Comparative analyses of classical phenotypic method and ribosomal RNA gene sequencing for identification of medically relevant Candida species

As the distribution of Candida species and their susceptibility to antifungal agents have changed, a new means of accurately and rapidly identifying these species is necessary for the successful early resolution of infection and the subsequent reduction of morbidity and mortality. The current work aimed to evaluate ribosomal RNA gene sequencing for the identification of medically relevant Candida species in comparison with a standard phenotypic method. Eighteen reference strains (RSs), 69 phenotypically identified isolates and 20 inconclusively identified isolates were examined. Internal transcribed spaces (ITSs) and D1/D2 of the 26S ribosomal RNA gene regions were used as targets for sequencing. Additionally, the sequences of the ITS regions were used to establish evolutionary relationships. The sequencing of the ITS regions was successful for 88% (94/107) of the RS and isolates, whereas 100% of the remaining 12% (13/107) of the samples were successfully analysed by sequencing the D1/D2 region. Similarly, genotypic analysis identified all of the RS and isolates, including the 20 isolates that were not phenotypically identified. Phenotypic analysis, however, misidentified 10% (7/69) of the isolates. Phylogenetic analysis allowed the confirmation of the relationships between evolutionarily close species. Currently, the use of genotypic methods is necessary for the correct identification of Candida species.

Phylogenetic analyses of chikungunya virus among travelers in Rio de Janeiro, Brazil, 2014-2015

Chikungunya virus (CHIKV) is a mosquito-borne pathogen that emerged in Brazil by late 2014. In the country, two CHIKV foci characterized by the East/Central/South Africa and Asian genotypes, were established in North and Northeast regions. We characterized, by phylogenetic analyses of full and partial genomes, CHIKV from Rio de Janeiro state (2014-2015). These CHIKV strains belong to the Asian genotype, which is the determinant of the current Northern Brazilian focus, even though the genome sequence presents particular single nucleotide variations. This study provides the first genetic characterisation of CHIKV in Rio de Janeiro and highlights the potential impact of human mobility in the spread of an arthropod-borne virus.

Phylogenetic relationships among four species of the guarani group of Drosophila (Diptera, Drosophilidae) as inferred by molecular and morphological analyses

Traditionally, the Drosophila guarani species group has been divided into two subgroups: the guarani and the guaramunu subgroups. Two, out of the four species included in this research, are members of the guarani subgroup (D. ornatifrons Duda, 1927 and D. subbadia Paterson & Mainland, 1943) and two are included in the guaramunu subgroup (D. maculifrons Duda, 1927 and D. griseolineata Duda, 1927). However, some authors have suggested that D. maculifrons and D. griseolineata are much closer to some species of the Drosophila tripunctata group than to some of the species of the guarani group. To add new data to the matter under dispute, Polyacrylamide Gel Eletrophoresis (PAGE-SDS) was used for the analysis and comparison of protein composition and Random Amplified Polymorphic DNA (RAPD) analysis to find differences in genomic DNA, in addition to the analysis of quantitative morphological characters previously described. Analysis of PAGE-SDS results in a dendrogram that pointed out D. subbadia as being the most distant within the Drosophila guarani group. However, these results were not supported either by RAPD analysis or by the analysis of continuous morphological characters, which supplied the clustering of D. subbadia with D. ornatifrons. Although our data give strong support to the clustering of D. subbadia and D. ornatifrons, none of the dendrograms provided a clade comprising D. maculifrons and D. griseolineata. Thus, this research does not support the traditional subdivision of the D. guarani group into those two subgroups.

Fertilization response likelihood for the interpretation of leaf analyses

Leaf analysis is the chemical evaluation of the nutritional status where the nutrient concentrations found in the tissue reflect the nutritional status of the plants. Thus, a correct interpretation of the results of leaf analysis is fundamental for an effective use of this tool. The purpose of this study was to propose and compare the method of Fertilization Response Likelihood (FRL) for interpretation of leaf analysis with that of the Diagnosis and Recommendation Integrated System (DRIS). The database consisted of 157 analyses of the N, P, K, Ca, Mg, S, Cu, Fe, Mn, Zn, and B concentrations in coffee leaves, which were divided into two groups: low yield (< 30 bags ha-1) and high yield (> 30 bags ha-1). The DRIS indices were calculated using the method proposed by Jones (1981). The fertilization response likelihood was computed based on the approximation of normal distribution. It was found that the Fertilization Response Likelihood (FRL) allowed an evaluation of the nutritional status of coffee trees, coinciding with the DRIS-based diagnoses in 84.96 % of the crops.

Genetical and environmental analyses of yield in six biparental soybean crosses

The yearly genetic progress obtained by breeding for increased soybean yield has been considered acceptable worldwide. It is common sense, however, that this progress can be improved further if refined breeding techniques, developed from the knowledge of the genetic mechanisms controlling soybean yield, are used. In this paper, data from four cultivars and/or lines and their derived sets of F2, F3, F7, F8, F9 and F10 generations assayed in 17 environments were analyzed to allow an insight of the genetic control of soybean yield under different environmental conditions. The general picture was of a complex polygene system controlling yield in soybeans. Additive genetic effects predominated although dominance was often found to be significant. Complications such as epistasis, linkage and macro and micro genotype x environment (G x E) interactions were also commonly detected. The overall heritability was 0.29. The relative magnitude of the additive effects and the complicating factors allowed the inference that the latter are not a serious problem to the breeder. The low heritability values and the considerable magnitude of G x E interactions for yield, however, indicated that careful evaluation through experiments designed to allow for the presence of these effects is necessary for successful selection.

Characterization of mandarin citrus germplasm from Southern Brazil by morphological and molecular analyses

The objective of this work was to characterize mandarin (Citrus spp.) germplasm from Southern Brazil by morphological and molecular analyses. Thirty seven cultivars from 34 distinct mandarin varieties were evaluated by morphological and agronomic traits of leaves, flowers and fruits, and by microsatellite markers. The morphological and agronomic characteristics suggested that almost all varieties can be produced for commercial use, and some, as the Satsuma variety, are recommended for breeding programs. Pooled DNA samples from 1-5 plants belonging to each cultivar were tested. Eight of the nine primers detected polymorphisms. Specific markers were found for some accessions. The dendrogram constructed with the morphological results divided the 37 cultivars into four groups, while that obtained with the microsatellites clustered 35 of the 37 cultivars into three groups only. Generally, intervarietal differences are not high, and this lack of agreement in the two multifactorial analyses indicates that diverse evolutionary factors are acting at these two levels of investigation.

Multivariate analyses of genotype x environment interaction of popcorn

The objectives of this work were to evaluate the genotype x environment (GxE) interaction for popcorn and to compare two multivariate analyses methods. Nine popcorn cultivars were sown on four dates one month apart during each of the agricultural years 1998/1999 and 1999/2000. The experiments were carried out using randomized block designs, with four replicates. The cv. Zélia contributed the least to the GxE interaction. The cv. Viçosa performed similarly to cv. Rosa-claro. Optimization of GxE was obtained for cv. CMS 42 for a favorable mega-environment, and for cv. CMS 43 for an unfavorable environment. Multivariate analysis supported the results from the method of Eberhart & Russell. The graphic analysis of the Additive Main effects and Multiplicative Interaction (AMMI) model was simple, allowing conclusions to be made about stability, genotypic performance, genetic divergence between cultivars, and the environments that optimize cultivar performance. The graphic analysis of the Genotype main effects and Genotype x Environment interaction (GGE) method added to AMMI information on environmental stratification, defining mega-environments and the cultivars that optimized performance in those mega-environments. Both methods are adequate to explain the genotype x environment interactions.

Incidence of Garlic common latent virus in Argentina, and phylogenetic and recombination analyses of isolates

The objective of this work was to estimate the incidence and prevalence of Garlic common latent virus (GarCLV) in the main production regions of garlic (Allium sativum) in Argentina, and to perform phylogenetic and recombination analyses in isolates from these regions. Leaf samples (3,050) were taken from four garlic commercial types, in 13 departments of the four main garlic-producing provinces of Argentina, in a 1,175-ha sampling area. Virus infection was evaluated with DAS-Elisa test using specific antiserum, and the phylogenetic and recombination analyses were done with capsid protein (CP) nucleotide sequence of seven GarCLV isolates from the provinces. The incidence of GarCLV in the evaluated provinces varied between 6.7 and 22% of the samples, whereas the prevalence varied between 52.6 and 70%. In the analysis of garlic commercial types, Morado showed the highest incidence of the virus, in the province of San Juan, whereas Rosado Paraguayo had the lowest incidence, in the province of Cordoba. Nucleotide identity in the CP sequences ranged between 80.3 and 97.6%. The phylogenetic analysis shows the presence of two main groups of GarCLV and of a possible third group that would include only a German isolate. The recombination analysis between isolates from different parts of the world evidences the presence of recombinant isolates from Poland and Australia.

Analysis of translational errors in frame-based and frameless cranial radiosurgery using an anthropomorphic phantom

Abstract Objective: To evaluate three-dimensional translational setup errors and residual errors in image-guided radiosurgery, comparing frameless and frame-based techniques, using an anthropomorphic phantom. Materials and Methods: We initially used specific phantoms for the calibration and quality control of the image-guided system. For the hidden target test, we used an Alderson Radiation Therapy (ART)-210 anthropomorphic head phantom, into which we inserted four 5mm metal balls to simulate target treatment volumes. Computed tomography images were the taken with the head phantom properly positioned for frameless and frame-based radiosurgery. Results: For the frameless technique, the mean error magnitude was 0.22 ± 0.04 mm for setup errors and 0.14 ± 0.02 mm for residual errors, the combined uncertainty being 0.28 mm and 0.16 mm, respectively. For the frame-based technique, the mean error magnitude was 0.73 ± 0.14 mm for setup errors and 0.31 ± 0.04 mm for residual errors, the combined uncertainty being 1.15 mm and 0.63 mm, respectively. Conclusion: The mean values, standard deviations, and combined uncertainties showed no evidence of a significant differences between the two techniques when the head phantom ART-210 was used.

Structural and reactivity analyses of 2-benzylamino-1,4-naphthoquinone by X-ray characterization, electrochemical measurements, and dft single-molecule calculations

This study represents an integrated approach towards understanding the electronic and structural aspects of 2-benzylamino-1,4-naphthalenedione, a representative 2-amino-napfthoquinone. To this end, theoretical calculations performed at the B3PW91/6-31+G(d) level of density functional theory, electrochemical and X-ray structural investigation were employed. Two intramolecular H-bonds and other two intermolecular H-bonds were observed, including non-classical interactions. Cyclic voltammogram (CV) and differential pulse voltammetry (DPV) show two pairs of peaks, being each one a monoelectronic process.

Self-condensation of n-(N-propyl)butanimine: NMR and mass spectral analyses and investigation by theoretical calculation

The stability of N-propylbutanimine (1) was investigated under different experimental conditions. The acid-catalyzed self-condensation that produced the E-enimine (4) and Z-inimine (5) was studied by experimental analyses and theoretical calculations. Since the calculations for the energy of 5 indicated that it had a lower energy than 4, yet 4 was the principal product, the self-condensation of 1 must be kinetically controlled.

Least squares regression with errors in both variables: case studies

Analytical curves are normally obtained from discrete data by least squares regression. The least squares regression of data involving significant error in both x and y values should not be implemented by ordinary least squares (OLS). In this work, the use of orthogonal distance regression (ODR) is discussed as an alternative approach in order to take into account the error in the x variable. Four examples are presented to illustrate deviation between the results from both regression methods. The examples studied show that, in some situations, ODR coefficients must substitute for those of OLS, and, in other situations, the difference is not significant.

Grape juice quality control by means of ¹H nmr spectroscopy and chemometric analyses

This work shows the application of ¹H NMR spectroscopy and chemometrics for quality control of grape juice. A wide range of quality assurance parameters were assessed by single ¹H NMR experiments acquired directly from juice. The investigation revealed that conditions and time of storage should be revised and indicated on all labels. The sterilization process of homemade grape juices was efficient, making it possible to store them for long periods without additives. Furthermore, chemometric analysis classified the best commercial grape juices to be similar to homemade grape juices, indicating that this approach can be used to determine the authenticity after adulteration.

Efeitos da rugosidade superficial nas propriedades de passivação de monocamadas orgânicas automontadas

Precise surface area is needed for accurate characterization of self-assembled monolayers (SAMs) on metallic surfaces. The aim of this manuscript was to emphasize that miscalculation of surface area is the major source of errors in SAM electrochemical characterization. Limitations are discussed and recommendations given for beginners in analyses of SAM functionalized electrodes. The electrochemical measurements and examples were based on bare gold electrode immobilized with dodecanethiol. The degree of compression of the monolayer properties of formation and reproducibility of the electrochemical response depends on roughness factor, with values closer to the unit being better.

Application of fourier transform infrared spectroscopy, chemical and chemometrics analyses to the characterization of agro-industrial waste

Agroindustrial waste in general presents significant levels of nutrients and organic matter and has therefore been frequently put to agricultural use. In this context, the objective of this study was to determine the chemical composition, nitrogen, phosphorus, potassium, calcium, magnesium and carbon content, as well as the qualitative characteristics through Fourier transform infrared spectroscopy of four samples of poultry litter and one sample of cattle manure, from the southwestern region of Paraná, Brazil. Results revealed that, in general, the poultry litter presented higher amount of nutrients and carbon than the cattle manure. The infrared spectra allowed identification of the functional groups present and the differences in degree of sample humification. The statistical treatment confirmed the quantitative and qualitative differences revealed.