Optimisation of a quantitative polymerase chain reaction-based strategy for the detection and quantification of human herpesvirus 6 DNA in patients undergoing allogeneic haematopoietic stem cell transplantation

Human herpesvirus 6 (HHV-6) may cause severe complications after haematopoietic stem cell transplantation (HSCT). Monitoring this virus and providing precise, rapid and early diagnosis of related clinical diseases, constitute essential measures to improve outcomes. A prospective survey on the incidence and clinical features of HHV-6 infections after HSCT has not yet been conducted in Brazilian patients and the impact of this infection on HSCT outcome remains unclear. A rapid test based on real-time quantitative polymerase chain reaction (qPCR) has been optimised to screen and quantify clinical samples for HHV-6. The detection step was based on reaction with TaqMan® hydrolysis probes. A set of previously described primers and probes have been tested to evaluate efficiency, sensitivity and reproducibility. The target efficiency range was 91.4% with linearity ranging from 10-106 copies/reaction and a limit of detection of five copies/reaction or 250 copies/mL of plasma. The qPCR assay developed in the present study was simple, rapid and sensitive, allowing the detection of a wide range of HHV-6 loads. In conclusion, this test may be useful as a practical tool to help elucidate the clinical relevance of HHV-6 infection and reactivation in different scenarios and to determine the need for surveillance.

An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA

This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy.

Spectroscopic quantification of soil phosphorus forms by 31p-nmr after nine years of organic or mineral fertilization

Long-standing applications of mineral fertilizers or types of organic wastes such as manure can cause phosphorus (P) accumulation and changes in the accumulated P forms in the soil. The objective of this research was to evaluate the forms of P accumulated in soils treated with mineral fertilizer or different types of manure in a long-term experiment. Soil was sampled from the 0-5 cm layer of plots fertilized with five different nutrient sources for nine years: 1) control without fertilizer; 2) mineral fertilizer at recommended rates for local conditions; 3) 5 t ha-1 year-1 of moist poultry litter; 4) 60 m³ ha-1 year-1 of liquid cattle manure and 5) 40 m³ ha-1 year-1 of liquid swine manure. The 31P-NMR spectra of soil extracts detected the following P compounds: orthophosphate, pyrophosphate, inositol phosphate, glycerophosphate, and DNA. The use of organic or mineral fertilizer over nine years did not change the soil P forms but influenced their concentration. Fertilization with mineral or organic fertilizers stimulated P accumulation in inorganic forms. Highest inositol phosphate levels were observed after fertilization with any kind of manure and highest organic P concentration in glycerophosphate form in after mineral or no fertilization.

Quantification of aluminium in soil of the Solimões Formation, Acre State, Brazil

The variety of soils in the State of Acre is wide and their chemical profiles are still not fully understood. The nature of the material of origin of these soils is indicated by the high aluminium (Al) content, commonly associated with high calcium (Ca) and magnesium (Mg) contents. The study objective was to use different methods to quantify Al in soils from toposequences formed from material of a sedimentary nature originating from the Solimões Formation, in Acre, Brazil. Trenches were opened at three distinct points in the landscape: shoulder, backslope and footslope positions. Soil samples were collected for physical, chemical, mineralogical analyses. The Al content was quantified using different methods. High Al contents were found in most of these horizons, associated with high Ca and Mg levels, representing the predominant cations in the sum of exchangeable bases. The mineralogy indicates that the soils are still in a low weathering phase, with the presence of significant quantities of 2:1 minerals. Similar Al contents were determined by the methods of NaOH titration, xylenol orange spectrometry and inductively coupled plasma optical emission spectrometry. However, no consistent data were obtained by the pyrocatechol violet method. Extraction with KCl overestimated the exchangeable Al content due to its ability to extract the non-exchangeable Al present in the smectite interlayers. It was observed that high Al contents are related to the instability of the hydroxyl-Al smectite interlayers.

Quantification of permanent and variable charges in reference soils of the State of Pernambuco, Brazil

The electrical charges in soil particles are divided into structural or permanent charges and variable charges. Permanent charges develop on the soil particle surface by isomorphic substitution. Variable charges arise from dissociation and association of protons (H+), protonation or deprotonation, and specific adsorption of cations and anions. The aim of this study was to quantify the permanent charges and variable charges of Reference Soils of the State of Pernambuco, Brazil. To do so, 24 subsurface profiles from different regions (nine in the Zona da Mata, eight in the Agreste, and seven in the Sertão) were sampled, representing approximately 80 % of the total area of the state. Measurements were performed using cesium chloride solution. Determination was made of the permanent charges and the charges in regard to the hydroxyl functional groups through selective ion exchange of Cs+ by Li+ and Cs+ by NH4+, respectively. All the soils analyzed exhibited variable cation exchange capacity, with proportions from 0.16 to 0.60 and an average of 0.40 when related to total cation exchange capacity.

Quantification of the least limiting water range in an oxisol using two methodological strategies

The least limiting water range (LLWR) has been used as an indicator of soil physical quality as it represents, in a single parameter, the soil physical properties directly linked to plant growth, with the exception of temperature. The usual procedure for obtaining the LLWR involves determination of the water retention curve (WRC) and the soil resistance to penetration curve (SRC) in soil samples with undisturbed structure in the laboratory. Determination of the WRC and SRC using field measurements (in situ ) is preferable, but requires appropriate instrumentation. The objective of this study was to determine the LLWR from the data collected for determination of WRC and SRC in situ using portable electronic instruments, and to compare those determinations with the ones made in the laboratory. Samples were taken from the 0.0-0.1 m layer of a Latossolo Vermelho distrófico (Oxisol). Two methods were used for quantification of the LLWR: the traditional, with measurements made in soil samples with undisturbed structure; and in situ , with measurements of water content (θ), soil water potential (Ψ), and soil resistance to penetration (SR) through the use of sensors. The in situ measurements of θ, Ψ and SR were taken over a period of four days of soil drying. At the same time, samples with undisturbed structure were collected for determination of bulk density (BD). Due to the limitations of measurement of Ψ by tensiometer, additional determinations of θ were made with a psychrometer (in the laboratory) at the Ψ of -1500 kPa. The results show that it is possible to determine the LLWR by the θ, Ψ and SR measurements using the suggested approach and instrumentation. The quality of fit of the SRC was similar in both strategies. In contrast, the θ and Ψ in situ measurements, associated with those measured with a psychrometer, produced a better WRC description. The estimates of the LLWR were similar in both methodological strategies. The quantification of LLWR in situ can be achieved in 10 % of the time required for the traditional method.

Quantification of the diversity among common bean accessions using Ward-MLM strategy

The present work aimed at evaluating the divergence among common bean accessions by their agronomic, morphological and molecular traits, based on the Ward-MLM procedure. A collection of 57 accessions from the gene bank of Universidade Federal do Espírito Santo was used in this study, from which: 31 were landraces belonging to the community Fortaleza, in the municipality of Muqui, ES, Brazil; 20 accessions were provided by Embrapa Trigo; and 6 were commercial cultivars. Five agronomic traits (plant cycle, number of seeds per pod, number of pods per plant, weight of 100 seeds, and grain yield), five morphological traits (growth habit, plant size, seed shape, seed color, and commercial group) and 16 microsatellite primers were evaluated. High genetic variability was detected considering morphological, agronomic and molecular traits in the 57 common bean accessions studied. The Ward-MLM procedure showed that the ideal number of groups was five, according to the pseudo F and pseudo t² criteria. The accessions from Andean origin had heavier seeds than others and formed a cluster. The Ward-MLM statistical procedure is a useful technique to detect genetic divergence and to cluster genotypes by simultaneously using morphological, agronomic and molecular data.

Comparison of GC and HPLC for quantification of organic acids in two jaboticaba (Myrciaria) fruit varieties

Gas chromatography (GC) with trimethylsilyl derivative formation was compared to high-performance liquid chromatography (HPLC) for quantification of organic acids (OAs) in two jaboticaba (Myrciaria) fruit (pulp and pericarp) varieties (Sabará and Açu Paulista). Succinic and citric acids were the major OAs found in all the samples analyzed. Besides being much more tedious, the results obtained with GC were significantly lower than HPLC (p<0.05) when the data (acids, variety, two parts and flowering days) were considered together. The presence of both acids was confirmed by gas chromatography-mass spectrometry (GC-MS).

High performance liquid chromatography method for quantification of the N-phenylpiperazine derivative LASSBio-579 in rat plasma

A rapid HPLC analytical method was developed and validated for the determination of the N-phenylpiperazine derivative LASSBio-579in plasma rat. Analyses were performed using a C18 column and elution with 20 mM sodium dihydrogen phosphate monohydrate - methanol. The analyte was monitored using a photodiode array detector (257 nm). Calibration curves in spiked plasma were linear over the concentration range of 0.3-8 mg/mL with determination coefficient > 0.99. The lower limit of quantification was 0.3 mg/mL. The applicability of the HPLC method for pharmacokinetic studies was tested using plasma samples obtained after administration of LASSBio-579 to Wistar rats, showing the specificity of the method.

A validated method using RP-HPLC for quantification of reserpine in the Brazilian tree Rauvolfia sellowii Müll. Arg. (Apocynaceae)

This study describes a simple, fast and reproducible method using RP-HPLC-UV, in a gradient system, for quantification of reserpine in Rauvolfia sellowii stem bark. The analysis were carried out on a C18 column; mobile phase was water and acetonitrile, and separations were carried out in 10 min, flow rate of 1.0 mL min-1, 25 ºC and 268 nm. The validation data showed that the method was specific, accurate, precise and robust. Results were linear over a range of 0.625-40.0 μg mL-1, and the mean recovery was 95.1%. The amount of reserpine found in the dried stem bark was 0.01% (m/m).

Quantification of tryptophan in plasma by high performance liquid chromatography

A simple, rapid and selective method using high-performance liquid chromatography with ultraviolet detection (267 nm) was applied for the determination of tryptophan in plasma. Separation was carried out on a C18 column (150 x 4.6 mm internal diameter) in 6 min. The mobile phase consisted of 5 mM the sodium acetate and acetonitrile (92:8, v/v). The method was shown to be precise and accurate, and good recovery of analyte was achieved, characterizing the method as efficient and reliable for use in laboratory analysis.

Quantification of the uranium concentration in human urine by inductively coupled plasma-sector field mass spectrometry (ICP-SFMS)

In this study, the validation of a method for analyzing the uranium (U) concentration in human urine samples by inductively coupled plasma-sector field mass spectrometry (ICP-SFMS) was conducted. PROCORAD (the Association for the Promotion of Quality Control in Radiotoxicological Analysis) provided two urine samples spiked with unknown contents of U (Sample A = 33.6 ± 1.0 µg/L and Sample B = 3.3 ± 0.1 µg/L) and one unspiked sample as a blank. The analyses were directly performed on the diluted urine samples (dilution factor = 1:20) in 5% v/v HNO3. The results obtained by ICP-SFMS corresponded well with the reference values, and the limits of detection were 235U = 0.049 × 10-3 µg/L and 238U = 7.37 × 10-3 µg/L. The ICP-SFMS technique has been shown to be successful in the analysis of the U concentration in human urine samples and for the quantification of isotopic ratios.

A reliable method of quantification of trace copper in beverages with and without alcohol by spectrophotometry after cloud point extraction

A new cloud point extraction (CPE) method was developed for the separation and preconcentration of copper (II) prior to spectrophotometric analysis. For this purpose, 1-(2,4-dimethylphenyl) azonapthalen-2-ol (Sudan II) was used as a chelating agent and the solution pH was adjusted to 10.0 with borate buffer. Polyethylene glycol tert-octylphenyl ether (Triton X-114) was used as an extracting agent in the presence of sodium dodecylsulphate (SDS). After phase separation, based on the cloud point of the mixture, the surfactant-rich phase was diluted with acetone, and the enriched analyte was spectrophotometrically determined at 537 nm. The variables affecting CPE efficiency were optimized. The calibration curve was linear within the range 0.285-20 µg L-1 with a detection limit of 0.085 µg L-1. The method was successfully applied to the quantification of copper in different beverage samples.

Quantification of beta-lactam antibiotics in veterinary drugs: amoxicillin and ampicillin determination by high performance liquid chromatography

This work focused on the development and validation of an RP-HPLC-UV method for quantification of beta-lactam antibiotics in three pharmaceutical samples. Active principles analyzed were amoxicillin and ampicillin, in 3 veterinary drugs. Mobile phase comprised 5 mmol L-1 phosphoric acid solution at pH 2.00, acetonitrile with gradient elution mode and detection wavelength at 220 nm. The method was validated according to the Brazilian National Health Surveillance regulation, where linear range and linearity, selectivity, precision, accuracy and ruggedness were evaluated. Inter day precision and accuracy for pharmaceutical samples 1, 2 and 3 were: 1.43 and 1.43%; 4.71 and 3.74%; 2.72 and 1.72%, respectively, while regression coefficients for analytical curves exceeded 0.99. The method had acceptable merit figure values, indicating reliable quantification. Analyzed samples had active principle concentrations varying from -12 to +21% compared to manufacturer label claims, rendering the medicine unsafe for administration to animals.

Bioanalytical method for the quantification of the monastrol derivative anticancer candidate lasom 65 in pre-clinical pharmacokinetic investigations

A simple HPLC/UV method was developed for the determination of the anticancer candidate LaSOM 65 in rat plasma. Samples were cleaned by protein precipitation with acetonitrile (recovery > 95%), after which they were subjected to chromatography under the isocratic elution of an acetonitrile:water (45:55, ν/ν) solution with detection at 303 nm. The method was linear (r² > 0.98) over the concentration range (0.05-2 µg mL-1) with intra- and inter-day precision ranging from 9.6% to 13.6% and 4.3% to 5.4%, respectively. The accuracy of the method ranged from 85% to 113.6%, and it showed sufficient sensitivity to determine pharmacokinetic parameters of LaSOM 65 after intravenous administration to Wistar rats.