Whole blood assay to access T cell-immune responses to Mycobacterium tuberculosis antigens in healthy Brazilian individuals

The production of interferon gamma (IFNgamma) guarantees effective T cell-mediated immunity against Mycobacterium tuberculosis infection. In the present study, we simply compare the in vitro immune responses to Mycobacterium antigens in terms of IFNg production in a total of 10 healthy Brazilian volunteers. Whole blood and mononuclear cells were cultivated in parallel with PPD, Ag85B, and M. bovis hsp65, and five-days supernatants were harvested for cytokine detection by ELISA. The inter-assay result was that the overall profile of agreement in response to antigens was highly correlated (r² = 0.9266; p = 0.0102). Potential analysis is in current progress to dictate the usefulness of this method to access the immune responses also in tuberculosis patients and its contacts.

Four whole-istic aspects of schistosome granuloma biology: fractal arrangement, internal regulation, autopoietic component and closure

This paper centers on some whole-istic organizational and functional aspects of hepatic Schistosoma mansoni granuloma, which is an extremely complex system. First, it structurally develops a collagenic topology, originated bidirectionally from an inward and outward assembly of growth units. Inward growth appears to be originated from myofibroblasts derived from small portal vessel around intravascular entrapped eggs, while outward growth arises from hepatic stellate cells. The auto-assembly of the growth units defines the three-dimensional scaffold of the schistosome granulomas. The granuloma surface irregularity and its border presented fractal dimension equal to 1.58. Second, it is internally regulated by intricate networks of immuneneuroendocrine stimuli orchestrated by leptin and leptin receptors, substance P and Vasoactive intestinal peptide. Third, it can reach the population of ± 40,000 cells and presents an autopoietic component evidenced by internal proliferation (Ki-67+ Cells), and by expression of c-Kit+ Cells, leptin and leptin receptor (Ob-R), granulocyte-colony stimulating factor (G-CSF-R), and erythropoietin (Epo-R) receptors. Fourth, the granulomas cells are intimately connected by pan-cadherins, occludin and connexin-43, building a state of closing (granuloma closure). In conclusion, the granuloma is characterized by transitory stages in such a way that its organized structure emerges as a global property which is greater than the sum of actions of its individual cells and extracellular matrix components.

Evaluation of buffy coat 16S rRNA PCR, buffy coat culture and whole blood PCR for detection of bacteraemia

The use of Gram type-specific PCR on buffy coat from clinical specimens for the detection of bacteraemia was evaluated for the first time using whole blood culture as the gold standard. In addition, the established buffy coat culture and whole blood PCR were also compared. Gram-positive bacteria belonging to six species and Gram-negative bacteria from 10 species were isolated and identified by culture and detected using broad-range 16S rDNA primers and Gram-specific primers. Data from the three methods all conferred very high sensitivity, specificity, positive and negative predictive values when compared to whole blood culture. The Kappa coefficients of agreement were 0.9819 (buffy coat PCR), 0.9458 (whole blood PCR) and 1.0 (buffy coat culture), which establishes their validity as alternative methods to routine blood culture in detecting bacteraemia. In addition, results showed that there was a direct correlation of WBC counts greater than 12,000 cells per mm³ to the occurrence of bacteraemia as detected by the four methods (p < 0.05).

An indirect immunofluorescence antibody test employing whole eggs as the antigen for the diagnosis of abdominal angiostrongyliasis

Abdominal angiostrongyliasis is a potentially fatal zoonotic disease with a broad geographical distribution throughout Central and South America. This study assessed the performance of Angiostrongylus costaricensis eggs as the antigen in an indirect immunofluorescence assay for the determination of parasite-specific IgG and IgG1 antibodies. For prevalence studies, an IgG antibody titre > 16 was identified as the diagnostic threshold with the best performance, providing 93.7% sensitivity and 84.6% specificity. Cross reactivity was evaluated with 65 additional samples from patients with other known parasitic infections. Cross reactivity was observed only in samples from individuals infected with Strongyloides stercoralis. For clinical diagnosis, we recommend the determination of IgG only as a screening test. IgG1 determination may be used to increase the specificity of the results for patients with a positive screening test.

Whole-cell antigenicity data support sequence-based kinetoplastid taxonomy

Early immunological data, obtained by immunodiffusion and immunoelectrophoresis, on the whole-cell antigenicity of kinetoplastid protozoa were retrieved and used to construct a dendrogram of antigenic distances. Remarkably, they supported the same taxonomic conclusions as analyses based on DNA and protein sequence data.

Whole-genome sequences of influenza A(H3N2) viruses isolated from Brazilian patients with mild illness during the 2014 season

The influenza A(H3N2) virus has circulated worldwide for almost five decades and is the dominant subtype in most seasonal influenza epidemics, as occurred in the 2014 season in South America. In this study we evaluate five whole genome sequences of influenza A(H3N2) viruses detected in patients with mild illness collected from January-March 2014. To sequence the genomes, a new generation sequencing (NGS) protocol was performed using the Ion Torrent PGM platform. In addition to analysing the common genes, haemagglutinin, neuraminidase and matrix, our work also comprised internal genes. This was the first report of a whole genome analysis with Brazilian influenza A(H3N2) samples. Considerable amino acid variability was encountered in all gene segments, demonstrating the importance of studying the internal genes. NGS of whole genomes in this study will facilitate deeper virus characterisation, contributing to the improvement of influenza strain surveillance in Brazil.

Whole-genome sequencing of a Plasmodium vivax isolate from the China-Myanmar border area

Currently, there is a trend of an increasing number of Plasmodium vivaxmalaria cases in China that are imported across its Southeast Asia border, especially in the China-Myanmar border area (CMB). To date, little is known about the genetic diversity of P. vivaxin this region. In this paper, we report the first genome sequencing of a P. vivaxisolate (CMB-1) from a vivax malaria patient in CMB. The sequencing data were aligned onto 96.43% of the P. vivaxSalvador I reference strain (Sal I) genome with 7.84-fold coverage as well as onto 98.32% of 14 Sal I chromosomes. Using the de novoassembly approach, we generated 8,541 scaffolds and assembled a total of 27.1 Mb of sequence into CMB-1 scaffolds. Furthermore, we identified all 295 known virgenes, which is the largest subtelomeric multigene family in malaria parasites. These results provide an important foundation for further research onP. vivaxpopulation genetics.

Whole genome sequence of Klebsiella pneumoniae U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India

Klebsiella pneumoniae U25 is a multidrug resistant strain isolated from a tertiary care hospital in Chennai, India. Here, we report the complete annotated genome sequence of strain U25 obtained using PacBio RSII. This is the first report of the whole genome of K. pneumoniaespecies from Chennai. It consists of a single circular chromosome of size 5,491,870-bp and two plasmids of size 211,813 and 172,619-bp. The genes associated with multidrug resistance were identified. The chromosome of U25 was found to have eight antibiotic resistant genes [blaOXA-1,blaSHV-28, aac(6’)1b-cr,catB3, oqxAB, dfrA1]. The plasmid pMGRU25-001 was found to have only one resistant gene (catA1) while plasmid pMGRU25-002 had 20 resistant genes [strAB, aadA1,aac(6’)-Ib, aac(3)-IId,sul1,2, blaTEM-1A,1B,blaOXA-9, blaCTX-M-15,blaSHV-11, cmlA1, erm(B),mph(A)]. A mutation in the porin OmpK36 was identified which is likely to be associated with the intermediate resistance to carbapenems in the absence of carbapenemase genes. U25 is one of the few K. pneumoniaestrains to harbour clustered regularly interspaced short palindromic repeats (CRISPR) systems. Two CRISPR arrays corresponding to Cas3 family helicase were identified in the genome. When compared to K. pneumoniaeNTUHK2044, a transposase gene InsH of IS5-13 was found inserted.

Effects of isoflavones on beany flavor and astringency of soymilk and cooked whole soybean grains

Flavor is the main limiting factor affecting soybean acceptability in the Occidental countries. The purpose of this study was to determine the effetcs of isoflavones on soybean flavor. Differences in beany flavor and astringency of soymilk and cooked whole soybean grains, prepared with cultivars IAS 5 and BR-36 (136 and 54 mg of total isoflavones /100 g of sample, respectively) with pre-soaking and pre-heating of grains, were sensorially analised, by an unstructured category scale of ascending intensity. Differences in isoflavone contents for both soybean cultivars were maintained in the two products, despite the pre-treatments in the processing. Pre-soaking of grains intensified beany flavor in the soymilk, reducing the perception of astringency, which is caused by the aglucones that were developed in reduced amounts.The whole soybeans grains cooked under pressure (1.5 kgf/cm² at 127°C) presented reduced levels of isoflavones malonyl-glucosides. Due to thermal instability, these compounds were converted to conjugated glucosides, genistin and daidzin. In the cooked whole soybean grains, no aglucones were formed and consequently it was not possible to detect differences in astringency. Results suggest that pre-heating of grains promote better flavor in soybean products.

Comparison of citrus rooting evaluation methods using root images in soil profiles and root weight

A digitized image method was compared with a standard washing technique for measuring citrus roots in the field. Video pictures of roots were taken in a soil profile. The profile area analyzed was defined by iron rings, which were also used to remove the roots to determine their dry weight. The roots presented in the pictures were quantified using SIARCS software developed by Embrapa. The root length and area determined by digital images provided a good estimate of root quantity present in the profile.

Description of a pure seed fraction of oat through usual evaluations and radiographic images

The objective of this work was to evaluate the width and length incidence in a single seed fraction of oat [Avena sativa (L.)] cv. Cristal. The seeds were selected by a mechanical divider and by hand, and their correspondence to radiographic images in seeds with glumes and their caryopses. The width and length of the seeds with glumes and their caryopses were measured with electronic calliper, and their weight, with precision balance. Radiographic images of seeds with glumes were taken with an X-ray experimental equipment. The analyst selected seeds with glumes by the width and by the length previously determined and so with more weight, than that obtained by hand selection was slightly narrower, larger and lighter. The presence of the glumes masked the caryopses real dimensions (width and length), and conduced the analyst to select seeds that differed more by the width than by the length. The radiographic images showed the presence, or not, of caryopses inside the seed and its real dimensions. The mechanical partition method for seeds showed to be more efficient because the analyst subjectivity was not considered when the selection upon its dimensions was done. The X-ray analysis was a useful tool that complements the pure seed fraction selection as another factor of seed quality.

Estimating soybean crop areas using spectral-temporal surfaces derived from MODIS images in Mato Grosso, Brazil

The objective of this work was to evaluate the application of the spectral-temporal response surface (STRS) classification method on Moderate Resolution Imaging Spectroradiometer (MODIS, 250 m) sensor images in order to estimate soybean areas in Mato Grosso state, Brazil. The classification was carried out using the maximum likelihood algorithm (MLA) adapted to the STRS method. Thirty segments of 30x30 km were chosen along the main agricultural regions of Mato Grosso state, using data from the summer season of 2005/2006 (from October to March), and were mapped based on fieldwork data, TM/Landsat-5 and CCD/CBERS-2 images. Five thematic classes were considered: Soybean, Forest, Cerrado, Pasture and Bare Soil. The classification by the STRS method was done over an area intersected with a subset of 30x30-km segments. In regions with soybean predominance, STRS classification overestimated in 21.31% of the reference values. In regions where soybean fields were less prevalent, the classifier overestimated 132.37% in the acreage of the reference. The overall classification accuracy was 80%. MODIS sensor images and the STRS algorithm showed to be promising for the classification of soybean areas in regions with the predominance of large farms. However, the results for fragmented areas and smaller farms were less efficient, overestimating soybean areas.

Land use/cover classification in the Brazilian Amazon using satellite images

Land use/cover classification is one of the most important applications in remote sensing. However, mapping accurate land use/cover spatial distribution is a challenge, particularly in moist tropical regions, due to the complex biophysical environment and limitations of remote sensing data per se. This paper reviews experiments related to land use/cover classification in the Brazilian Amazon for a decade. Through comprehensive analysis of the classification results, it is concluded that spatial information inherent in remote sensing data plays an essential role in improving land use/cover classification. Incorporation of suitable textural images into multispectral bands and use of segmentation‑based method are valuable ways to improve land use/cover classification, especially for high spatial resolution images. Data fusion of multi‑resolution images within optical sensor data is vital for visual interpretation, but may not improve classification performance. In contrast, integration of optical and radar data did improve classification performance when the proper data fusion method was used. Among the classification algorithms available, the maximum likelihood classifier is still an important method for providing reasonably good accuracy, but nonparametric algorithms, such as classification tree analysis, have the potential to provide better results. However, they often require more time to achieve parametric optimization. Proper use of hierarchical‑based methods is fundamental for developing accurate land use/cover classification, mainly from historical remotely sensed data.

Parboiled rice whole bran in laying diets for Japanese quails

The objective of this work was to evaluate the effects of parboiled rice whole bran (PRWB) inclusion in laying diets for Japanese quails, on their performance, egg quality, and economic viability. A total of 448 17-week-old quails were weighed and distributed in a completely randomized design with seven treatments and eight replicates of eight birds each. A control diet (no PRWB) and six diets, containing 5, 10, 15, 20, 25, and 30% of PRWB, were tested. The increasing levels of PRWB did not affected nutrient digestibility coefficient, dietary energy use, feed intake, egg production, egg weight, egg mass, and the economic viability indices. However, there was a linear decrease in egg shell percentage, specific weight, and yolk color. The inclusion of up to 30% PRWB in the diet allows nutrient utilization and performance similar to those obtained by the control group, and it is economically viable.

Development of a shelling method to recover whole kernels of the Cutia nut (Couepia edulis)

The kernel of the cutia nut (castanha-de-cutia, Couepia edulis (Prance) Prance) of the western Amazon, which is consumed by the local population, has traditionally been extracted from the nut with a machete, a dangerous procedure that only produces kernels cut in half. A shelling off machine prototype, which produces whole kernels without serious risks to its operator, is described and tested. The machine makes a circular cut in the central part of the fruit shell, perpendicular to its main axis. Three ways of conditioning the fruits before cutting were compared: (1) control; (2) oven drying immediately prior to cutting; (3) oven drying, followed by a 24-hour interval before cutting. The time needed to extract and separate the kernel from the endocarp and testa was measured. Treatment 3 produced the highest output: 63 kernels per hour, the highest percentage of whole kernels (90%), and the best kernel taste. Kernel extraction with treatment 3 required 50% less time than treatment 1, while treatment 2 needed 38% less time than treatment 1. The proportion of kernels attached to the testa was 93%, 47%, and 8% for treatments 1, 2, and 3, respectively, and was the main reason for extraction time differences.