One-step reverse transcriptase polymerase chain reaction for the diagnosis of respiratory syncytial virus in children

Human respiratory syncytial virus (HRSV) is the main cause of acute lower respiratory tract infections in infants and children. Rapid diagnosis is required to permit appropriate care and treatment and to avoid unnecessary antibiotic use. Reverse transcriptase (RT-PCR) and indirect immunofluorescence assay (IFA) methods have been considered important tools for virus detection due to their high sensitivity and specificity. In order to maximize use-simplicity and minimize the risk of sample cross-contamination inherent in two-step techniques, a RT-PCR method using only a single tube to detect HRSV in clinical samples was developed. Nasopharyngeal aspirates from 226 patients with acute respiratory illness, ranging from infants to 5 years old, were collected at the University Hospital of the University of Sao Paulo (HU-USP), and tested using IFA, one-step RT-PCR, and semi-nested RT-PCR. One hundred and two (45.1%) samples were positive by at least one of the three methods, and 75 (33.2%) were positive by all methods: 92 (40.7%) were positive by one-step RT-PCR, 84 (37.2%) by IFA, and 96 (42.5%) by the semi-nested RT-PCR technique. One-step RT-PCR was shown to be fast, sensitive, and specific for RSV diagnosis, without the added inconvenience and risk of false positive results associated with semi-nested PCR. The combined use of these two methods enhances HRSV detection. (C) 2007 Elsevier B.V. All rights reserved.

Characterization of Metal and Trace Element Contents of Particulate Matter (PM10) Emitted by Vehicles Running on Brazilian FuelsHydrated Ethanol and Gasoline with 22% of Anhydrous Ethanol

Emission of fine particles by mobile sources has been a matter of great concern due to its potential risk both to human health and the environment. Although there is no evidence that one sole component may be responsible for the adverse health outcomes, it is postulated that the metal particle content is one of the most important factors, mainly in relation to oxidative stress. Data concerning the amount and type of metal particles emitted by automotive vehicles using Brazilian fuels are limited. The aim of this study was to identify inhalable particles (PM10) and their trace metal content in two light-duty vehicles where one was fueled with ethanol while the other was fueled with gasoline mixed with 22% of anhydrous ethanol (gasohol); these engines were tested on a chassis dynamometer. The elementary composition of the samples was evaluated by the particle-induced x-ray emission technique. The experiment showed that total emission factors ranged from 2.5 to 11.8 mg/km in the gasohol vehicle, and from 1.2 to 3 mg/km in the ethanol vehicle. The majority of particles emitted were in the fine fraction (PM2.5), in which Al, Si, Ca, and Fe corresponded to 80% of the total weight. PM10 emissions from the ethanol vehicle were about threefold lower than those of gasohol. The elevated amount of fine particulate matter is an aggravating factor, considering that these particles, and consequently associated metals, readily penetrate deeply into the respiratory tract, producing damage to lungs and other tissues.

Cytochrome-b variation in Apis mellifera samples and its association with COI-COII patterns

Five Mbo I (Mbo-A, Mbo-M, Mbo-C(1), Mbo-C(2) and Mbo-C(3)) and Hinf I (Hinf-1 to Hinf-5) patterns were observed in Apis mellifera samples after restriction of a 485 bp fragment of the mitochondrial cytochrome-b (cyt-b) gene. Associating the cyt-b Restriction fragment length polymorphism (RFLP) pattern of each sample to its respective previously established COI-COII (Dra I sites) pattern, five restriction patterns (Mbo-C(1), Mbo-C(2), Mbo-C(3), Hinf-1 and Hinf-4) were observed in samples of maternal origin associated to the evolutionary branch C. No deletions or insertions were observed and the nucleotide substitution rate was estimated at 5.4%. Higher nucleotide diversity was observed among the branch C-haplotypes when compared with A and M lineages. Further studies are needed to confirm if the cyt-b + COI-COII haplotypes help to assign certain phylogeographic patterns to the branch C and to clarify phylogenetic relationships among A. mellifera subspecies.

Next Generation Sequencing of Pooled Samples Reveals New SNRNP200 Mutations Associated with Retinitis Pigmentosa

The gene SNRNP200 is composed of 45 exons and encodes a protein essential for pre-mRNA splicing, the 200 kDa helicase hBrr2. Two mutations in SNRNP200 have recently been associated with autosomal dominant retinitis pigmentosa (adRP), a retinal degenerative disease, in two families from China. In this work we analyzed the entire 35-Kb SNRNP200 genomic region in a cohort of 96 unrelated North American patients with adRP. To complete this large-scale sequencing project, we performed ultra high-throughput sequencing of pooled, untagged PCR products. We then validated the detected DNA changes by Sanger sequencing of individual samples from this cohort and from an additional one of 95 patients. One of the two previously known mutations (p.S1087L) was identified in 3 patients, while 4 new missense changes (p.R681C, p.R681H, p.V683L, p.Y689C) affecting highly conserved codons were identified in 6 unrelated individuals, indicating that the prevalence of SNRNP200-associated adRP is relatively high. We also took advantage of this research to evaluate the pool-and-sequence method, especially with respect to the generation of false positive and negative results. We conclude that, although this strategy can be adopted for rapid discovery of new disease-associated variants, it still requires extensive validation to be used in routine DNA screenings. (C) 2011 Wiley-Liss, Inc.

Adherence and invasion of Bacteroidales isolated from the human intestinal tract

Members of the genera Bacteroides and Parabacteroides are important constituents of both human and animal intestinal microbiota, and are significant facultative pathogens. In this study, the ability of Bacteroides spp. and Parabacteroides distasonis isolated from both diarrhoeal and normal stools (n = 114) to adhere to and invade HEp-2 cells was evaluated. The presence of putative virulence factors such as capsule and fimbriae was also investigated. Adherence to HEp-2 cells was observed in 75.4% of the strains, which displayed non-localized clusters. Invasion was observed in 37.5% and 26% of the strains isolated from diarrhoeal and non-diarrhoeal stools, respectively. All strains displayed a capsule, whereas none of them showed fimbriae-like structures. This is the first report of the ability of Bacteroides spp. and P. distasonis to adhere to and invade cultured HEp-2 epithelial cells.

Effects of gamma-radiation on the fungus Alternaria alternata in artificially inoculated cereal samples

The objective of this study was to evaluate the effects of different gamma-radiation doses on the growth of Alternaria alternata in artificially inoculated cereal samples. Seeds and grains were divided into four groups: Control Group (not irradiated), and Groups 1, 2 and 3, inoculated with an A. alternata spore suspension (1 x 10(6) spores/mL) and exposed to 2, 5 and 10 kGy, respectively. Serial dilutions of the samples were prepared and seeded on DRBC (dichloran rose bengal chloramphenicol agar) and DCMA (dichloran chloramphenicol malt extract agar) media, after which the number of colony-forming units per gram was determined in each group. In addition, fungal morphology after irradiation was analyzed by scanning electron microscopy (SEM). The results showed that ionizing radiation at a dose of 5 kGy was effective in reducing the growth of A. alternata. However, a dose of 10 kGy was necessary to inhibit fungal growth completely. SEM made it possible to visualize structural alterations induced by the different gamma-radiation doses used. (C) 2009 Elsevier Ltd. All rights reserved.

Evaluation of laccases and melanization in clinical and environmental Cryptococcus neoformans samples by non-denaturing PAGE

The increased incidence of infections caused by the opportunistic pathogen Cryptococcus neoformans, which mainly affects immunocompromised patients but can also infect immunocompetent individuals, has needed additional studies on this micro-organism`s pathogenicity and factors related to virulence, such as enzyme production, for a better understanding of the aetiology of cryptococcosis. The aim of this study was to verify the applicability of non-denaturing PAGE for analysis of laccases by quantification of the amount of melanin pigment produced by clinical and environmental strains of C. neoformans. After incubation of the gel with the substrate L-dopa, strains produced melanin spots of a bright brown to black colour. Quantification of these spots was performed by densitometry analysis and the amount of melanin produced was calculated and compared among the strains. All strains showed laccase activity. Serotype B strains showed a higher melanin intensity than serotype A strains. Over half of the clinical strains (56.2%) showed the lowest melanin intensities, suggesting that melanin production may not be the main virulence factor against host defence. The clinical strain ICB 88 revealed two melanin spots on the gel, indicating the presence of two laccase isoforms. The environmental strains showed the highest values of melanin intensity, which may be related to previous exposure to environmental stress conditions.

Study of DNA damage with a new system for irradiation of samples in a nuclear reactor

In this paper, we report results of a quantitative analysis of the effects of neutrons on DNA, and, specifically, the production of simple and double breaks of plasmid DNA in aqueous solutions with different concentrations of free-radical scavengers. The radiation damage to DNA was evaluated by electrophoresis through agarose gels. The neutron and gamma doses were measured separately with thermoluminescent detectors. In this work, we have also demonstrated usefulness of a new system for positioning and removing samples in channel BH#3 of the IEA-R1 reactor at the Instituto de Pesquisas Energeticas e Nucleares (Brazil) without necessity of interrupting the reactor operation. (C) 2010 Elsevier Ltd. All rights reserved.

New mechanical samples positioning system for irradiations on a radial channel at nuclear research reactor in a full-power continuous operation

This paper describes a new mechanical samples positioning system that allows the safe placement and removal of biological samples for prolonged irradiation, in a nuclear reactor during full-power continuous operation. Also presented herein the materials of construction and operating principles. Additionally, this sample positioning system is compared with an existing pneumatic and automated transfer system, already available at the research reactors. The system consists of a mechanical arm with a claw, which can deliver the samples for irradiations without reactor shutdown. It was installed in the lEA-R1 research reactor at Instituto de Pesquisas Energeticas e Nucleares (IPEN), Sao Paulo, Brazil, and for the past 5 years, the system has successfully operated and allowed the conducting of important experiments. As a result of its introduction, the facility has been in a position to positively respond to the increased demand in studies of biology, medicine, physics, engineering, detector/dosimeter calibrations, etc. It is one example of the appropriated technologies that save energy and resources. (C) 2010 Elsevier Ltd. All rights reserved.

Temperature Dependence of the Intergranular Critical Current Density in Uniaxially Pressed Bi(1.65)Pb(0.35)Sr(2)Ca(2)Cu(3)O(10+delta) Samples

We have studied the normal and superconducting transport properties of Bi(1.65)Pb(0.35)Sr(2)Ca(2)Cu(3)O(10+delta) (Bi-2223) ceramic samples. Four samples, from the same batch, were prepared by the solid-state reaction method and pressed uniaxially at different compacting pressures, ranging from 90 to 250 MPa before the last heat treatment. From the temperature dependence of the electrical resistivity, combined with current conduction models for cuprates, we were able to separate contributions arising from both the grain misalignment and microstructural defects. The behavior of the critical current density as a function of temperature at zero applied magnetic field, J (c) (T), was fitted to the relationship J (c) (T)ae(1-T/T (c) ) (n) , with na parts per thousand 2 in all samples. We have also investigated the behavior of the product J (c) rho (sr) , where rho (sr) is the specific resistance of the grain-boundary. The results were interpreted by considering the relation between these parameters and the grain-boundary angle, theta, with increasing the uniaxial compacting pressure. We have found that the above type of mechanical deformation improves the alignment of the grains. Consequently the samples exhibit an enhance in the intergranular properties, resulting in a decrease of the specific resistance of the grain-boundary and an increase in the critical current density.

Intergranular properties of uniaxially pressed YBa(2)Cu(3)O(7-delta) ceramic samples

We performed measurements of electrical resistivity as a function of temperature, rho(T), in polycrystalline samples of YBa(2)Cu(3)O(7-delta) (Y-123) subjected to different uniaxial compacting pressures. We observed by using X-ray diffractometry that samples have a very similar composition. Most of the identified peaks are related to the superconducting Y-123 phase. Also, from the X-ray diffraction patterns performed, in powder and pellet samples, we estimated the Lotgering factor along the (00l) direction, F((00l)). The results indicate that F((00l)) increases from 0.13 to 0.16. From electrical resistivity measurements as a function of temperature, we were able to separate contributions arising from both the grain misalignment and microstructural defects. We found appreciable degradation in the normal-state transport properties of samples with an increase in uniaxial compacting pressure. It seems that this type of behavior is associated with an increase in the influence of microstructural defects at the intergranular level. The experimental results are analyzed in the framework of a current conduction model of granular samples.

Enhanced visualization of histological samples with an adjustable RGB contrast system with application for tissue used in photodynamic therapy

The analysis of histological sections has long been a valuable tool in the pathological studies. The interpretation of tissue conditions, however, relies directly on visual evaluation of tissue slides, which may be difficult to interpret because of poor contrast or poor color differentiation. The Chromatic Contrast Visualization System (CCV) combines an optical microscope with electronically controlled light-emitting diodes (LEDs) in order to generate adjustable intensities of RGB channels for sample illumination. While most image enhancement techniques rely on software post-processing of an image acquired under standard illumination conditions, CCV produces real-time variations in the color composition of the light source itself. The possibility of covering the entire RGB chromatic range, combined with the optical properties of the different tissues, allows for a substantial enhancement in image details. Traditional image acquisition methods do not exploit these visual enhancements which results in poorer visual distinction among tissue structures. Photodynamic therapy (PDT) procedures are of increasing interest in the treatment of several forms of cancer. This study uses histological slides of rat liver samples that were induced to necrosis after being exposed to PDT. Results show that visualization of tissue structures could be improved by changing colors and intensities of the microscope light source. PDT-necrosed tissue samples are better differentiated when illuminated with different color wavelengths, leading to an improved differentiation of cells in the necrosis area. Due to the potential benefits it can bring to interpretation and diagnosis, further research in this field could make CCV an attractive technique for medical applications.

Grain size and heavy minerals of the Late Quaternary eolian sediments from the Imbituba-Jaguaruna coast, Southern Brazil: Depositional controls linked to relative sea-level changes

The stratigraphic subdivision and correlation of dune deposits is difficult, especially when age datings are not available. A better understanding of the controls on texture and composition of eolian sands is necessary to interpret ancient eolian sediments. The Imbituba-Jaguaruna coastal zone (Southern Brazil, 28 degrees-29 degrees S) stands out due to its four well-preserved Late Pleistocene (eolian generation 1) to Holocene eolian units (eolian generations 2, 3, and 4). In this study, we evaluate the grain-size and heavy-mineral characteristics of the Imbituba-Jaguartma eolian units through statistical analysis of hundreds of sediment samples. Grain-size parameters and heavy-mineral content allow us to distinguish the Pleistocene from the Holocene units. The grain size displays a pattern of fining and better sorting from generation 1 (older) to 4 (younger), whereas the content of mechanically stable (dense and hard) heavy minerals decreases from eolian generation 1 to 4. The variation in grain size and heavy-mineral content records shifts in the origin and balance (input versus output) of eolian sediment supply attributable mainly to relative sea-level changes. Dunefields submitted to relative sea-level lowstand conditions (eolian generation 1) are characterized by lower accumulation rates and intense post-depositional dissection by fluvial incision. Low accumulation rates favor deflation in the eolian system, which promotes concentration of denser and stable heavy minerals (increase of ZTR index) as well as coarsening of eolian sands. Dissection involves the selective removal of finer sediments and less dense heavy minerals to the coastal source area. Under a high rate of relative sea-level rise and transgression (eolian generation 2), coastal erosion prevents deflation through high input of sediments to the coastal eolian source. This condition favors dunefield growth. Coastal erosion feeds sand from local sources to the eolian system. including sands from previous dunefields (eolian generation 1) and from drowned incised valleys. Therefore, dunefields corresponding to transgressive phases inherit the grain-size and heavy-mineral characteristics of previous dunefields, leading to selective enrichment of finer sands and lighter minerals. Eolian generations 3 and 4 developed during a regressive-progradational phase (Holocene relative sea level highstand). The high rate of sediment supply during the highstand phase prevents deflation. The lack of coastal erosion favors sediment supply from distal sources (fluvial sediments rich in unstable heavy minerals). Thus, dunefields of transgressive and highstand systems tracts may be distinguished from dunefields of the lowstand systems tract through high rates of accumulation (low deflation) in the former. The sediment source of the transgressive dunefields (high input of previously deposited coastal sands) differs from that of the highstand dunefields (high input of fluvial distal sands). Based on this case study, we propose a general framework for the relation between relative sea level, sediment supply and the texture and mineralogy of eolian sediments deposited in siliciclastic wet coastal zones similar to the Imbituba-Jaguaruna coast (C) 2009 Elsevier B.V. All rights reserved.

Morphometric analysis of the urethra of castrated female rats treated with tamoxifen

Objectives: The aim of this study was to evaluate the effects of tamoxifen on the weight and thickness of the urethral epithelium of castrated female rats. Methods: Forty castrated adult female Wistar-Hannover rats were randomly divided into two groups: Group I (n = 20) in which the animals received only the vehicle (propylene glycol) and Group 11 (n = 20) in which the rats received tamoxifen 250 mu g/day by gavage. After 30 days of treatment, all animals were sacrificed and the urethra was immediately removed for weighing. Next, the urethra was divided into the proximal and distal segments, which were fixed in 10% formaldehyde and submitted to routine histological techniques for morphometric study. The data were analyzed using the weighted minimum mean-square error method and Student`s t-test for two independent samples (p < 0.05). Results: There was a significant increase in the mean weight of the urethra in the rats of Group 11 compared to the control group, 32.0 +/- 2.0 mg and 22.0 +/- 1.6 mg, respectively (p < 0.001). The mean thickness of the distal urethral epithelium of the animals treated with tamoxifen was significantly greater than that of the control group, 42.8 +/- 2.0 mu m and 36.6 +/- 1.5 mu m, respectively (p < 0.001). There was no statistically significant difference between the two groups with respect to the epithelial thickness of the proximal urethra (p = 0.514). Conclusion: Treating castrated adult rats with 250 mu g/day of tamoxifen for 30 days may increase the weight of the urethra and the thickness of the distal urethral epithelium. (c) 2008 Elsevier Ireland Ltd. All rights reserved.

Testing hypotheses in the Birnbaum-Saunders distribution under type-II censored samples

The two-parameter Birnbaum-Saunders distribution has been used successfully to model fatigue failure times. Although censoring is typical in reliability and survival studies, little work has been published on the analysis of censored data for this distribution. In this paper, we address the issue of performing testing inference on the two parameters of the Birnbaum-Saunders distribution under type-II right censored samples. The likelihood ratio statistic and a recently proposed statistic, the gradient statistic, provide a convenient framework for statistical inference in such a case, since they do not require to obtain, estimate or invert an information matrix, which is an advantage in problems involving censored data. An extensive Monte Carlo simulation study is carried out in order to investigate and compare the finite sample performance of the likelihood ratio and the gradient tests. Our numerical results show evidence that the gradient test should be preferred. Further, we also consider the generalized Birnbaum-Saunders distribution under type-II right censored samples and present some Monte Carlo simulations for testing the parameters in this class of models using the likelihood ratio and gradient tests. Three empirical applications are presented. (C) 2011 Elsevier B.V. All rights reserved.