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PubMed1974

Characterization of ribonucleic acids from the venom glands of Crotalus durissus terrifucus (Ophidia, Reptilia) after manual extraction of the venom. Studies on template activity and base composition.

RNA synthesis in the venom glands of Crotalus durissus terrificus was stimulated by the manual extraction of the venom (milking). RNA was extracted from venom glands activated by milking and fractionated by centrifugation through sucrose density gradients. Template activity for protein synthesis and base composition of the RNA fractions were studied. RNA fractions that sediment between 18S and 4S had the highest template activity. The base composition analysis indicated that the 28S and 18S rRNA have a C+G content of 65.4 and 58% respectively. The ;melting' temperature (T(m)) of DNA in 0.15m-NaCl-0.015m-trisodium citrate, pH7.0, was 85 degrees C, corresponding to a C+G content of 38%. The base ratio of the RNA fractions that showed a high template activity was intermediate between that of rRNA and homologous DNA. The possible role of these fractions in the synthesis of the two main toxins (crotoxin and crotamine) of the South American rattlesnake's venom is discussed.

Animals↗
PubMed1994

Effects of base composition on the negative cooperativity and binding mode transitions of Escherichia coli SSB-single-stranded DNA complexes.

We have examined the ability of the Escherichia coli single-stranded DNA binding protein (SSB) tetramer to form its different binding modes on poly(dC), poly(U), and poly(A) over a range of NaCl and NaF concentrations for comparison with previous studies with poly(dT). In reverse titrations with poly(U) and poly(A) at 25 degrees C, pH 8.1, SSB forms all four binding modes previously observed with poly(dT), namely, (SSB)35, (SSB)40, (SSB)56, and (SSB)65, where the subscript denotes the site size (i.e., the average number of nucleotides occluded per SSB tetramer). As with poly(dT), the low site size modes are favored at low monovalent salt concentration (< 10 mM), whereas increasing salt concentration facilitates the transitions to the higher site size modes. Surprisingly, SSB does not form a stable (SSB)35 complex on poly(dC), even at 1 mM NaCl; rather, the (SSB)56 mode is formed under these conditions. Upon raising the [NaCl], the (SSB)56 complex undergoes a transition to the (SSB)65 complex (transition midpoint, 40 mM NaCl). On the basis of studies with dC(pC)34, dT(pT)34, and dA(pA)34, the inability of the SSB tetramer to form the (SSB)35 complex with poly(dC) is due mainly to a much lower degree of negative cooperativity for binding oligodeoxycytidylates to the SSB tetramer. At low salt concentration, the negative cooperativity parameter, sigma 35, is lowest for dA(pA)34, intermediate for dT(pT)34, and highest for dC(pC)34, indicating that it is most difficult to saturate the SSB tetramer with two molecules of dA(pA)34. We have also measured the equilibrium constants for binding the oligodeoxynucleotides dC(pC)34, dC(pC)69, dA(pA)34, and dA(pA)69 as a function of [NaCl] and [NaBr] and find that the salt dependencies of these oligonucleotides are dependent upon base composition. These studies also indicate that ion binding accompanies formation of these SSB-ss-DNA complexes, although there is a net release of ions upon formation of the complex. This influence of both salt concentration and base composition indicates that both electrostatic and nonelectrostatic factors contribute to the negative cooperativity associated with ss-DNA binding to the SSB tetramer.

Base Composition↗
PubMed1996

Estrogenicity of resin-based composites and sealants used in dentistry.

We tested some resin-based composites used in dentistry for their estrogenic activity. A sealant based on bisphenol-A diglycidylether methacrylate (bis-GMA) increased cell yields, progesterone receptor expression, and pS2 secretion in human estrogen-target, serum-sensitive MCF7 breast cancer cells. Estrogenicity was due to bisphenol-A and bisphenol-A dimethacrylate, monomers found in the base paste of the dental sealant and identified by mass spectrometry. Samples of saliva from 18 subjects treated with 50 mg of a bis-GMA-based sealant applied on their molars were collected 1 hr before and after treatment. Bisphenol-A (range 90-931 micrograms) was identified only in saliva collected during a 1-hr period after treatment. The use of bis-GMA-based resins in dentistry, and particularly the use of sealants in children, appears to contribute to human exposure to xenoestrogens.

Adult↗
PubMed2005

Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes.

To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, M. smegmatis had been determined and compared. As all the organisms are GC-rich, the GC contents at third codon positions were found in fact higher than the second codon positions as well as the first + second codon positions in all the organisms indicating that directional mutational pressure is strongly operative at the synonymous third codon positions. Nc plot indicates that codon usage variation in all these organisms are governed by the forces other than compositional constraints. Correspondence analysis suggests that: (i) there are codon usage variation among the genes and genomes of the fourteen mycobacteriophages and M. smegmatis, i.e., codon usage patterns in the mycobacteriophages is phage-specific but not the M. smegmatis-specific; (ii) synonymous codon usage patterns of Barnyard, Che8, Che9d, and Omega are more similar than the rest mycobacteriophages and M. smegmatis; (iii) codon usage bias in the mycobacteriophages are mainly determined by mutational pressure; and (iv) the genes of comparatively GC rich genomes are more biased than the GC poor genomes. Translational selection in determining the codon usage variation in highly expressed genes can be invoked from the predominant occurrences of C ending codons in the highly expressed genes. Cluster analysis based on codon usage data also shows that there are two distinct branches for the fourteen mycobacteriophages and there is codon usage variation even among the phages of each branch.

Bacteriophages↗
PubMed2005

[Bias of base composition and codon usage in pseudorabies virus genes].

The complete sequence of the Pseudorabies Virus (PRV) genomic DNA has not yet been determined, primarily because of the high content of G + C nucleotides of about 74%. We examined the base composition and codon usage of the 68 known PRV genes. As a result, we found a strong bias towards GC-rich codons especially NNC or NNG (N represents any one of four nucleotides) in PRV genes. This demonstrated that the usage bias of synonymous codon and amino acid is the main cause of the high G + C content of PRV. The results showed that the genome regions adjacent UL48, UL40, UL14, IE180 genes where the G + C content occurs as pronounced waves are corresponding to the replication origins. It was also found that the codon usage patterns of regulatory genes are apparently different from other PRV genes. A corresponding analysis of amino acid compositions indicated that the bias of codon usage could be related to the differences of gene function.

Amino Acids↗
PubMed1996

Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase.

We have characterized the inhibition exerted by histone H1 on the activity of human placenta DNA (cytosine-5-)-methyltransferase. Our experiments demonstrate that the extent of inhibition depends on the DNA base composition, AT-rich substrates being more severely affected than GC-rich substrates and CpG-rich islands. With bacterial SssI methylase, the effect is completely reversed since its activity on AT-rich substrates undergoes a 4-5-fold stimulation upon the addition of H1. Poly(L-lysine) mimicks H1 effects, suggesting an essential role of lysine residues in both the inhibitory and stimulatory effects of H1. By comparison of the different behaviors of the two enzymes, the inhibitory effect over the eukaryotic enzyme might be accounted for by hypothesizing a competition between minor groove-binding motifs (SPKK-like) present in placenta methylase as well as in histone H1.

Base Composition↗
PubMed1976

Cardiac and skeletal muscle acid-base composition during metabolic acidosis in dogs.

Nephrectomized, open chested dogs were infused with 25-30 ml.kg(-1) body weight of 0.15 M NaCl (group I), 0.15 MHCl (Group II) or 0.3 M lactic acid (Group) III). Pulmonary ventilation was maintained constant in the three groups. Intracellular pH was calculated with the CO2 method. No significant intracellular or extracellular acid-base changes were produced in Group I. A similar degree of extracellular acidosis was achieved in Groups II and III. In spite of constant arterial PCO2, the PCO2 of mixed, coronary sinus and femoral vanous blood increased moderately after the infusion in Groups II and III. It was calculated that less than half of the HCl acid infused remained in the extracellular space. However, no significant changes were observed in the acid-base composition of skeletal muscle in either Group II or III. Comparison of the cardiac muscle cell acid-base composition of Group I with that of Groups II and III whows that metabolic acidosis of the degree and duration produced in these experiments does not produce appreciable myocardial acidosis.

Acid-Base Equilibrium↗
PubMed2006

A comparative evaluation of radiation-induced DNA damage using real-time PCR: influence of base composition.

To study the radiosensitivity of DNA segments at the open reading frame (gene) level, real-time PCR was used to analyze DNA damages induced by ionizing radiation. After irradiation (1, 3 and 5 kGy) of genomic DNA purified from Salmonella typhimurium, real-time PCR based on SYBR Green fluorescence and melting temperature was performed using various primer sets targeting the rfbJ, rfaJ, rfaB, hilD, ssrB, pipB, sopD, pduQ, eutG, oadB, ccmB and ccmA genes. The ccmA and ccmB genes, which existed as two copies on the chromosome and had a high GC content ( approximately 70%), showed much lower radiosensitivities than the other genes tested, particularly at 5 kGy; this distinctive feature was seen only when the genes were located on the chromosome, regardless of copy number. Our results reinforce the concept that gene sensitivity to ionizing radiation depends on the base composition and/or the spatial localization of the gene on the chromosome.

Base Composition↗
PubMed1963

THE BASE COMPOSITION OF RIBONUCLEIC ACID IN LAMPBRUSH CHROMOSOMES, NUCLEOLI, NUCLEAR SAP, AND CYTOPLASM OF TRITURUS OOCYTES.

The base composition of RNA's extracted from chromosomes, nucleoli, nuclear sap, and cytoplasm of Triturus oocytes has been determined by microelectrophoresis. The chromosomal RNA has a content of guanine+cytosine equal to that of DNA, but there is no complementarity in the composition as for DNA. Nuclear sap contains a highly variable RNA with a tendency towards high uracil values. Nucleolar and cytoplasmic RNA's are similar in composition and both are of the guanine-cytosine rich type. The chromosomes and nucleoli contain roughly equivalent amounts of RNA, somewhat less than is present in the nuclear sap. The RNA/DNA ratio of the whole chromosomes is about 10. However, the ratio in the synthetically active regions, the loops, is much higher, since the loops contain all the chromosomal RNA but only a small fraction of the DNA.

Adenine↗
PubMed1991

A simple and rapid experimental protocol for studies of nucleic acids metabolism and their base composition.

A suitable, simple and rapid protocol for metabolic studies of nucleic acids and determining their base composition, using reversed-phase high-performance liquid chromatography is described. Modified classic methods of isolation of the nucleic acids fraction from a biological material, in our particular case Artemia sp., were used. Then analysis of their constituents and the incorporated radioactivity, after hydrolytic processes, was performed by high-performance liquid chromatography under isocratic conditions, with 9 min total retention time. This method may be applied in several aspects of nucleic acids research, such as molecular cloning or metabolic and phylogenetic studies.

Animals↗
PubMedDate not supplied

Barcoll hardness of different resin-based composites cured by halogen or light emitting diode (LED).

The clinical performance of light curing resin composites is greatly influenced by the quality of the light-curing unit (LCU). Halogen LCUs are commonly used for curing composite materials. However, they have some drawbacks. The development of new, blue, super bright light emitting diodes (LED LCU) of 470-nm wavelength with high light irradiance comes as an alternative to standard halogen LCUs of 450-470-nm wavelengths. This study evaluated the surface hardness of the different resin-based composites (flowable, hybrid and packable resin composites) cured by LED LCU or halogen LCU. A Teflon mold 10-mm in diameter and 2-mm in depth was made to obtain five disk-shaped specimens for each experimental group. Then, the specimens were cured by an LED LCU or halogen LCU for 40 seconds. The hardness of the upper and lower surfaces was measured with a Barcoll hardness-measuring instrument. The statistical analysis was performed using one-way analysis of variance (ANOVA) and Duncan test at a p=0.05 significance level. The results of the hardness test indicated that the hardness of resin composites cured by an LED LCU were greater than those cured by a halogen LCU. Additionally, for all resin-based composites, the hardness values for the upper surfaces were higher than the lower surfaces. However, for both results no statistically significant differences were observed (p>0.05).

Analysis of Variance↗
PubMedDate not supplied

[Base composition and DNA content in single-cell Cyanobacteria].

The base composition and DNA content were determined in 19 strains of cyanobacteria. The content of GC varied within the range of 33.6 to 70.7 mol%, and the content of DNA, from 1.05 X 10(-14) to 28.7 X 10(-14) g per cell. The latter parameter almost directly depended on the cell volume. The cultures were subdivided into six groups according to the results obtained.

Bacteria↗
PubMed1999

Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition.

CspB is a small acidic protein of Bacillus subtilis, the induction of which is increased dramatically in response to cold shock. Although the exact functional role of CspB is unknown, it has been demonstrated that this protein binds single-stranded deoxynucleic acids (ssDNA). We addressed the question of the effect of base composition on the CspB binding to ssDNA by analyzing the thermodynamics of CspB interactions with model oligodeoxynucleotides. Combinations of four different techniques, fluorescence spectroscopy, gel shift mobility assays, isothermal titration calorimetry, and analytical ultracentrifugation, allowed us to show that: 1) CspB can preferentially bind poly-pyrimidine but not poly-purine ssDNA templates; 2) binding to T-based ssDNA template occurs with high affinity (K(d(25 degrees C)) approximately 42 nM) and is salt-independent, whereas binding of CspB to C-based ssDNA template is strongly salt-dependent (no binding is observed at 1 M NaCl), indicating large electrostatic component involved in the interactions; 3) upon binding each CspB covers a stretch of 6-7 thymine bases on T-based ssDNA; and 4) the binding of CspB to T-based ssDNA template is enthalpically driven, indicating the possible involvement of interactions between aromatic side chains on the protein with the thymine bases. The significance of these results with respect to the functional role of CspB in the bacterial cold shock response is discussed.

Bacterial Proteins↗
PubMed1990

Rapid procedure to determine the DNA base composition from small amounts of gram-positive bacteria.

A universal rapid procedure to determine the DNA base composition (mol% guanine + cytosine) of Gram-positive bacteria is described. Cells of Gram-positive bacteria were lysed with achromo-peptidase and the mol% G + C of their DNAs were determined by using high performance liquid chromatography. One ml of a Gram-positive bacterial suspension which matched MacFarland No. 3 standard turbidity was sufficient to determine the mol% G + C within 3 h.

Base Composition↗
PubMed1979

DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels.

The specific influence of the four nucleobases on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels under denaturing and nondenaturing conditions has been investigated using homooligomers from the four deoxyribonucleotides as chain length standards. Homooligomers of same chain lengths exhibit remarkable differences in mobility. Specific retardation of any other oligonucleotide investigated was found to be mainly dependent on base composition but not on sequence. A simple procedure is presented for calculating mobilities relative to the standards on denaturing gels. This allows a reliable identification of oligonucleotides on acrylamide-gels by exact chain length determination with respect to base composition and furthermore a detailed interpretation of complex reaction mixtures. The homooligomers also show the same differences in mobility on nondenaturing gels. The significance of this effect for strand separation is discussed.

Base Sequence↗
PubMed2006

Influence of surface roughness on crack formation in a glass-ceramic bonded to a resin composite base.

The objective of the present study was to assess the influence of the roughness of a loaded surface on crack formation in a mica-based glass-ceramic bonded to a resin composite base. Five different surface roughnesses were created on glass-ceramic discs by serial wet-grinding with silicone carbide abrasives. The thicknesses of the ceramic discs were 1.50 +/- 0.01 mm. Resin composite discs were bonded to the ceramic surfaces opposite to the ground surfaces using an adhesive resin composite cement and a silane coupling agent. A compressive load was then applied at the center of the ground ceramic surface. The loads at initial radial and cone crack formations in the ceramic were measured macroscopically. In three of the five groups, the initial radial crack formations could not be observed due to the high roughness of these surfaces. Statistical analysis was performed using Student's t test for initial radial cracks and one-way ANOVA for the cone cracks. There were no significant differences between the two groups for the initial radial cracks or among the five groups for the cone cracks (P < 0.05). The roughness of the loaded surface had no influence on crack formation in the bonded mica-based glass-ceramic.

Aluminum Silicates↗