A comparison of four DNA extraction protocols for the analysis of urine from patients with visceral leishmaniasis

Introduction Polymerase chain reaction (PCR) may offer an alternative diagnostic option when clinical signs and symptoms suggest visceral leishmaniasis (VL) but microscopic scanning and serological tests provide negative results. PCR using urine is sensitive enough to diagnose human visceral leishmaniasis (VL). However, DNA quality is a crucial factor for successful amplification. Methods A comparative performance evaluation of DNA extraction methods from the urine of patients with VL using two commercially available extraction kits and two phenol-chloroform protocols was conducted to determine which method produces the highest quality DNA suitable for PCR amplification, as well as the most sensitive, fast and inexpensive method. All commercially available kits were able to shorten the duration of DNA extraction. Results With regard to detection limits, both phenol: chloroform extraction and the QIAamp DNA Mini Kit provided good results (0.1 pg of DNA) for the extraction of DNA from a parasite smaller than Leishmania (Leishmania) infantum (< 100fg of DNA). However, among 11 urine samples from subjects with VL, better performance was achieved with the phenol:chloroform method (8/11) relative to the QIAamp DNA Mini Kit (4/11), with a greater number of positive samples detected at a lower cost using PCR. Conclusion Our results demonstrate that phenol:chloroform with an ethanol precipitation prior to extraction is the most efficient method in terms of yield and cost, using urine as a non-invasive source of DNA and providing an alternative diagnostic method at a low cost.

Molecular identification and antifungal susceptibility profiles of Candida parapsilosis complex species isolated from culture collection of clinical samples

AbstractINTRODUCTION:Candida parapsilosis is a common yeast species found in cases of onychomycosis and candidemia associated with infected intravascular devices. In this study, we differentiated Candida parapsilosis sensu stricto, Candida orthopsilosis , and Candida metapsilosis from a culture collection containing blood and subungual scraping samples. Furthermore, we assessed the in vitro antifungal susceptibility of these species to fluconazole, itraconazole, voriconazole, posaconazole, amphotericin B, and caspofungin.METHODS:Differentiation of C. parapsilosis complex species was performed by amplification of the secondary alcohol dehydrogenase (SADH) gene and digestion by the restriction enzyme Ban I. All isolates were evaluated for the determination of minimal inhibitory concentrations using Etest, a method for antifungal susceptibility testing.RESULTS:Among the 87 isolates, 78 (89.7%) were identified as C. parapsilosis sensu stricto , five (5.7%) were identified as C. orthopsilosis , and four (4.6%) were identified as C. metapsilosis . Analysis of antifungal susceptibility showed that C. parapsilosis sensu strictoisolates were less susceptible to amphotericin B and itraconazole. One C. parapsilosis sensu stricto isolate was resistant to amphotericin B and itraconazole. Moreover, 10.2% of C. parapsilosis sensu stricto isolates were resistant to caspofungin. Two C. parapsilosis sensu strictoisolates and one C. metapsilosis isolate were susceptible to fluconazole in a dose-dependent manner.CONCLUSIONS:We reported the first molecular identification of C. parapsilosiscomplex species in State of Goiás, Brazil. Additionally, we showed that although the three species exhibited differences in antifungal susceptibility profiles, the primary susceptibility of this species was to caspofungin.

Microsatellite instability in solitary and sporadic gastric cancer

Recently, the presence of microsatellite instability (MSI) has been reported in gastric cancer and associated with older age of presentation, distal tumor location, early disease staging, and better overall prognosis. Different characteristics in presentation and in tumor behavior may be explained by different genetic alterations during carcinogenesis of gastric cancer. Identification of specific genetic pathways in gastric cancer may have direct impact on prognosis and selection of treatment strategies. PATIENTS AND METHODS: All 24 patients were treated by radical surgery. Fragments of normal and tumor tissues were extracted from the specimen and stored at -80ºC before DNA purification and extraction. PCR amplification utilizing microsatellite markers was performed. Tumors presenting PCR products of abnormal sizes were considered positive for microsatellite instability (MSI+). RESULTS: Five patients (21%) had tumors that were MSI+ in at least 1 marker. In the group of patients with Lauren's intestinal-type gastric carcinoma, 3 had tumors that were MSI+ (23%), while in the group of diffuse-type gastric cancer, 2 patients had tumors that were MSI+ (19%). The mean age of presentation and the male:female ratio was similar in both groups. Tumors that were MSI+ were more frequently located in proximal portion of the stomach compared to microsatellite-stable (MSS) tumors (40% vs. 16%). Although there was a trend of patients with MSI+ tumors towards a proximal gastric tumor location, early staging, and negative lymph node metastasis, there was no statistical significance compared to those with MSS tumors (P >.1). Comparison of overall and disease-free survival between gastric tumors that were MSI+ and those that were MSS found no statistically significant differences (P >.1). CONCLUSIONS: Microsatellite instability is a frequent event in gastric carcinogenesis and shows a trend towards distinct clinical and pathological characteristics of gastric cancer.

Ecology of sandflies (Diptera: Psychodidae) in a restricted focus of cutaneous leishmaniasis en Northern Venezuela: I. Description of the study area, catching methods and species composition

A study on the ecology of phlebotomine sandfly fauna in a restricted focus of cutaneous leishmaniasis in northern Venezuela was undertaken in order to investigate the species responsible for the transmission. The study area and catching methods for phlebotomine sandflies are described. A total of 9,061 females and 1,662 males were collected during a year-term study. 12 species of Lutzomya and 1 species of Brumptomya sp. were identified. Absolute and relative abundance and ocurrence for each species were determined. The rel ative occurrence allowed to distinguish the common species, viz. L. panamensis, L. ovallesi, L. gomezi, L. tinidadensis, L. atroclavata, L. cayennensis, L. shannoni and L. olmeca bicolor from the rare species vis., L. punctigeniculata, L. rangeliana, L. evansi and L. dubitans. General comments on the species composition of the sandfly fauna in this locality are made.

Isolation and molecular identification of Leishmania chagasi from a bat (Carollia perspicillata) in northeastern Venezuela

This report describes the isolation of a Leishmania chagasi strain from a bat (Carollia perspicillata), and its identification using biological methods and molecular characterization. The parasites were isolated in an artificial culture medium from a blood sample extracted from a bat heart. The isolate was then inoculated into the footpads of Balb/c mice, which subsequently developed a typical nodular leishmanial lesion; the parasites were confirmed as Leishmania by smear and histopathology. Molecular characterization of the parasites was performed by polymerase chain reaction with species-specific primers, kDNA restriction pattern following Hae III endonuclease digestion and dot blot hybridization using a kDNA probe. This report demonstrates that bats can be hosts for L. chagasi species and suggests the need for studies to determine whether they may be involved in foci of visceral leishmaniasis.

Integrative Review: Concepts And Methods Used In Nursing


Integrative review (IR) has an international reputation in nursing research and evidence-based practice. This IR aimed at identifying and analyzing the concepts and methods recommended to undertaking IR in nursing. Nine information resources,including electronic databases and grey literature were searched. Seventeen studies were included. The results indicate that: primary studies were mostly from USA; it is possible to have several research questions or hypotheses and include primary studies in the review from different theoretical and methodological approaches; it is a type of review that can go beyond the analysis and synthesis of findings from primary studies allowing exploiting other research dimensions, and that presents potentialities for the development of new theories and new problems for research. Conclusion: IR is understood as a very complex type of review and it is expected to be developed using standardized and systematic methods to ensure the required rigor of scientific research and therefore the legitimacy of the established evidence.


Lead and zinc in the structure of organic and mineral soil components

In addition to the more reactive forms, metals can occur in the structure of minerals, and the sum of all these forms defines their total contents in different soil fractions. The isomorphic substitution of heavy metals for example alters the dimensions of the unit cell and mineral size. This study proposed a method of chemical fractionation of heavy metals, using more powerful extraction methods, to remove the organic and different mineral phases completely. Soil samples were taken from eight soil profiles (0-10, 10-20 and 20-40 cm) in a Pb mining and metallurgy area in Adrianópolis, Paraná, Brazil. The Pb and Zn concentrations were determined in the following fractions (complete phase removal in each sequential extraction): exchangeable; carbonates; organic matter; amorphous and crystalline Fe oxides; Al oxide, amorphous aluminosilicates and kaolinite; and residual fractions. The complete removal of organic matter and mineral phases in sequential extractions resulted in low participation of residual forms of Pb and Zn in the total concentrations of these metals in the soils: there was lower association of metals with primary and 2:1 minerals and refractory oxides. The powerful methods used here allow an identification of the complete metal-mineral associations, such as the occurrence of Pb and Zn in the structure of the minerals. The higher incidence of Zn than Pb in the structure of Fe oxides, due to isomorphic substitution, was attributed to a smaller difference between the ionic radius of Zn2+ and Fe3+.

Incubation methods for assessing mineralizable nitrogen in soils under sugarcane

Considering nitrogen mineralization (N) of soil organic matter is a key aspect for the efficient management of N fertilizers in agricultural systems. Long-term aerobic incubation is the standard technique for calibrating the chemical extraction methods used to estimate the potentially mineralizable N in soil. However, the technique is laborious, expensive and time-consuming. In this context, the aims of this study were to determine the amount of soil mineralizable N in the 0-60 cm layer and to evaluate the use of short-term anaerobic incubation instead of long-term aerobic incubation for the estimation of net N mineralization rates in soils under sugarcane. Five soils from areas without previous N fertilization were used in the layers 0-20, 20-40 and 40-60 cm. Soil samples were aerobically incubated at 35 ºC for 32 weeks or anaerobically incubated (waterlogged) at 40 ºC for seven days to determine the net soil N mineralization. The sand, silt and clay contents were highly correlated with the indexes used for predicting mineralizable N. The 0-40 cm layer was the best sampling depth for the estimation of soil mineralizable N, while in the 40-60 cm layer net N mineralization was low in both incubation procedures. Anaerobic incubation provided reliable estimates of mineralizable N in the soil that correlated well with the indexes obtained using aerobic incubation. The inclusion of the pre-existing NH4+-N content improved the reliability of the estimate of mineralizable N obtained using anaerobic incubation.

Phosphorus extracted by ion exchange resins and mehlich-1 from oxisols (latosols) treated with different phosphorus rates and sources for varied soil-source contact periods

Despite the large number of studies addressing the quantification of phosphorus (P) availability by different extraction methods, many questions remain unanswered. The aim of this paper was to compare the effectiveness of the extractors Mehlich-1, Anionic Resin (AR) and Mixed Resin (MR), to determine the availability of P under different experimental conditions. The laboratory study was arranged in randomized blocks in a [(3 x 3 x 2) + 3] x 4 factorial design, with four replications, testing the response of three soils with different texture: a very clayey Red Latosol (LV), a sandy clay loam Red Yellow Latosol (LVA), and a sandy loam Yellow Latosol (LA), to three sources (triple superphosphate, reactive phosphate rock from Gafsa-Tunisia; and natural phosphate from Araxá-Minas Gerais) at two P rates (75 and 150 mg dm-3), plus three control treatments (each soil without P application) after four contact periods (15, 30, 60, and 120 days) of the P sources with soil. The soil acidity of LV and LVA was adjusted by raising base saturation to 60 % with the application of CaCO3 and MgCO3 at a 4:1 molar ratio (LA required no correction). These samples were maintained at field moisture capacity for 30 days. After the contact periods, the samples were collected to quantify the available P concentrations by the three extractants. In general, all three indicated that the available P-content in soils was reduced after longer contact periods with the P sources. Of the three sources, this reduction was most pronounced for triple superphosphate, intermediate for reactive phosphate, while Araxá phosphate was least sensitive to the effect of time. It was observed that AR extracted lower P levels from all three soils when the sources were phosphate rocks, while MR extracted values close to Mehlich-1 in LV (clay) and LVA (medium texture) for reactive phosphate. For Araxá phosphate, much higher P values were determined by Mehlich-1 than by the resins, because of the acidity of the extractor. For triple superphosphate, both resins extracted higher P levels than Mehlich-1, due to the consumption of this extractor, particularly when used for LV and LVA.

Phosphorus availability in oxidic soils treated with lime and silicate applications

Based on the assumption that silicate application can raise soil P availability for crops, the aim of this research was to compare the effect of silicate application on soil P desorption with that of liming, in evaluations based on two extractors and plant growth. The experiment was carried out in randomized blocks with four replications, in a 3 × 3 × 5 factorial design, in which three soil types, three P rates, and four soil acidity correctives were evaluated in 180 experimental plots. Trials were performed in a greenhouse using corn plants in 20-dm³ pots. Three P rates (0, 50 and 150 mg dm-3) were applied in the form of powder triple superphosphate and the soil was incubated for 90 days. After this period, soil samples were collected for routine chemical analysis and P content determination by the extraction methods resin, Mehlich-1 and remaining P. Based on the results, acidity correctives were applied at rates calculated for base saturation increased to 70 %, with subsequent incubation for 60 more days, when P content was determined again. The acidity correctives consisted of: dolomitic lime, steelmaking slag, ladle furnace slag, and wollastonite. Therefore, our results showed that slags raised the soil P content more than lime, suggesting a positive correlation between P and Si in soil. Silicon did not affect the extractor choice since both Mehlich-1 and resin had the same behavior regarding extracted P when silicon was applied to the soil. For all evaluated plant parameters, there was significant interaction between P rates and correctives; highest values were obtained with silicate.

MERCURY QUANTIFICATION IN SOILS USING THERMAL DESORPTION AND ATOMIC ABSORPTION SPECTROMETRY: PROPOSAL FOR AN ALTERNATIVE METHOD OF ANALYSIS

Despite the considerable environmental importance of mercury (Hg), given its high toxicity and ability to contaminate large areas via atmospheric deposition, little is known about its activity in soils, especially tropical soils, in comparison with other heavy metals. This lack of information about Hg arises because analytical methods for determination of Hg are more laborious and expensive compared to methods for other heavy metals. The situation is even more precarious regarding speciation of Hg in soils since sequential extraction methods are also inefficient for this metal. The aim of this paper is to present a technique of thermal desorption associated with atomic absorption spectrometry, TDAAS, as an efficient tool for quantitative determination of Hg in soils. The method consists of the release of Hg by heating, followed by its quantification by atomic absorption spectrometry. It was developed by constructing calibration curves in different soil samples based on increasing volumes of standard Hg2+ solutions. Performance, accuracy, precision, and quantification and detection limit parameters were evaluated. No matrix interference was detected. Certified reference samples and comparison with a Direct Mercury Analyzer, DMA (another highly recognized technique), were used in validation of the method, which proved to be accurate and precise.

Electrical Conductivity and Chemical Composition of Soil Solution: Comparison of Solution Samplers in Tropical Soils

ABSTRACT Soil solution samplers may have the same working principle, but they differ in relation to chemical and physical characteristics, cost and handling, and these aspects exert influence on the chemical composition of the soil solution obtained. This study was carried out to evaluate, over time, the chemical composition of solutions extracted by Suolo Acqua, with the hydrophilic membrane (HM) as a standard, using soils with contrasting characteristics, and to determine the relationship between electrical conductivity (EC) and concentration of ions and pH of soil solution samples. This study was carried out under laboratory conditions, using three soils samples with different clay and organic matter (OM) contents. Soil solution contents of F−, Cl−, NO−3, Br−, SO42−, Na+, NH4+, K+, Mg2+, Ca2+, were analyzed, as well as inorganic, organic, and total C contents, pH, and EC, in four successive sampling times. Soil solution chemical composition extracted by the Suolo Acqua sampler is similar to that collected by the HM, but the Suolo Acqua extracted more Na+ and soluble organic C than the HM solution. Solution EC, cation and anion concentrations, and soluble C levels are higher in the soil with greater clay and OM contents (Latossolo and Cambissolo in this case). Soil solution composition varied over time, with considerable changes in pH, EC, and nutrient concentrations, especially associated with soil OM. Thus, single and isolated sampling of the soil solution must be avoided, otherwise composition of the soil solution may not be correctly evaluated. Soil solution EC was regulated by pH, as well as the sum of cation and anion concentrations, and the C contents determined in the soil liquid phase.

Analytical methods for vancomycin determination in biological fluids and in pharmaceuticals

Vancomycin is a glycopeptide antibiotic employed in the treatment of infections caused by certain methicillin-resistant staphylococci. It is indicated also for patients allergic to penicillin or when there is no response to penicillins or cephalosporins. The adequate vancomycin concentration levels in blood serum lies between 5 and 10 mg/L. Higher values are toxic, causing mainly nephrotoxicity and ototoxicity. Various analytical methods are described in the literature: spectrophotometric, immunologic, biologic and chromatographic methods. This paper reviews the main analytical methods for vancomycin determination in biological fluids and in pharmaceutical preparations.

Development and validation of RP-LC and uv spectrophotometric methods to assay bromopride in oral and injectable solutions

A reversed-phase liquid chromatographic (LC) and ultraviolet (UV) spectrophotometric methods were developed and validated for the assay of bromopride in oral and injectable solutions. The methods were validated according to ICH guideline. Both methods were linear in the range between 5-25 μg mL-1 (y = 41837x - 5103.4, r = 0.9996 and y = 0.0284x - 0.0351, r = 1, respectively). The statistical analysis showed no significant difference between the results obtained by the two methods. The proposed methods were found to be simple, rapid, precise, accurate, and sensitive. The LC and UV methods can be used in the routine quantitative analysis of bromopride in oral and injectable solutions.

MÉTODOS DE EXTRAÇÃO DE POLI-HIDROXIALCANOATOS A PARTIR DE BIOMASSA BACTERIANA

Polyhydroxyalkanoates (PHAs) are biodegradable and biocompatible polyesters intracellularly accumulated by many bacteria as an energy reserve material and carbon source. These biopolymers may be extracted from cells after their production phase, and the extraction process involves various individual operations to ensure adequate removal of the biopolymer from the cells. During this process, the following aspects should be considered: reduction of product losses during different stages of the process to obtain a highly pure product, preservation of physical and thermal characteristics, and use of low toxicity chemicals to achieve sustainable production and avoid harming the environment. The impact of the costs of PHA extraction on the total cost of the production process may account for over 50% of the end-value of the product. Within this context, several methods of PHA extraction have been reported in the literature. These methods include the use of solvents, chemical digestion, enzymatic digestion, mechanical extraction with high-pressure homogenization and ultrasound, extraction using supercritical fluids, or a combination of these methods. The present review of the literature shows strategies for extraction processes of PHAs produced by bacteria involving cell destabilization and/or breakage, recovery, and purification of the biopolymer.