Performance of the Vitek 2 system software version 5.03 in the bacterial identification and antimicrobial susceptibility test: evaluation study of clinical and reference strains of Gram-positive cocci

Introduction. The genera Enterococcus, Staphylococcus and Streptococcus are recognized as important Gram-positive human pathogens. The aim of this study was to evaluate the performance of Vitek 2 in identifying Gram-positive cocci and their antimicrobial susceptibilities. Methods. One hundred four isolates were analyzed to determine the accuracy of the automated system for identifying the bacteria and their susceptibility to oxacillin and vancomycin. Results. The system correctly identified 77.9% and 97.1% of the isolates at the species and genus levels, respectively. Additionally, 81.8% of the Vitek 2 results agreed with the known antimicrobial susceptibility profiles. Conclusion. Vitek 2 correctly identified the commonly isolated strains; however, the limitations of the method may lead to ambiguous findings.

Background and Reference Values of Metals in Soils from Paraíba State, Brazil

ABSTRACT Soil contamination by heavy metals threatens ecosystems and human health. Environmental monitoring bodies need reference values for these contaminants to assess the impacts of anthropogenic activities on soil contamination. Quality reference values (QRVs) reflect the natural concentrations of heavy metals in soils without anthropic interference and must be regionally established. The aim of this study was to determine the natural concentrations and quality reference values for the metals Ag, Ba, Cd, Co, Cu, Cr, Mo, Ni, Pb, Sb and Zn in soils of Paraíba state, Brazil. Soil samples were collected from 94 locations across the state in areas of native vegetation or with minimal anthropic interference. The quality reference values (QRVs) were (mg kg-1): Ag (<0.53), Ba (117.41), Cd (0.08), Co (13.14), Cu (20.82), Cr (48.35), Mo (0.43), Ni (14.44), Sb (0.61), Pb (14.62) and Zn (33.65). Principal component analysis grouped the metals Cd, Cr, Cu, Ni, Pb and Sb (PC1); Ag (PC2); and Ba, Co, Fe, Mn and Zn (PC3). These values were made official by Paraíba state through Normativa Resolution 3602/2014.

Evapotranspiration and crop coefficient for potato in organic farming

The aim of this study was to quantify the water consumption and the crop coefficients (Kc) for the potato (Solanum tuberosum L.), in Seropédica, Rio de Janeiro (RJ), Brazil, under organic management, and to simulate the crop evapotranspiration (ETc) using the Kc obtained in the field and the ones recommended by the Food and Agriculture Organization (FAO). The water consumption was obtained through soil water balance, using TDR probes installed at 0.15m and 0.30m deep. At the different stages of development, the Kc was determined by the ratio of ETc and reference evapotranspiration, obtained by Penman-Monteith FAO 56. The crop coefficients obtained were 0.35, 0.45, 1.29 and 0.63. The accumulated ETc obtained in the field was 109.6 mm, while the ETc accumulated from FAO's Kc were 142.2 and 138mm, respectively, considering the classical values and the values adjusted to the local climatic conditions. The simulation of water consumption based on meteorological data of historical series from 1961 to 2007 provided higher value of ETc when compared with the one obtained in the field. From the meteorological data of historical series, it was observed that the use of Kc recommended by FAO may overestimate the amount of irrigation water by 9%, over the same growing season.

How and why to measure the germination process?

In the last two centuries, papers have been published including measurements of the germination process. High diversity of mathematical expressions has made comparisons between papers and some times the interpretation of results difficult. Thus, in this paper is included a review about measurements of the germination process, with an analysis of the several mathematical expressions included in the specific literature, recovering the history, sense, and limitations of some germination measurements. Among the measurements included in this paper are the germinability, germination time, coefficient of uniformity of germination (CUG), coefficient of variation of the germination time (CVt), germination rate (mean rate, weighted mean rate, coefficient of velocity, germination rate of George, Timson’s index, GV or Czabator’s index; Throneberry and Smith’s method and its adaptations, including Maguire’s rate; ERI or emergence rate index, germination index, and its modifications), uncertainty associated to the distribution of the relative frequency of germination (U), and synchronization index (Z). The limits of the germination measurements were included to make the interpretation and decisions during comparisons easier. Time, rate, homogeneity, and synchrony are aspects that can be measured, informing the dynamics of the germination process. These characteristics are important not only for physiologists and seed technologists, but also for ecologists because it is possible to predict the degree of successful of a species based on the capacity of their harvest seed to spread the germination through time, permitting the recruitment in the environment of some part of the seedlings formed.

Production and characterization of monoclonal antibodies to Brazilian isolates of bovine viral diarrhea virus

Three Brazilian isolates of bovine viral diarrhea virus (BVDV), antigenically distinct from the standard North American isolates, were selected to immunize BALB/c mice in order to obtain hybridoma cells secreting anti-BVDV monoclonal antibodies (mAbs). Two hybridoma clones secreting mAbs, reacting specifically with BVDV-infected cells (mAbs 3.1C4 and 6.F11), were selected after five fusions and screening of 1001 hypoxanthine-aminopterin-thymidine-resistant clones. These mAbs reacted in an indirect fluorescent antibody (IFA) assay with all 39 South and North American BVDV field isolates and reference strains available in our laboratory, yet failed to recognize other pestiviruses, namely the hog cholera virus. The mAbs reacted at dilutions up to 1:25,600 (ascitic fluid) and 1:100 (hybridoma culture supernatant) in IFA and immunoperoxidase (IPX) staining of BVDV-infected cells but only mAb 3.1C4 neutralized virus infectivity. Furthermore, both mAbs failed to recognize BVDV proteins by IPX in formalin-fixed paraffin-embedded tissues and following SDS-PAGE and immunoblot analysis of virus-infected cells, suggesting they are probably directed to conformational-type epitopes. The protein specificity of these mAbs was then determined by IFA staining of CV-1 cells transiently expressing each of the BVDV proteins: mAb 3.1C4 reacted with the structural protein E2/gp53 and mAb 6.F11 reacted with the structural protein E1/gp25. Both mAbs were shown to be of the IgG2a isotype. To our knowledge, these are the first mAbs produced against South American BVDV isolates and will certainly be useful for research and diagnostic purposes.

Lack of mutations of exon 2 of the MEN1 gene in endocrine and nonendocrine sporadic tumors

In addition to the mutations that underlie most cases of the multiple endocrine neoplasia type 1 (MEN1) syndrome, somatic mutations of the MEN1 gene have also been described in sporadic tumors like gastrinomas, insulinomas and bronchial carcinoid neoplasm. We examined exon 2 of this gene, where most of the mutations have been described, in 148 endocrine and nonendocrine sporadic tumors. DNA was obtained by phenol/chloroform extraction and ethanol precipitation from 92 formalin-fixed, paraffin-embedded samples, and from 40 fresh tumor tissue samples. We used 5 pairs of primers to encompass the complete coding sequence of exon 2 of the MEN1 gene that was screened by the polymerase chain reaction-single-stranded conformation polymorphism (PCR-SSCP) technique in 78 sporadic thyroid cancers: 28 follicular adenomas, 35 papillary carcinomas, 14 follicular carcinomas, and 1 anaplastic thyroid carcinoma. We also examined 46 adrenal lesions (3 hyperplasias, 3 adenomas and 35 adrenocortical carcinomas, 2 pheochromocytomas, 2 ganglioneuroblastomas, and 1 lymphoma) and 24 breast cancers (6 noninvasive, 16 infiltrating ductal, and 2 invasive lobular tumors). The PCR product of 5 tumors suspected to present band shifts by SSCP was cloned. Direct sense and antisense sequencing did not identify mutations. These results suggest that the MEN1 gene is not important in breast, thyroid or adrenal sporadic tumorigenesis. Because the frequency of mutations varies significantly among tumor subgroups and allelic deletions are frequently observed at 11q13 in thyroid and adrenal cancers, another tumor suppressor gene residing in this region is likely to be involved in the tumorigenesis of these neoplasms.

Dimensions and dynamics in integrin function

Integrins play crucial roles in cell adhesion, migration, and signaling by providing transmembrane links between the extracellular matrix and the cytoskeleton. Integrins cluster in macromolecular complexes to generate cell-matrix adhesions such as focal adhesions. In this mini-review, we compare certain integrin-based biological responses and signaling during cell interactions with standard 2D cell culture versus 3D matrices. Besides responding to the composition of the matrix, cells sense and react to physical properties that include three-dimensionality and rigidity. In routine cell culture, fibroblasts and mesenchymal cells appear to use focal adhesions as anchors. They then use intracellular actomyosin contractility and dynamic, directional integrin movements to stretch cell-surface fibronectin and to generate characteristic long fibrils of fibronectin in "fibrillar adhesions". Some cells in culture proceed to produce dense, three-dimensional matrices similar to in vivo matrix, as opposed to the flat, rigid, two-dimensional surfaces habitually used for cell culture. Cells within such more natural 3D matrices form a distinctive class of adhesion termed "3D-matrix adhesions". These 3D adhesions show distinctive morphology and molecular composition. Their formation is heavily dependent on interactions between integrin alpha5ß1 and fibronectin. Cells adhere much more rapidly to 3D matrices. They also show more rapid morphological changes, migration, and proliferation compared to most 2D matrices or 3D collagen gels. Particularly notable are low levels of tyrosine phosphorylation of focal adhesion kinase and moderate increases in activated mitogen-activated protein kinase. These findings underscore the importance of the dimensionality and dynamics of matrix substrates in cellular responses to the extracellular matrix.

Periodic mechanical stress activates MEK1/2-ERK1/2 mitogenic signals in rat chondrocytes through Src and PLCγ1

The mitogenic effects of periodic mechanical stress on chondrocytes have been studied extensively but the mechanisms whereby chondrocytes sense and respond to periodic mechanical stress remain a matter of debate. We explored the signal transduction pathways of chondrocyte proliferation and matrix synthesis under periodic mechanical stress. In particular, we sought to identify the role of the MEK1/2-ERK1/2 signaling pathway in chondrocyte proliferation and matrix synthesis following cyclic physiologic mechanical compression. Under periodic mechanical stress, both rat chondrocyte proliferation and matrix synthesis were significantly increased (P < 0.05) and were associated with increases in the phosphorylation of Src, PLCγ1, MEK1/2, and ERK1/2 (P < 0.05). Pretreatment with the MEK1/2-ERK1/2 selective inhibitor, PD98059, and shRNA targeted to ERK1/2 reduced periodic mechanical stress-induced chondrocyte proliferation and matrix synthesis (P < 0.05), while the phosphorylation levels of Src-Tyr418 and PLCγ1-Tyr783 were not inhibited. Proliferation, matrix synthesis and phosphorylation of MEK1/2-Ser217/221 and ERK1/2-Thr202/Tyr204 were inhibited after pretreatment with the PLCγ1 inhibitor U73122 in chondrocytes in response to periodic mechanical stress (P < 0.05), while the phosphorylation site of Src-Tyr418 was not affected. Inhibition of Src activity with PP2 and shRNA targeted to Src abrogated chondrocyte proliferation and matrix synthesis (P < 0.05) and attenuated PLCγ1, MEK1/2 and ERK1/2 activation in chondrocytes subjected to periodic mechanical stress (P < 0.05). These findings suggest that periodic mechanical stress promotes chondrocyte proliferation and matrix synthesis in part through the Src-PLCγ1-MEK1/2-ERK1/2 signaling pathway, which links these three important signaling molecules into a mitogenic cascade.

Relationship between the price of fish and its quality attributes: a study within a community at the University of São Paulo, Brazil

The aim of this study was to evaluate the associations between the products' market price and attributes related to fish purchase and consumption within a university community in Brazil. A structured questionnaire consisting of a five-point Likert scale was used. It was previously tested and made available to the university community via the Internet. The sample comprised 1966 voluntaries including university students and faculty and staff members. A descriptive analysis of data was performed using Spearman's correlation analysis. The results showed that the majority of the respondents (56%) consume fish at home; some consume fish at restaurants (39%), and 5% at family or friends' houses, reinforcing the idea that variables such as culture and reference groups are fundamental determinants of purchase and consumption behavior. It was identified a significant (p < 0.001) and very strong correlation between the attributes price and nutritional value (r = 0.92); price and availability at the usual places of purchase (r = 0.92); price and packaging (r = 0.92); price and brand name (r = 0.91); and price and of the Federal Inspection stamp (r = 0.91) and a low positive correlation (p < 0.001) between the price variable and the initiative for fish traceability (r = 0.16). This study demonstrated that the price of fish is associated with the quality of the product and the attributes related to it such as packaging, nutritional value, and availability of the product in the market.

Characterization of Leishmania infantum species in dogs from the urban area of Cuiabá, State of Mato Grosso, Brazil

INTRODUCTION: Visceral leishmaniasis presents urban behavior in some Brazilian cities, with domestic dogs as the main infection source. In Cuiabá, MT, canine visceral leishmaniasis was diagnosed and characterized as recommended by the Ministry of Health. METHODS: Biological samples from suspected canine carriers were analyzed by the isoenzyme electrophoresis technique. The 6PGDH enzyme and reference strain IOC/L0566 (MHOM/BR/1975/M2903) of Leishmania (Leishmania) infantum was used as one of the controls. RESULTS: Electrophoresis analysis revealed that the canine isolates belonged to the species L. (L.) infantum. CONCLUSIONS: The authors emphasize the importance of species characterization, particularly in areas of mixed infection like Cuiabá.

Para além das fronteiras da química: relações entre filosofia, psicologia e ensino de química

The concepts of molecule and of molecular structure are so central to understand chemical phenomena that seems to be no doubt about the uniqueness of its meanings. Nevertheless, the idea that the world exhibits a multiform structure and that to different spheres of the world correspond different ways of knowing (Berger & Luckmann, 1967) has received support from different areas of scientific inquiry. Bachelard (1940, 1982) showed that a single philosophical doctrine is not enough to describe all the different ways of thinking when we try to explain a single concept. Wooley's question about the possibility of deducing the concept of molecular structure from quantum theory (Wooley, 1978) strengthened the feasibility of thinking the concept of molecule as a profile that encompasses different meanings. Moreover, research on students' learning of scientific concepts have brought to light that students use several ideas to explain scientific and everyday phenomena which are different from those learned in formal schooling. These ideas are not extinguished or replaced by scientific concepts, despite the efforts to do so in science classes. The common sense and scientific ways of understanding and talking about reality seems to be complementary in the same sense of the Bohr's complementarity (Halliday & Martin, 1993). So, we have to include in our profile of the concept of molecule not only scientific but also common sense zones. Drawing from Bachelard's notion of epistemological profile, from the history of science and from the research on children's ideas in science, we have developed the idea of a conceptual profile and used it to analyse basic scientific concepts, such as the concepts of matter and physical states of matter (Mortimer, 1995) and to investigate new ways to teach them. In the present paper, we will discuss the zones that might constitute a conceptual profile of molecule. The need of complementary views to account for the molecular structure in different contexts bring important issues for understanding and teaching chemistry, which will be discussed further in the article.

Qualidade de medições em química analítica. Estudo de caso: determinação de cádmio por espectrofotometria de absorção atômica com chama

Calculation of uncertainty of results represents the new paradigm in the area of the quality of measurements in laboratories. The guidance on the Expression of Uncertainty in Measurement of the ISO / International Organization for Standardization assumes that the analyst is being asked to give a parameter that characterizes the range of the values that could reasonably be associated with the result of the measurement. In practice, the uncertainty of the analytical result may arise from many possible sources: sampling, sample preparation, matrix effects, equipments, standards and reference materials, among others. This paper suggests a procedure for calculation of uncertainties components of an analytical result due to sample preparation (uncertainty of weights and volumetric equipment) and instrument analytical signal (calibration uncertainty). A numerical example is carefully explained based on measurements obtained for cadmium determination by flame atomic absorption spectrophotometry. Results obtained for components of total uncertainty showed that the main contribution to the analytical result was the calibration procedure.

Determination of phenobarbital in human plasma by a specific liquid chromatography method: application to a bioequivalence study

A liquid chromatography method was developed and validated for the determination of phenobarbital in human plasma using phenytoin as internal standard. The drugs were extracted from plasma by liquid-liquid extraction and separated isocratically on a C12 analytical column, maintained at 35 ºC, with water:acetonitrile:methanol (58.8:15.2:26, v/v/v) as mobile phase, run at a flow rate of 1.2 mL/min with detection at 205 nm. The method was linear in the range of 0.1-4 μg/mL (r²=0.9999) and demonstrated acceptable results for the precision, accuracy and stability studies. The method was successfully applied for the bioequivalence study of two tablet formulations (test and reference) of phenobarbital 100 mg after single oral dose administration to healthy human volunteers.

Uso do bivalve límnico Anodontites tenebricosus (LEA, 1834) no biomonitoramento de metais do Rio Ribeira de Iguape

This study investigated the contamination of the Ribeira de Iguape River - RIR by Cd, Zn, Cr and Pb, using the bivalve Anodontites tenebricosus as a biomonitor. Metal concentrations in tissue samples were measured by HR-ICPMS. Bivalve tissues exhibited mean levels of 1.00 µg/g Cd; 152.89 µg/g Zn; 14.79 µg/g Cr and 4.40 µg/g Pb. Lead concentrations were comparable to those reported for moderately contaminated sites. The results showed that Pb is bioavailable to the bivalves, exhibiting high concentrations and exceeding both natural and reference values for human consumption. The freshwater bivalve Anodontites tenebricosus is a suitable biomonitor of contamination by metals.

Caracterização detalhada de material de referência certificado de carvão brasileiro

The use and characterization of the first Certified Reference Material (CRM) of Brazilian coal for analytical quality control are presented. All results were determined within the limits of repeatability and reproducibility allowed under the standards. Notable among the characterization parameters was the mineral matter content (45.39%) obtained by an alternative procedure showing a low relative error (-2.1%) compared to the standard technique (low ashing temperature). The possible expanded application of this CRM application in national laboratories, beyond the certificated and reference parameters, has advantages such as lower cost and easy availability, but round robin tests must be performed.