Analysis of the ethidium bromide bound to DNA by photoacoustic and FTIR spectroscopy

Under physiological conditions B-form DNA is an exceedingly stable structure. However, experimental evidences obtained through nuclear magnetic resonance and fluorescence anisotropy suggest that the structure of the double helix fluctuates substantially. We describe photoacoustic phase modulation frequency measurements of ethidium bromide (Eb) with calf thymus, DNA. As in fluorescence phase modulation measurements, we used an intercalating dye as a probe; however, we monitored the triplet excited state lifetime at different ionic strengths. The triplet lifetime of Eb varied from about 0.30 ms, with no DNA present, to 20 ms, (at a DNA:Eb molar ratio of 5). With salt titration, this value falls, to about 2.0 ms. This result suggests, a strong coupling between the phenantridinium ring of the ethidium and the base pairs because of the stacking movement of the DNA molecule under salt effect. This, effect may be understood considering DNA as a polyelectrolyte. The counterions, in the solution shield the phosphate groups, reducing the electrostatic repulsion force between them, hence compacting the DNA molecule. The results from Fourier transform infrared demonstrated two important bands: 3187 cm(-1) corresponding to the symmetric stretching of the NH group of the bases, and 1225 cm(-1) corresponding to the asymmetric stretching of phosphate groups shifted toward higher wavenumbers, suggesting a proximity between the intercalant and base pairs and a modification of the DNA backbone state, both induced by salt accretion.

Molecular organization of 5S rDNA in fishes of the genus Brycon

There are few reports on the genomic organization of 5S rDNA in fish species. To characterize the 5S rDNA nucleotide sequence and chromosomal localization in the Neotropical fishes of the genus Brycon, 5S rDNA copies from seven species were generated by PCR. The nucleotide sequences of the coding region (5S rRNA gene) and the nontranscribed spacer (NTS) were determined, revealing that the 5S rRNA genes were highly conserved, while the NTSs were widely variable among the species analyzed. Moreover, two classes of NTS were detected in each species, characterized by base substitutions and insertions-deletions. Using fluorescence in situ hybridization (FISH), two 5S rDNA chromosome loci that could be related to the two 5S rDNA NTS classes were observed in at least one of the species studied. 5S rDNA sequencing and chromosomal localization permitted the characterization of Brycon spp. and suggest a higher similarity among some of them. The data obtained indicate that the 5S rDNA can be an useful genetic marker for species identification and evolutionary studies.

A kinetic study of the effect of ultrasound power on the sonohydrolysis of tetraethyl orthosilicate

A kinetic study of the ultrasound-stimulated and acid-catalyzed sonohydrolysis of tetraethyl orthosilicate (TEOS) in solventless TEOS-water heterogeneous mixtures was carried out by means of a calorimetric method as a function of the ultrasound power. The hydrolysis reaction starts in acidulated heterogeneous water-TEOS mixtures after an induction period under ultrasonic stimulation. The ultrasound power seems to play a role on the dynamical coupling of the system originating a continuum upward shifting of the base line during the induction period of sonication. The rate in which the base line is upward shifted diminishes with the power. The best coupling between the ultrasound and the reactant heterogeneous mixtures for this experimental setup was found to occur at 50 W, for which the gelation time was found to be a minimum. The kinetics of the heterogeneous TEOS sonohydrolysis was studied on the basis of a dissolution and reaction modeling. The heterogeneous reaction pathway as deduced from the kinetic study was drawn in a ternary diagram as a function of the ultrasound power. (C) 2006 Elsevier B.V. All rights reserved.

Ultrastructure of the ovariole sheath in Diatraea saccharalis (Lepidoptera : Pyralidae)

The ultrastructure of the ovariole sheath along the Diatraea saccharalis ovariole was studied by scanning and transmission electron microscopy. Each ovariole is surrounded by an epithelial sheath, a tunica propria and scattered lumen cells. These three components of the ovariole sheath show different ultrastructural features along the ovariole, in the germarium or in the vitellarium; these differences are more evident in the epithelial sheath cells. The epithelial sheath is composed by two layers of cells, the external one running longitudinally and the internal one running circularly in the ovariole. These cells, in vitellarium, present cytoplasmic bundles of myofilaments that are arranged parallel to the long axis of the cells; these myofilaments are apparently related to the contraction movements of the follicles within the ovariole. The acellular tunica propria, composed of finely filamentous material, is attached to the adjacent follicle cells by adhesive dense plates. Between the epithelial sheath and the tunica propria there is a population of lumen cells, with morphological features of secretory activity.

Othonella araguaiana (Bivalvia, Megadesmidae) from the Corumbatai Formation (Midlle [Middle] Permian), Eastern Margin of the Parana Basin: systematic, evolutionary and biostratigraphic significances.

In this study, the occurrence of Othonella araguaiana Mendes, a rare bivalve species is reported for the first time in the Pinzonella illusa biozone, Middle Permian Corumbatai Formation, in the State of São Paulo. This species was originally described in coeval rocks of the Estrada Nova Formation (= Corumbatai) from the Alto Araguaia and Alto Garcas regions, State of Mato Grosso. The specimens of O. araguaiana were found in the base of a bioclastic sandstone bed, a proximal tempestite, in the middle of the Corumbatai Formation, in the city of Rio Claro, São Paulo State. The silicified shells and internal molds are well preserved, showing impressions of muscle scars and other internal anatomic characters (e.g., hinge), never illustrated by previous authors. In his original description, Mendes (1963) called attention to the similarity between O. araguaiana and Terraia aequilateralis, a common veneroid of the Corumbatai Formation. Conversely, Runnegar and Newell (1971) suggested that O. araguaiana belongs to Megadesmidae, being a junior synonym of Plesiocyprinella carinata (the commonest megadesmid of the Passa Dois Group). Our study indicates that O. araguaiana is indeed a megadesmid, but is distinct from the P. carinata. The new occurrence of O. araguaiana demonstrates that a) the paleobiogeographic distribution of this species is wider than previously thought (that it was restricted to the northern part of Parana Basin, Mato Grosso State); b) the molluscan fauna of the Corumbatai Formation (P. illusa biozone) in the State of São Paulo is more diverse and dominated by megadesmids; and c) the composition of the molluscan fauna of the Corumbatai Formation in Alto GarYas, State of Mato Grosso, is essentially the same as that of the P. illusa biozone of the eastern margin of the Parana Basin.

A stratigraphic chart of the Late Carboniferous/Permian succession of the eastern border of the Parana Basin, Brazil, South America

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Cloning and expression of the cDNA encoding rat granulocyte colony-stimulating factor

Granulocyte colony-stimulating factor (G-CSF) acts on precursor hematopoietic cells to control the production and maintenance of neutrophils. Recombinant G-CSF (re-G-CSF)is used clinically to treat patients with neutropenia and has greatly reduced the infection risk associated with bone marrow transplantation. Cyclic hematopoiesis, a stem cell defect characterized by severe recurrent neutropenia, occurs in man and grey collie dogs, and can be treated by administration of re-G-CSF. Availability of the rat G-CSF cDNA would benefit the use of rats as models of gene therapy for the treatment of cyclic hematopoiesis. In preliminary rat experiments, retroviral-mediated expression of canine G-CSF caused neutralizing antibody formation which precluded long-term increases in neutrophil counts. To overcome this problem we cloned the rat G-CSF cDNA from RNA isolated from skin fibroblasts. The rat G-CSF sequence shared a high degree of identity in both the coding and non-coding regions with both the murine G-CSF (85%) and human G-CSF (74%). The signal peptides of murine and human G-CSF both contained 30 amino acids (aa), whereas the deduced signal sequence for rat G-CSF possessed 21 aa. A retrovirus encoding the rat G-CSF cDNA synthesized bioactive G-CSF from transduced vascular smooth muscle cells.

Determination of neutral polymorphisms (frameworks) of the human beta globin gene in beta thalassaemias by PCR/DGGE

Purpose: Considering the importance of type beta thalassaemias as hereditary syndromes of high significance in different populations of Mediterranean origin and, by extension, in the Brazilian population, the objective of the present study was to determine by PCR/DGGE the gene structures responsible for neutral polymorphisms (frameworks) observed in the human beta globin gene associated with the mutations responsible for type beta thalassaemias in a sample of the Brazilian population and, more specifically, of the population of the State of São Paulo. Patients and methods: Thirty individuals with beta thalassaemic mutations were analyzed: 22 mutations were in codon 39 (C->T), 5 in IVS1-110 (G->A), 2 in IVS1-6 (T->C) and 1 in IVS1-1 (G->A). DNA was extracted and selective amplification was performed by PCR extending from position IVS1 nt 46 to IVS2 nt 126 (474 pb). The product was then analyzed by polyacrylamide gel electrophoresis on a denaturing 10-60% urea/formamide gradient. Results: The results demonstrated that, as expected, the mutations responsible for type beta thalassaemia observed in this population are of Mediterranean origin, with 73% distribution represented by codon 39,17% by IVS1-110, 7% by IVS1-6 and 3% by IVS1-1. In turn, framework distribution seems to indicate a higher frequency of Fr 1-1 in codon 39 and IVS1-110, of Fr 1-3 in IVS1-6 and of Fr 1-2 in IVS1-1. Conclusions: These results permit us to conclude that gene amplification by PCR followed by DGGE is an appropriate method for the separation of DNA molecules that differ even by a single base change and therefore can be utilized to detect the alterations observed in the human beta globin gene. This methodology shows that, using only a pair of primers, it is possible to define the frameworks that are observed in the beta globin gene.

Nucleotide sequence of 5S rDNA and localization of the ribosomal RNA genes to metaphase chromosomes of the Tilapiine cichlid fish, Oreochromis niloticus

In this study, we report the cloning and nucleotide sequence of PCR-generated 5S rDNA from the Tilapiine cichlid fish, Oreochromis niloticus. Two types of 5S rDNA were detected that differed by insertions and/or deletions and base substitutions within the non-transcribed spacer (NTS). Two 5S rDNA loci were observed by fluorescent in situ hybridization (FISH) in metaphase spreads of tilapia chromosomes. FISH using an 18S rDNA probe and silver nitrate sequential staining of 5S-FISH slides showed three 18S rDNA loci that are not syntenic to the 5S rDNA loci.

Complete replacement of the mitochondrial genotype in a Bos indicus calf reconstructed by nuclear transfer to a bos taurus oocyte

Due to the exclusively maternal inheritance of mitochondria, mitochondrial genotypes can be coupled to a particular nuclear genotype by continuous mating of founder females and their female offspring to males of the desired nuclear genotype. However, backcrossing is a gradual procedure that, apart from being lengthy, cannot ascertain that genetic and epigenetic changes will modify the original nuclear genotype. Animal cloning by nuclear transfer using host ooplasm carrying polymorphic mitochondrial genomes allows, among other biotechnology applications, the coupling of nuclear and mitochondrial genotypes of diverse origin within a single generation. Previous attempts to use Bos taurus oocytes as hosts to transfer nuclei from unrelated species led to the development to the blastocyst stage but none supported gestation to term. Our aim in this study was to determine whether B. taurus oocytes support development of nuclei from the closely related B. indicus cattle and to examine the fate of their mitochondrial genotypes throughout development. We show that indicus:taurus reconstructed oocytes develop to the blastocyst stage and produce live offspring after transfer to surrogate cows. We also demonstrate that, in reconstructed embryos, donor cell-derived mitochondria undergo a stringent genetic drift during early development leading, in most cases, to a reduction or complete elimination of B. indicus mtDNA. These results demonstrate that cross-subspecies animal cloning is a viable approach both for matching diverse nuclear and cytoplasmic genes to create novel breeds of cattle and for rescuing closely related endangered cattle.

In vitro evaluation of the antimicrobial activity of a castor oil-based irrigant

The antimicrobial activity of irrigating solutions - Endoquil (castor oil detergent), 2% chlorhexidine gluconate solution, and 0.5% NaOCI solution - was evaluated against Gram-positive cocci (Micrococcus luteus, Staphylococcus aureus, Enterococcus faecalis, Staphylococcus epidermidis, Streptococcus mutans, and Streptococcus sobrinus), Gramnegative rods (Escherichia coli and Pseudomonas aeruginosa), and the yeast Candida albicans. Activity was evaluated using the two-layer agar diffusion technique. The base layer was obtained by pouring 10.0 ml of Muller Hinton Medium or 10.0 ml of Brain Heart Infusion agar in a Petri dish. After solidification a 5.0 ml seed layer of Muller Hinton Medium or Brain Heart Infusion agar with inoculum (106/ml) was added. Absorbent paper disks (6.0 mm in diameter) immersed in the solutions were placed at equidistant points. Plates were maintained at room temperature for 2 h for prediffusion of the solutions and incubated at 37°C for 24 h. The candle jar system was used for the Brain Heart Infusion agar plates. All tests were performed in duplicate. After incubation the medium was optimized with 0.05 g% triphenyltetrazolium chlorate gel and inhibition halos were measured. All bacterial strains were inhibited by 2.0% chlorhexidine gluconate. Endoquil was effective against Grampositive microorganisms, and 0.5% NaOCI was effective only against S. aureus. Copyright © 2001 by The American Association of Endodontists.

RAPD analysis in the Neotropical fish Brycon lundii: Genetic diversity and its implications for the conservation of the species

Random amplified polymorphic DNA (RAPD) technique was used to examine the genetic variability on an endangered Neotropical fish species, Brycon lundii, collected on two regions with distinct environmental conditions in the São Francisco River (Brazil), downstream from a hydroelectric station. Using decamer oligonucleotides as single primers in Polymerase Chain Reaction (PCR), genetic similarity index, mean allele frequency and mean heterozigosity were estimated, revealing variations between samples from the two regions. Moreover, a fragment of about 1200 base pairs was found in 100% of the examined animals collected at the region closer to the hydroelectric dam, while its frequency was much lower (27.3%) within the sample from the second collecting site, 30 km downstream from the dam, indicating a possible correlation between genetic variation and geographical area. A dendogram representing the relationships among genotypes was obtained, demonstrating at least two major clusters of animals. Based on the data, a model of population structuring in Brycon lundii is suggested. The described approach holds great promise for further analyses and gives support to biodiversity maintenance and recovery efforts of B. lundii.

Collateral cartilage ossification of the distal phalanx in the Brazilian Jumper horse

Collateral cartilage ossification of the distal phalanx in the Brazilian Jumper horse is a common finding. The objective of this study was to evaluate the prevalence and the degree of ossification of the collateral cartilages of the distal phalanx in Brazilian Jumper horses. In an analysis of 652 collateral cartilages from the front feet of 163 horses, 93% of these cartilages had collateral cartilage ossification (P < 0.005), and 7% of these cartilages did not have any type of ossification. In ossified cartilages, 86.4% had ossification beginning from the base, and 6.6% had a separate center of ossification.

The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.