Evaluation of three different DNA extraction methods from blood samples collected in dried filter paper in Plasmodium subpatent infections from the Amazon region in Brazil

Asymptomatic Plasmodium infection is a new challenge for public health in the American region. The polymerase chain reaction (PCR) is the best method for diagnosing subpatent parasitemias. In endemic areas, blood collection is hampered by geographical distances and deficient transport and storage conditions of the samples. Because DNA extraction from blood collected on filter paper is an efficient method for molecular studies in high parasitemic individuals, we investigated whether the technique could be an alternative for Plasmodium diagnosis among asymptomatic and pauciparasitemic subjects. In this report we compared three different methods (Chelex®-saponin, methanol and TRIS-EDTA) of DNA extraction from blood collected on filter paper from asymptomatic Plasmodium-infected individuals. Polymerase chain reaction assays for detection of Plasmodium species showed the best results when the Chelex®-saponin method was used. Even though the sensitivity of detection was approximately 66% and 31% for P. falciparum and P. vivax, respectively, this method did not show the effectiveness in DNA extraction required for molecular diagnosis of Plasmodium. The development of better methods for extracting DNA from blood collected on filter paper is important for the diagnosis of subpatent malarial infections in remote areas and would contribute to establishing the epidemiology of this form of infection.

EVALUATION OF FOUR DIFFERENT DNA EXTRACTION METHODS IN COAGULASE-NEGATIVE STAPHYLOCOCCI CLINICAL ISOLATES

Currently there are several methods to extract bacterial DNA based on different principles. However, the amount and the quality of the DNA obtained by each one of those methods is highly variable and microorganism dependent, as illustrated by coagulase-negative staphylococci (CoNS) which have a thick cell wall that is difficult to lyse. This study was designed to compare the quality and the amount of CoNS DNA, extracted by four different techniques: two in-house protocols and two commercial kits. DNA amount and quality determination was performed through spectrophotometry. The extracted DNA was also analyzed using agarose gel electrophoresis and by PCR. 267 isolates of CoNS were used in this study. The column method and thermal lyses showed better results with regard to DNA quality (mean ratio of A260/280 = 1.95) and average concentration of DNA (), respectively. All four methods tested provided appropriate DNA for PCR amplification, but with different yields. DNA quality is important since it allows the application of a large number of molecular biology techniques, and also it's storage for a longer period of time. In this sense the extraction method based on an extraction column presented the best results for CoNS.

Comparative study of two extraction methods for enteric virus recovery from sewage sludge by molecular methods

The aim of this study was to compare two nucleic acid extraction methods for the recovery of enteric viruses from activated sludge. Test samples were inoculated with human adenovirus (AdV), hepatitis A virus (HAV), poliovirus (PV) and rotavirus (RV) and were then processed by an adsorption-elution-precipitation method. Two extraction methods were used: an organic solvent-based method and a silica method. The organic-based method was able to recoup 20% of the AdV, 90% of the RV and 100% of both the PV and HAV from seeded samples. The silica method was able to recoup 1.8% of the AdV and 90% of the RV. These results indicate that the organic-based method is more suitable for detecting viruses in sewage sludge.

COMPARISON OF RNA EXTRACTION METHODS FOR Passiflora edulis SIMS LEAVES

ABSTRACT Functional genomic analyses require intact RNA; however, Passiflora edulis leaves are rich in secondary metabolites that interfere with RNA extraction primarily by promoting oxidative processes and by precipitating with nucleic acids. This study aimed to analyse three RNA extraction methods, Concert™ Plant RNA Reagent (Invitrogen, Carlsbad, CA, USA), TRIzol® Reagent (Invitrogen) and TRIzol® Reagent (Invitrogen)/ice -commercial products specifically designed to extract RNA, and to determine which method is the most effective for extracting RNA from the leaves of passion fruit plants. In contrast to the RNA extracted using the other 2 methods, the RNA extracted using TRIzol® Reagent (Invitrogen) did not have acceptable A260/A280 and A260/A230 ratios and did not have ideal concentrations. Agarose gel electrophoresis showed a strong DNA band for all of the Concert™ method extractions but not for the TRIzol® and TRIzol®/ice methods. The TRIzol® method resulted in smears during electrophoresis. Due to its low levels of DNA contamination, ideal A260/A280 and A260/A230 ratios and superior sample integrity, RNA from the TRIzol®/ice method was used for reverse transcription-polymerase chain reaction (RT-PCR), and the resulting amplicons were highly similar. We conclude that TRIzol®/ice is the preferred method for RNA extraction for P. edulis leaves.

Cat's claw oxindole alkaloid isomerization induced by common extraction methods

Cat's claw oxindole alkaloids are prone to isomerization in aqueous solution. However, studies on their behavior in extraction processes are scarce. This paper addressed the issue by considering five commonly used extraction processes. Unlike dynamic maceration (DM) and ultrasound-assisted extraction, substantial isomerization was induced by static maceration, turbo-extraction and reflux extraction. After heating under reflux in DM, the kinetic order of isomerization was established and equations were fitted successfully using a four-parameter Weibull model (R² > 0.999). Different isomerization rates and equilibrium constants were verified, revealing a possible matrix effect on alkaloid isomerization.

VIS-NIR SPECTROMETRY, SOIL PHOSPHATE EXTRACTION METHODS AND INTERACTIONS OF SOIL ATTRIBUTES

The objective of this study was to evaluate the relationships between the spectra in the Vis-NIR range and the soil P concentrations obtained from the PM and Prem extraction methods as well as the effects of these relationships on the construction of models predicting P concentration in Oxisols. Soil samples' spectra and their PM and Prem extraction solutions were determined for the Vis-NIR region between 400 and 2500 nm. Mineralogy and/or organic matter content act as primary attributes allowing correlation of these soil phosphorus fractions with the spectra, mainly at wavelengths between 450-550, 900-1100 nm, near 1400 nm and between 2200-2300 nm. However, the regression models generated were not suitable for quantitative phosphate analysis. Solubilization of organic matter and reactions during the PM extraction process hindered correlations between the spectra and these P soil fractions. For Prem,, the presence of Ca in the extractant and preferential adsorption by gibbsite and iron oxides, particularly goethite, obscured correlations with the spectra.

Evaluation of protein extraction methods to obtain protein concentrate from cassava leaf

The cassava leaf, waste generated in the harvest of the roots, is characterized by high content of protein, vitamins and minerals; however, its use is limited due to the high fiber content and antinutritional substances, which can be removed by obtaining protein concentrates. In this context, the objective of this study was to evaluate protein extraction processes, aiming the use of cassava leaves (Manihot esculenta Crantz) as an alternative protein. Four methods were tested: 1) Coagulation of Proteins by Lowering the Temperature, 2) Extraction by Isoelectric Precipitation, 3) Solubilization of Proteins and 4) Fermentation of Filter Leaf Juice. To obtain the concentrates, the use of fresh or dried leaves and extraction in one or two steps were also evaluated. The solubilization of proteins (method 3) showed a higher extraction yield; however, with concentrate of low quality. The fermentation of the juice (method 4) produced concentrates with higher quality and lower costs and the isoelectric precipitation (method 2) promoted the obtention of concentrates in less time, both with good prospects for use. The use of two extraction steps was not advantageous to the process and there was no difference between the use of fresh or dried leaf, and the use of fresh leaves is presented as a good option for the simplicity of the method.

Comparison of two commercial kits and two extraction methods for fecal glucocorticoid analysis in ocelots (Leopardus pardalis) submitted to ACTH challenge

The ocelot (Leopardus pardalis) is included in list of wild felid species protected by CITES and is part of conservation strategies that necessarily involve the use of assisted reproduction techniques, which requires practical and minimally invasive techniques of high reproducibility that permit the study of animal reproductive physiology. The objective of this study was to compare and validate two commercial assays: ImmuChem Double Antibody Corticosterone 125I RIA from ICN Biomedicals, Costa Mesa, CA, USA; and Coat-a-Count Cortisol 125I RIA from DPC, Los Angeles, CA, USA, for assessment of fecal glucocorticoid metabolites in ocelots submitted to ACTH (adrenocorticotropic hormone) challenge. Fecal samples were collected from five ocelots kept at the Brazilian Center of Neotropical Felines, Associação Mata Ciliar, São Paulo, Brazil, and one of the animals was chosen as a negative control. The experiment was conducted over a period of 9 days. On day 0, a total dose of 100 IU ACTH was administered intramuscularly. Immediately after collection the samples were stored at 20C in labeled plastic bags. The hormone metabolites were subsequently extracted and assayed using the two commercial kits. Previously it was performed a trial with the DPC kit to check the best extraction method for hormones metabolites. Data were analyzed with the SAS program for Windows V8 and reported as means ± SEM. The Schwarzenberger extraction method was slightly better when compared with the Wasser extraction method (103,334.56 ± 19,010.37ng/g of wet feces and 59,223.61 ± 12,725.36ng/g of wet feces respectively; P=0,0657). The ICN kit detected an increase in glucocorticoid metabolite concentrations in a more reliable manner. Metabolite concentrations (ng/g wet feces) on day 0 and day 1 were 66,956.28 ± 36,786.93 and 92,991.19 ± 28,555.63 for the DPC kit, and 205,483.32 ± 83,811.32 and 814,578.75 ± 292,150.47 for the ICN kit, respectively. The limit of detection for the ICN kit was 7.7 ng/mL for 100% B/Bo (25ng/mL for 88%B/Bo) and for the DPC kit it was 0.2ug/dL for 90.95% B/Bo (1ug/dL for 81.27% B/Bo). In conclusion it was confirmed that the Schwarzenberger extraction method and the ICN kit are superior for extracting and measuring fecal glucocorticoid metabolites in ocelot fecal samples.

Use of real-time PCR to evaluate two DNA extraction methods from food

The DNA extraction is a critical step in Genetically Modified Organisms analysis based on real-time PCR. In this study, the CTAB and DNeasy methods provided good quality and quantity of DNA from the texturized soy protein, infant formula, and soy milk samples. Concerning the Certified Reference Material consisting of 5% Roundup Ready® soybean, neither method yielded DNA of good quality. However, the dilution test applied in the CTAB extracts showed no interference of inhibitory substances. The PCR efficiencies of lectin target amplification were not statistically different, and the coefficients of correlation (R²) demonstrated high degree of correlation between the copy numbers and the threshold cycle (Ct) values. ANOVA showed suitable adjustment of the regression and absence of significant linear deviations. The efficiencies of the p35S amplification were not statistically different, and all R² values using DNeasy extracts were above 0.98 with no significant linear deviations. Two out of three R² values using CTAB extracts were lower than 0.98, corresponding to lower degree of correlation, and the lack-of-fit test showed significant linear deviation in one run. The comparative analysis of the Ct values for the p35S and lectin targets demonstrated no statistical significant differences between the analytical curves of each target.

Physicochemical properties and antioxidant activity of Tunisian date palm (Phoenix dactylifera L.) oil as affected by different extraction methods

The chemical analysis of flesh and seed of date palm fruit (Kentichi) was evaluated. Carbohydrates were the predominant component in all studied date cultivars (~78.69-83.46 g/100g dry matter), followed by moisture content (~9.23-11.17%), along with moderate amount of fat (~0.56-7.10 g/100g dry matter), protein (~2.16-2.80 g/100g dry matter), and ash (~1.18-1.64 g/100 g dry matter). Some antioxidants (Ascorbic acid, total phenolic, total flavonoid, chlorophyll and carotenoids) were found in different values in both date fruit and seed. The physicochemical properties and antioxidant activity of both flesh and seed oil which was extracted using Hexane, Soxhlet and Modified Bligh - Dyer extraction methods were determined. The experimental results showed that temperature, different solvents and extraction time had significant effect on the yield of the date palm oil and physicochemical properties. Date Flesh oil showed an important free radical scavenging activity towards 1-1-diphenyl-2-picrylhydrazyl (DPPH) free radical.

The influence of extraction methods on composition and antioxidant properties of rice bran oil

AbstractThe current study was employed to assess the influence of the different extraction methods on total tocols, γ-oryzanol content, and antioxidant properties of Chiang Mai Black rice, Mali Red rice, and Suphanburi-1 Brown rice bran oil. Rice bran oil (RBO) was extracted by Hexane, Hot pressed, Cold pressed, and Supercritical Fluid Extraction (SFe) methods. High yield of RBO was extracted by hexane and SFe methods. Total and subgroups of tocols, and γ-oryzanol content were determined by HPLC. The hexane extracted sample accounts for high content of γ-oryzanol and tocols. Besides, all of RBO extracts contain a significantly high amount of γ-tocotrienol. In vitro antioxidant assay results indicated that superior quality of oil was recovered by hexane extraction. The temperature in the extraction process also affects the value of the oil. Superior quality of oil was recovered by hexane extraction, in terms of phytochemical contents and antioxidant properties compared to other tested extraction methods. Further, thorough study of factors compromising the quality and quantity of RBO recovery is required for the development of enhanced functional foods and other related products.

Optimization of chromatographic conditions and comparison of extraction efficiencies of four different methods for determination and quantification of pesticide content in bovine milk by UFLC-MS/MS

This paper describes the optimization of a multiresidue chromatographic analysis for the identification and quantification of 20 pesticides in bovine milk, including three carbamates, a carbamate oxime, six organophosphates, two strobilurins, a pyrethroid, an oxazolidinedione, an aryloxyphenoxypropionate acid/ester, a neonicotinoid, a dicarboximide, and three triazoles. The influences of different chromatographic columns and gradients were evaluated. Furthermore, four different extraction methods were evaluated; each utilized both different solvents, including ethyl acetate, methanol, and acetonitrile, and different workup steps. The best results were obtained by a modified QuEChERS method that lacked a workup step, and that included freezing the sample for 2 hours at -20 ºC. The results were satisfactory, yielding coefficients of variation of less than 20%, with the exception of the 50 µg L-1 sample of famoxadone, and recoveries between 70 and 120%, with the exception of acephate and bifenthrin; however, both analytes exhibited coefficients of variation of less than 20%.

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.

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.

Flavonoid extraction from Alpinia zerumbet (Pers.) Burtt et Smith leaves using different techniques and solvents

The current study aims to verify the best method for a rapid and efficient extraction of flavonoids from Alpinia zerumbet. Dried leaves were extracted using distillated water and ethanol 70% by extraction methods of shaking maceration, ultrasonic, microwave and stirring. By the application of TLC and reversed-phase HPLC techniques the rutin and kaempferol-3-O-glucuronide were detected. Ethanol 70% was more efficient for flavonoids extraction than water. No significant yielding variation was verified for ultrasonic, microwave and stirring methods using ethanol 70% (11 to 14%). The relative concentration of rutin and kaempferol-3-O-glucuronide, respectively, was higher by ultrasonic (1.5 and 5.62 mg g-1 dried leaves, respectively) and by microwave (1.0 and 6.64 mg g-1 dried leaves) methods using ethanol. Rapid and simplified extraction proceeding optimize phytochemical work and acquisition of secondary metabolites.