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At least 469 records · Page 26Linked to original sources
PubMed1991

Bacillus brevis Migula 1900 taxonomy: reassociation and base composition of DNA.

Of 87 strains previously identified as Bacillus brevis Migula 1900, 58 had G + C contents of 47.0 to 51.9 mol%, a range that included the G + C content (48.7 mol%) of the type strain. The G + C contents for three other groups consisting of 5, 7, and 17 strains were 37.0 to 41.9, 42.0 to 46.9, and 52.0 mol% or higher, respectively. DNA reassociation studies showed that 25 of the 58 strains with G + C contents of 47.0 to 51.9 mol% were closely related genetically to the type strain and to each other. For the most part, this genetically related group was phenotypically homogeneous; variations in the fermentation of mannitol and mannose were observed. My results strongly suggest that many of the strains were misclassified as B. brevis. Consequently, much of the phenotypic heterogeneity of the species B. brevis Migula 1900 is not due to variations exhibited by genetically related organisms, but is the result of variability introduced by the presence of genetically unrelated strains.

Bacillus↗
PubMed1987

Co-evolution of base composition and codon usage in Xenopus laevis and human globin genes with long-range DNA organization of their genome.

Eucaryotic DNA is punctuated by many A+T-rich segments that we named A+T-rich linkers. Two types of these A+T-rich linkers can be distinguished: (i) isolated A+T-rich linkers, and (ii) A+T-rich linkers crowded in clusters. We have analysed the distribution of A+T-rich linker across the alpha- and beta-globin gene domain in Xenopus laevis and human genomes using isodenaturation and electron microscopy. Comparison of our data with those previously obtained for the avian globin genes leads us to conclude that genes can be harboured indifferently in either domain. A correlation is established between the presence of A+T-rich linker inside introns and flanking regions and the A+T content of the coding sequence. For the coding sequence, a high A+T content is strongly correlated with high A+T content in the codon's third position and weakly in the first position.

Animals↗
PubMed2006

The RAG-1 exon in the avian order Caprimulgiformes: phylogeny, heterozygosity, and base composition.

We sequenced 2.8 kb of the RAG-1 exon for most of the extant genera in the avian order Caprimulgiformes to investigate monophyly of the order and phylogeny within the traditional families. The order is not monophyletic: the Aegothelidae (owlet-nightjars) were the sister group of the Apodiformes (swifts and hummingbirds). There was no support for the monophyly of a clade containing the remaining families of Caprimulgiformes. However, the RAG-1 data strongly supported a relationship between the Podargidae (frogmouths) and Caprimulgidae (nightjars). Within the Caprimulgidae, the Australasian genus Eurostopodus was sister to the rest of the family, which in turn was composed of four major clades, three of which were restricted to the New World and primarily to the Neotropics. The Old World caprimulgids form a monophyletic clade embedded within the New World taxa; consequently, most Old World nightjars are probably the result of a single expansion out of the Neotropics. The genus Caprimulgus was not found to be monophyletic. Several species in the Caprimulgidae have both elevated heterozygosity and high GC3 content; it is likely that these are causally related.

Animals↗
PubMed1992

Rates of synonymous substitution and base composition of nuclear genes in Drosophila.

We compared the rates of synonymous (silent) substitution among various genes in a number of species of Drosophila. First, we found that even for a particular gene, the rate of synonymous substitution varied considerably with Drosophila lineages. Second, we showed a large variation in synonymous substitution rates among nuclear genes in Drosophila. These rates of synonymous substitution were correlated negatively with C content and positively with A content at the third codon positions. Nucleotide sequences were also compared between pseudogenes and their functional homologs. The C content of the pseudogenes was lower than that of the functional genes and the A content of the former was higher than that of the latter. Because the synonymous substitution for functional genes and the nucleotide substitution for pseudogenes are exempted from any selective constraint at the protein level, these observations could be explained by a biased pattern of mutation in the Drosophila nuclear genome. Such a bias in the mutation pattern may affect the molecular clock (local clock) of each nuclear gene of each species. Finally, we obtained the average rates of synonymous substitution for three gene groups in Drosophila; 11.0 x 10(-9), 17.5 x 10(-9) and 27.1 x 10(-9)/site/year.

Animals↗
PubMed2003

The evolution of genomic base composition in bacteria.

Guanine plus cytosine (GC) content ranges broadly among bacterial genomes. In this study, we explore the use of a Brownian-motion model for the evolution of GC content over time. This model assumes that GC content varies over time in a continuous and homogeneous manner. Using this model and a maximum-likelihood approach, we analyzed the evolution of GC content across several bacterial phylogenies. Using three independent tests, we found that the observed divergence in GC content was consistent with a homogeneous Brownian-motion model. For example, similar rates of GC content evolution were inferred in several different bacterial subclades, indicating that there is relatively little rate heterogeneity in GC content evolution over broad evolutionary time scales. We thus argue that the homogeneous Brownian-motion model provides a good working model for GC content evolution. We then use this model to determine the overall rate of GC content evolution among eubacteria. We also determine the time frame over which GC content remains similar in related taxa, using a flexible definition for "similarity" in GC content so that, depending on the context, more or less stringent criteria may be applied. Our results have implications for models of sequence evolution, including those used for phylogenetic reconstruction and for inferring unusual changes in GC content.

Bacteria↗
PubMed1994

Flow cytometric detection of chromosome abnormalities by measuring centromeric index, DNA content, and DNA base composition.

This paper highlights two improvements of the on-line centromeric index (CI) analysis for the detection of chromosome abnormalities. On-line CI versus DNA content analysis of an EBV-transformed cell line, with a deletion (11)(p13p15.1), of a patient with aniridia and Wilms' tumour demonstrates the first improvement of the method of on-line CI analysis for flow karyotyping and sorting; a reciprocal translocation, insertion, or deletion can, when the cell type contains not more than a few of these types of abnormalities, be traced to the p-arm or q-arm of the relevant chromosome. On-line CI analysis was also performed with chromosomes isolated from a transitional cell carcinoma of the bladder. Cytogenetic analysis of this cell line showed numerous chromosomal abnormalities. Chromosomes of this cell line were also karyotyped by bivariate flow cytometry using a different set of parameters: Hoechst 33,258 fluorescence intensity (HOfl) versus chromomycin A3 fluorescence intensity (CAfl). A comparison of these results reveals the second improvement of the CI method for the detection of chromosome abnormalities; bivariate analysis of CI versus propidium fluorescence (PIfl) are complementary to bivariate analysis of HOfl versus CAfl. Chromosomes with distributions that fuse together in the HO/CA flow karyotype may be distinguished as individual peaks on the basis of their CI values.

Aniridia↗
PubMed1988

Trophozoite and nuclear size, DNA base composition, and nucleotide sequence homology of several Entamoeba strains in axenic culture.

We carried out a comparative study of nuclear and trophozoite diameters and of DNA thermal denaturation in eight Entamoeba strains cultured axenically (four of them E. histolytica, two initially designated as E. invadens, one E. moshkovskii, and one E. histolytica-like), as well as an analysis of the overall DNA sequence homology of the non-E. histolytica strains. The average nuclear (N) and trophozoite (T) diameters (in micron) were, respectively: global averages +/- SD for E. histolytica strains, 6.5 +/- 2.5 and 28.8 +/- 3.7; E. invadens IP101, 5.8 and 27.5, and PZ, 7.8 and 33.6; E. moshkovskii FIC, 4.1 and 12.9; E. histolytica-like Laredo strain, 5.0 and 20.6. The GC content of DNA, estimated by thermal elution in hydroxyapatite, was around 23% in HK9 and its clone HK9-1 and around 27% in the HM2 and HM3 E. histolytica strains; it was 37% in the Laredo strain, 26% in IP101, 35% in PZ, and 33% in FIC. The reassociation kinetics of PZ strain DNA showed that it consists of 40% repeated sequences and 60% unique sequences. By means of DNA association experiments in which one of each pair of DNAs tested had been labeled in vitro with 125I, we found the following overall sequence homology among the strains tested: PZ-FIC, 38%; IP101-Laredo, 38%; IP101-FIC, 47%; PZ-Laredo, 49%; Laredo-FIC, 69%; and IP101-PZ, 83%. We conclude that trophozoites of different E. histolytica strains have similar nuclear size and GC content, whereas these parameters and the nucleotide sequences are clearly different in every other Entamoeba species.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Base-compositional biases and the bat problem. III. The questions of microchiropteran monophyly.

Using single-copy DNA hybridization, we carried out a whole genome study of 16 bats (from ten families) and five outgroups (two primates and one each dermopteran, scandentian, and marsupial). Three of the bat species represented as many families of Rhinolophoidea, and these always associated with the two representatives of Pteropodidae. All other microchiropterans, however, formed a monophyletic unit displaying interrelationships largely in accord with current opinion. Thus noctilionoids comprised one clade, while vespertilionids, emballonurids, and molossids comprised three others, successively more closely related in that sequence. The unexpected position of rhinolophoids may be due either to the high AT bias they share with pteropodids, or it may be phylogenetically authentic. Reanalysis of the data with varying combinations of the five outgroups does not indicate a rooting problem, and the inclusion of many bat lineages divided at varying levels similarly discounts long branch attraction as an explanation for the pteropodid-rhinolophoid association. If rhinolophoids are indeed specially related to pteropodids, many synapomorphies of Microchiroptera are called into question, not least the unitary evolution of echolocation (although this feature may simply have been lost in pteropodids). Further, a rhinolophoid-pteropodid relationship--if true--has serious implications for the classification of bats. Finally, among the outgroups, an apparent sister-group relation of Dermoptera and Primates suggests that flying lemurs do not represent the ancestors of some or all bats; yet, insofar as gliding of the type implemented in dermopterans is an appropriate model for the evolution of powered mammalian flying, the position of Cynocephalus in our tree indirectly strengthens the argument that true flight could have evolved more than once among bats.

Animals↗
PubMed1999

Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A = T and G = C.

The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon position from Parity Rule 2 (PR2), where A = T and G = C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available, it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition, PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint.

Bacteria↗
PubMed1979

Serum electrolyte and acid base composition. The influence of graded degrees of chronic renal failure.

Data from 41 ambulatory patients with graded degrees of uncomplicated, chronic renal failure were used to define the quantitative relationship between serum acid-base and electrolyte composition and the serum creatinine level. Even in patients with only moderate renal insufficiency, serum total carbon dioxide (tCO2) content was reduced significantly. This early fall in tCO2 was offset by an increase in serum chloride (Cl-), serum undetermined anton concentration (A-) remaining normal. In patients with more severe degrees of renal insufficiency, further decrements in tCO2 occurred that were proportional to the increment in serum creatinine. These latter decrements in tCO2 were associated with equivalent increments in A-, serum Cl- remaining unchanged at the elevated level observed during moderate renal insufficiency. Confidence limits of 95% for tCO2 and A- were calculated from the data.

Acid-Base Equilibrium↗
PubMed2007

Fabrication and in vitro characterization of porous biodegradable composites based on phosphate glasses and oligolactide-containing polymer networks.

Degradable porous composite materials for use as temporary bone replacement or tissue engineering scaffolds were produced using a methacrylate-modified oligolactide polymer network and phosphate invert glasses in the system P2O5-CaO-MgO-Na2O-(TiO2). Porous glasses with an open interconnective porosity were produced by a salt sintering process. Compressive strengths were significantly enhanced by polymer coating of the inner surface of the porous glasses or by fabrication of glass powder-reinforced porous polymer specimens. In vitro degradation in simulated body fluid showed a degradation pattern of the composites which could be modulated by the composition and resulting solubility of the incorporated glass phase. Cytocompatibility of the composites was investigated in a FDA/EtBr viability assay using an MC3T3-E1 osteoblast-like cell line and showed good biocompatibility of the materials in vitro.

3T3 Cells↗
PubMed2002

The base composition of the genes is correlated with the secondary structures of the encoded proteins.

The analysis of a non-redundant set of human proteins, for which both the crystallographic structures and the corresponding gene sequences are available, show that bases at third codon position are non-uniformly distributed along the coding sequences. Significant compositional differences are found by comparing the gene regions corresponding to the different secondary structures of the proteins. Inter-and intra-structure differences were most pronounced in the GC-richest genes. These results are not compatible with any proposed hypotheses based on a neutral process of formation/maintenance of the high GC(3) levels of the genes localized in the GC-richest isochores of the human genome.

Amino Acids↗
PubMed2003

Sol-gel-derived titanium oxide/copolymer composite based glucose biosensor.

A new type of sol-gel-derived titanium oxide/copolymer composite material was developed and used for the construction of glucose biosensor. The composite material merged the best properties of the inorganic species, titanium oxide and the organic copolymer, poly(vinyl alcohol) grafting 4-vinylpyridine (PVA-g-PVP). The glucose oxidase entrapped in the composite matrix retained its bioactivity. Morphologies of the composite-modified electrode and the enzyme electrode were characterized with a scanning electron microscope. The dependence of the current responses on enzyme-loading and pH was studied. The response time of the biosensor was < 20 s and the linear range was up to 9 microM with a sensitivity of 405 nA/microM. The biosensor was stable for at least 1 month. In addition, the tetrathiafulvalene-mediated enzyme electrode was constructed for the decrease of detection potential and the effect of three common physiological sources that might interfere was also investigated.

Adsorption↗
PubMed2003

Preparation, characterization, and in vitro degradation of bioresorbable and bioactive composites based on Bioglass-filled polylactide foams.

Highly porous poly(D,L-lactide)/Bioglass composites scaffolds were prepared by thermally induced phase separation process of polymer solutions and subsequent solvent sublimation. A series of composite foams with different polymer/Bioglass weight ratios was prepared to study the influence of Bioglass content on the foam characteristics such as porous structure, density, and pore volume. The pore volume was decreased from 9.5 to 5.7 cm(3)/g when the Bioglass content was increased up to 40 wt %, but the overall pore morphology was not affected very much by changing the polymer/glass composition ratio. The composites foams were then incubated in phosphate-buffered saline at 37 degrees C to study the in vitro degradation of the polymer and to detect hydroxyapatite (HA) formation as an indication of their bioactivity. The addition of Bioglass to polymer foams increased the water absorption and weight loss as compared with pure polymer foams. However, the polymer molecular weight, determined by size exclusion chromatography, was found to decrease more rapidly and to a larger extent in absence of Bioglass. This delayed degradation rate in the composite foams was probably caused by the dissolution of alkaline ions from the Bioglass, resulting in a buffering effect of the incubation medium. After incubation for 7 days, HA was detected by X-ray diffractometry and Raman spectroscopy and confirmed by environmental scanning electron microscopy and energy-dispersive X-ray analysis. The porous composites developed here are promising materials for bone regeneration applications because the formation of HA on the surface of the pore walls should provide good environment for the adhesion and proliferation of osteoblasts and osteoprogenitor cells.

Bone Substitutes↗
PubMed2007

In vitro cytotoxicity of dental composites based on new and traditional polymerization chemistries.

UNLABELLED: The biological response to dental restorative polymer composites is mediated by the release of unpolymerized residual monomers. Several new composite formulations claim to reduce unpolymerized residual mass. The current study assessed the cytotoxic responses to several of these new formations and compared them with more traditional formulations. Our hypothesis predicted that if these new polymerization chemistries reduce unpolymerized residual mass, the cytotoxicity of these materials also should be reduced relative to traditional formulations. METHODS: Materials (HerculiteXRV, Premise, Filtek Supreme, CeramxDuo, Hermes, and Quixfil) were tested in vitro in direct contact with Balb mouse fibroblasts, initially, then after aging in artificial saliva for 0, 1, 3, 5, or 8 weeks. The toxicity was determined by using the MTT assay to the estimate SDH activity. Knoop hardness of the materials also was measured at 0 and 8 weeks to determine whether surface breakdown of the materials in artificial saliva contributed to cytotoxic responses. RESULTS: Materials with traditional methacrylate chemistries (Herculite, Premise, Filtek Supreme) were severely (>50%) cytotoxic throughout the 8-week interval, but materials with newer chemistries or filling strategies (Hermes, CeramXDuo, and Quixfil) improved over time of aging in artificial saliva. Hermes showed the least cytotoxicity at 8 weeks, and was statistically equivalent to Teflon negative controls. Hardness of the materials was unaffected by exposure to artificial saliva. CONCLUSIONS: Newer polymerization and filling strategies for dental composites show promise for reducing the release of unpolymerized components and cytotoxicity.

Animals↗