Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses

Selection of reference genes is an essential consideration to increase the precision and quality of relative expression analysis by the quantitative RT-PCR method. The stability of eight expressed sequence tags was evaluated to define potential reference genes to study the differential expression of common bean target genes under biotic (incompatible interaction between common bean and fungus Colletotrichum lindemuthianum) and abiotic (drought; salinity; cold temperature) stresses. The efficiency of amplification curves and quantification cycle (C (q)) were determined using LinRegPCR software. The stability of the candidate reference genes was obtained using geNorm and NormFinder software, whereas the normalization of differential expression of target genes [beta-1,3-glucanase 1 (BG1) gene for biotic stress and dehydration responsive element binding (DREB) gene for abiotic stress] was defined by REST software. High stability was obtained for insulin degrading enzyme (IDE), actin-11 (Act11), unknown 1 (Ukn1) and unknown 2 (Ukn2) genes during biotic stress, and for SKP1/ASK-interacting protein 16 (Skip16), Act11, Tubulin beta-8 (beta-Tub8) and Unk1 genes under abiotic stresses. However, IDE and Act11 were indicated as the best combination of reference genes for biotic stress analysis, whereas the Skip16 and Act11 genes were the best combination to study abiotic stress. These genes should be useful in the normalization of gene expression by RT-PCR analysis in common bean, the most important edible legume.

Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays

Abstract Background Spotted cDNA microarrays generally employ co-hybridization of fluorescently-labeled RNA targets to produce gene expression ratios for subsequent analysis. Direct comparison of two RNA samples in the same microarray provides the highest level of accuracy; however, due to the number of combinatorial pair-wise comparisons, the direct method is impractical for studies including large number of individual samples (e.g., tumor classification studies). For such studies, indirect comparisons using a common reference standard have been the preferred method. Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard. Results We performed hybridizations using a fixed amount of Cy3-labeled reference oligonucleotide (RefOligo) against distinct Cy5-labeled targets from prostate, breast and kidney tumor samples. Reconstructed ratios between all tissue pairs were derived from ratios between each tissue sample and RefOligo. Reconstructed ratios were compared to (i) ratios obtained in parallel from direct pair-wise hybridizations of tissue samples, and to (ii) reconstructed ratios derived from hybridization of each tissue against a reference RNA pool (RefPool). To evaluate the effect of the external references, reconstructed ratios were also calculated directly from intensity values of single-channel (One-Color) measurements derived from tissue sample data collected in the RefOligo experiments. We show that the average coefficient of variation of ratios between intra- and inter-slide replicates derived from RefOligo, RefPool and One-Color were similar and 2 to 4-fold higher than ratios obtained in direct hybridizations. Correlation coefficients calculated for all three tissue comparisons were also similar. In addition, the performance of all indirect methods in terms of their robustness to identify genes deemed as differentially expressed based on direct hybridizations, as well as false-positive and false-negative rates, were found to be comparable. Conclusion RefOligo produces ratios as precise and accurate as ratios reconstructed from a RNA pool, thus representing a reliable alternative in reference-based hybridization experiments. In addition, One-Color measurements alone can reconstruct expression ratios without loss in precision or accuracy. We conclude that both methods are adequate options in large-scale projects where the amount of a common reference RNA pool is usually restrictive.

Spatial reference of black capuchin monkeys in Brazilian Atlantic Forest: egocentric or allocentric?

Wild primates occupy large home ranges and travel long distances to reach goals. However, how primates are able to remember goal locations and travel efficiently is unclear. Few studies present consistent results regarding what reference system primates use to navigate, and what kind of spatial information they recognize. We analysed the pattern of navigation of one wild group of black capuchin monkeys, Cebus nigritus, at Atlantic Forest for 100 days in Carlos Botelho State Park (PECB), Brazil. We tested predictions based on the alternative hypotheses that black capuchin monkeys navigate using a sequence of landmarks as an egocentric reference system or an allocentric reference system, or both, depending on availability of food resources. The group location was recorded using a GPS device collecting coordinates at 5 min intervals, and route maps were generated using ArcView v9.3.1. The study group travelled through habitual routes during less than 30% of our study sample, and revisited resources from different starting points, using different paths and routes, even when prominent landmarks near feeding locations were not visible. The study group used habitual routes more frequently when high-quality foods were scarce, and navigated using different paths when revisiting food sources. Results support the hypothesis that black capuchin monkeys at PECB navigate using both egocentric and allocentric systems of reference, depending on the quality and distribution of the food resource they find. (C) 2010 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Experimental Investigation of the Hydrodynamic Coefficients of a Remotely Operated Vehicle Using a Planar Motion Mechanism

The determination of hydrodynamic coefficients of full scale underwater vehicles using system identification (SI) is an extremely powerful technique. The procedure is based on experimental runs and on the analysis of on-board sensors and thrusters signals. The technique is cost effective and it has high repeatability; however, for open-frame underwater vehicles, it lacks accuracy due to the sensors' noise and the poor modeling of thruster-hull and thruster-thruster interaction effects. In this work, forced oscillation tests were undertaken with a full scale open-frame underwater vehicle. These conducted tests are unique in the sense that there are not many examples in the literature taking advantage of a PMM installation for testing a prototype and; consequently, allowing the comparison between the experimental results and the ones estimated by parameter identification. The Morison's equation inertia and drag coefficients were estimated with two parameter identification methods, that is, the weighted and the ordinary least-squares procedures. It was verified that the in-line force estimated from Morison's equation agrees well with the measured one except in the region around the motion inversion points. On the other hand, the error analysis showed that the ordinary least-squares provided better accuracy and, therefore, was used to evaluate the ratio between inertia and drag forces for a range of Keulegan-Carpenter and Reynolds numbers. It was concluded that, although both experimental and estimation techniques proved to be powerful tools for evaluation of an open-frame underwater vehicle's hydrodynamic coefficients, the research provided a rich amount of reference data for comparison with reduced models as well as for dynamic motion simulation of ROVs. [DOI: 10.1115/1.4004952]

Perfomance of methods for estimating reference evapotranspiration in the municipalities of Frederico Westphalen and Palmeira das Missoes, State of Rio Grande do Sul, Brazil

The estimation of reference evapotranspiration (ETo), used in water balance, allows to determine soil water content, assisting on irrigation management. The present study aimed to compare simple ETo estimating methods with the Penman-Monteith (FAO), in the folowing time scales: daily, 5, 10, 15 and 30 days and monthly in the counties of Frederico Westphalen and Palmeira das Missoes, in the Rio Grande do Sul state, Brazil. The methods tested had their efficiency improved by increasing the time scale of analysis, keeping the same performance for both locations. The highest and lowest ETo values occurred in December and June, respectively. Most methods underestimated ETo. For any of the time scales Makking and Radiaton FAO24 methods can replace the Penman-Monteith for estimating ETo.

Effect of EVA on the fresh properties of cement paste

The improved workability effect of latex in dry mortars has not been fully clarified. The purpose of this research was to investigate the influence cif the EVA copolymer on the cement hydration and on the rheological properties of cement pastes. The results pointed to a minor influence of EVA on cement hydration and to a ball-bearing effect. In fact, the shear thinning behavior of reference paste at 15 min after mixing changed to shear thickening owing to the EVA addition. This behavior could be explained by the decrease in the interparticle separation distance as consequence of the solid content increase in case of shearing detachment of weakly adhered EVA particles from the cement particles surfaces. The expected EVA plasticizing effect was observed at 60 min. Such behavior points to the stabilization of EVA on the cement particles surfaces, thus resulting in a steric barrier effect. (C) 2011 Elsevier Ltd. All rights reserved.

Use of Leptospira spp. strains isolated in Brazil in the microscopic agglutination test applied to diagnosis of leptospirosis in cattle herds in eight brazilian states

Sarmento A.M.C., Azevedo S.S., Morais Z.M., Souza G.O., Oliveira F.C.S., Goncales A.P., Miraglia F. & Vasconcellos S.A. 2012. [Use of Leptospira spp. strains isolated in Brazil in the microscopic agglutination test applied to diagnosis of leptospirosis in cattle herds in eight brazilian states.] Emprego de estirpes Leptospira spp. isoladas no Brasil na microtecnica de soroaglutinacao microscopica aplicada ao diagnostico da leptospirose em rebanhos bovinos de oito estados brasileiros. Pesquisa Veterinaria Brasileira 32(7);601-606. Universidade de Sao Paulo, Faculdade de Medicina Veterinaria e Zootecnia, Departamento de Medicina Veterinaria Preventiva e Saude Animal, Av. Prof. Dr. Orlando Marques de Paiva 87, Sao Paulo, SP 05508-270, Brazil. E-mail: savasco@usp.br The aim of this study was to investigate the adequacy of the use of autochthonous strains of leptospires isolated in Brazil, added to antigen collection of the microscopic agglutination test (MAT) applied to the diagnosis of bovine leptospirosis. By means of non-probability sampling, 109 farms and 9,820 cattle, females at reproductive age were chosen from 85 municipalities in the states of Goias, Mato Grosso, Mato Grosso do Sul, Minas Gerais, Parana, Rio Grande do Sul, Santa Catarina and Sao Paulo. Among the 9,820 examined animals, 5,806 (59.12%) were reactants at MAT for at least one serovar using the 23 reference serovars. Employing the collection of reference serovars and the ten autochthonous strains, 6,400 (65.24%) reactants and significant difference (p=0.001) was found. The most probable serovars identified by the collection of reference antigens were Hardjo (43.03%), Shermani (20%), Wolfi (9.96%), Grippothyphosa (5.42%) and Pomona (4.28%). With the collection amplified with the ten strains isolated in Brazil, the most probable serovars were Hardjo (31%), Guaricura-M4/84 (22.50%), Shermani (15.43%), Wolffi (4.76%), Grippothyphosa (3.71%) and Autumnalis (3.24%). The serovar Guaricura, strain M4/84, isolated from bovines and buffaloes in the State of Sao Paulo, was ranked as one of the three most probable serovars in the states of Goias, Mato Grosso, Mato Grosso do Sul, Minas Gerais and Sao Paulo. The addition of autochthonous strains to the MAT antigen collection provided the confirmation of the diagnosis of leptospirosis in 594 cattle (6%) which have been classified as non-reactants by the reference collection (p=0.001).

The eagle and the starlings: Galileo's argument for the autonomy of science-how pertinent is it today?

After Galileo's argument for the autonomy of science is analysed and adapted to take into account later developments of scientific practices, we conclude that, in the final analysis, it is not compelling. Nevertheless, Galileo's argument still provides a useful point of reference, for aspects of it can be interpreted to anticipate central components of the often acclaimed ideal of science as value free, so that appraising it contributes to the larger purpose of exploring how well that ideal stands up today. Finally, we will argue that residue from Galileo's struggle with the Church remains with us, making it difficult to identify the conditions that would need to be put into place today for any robust sense of the autonomy of science to be defensible. (C) 2011 Elsevier Ltd. All rights reserved.

Brazilian research on extremophiles in the context of astrobiology

Extremophiles are organisms adapted to grow at extreme ranges of environmental variables, such as high or low temperatures, acid or alkaline medium, high salt concentration, high pressures and so forth. Most extremophiles are micro-organisms that belong to the Archaea and Bacteria domains, and are widely spread across the world, which include the polar regions, volcanoes, deserts, deep oceanic sediments, hydrothermal vents, hypersaline lakes, acid and alkaline water bodies, and other extreme environments considered hostile to human life. Despite the tropical climate, Brazil has a wide range of ecosystems which include some permanent or seasonally extreme environments. For example, the Cerrado is a biome with very low soil pH with high Al+3 concentration, the mangroves in the Brazilian coast are anaerobic and saline, Pantanal has thousands of alkaline-saline lakes, the Caatinga arid and hot soils and the deep sea sediments in the Brazilian ocean shelf. These environments harbour extremophilic organisms that, coupled with the high natural biodiversity in Brazil, could be explored for different purposes. However, only a few projects in Brazil intended to study the extremophiles. In the frame of astrobiology, for example, these organisms could provide important models for defining the limits of life and hypothesize about life outside Earth. Brazilian microbiologists have, however, studied the extremophilic micro-organisms inhabiting non-Brazilian environments, such as the Antarctic continent. The experience and previous results obtained from the Brazilian Antarctic Program (PROANTAR) provide important results that are directly related to astrobiology. This article is a brief synopsis of the Brazilian experience in researching extremophiles, indicating the most important results related to astrobiology and some future perspectives in this area. Received 29 February 2012, accepted 25 May 2012, first published online 11 July 2012

Cost-effectiveness and budget impact of saxagliptine as additional therapy to metformin for the treatment of diabetes mellitus type 2 in the Brazilian private health system

Cost-effectiveness and budget impact of saxagliptine as additional therapy to metformin for the treatment of diabetes mellitus type 2 in the Brazilian private health system Objectives: To compare costs and clinical benefits of three additional therapies to metformin (MF) for patients with diabetes mellitus type 2 (DM2). Methods: A discrete event simulation model seas built to estimate the cost-utility ratio (cost per quality-adjusted life years [QALY)) of saxagliptine as an additional therapy to MF when compared to rosiglitazone or pioglitazone. A budget impact model (BIM) was built to simulate the economic impact of saxagliptine use in the context of the Brazilian private health system. Results: The acquiring medication costs for the hypothetical patient group analyzed in a time frame of three years, were R$ 10,850,185, R$ 14,836,265 and R$ 14,679,099 for saxagliptine, pioglitazone and rosiglitazone, respectively. Saxagliptine showed lower costs and greater effectiveness in both comparisons, with projected savings for the first three years of R$ 3,874 and R$ 3,996, respectively. The BIM estimated cumulative savings of R$ 417,958 with the repayment of saxagliptine in three years from the perspective of a health plan with 1,000,000 covered individuals. Conclusion: From the perspective of private paying source, the projection is that adding saxagliptine with MF save costs when compared with the addition of rosiglitazone or pioglitazone in patients with DM2 that have not reached the HbA1c goal with metformin monotherapy. The BIM of including saxagliptine in the reimbursement lists of health plans indicated significant savings on the three-year horizon.

rpb2 is a reliable reference gene for quantitative gene expression analysis in the dermatophyte Trichophyton rubrum

The selection of reference genes used for data normalization to quantify gene expression by real-time PCR amplifications (qRT-PCR) is crucial for the accuracy of this technique. In spite of this, little information regarding such genes for qRT-PCR is available for gene expression analyses in pathogenic fungi. Thus, we investigated the suitability of eight candidate reference genes in isolates of the human dermatophyte Trichophyton rubrum subjected to several environmental challenges, such as drug exposure, interaction with human nail and skin, and heat stress. The stability of these genes was determined by geNorm, NormFinder and Best-Keeper programs. The gene with the most stable expression in the majority of the conditions tested was rpb2 (DNA-dependent RNA polymerase II), which was validated in three T. rubrum strains. Moreover, the combination of rpb2 and chs1 (chitin synthase) genes provided for the most reliable qRT-PCR data normalization in T. rubrum under a broad range of biological conditions. To the best of our knowledge this is the first report on the selection of reference genes for qRT-PCR data normalization in dermatophytes and the results of these studies should permit further analysis of gene expression under several experimental conditions, with improved accuracy and reliability.

Development of a slow-wave MEMS phase shifter on CMOS technology for millimeter wave frequencies

We propose a slow-wave MEMS phase shifter that can be fabricated using the CMOS back-end and an additional maskless post-process etch. The tunable phase shifter concept is formed by a conventional slow-wave transmission line. The metallic ribbons that form the patterned floating shield of this type of structure are released to allow motion when a control voltage is applied, which changes the characteristic impedance and the phase velocity. For this device a quality factor greater than 40 can be maintained, resulting in a figure of merit on the order of 0.7 dB/360 degrees and a total area smaller than 0.14 mm(2) for a 60-GHz working frequency. (C) 2011 Elsevier B.V. All rights reserved.

Characterization of a thermostable extracellular tannase produced under submerged fermentation by Aspergillus ochraceus

Background: Tannases are enzymes that may be used in different industrial sectors as, for example, food and pharmaceutical. They are obtained mainly from microorganisms, as filamentous fungi. However, the diversity of fungi stays poorly explored for tannase production. In this article, Aspergillus ochraceus is presented as a new source of tannase with interesting features for biotechnological applications. Results: Extracellular tannase production was induced when the fungus was cultured in Khanna medium with tannic acid as carbon source. The extracellular tannase was purified 9-fold with 2% recovery and a single band corresponding to 85 kDa was observed in SDS-PAGE. The native apparent molecular mass was estimated as 112 kDa. Optima of temperature and pH were 40 degrees C and 5.0, respectively. The enzyme was fully stable from 40 degrees C to 60 degrees C during 1 hr. The activity was enhanced by Mn2+ (33-39%) and NH4+ (15%). The purified tannase hydrolyzed tannic acid and methyl gallate with Km of 0.76 mM and 0.72 mM, respectively, and Vmax of 0.92 U/mg protein and 0.68 U/mg protein, respectively. The analysis of a partial sequence of the tannase encoding gene showed an open read frame of 567 bp and a sequence of 199 amino acids were predicted. TLC analysis revealed the presence of gallic acid as a tannic acid hydrolysis product. Conclusion: The extracellular tannase produced by A. ochraceus showed distinctive characteristics such as monomeric structure and activation by Mn2+, suggesting a new kind of fungal tannases with biotechnological potential. Further, it was the first time that a partial gene sequence for A. ochraceus tannase was described.

Recombinant expression, localization and in vitro inhibition of midgut cysteine peptidase (Sl-CathL) from sugarcane weevil, Sphenophorus levis

A cDNA coding for a digestive cathepsin L, denominated Sl-CathL, was isolated from a cDNA library of Sphenophorus levis larvae, representing the most abundant EST (10.49%) responsible for proteolysis in the midgut. The open reading frame of 972 bp encodes a preproenzyme similar to midgut cathepsin L-like enzymes in other coleopterans. Recombinant Sl-CathL was expressed in Pichia pastoris, with molecular mass of about 42 kDa. The recombinant protein was catalytically activated at low pH and the mature enzyme of 39 kDa displayed thermal instability and maximal activity at 37 degrees C and pH 6.0. Immunocytochemical analysis revealed Sl-CathL production in the midgut epithelium and secretion from vesicles containing the enzyme into the gut lumen, confirming an important role for this enzyme in the digestion of the insect larvae. The expression profile identified by RT-PCR through the biological cycle indicates that Sl-CathL is mainly produced in larval stages, with peak expression in 30-day-old larvae. At this stage, the enzyme is 1250-fold more expressed than in the pupal fase, in which the lowest expression level is detected. This enzyme is also produced in the adult stage, albeit in lesser abundance, assuming the presence of a different array of enzymes in the digestive system of adults. Tissue-specific analysis revealed that Sl-CathL mRNA synthesis occurs fundamentally in the larval midgut, thereby confirming its function as a digestive enzyme, as detected in immunolocalization assays. The catalytic efficiency of the purified recombinant enzyme was calculated using different substrates (Z-Leu-Arg-AMC, Z-Arg-Arg-AMC and Z-Phe-Arg-AMC) and rSl-CathL exhibited hydrolysis preference for Z-Leu-Arg-AMC (k(cat)/K-m = 37.53 mM S-1), which is similar to other insect cathepsin L-like enzymes. rSl-CathL activity inhibition assays were performed using four recombinant sugarcane cystatins. rSl-CathL was strongly inhibited by recombinant cystatin CaneCPI-4 (K-i = 0.196 nM), indicating that this protease is a potential target for pest control. (C) 2011 Elsevier Ltd. All rights reserved.

Preparation of percentile tables through anthropometric, performance, biochemical, hematological, hormonal and psychological parameters in professional soccer players

Introduction: The lack of reference values of anthropometric, performance, biochemical, hematological, hormonal and psychological parameters is an important limitation in the investigations with soccer players. Objective: To elaborate percentile tables to be used as comparison reference for further studies. Methods: 82 professional soccer players were evaluated approximately 30 days after the beginning of the main competition played by their teams. On the first day of evaluation, fast blood samples were collected for measurement of hematological parameters (i.e. erythrocytes, hemoglobin, hematocrit, mean corpuscular volume - MCV, mean corpuscular hemoglobin - MCH, mean corpuscular hemoglobin concentration - MCHC, leukocytes, eosinophils, lymphocytes, monocytes and platelets) and of concentrations of adrenaline, cortisol, creatine kinase, creatinine, norepinephrine, testosterone and urea. Subsequently, the soccer players had their anthropometric characteristics and psychological parameters assessed. In addition, the evaluation of the lactic anaerobic system efficiency was performed on a 400-m track. On the second day, both the alactic anaerobic and aerobic system efficiency was measured. Results: The percentile distribution (P-0, P-15, P-30, P-50, P-70, P-85 e P-100) was used to present the results. Conclusion: The elaboration of the percentile tables can be used as comparison reference for further studies.