer based) at 2 mm depth with a curing time of 40 s.

Composite Resins↗

PubMed1965

ADANSONIAN ANALYSIS AND DEOXYRIBONUCLEIC ACID BASE COMPOSITION OF SERRATIA MARCESCENS.

Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of Serratia marcescens. J. Bacteriol. 89:454-461. 1965.-A total of 33 strains of Serratia marcescens were subjected to Adansonian analysis for which more than 200 coded features for each of the organisms were included. In addition, the base composition [expressed as moles per cent guanine + cytosine (G + C)] of the deoxyribonucleic acid (DNA) prepared from each of the strains was determined. Except for four strains which were intermediate between Serratia and the Hafnia and Aerobacter group C of Edwards and Ewing, the S. marcescens species group proved to be extremely homogeneous, and the different strains showed high affinities for each other (mean similarity, S = 77%). The G + C ratio of the DNA from the Serratia strains ranged from 56.2 to 58.4% G + C. Many species names have been listed for the genus, but only a single clustering of the strains was obtained at the species level, for which the species name S. marcescens was retained. S. kiliensis, S. indica, S. plymuthica, and S. marinorubra could not be distinguished from S. marcescens; it was concluded, therefore, that there is only a single species in the genus. The variety designation kiliensis does not appear to be valid, since no subspecies clustering of strains with negative Voges-Proskauer reactions could be detected. The characteristics of the species are listed, and a description of S. marcescens is presented.

Anti-Bacterial Agents↗