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In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree) and beta diversity was found between the DNA samples extracted by the commercial kit and the developed protocol. The number of high-quality sequences of the samples extracted by the developed method was 20% higher than those obtained by the samples processed by the kit. The developed economic protocol successfully yielded high-quality pure mDNA compatible with complex molecular applications. Thus we propose the developed protocol as a gold standard for future metagenomic studies investigating a large number of samples.

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In this work a feasible method for chloride and sulfate determination in calcium carbonate pharmaceutical raw material and commercial tablets by ion chromatography after microwave-induced combustion was developed. The analytes were released from matrix by combustion in closed system pressurized with oxygen. Starch as volatilization aid, 100mmolL-1 HNO3 as absorbing solution and 5min of microwave irradiation time were used. Recovery tests using standard solutions were performed for the accuracy evaluation. A mixture of calcium carbonate pharmaceutical raw material or commercial tablets, starch and a certified reference material was also used as a type of recovery test. Recoveries ranging from 88% to 103% were obtained in both spike tests. Limits of detection (Cl-: 40µgg-1 and SO42-: 140µgg-1) were up to eighteen times lower than the maximum limits established for the analytes by Brazilian, British, European and Indian Pharmacopoeias. The limit tests recommended by the European Pharmacopoeia for Cl- and SO42- in CaCO3 were carried out to compare the results. Chloride and SO42- concentrations in the samples analyzed by proposed method were in agreement with those results obtained using the tests recommended by the European Pharmacopoeia. However, the proposed method presents several advantages for the routine analysis when compared to pharmacopoeial methods, such as the quantitative simultaneous determination, high sample preparation throughput (up to eight samples per run in less than 30min), reduced volume of reagents and waste generation. Thus, the proposed method is indicated as an excellent alternative for Cl- and SO42- determination in CaCO3 pharmaceutical raw material and commercial tablets.

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Abstract In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree) and beta diversity was found between the DNA samples extracted by the commercial kit and the developed protocol. The number of high-quality sequences of the samples extracted by the developed method was 20% higher than those obtained by the samples processed by the kit. The developed economic protocol successfully yielded high-quality pure mDNA compatible with complex molecular applications. Thus we propose the developed protocol as a gold standard for future metagenomic studies investigating a large number of samples.

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Responding to the need for green and efficient methods to determine catalyst residues with suitable precision and accuracy in samples with high fat content, the present work evaluates a microwave-assisted ultraviolet digestion (MW-UV) system for margarines and subsequent determination of Ni, Pd and Pt using inductively coupled plasma mass spectrometry (ICP-MS). It was possible to digest up to 500mg of margarine using only 10mL of 4molL-1 HNO3 with a digestion efficiency higher than 98%. This allowed the determination of catalyst residues using the ICP-MS and free of interferences. For this purpose, the following experimental parameters were evaluated: concentration of digestion solution, sample mass and microwave irradiation program. The residual carbon content was used as a parameter to evaluate the efficiency of digestion and to select the most suitable experimental conditions. The accuracy evaluation was performed by recovery tests using a standard solution and certified reference material, and recoveries ranging from 94% to 99% were obtained for all analytes. The limits of detection for Ni, Pd and Pt using the proposed method were 35.6, 0.264 and 0.302ngg-1, respectively. When compared to microwave-assisted digestion (MW-AD) in closed vessels using concentrated HNO3 (used as a reference method for sample digestion), the proposed MW-UV could be considered an excellent alternative for the digestion of margarine, as this method requires only a diluted nitric acid solution for efficient digestion. In addition, MW-UV provides appropriate solutions for further ICP-MS determination with suitable precision (relative standard deviation < 7%) and accuracy for all evaluated analytes. The proposed method was applied to margarines from different brands produced in Brazil, and the concentration of catalyst residues was in agreement with the current legislation or recommendations.

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RATIONALE: The analysis of stable isotopes in tissues such as teeth and bones has been used to study long-term trophic ecology and habitat use in marine mammals. However, carbon isotope ratios (δ(13) C values) can be altered by the presence of (12) C-rich lipids and carbonates. Lipid extraction and acidification are common treatments used to remove these compounds. The impact of lipids and carbonates on carbon and nitrogen isotope ratios (δ(15) N values), however, varies among tissues and/or species, requiring taxon-specific protocols to be developed. METHODS: The effects of lipid extraction and acidification and their interaction on carbon and nitrogen isotope values were studied for beaked whale (Ziphiidae) bone samples. δ(13) C and δ(15) N values were determined in quadruplicate samples: control, lipid-extracted, acidified and lipid-extracted followed by acidification. Samples were analyzed by means of elemental analysis isotope ratio mass spectrometry. Furthermore, the efficiency of five mathematical models developed for estimating lipid-normalized δ(13) C values from untreated δ(13) C values was tested. RESULTS: Significant increases in δ(13) C values were observed after lipid extraction. No significant changes in δ(13) C values were found in acidified samples. An interaction between both treatments was demonstrated for δ(13) C but not for δ(15) N values. No change was observed in δ(15) N values for lipid-extracted and/or acidified samples. Although all tested models presented good predictive power to estimate lipid-free δ(13) C values, linear models performed best. CONCLUSIONS: Given the observed changes in δ(13) C values after lipid extraction, we recommend a priori lipid extraction or a posteriori lipid normalization, through simple linear models, for beaked whale bones. Furthermore, acidification seems to be an unnecessary step before stable isotope analysis, at least for bone samples of ziphiids. Copyright © 2015 John Wiley & Sons, Ltd.

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OBJECTIVE/BACKGROUND: The diagnosis of leprosy has been a challenge due to the low sensibility of the conventional methods and the impossibility of culturing the causative organism. In this study, four methods for Mycobacterium leprae nucleic-acid extraction from Ziehl-Neelsen-stained slides (ZNS slides) were compared: Phenol/chloroform, Chelex 100 resin, and two commercial kits (Wizard Genomic DNA Purification Kit and QIAamp DNA Mini Kit). METHODS: DNA was extracted from four groups of slides: a high-codification-slide group (bacteriological index [BI]⩾4), a low-codification-slide group (BI=1), a negative-slide group (BI=0), and a negative-control-slide group (BI=0). Quality DNA was evidenced by the amplification of specific repetitive element present in M. leprae genomic DNA (RLEP) using a nested polymerase chain reaction. RESULTS: This is the first report comparing four different extraction methods for obtaining M. leprae DNA from ZNS slides in Cuban patients, and applied in molecular diagnosis. Good-quality DNA and positive amplification were detected in the high-codification-slide group with the four methods, while from the low-codification-slide group only the QIAGEN and phenol-chloroform methods obtained amplification of M. leprae. In the negative-slide group, only the QIAGEN method was able to obtain DNA with sufficient quality for positive amplification of the RLEP region. No amplification was observed in the negative-control-slide group by any method. Patients with ZNS negative slides can still transmit the infection, and molecular methods can help identify and treat them, interrupting the chain of transmission and preventing the onset of disabilities. CONCLUSION: The ZNS slides can be sent easily to reference laboratories for later molecular analysis that can be useful not only to improve the diagnosis, but also for the application of other molecular techniques.

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Didymosphenia geminata mats display few cells in relation to extracellular material and contain polysaccharides and heavy metals that interfere with molecular studies. We describe an optimized DNA extraction protocol that help to overcome these difficulties. Our protocol outperformed five previously described DNA extraction techniques.

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Bioactive compounds have become very important in the food and pharmaceutical markets leading research interests seeking efficient methods for extracting these bioactive substances. The objective of this research is to implement preparative scale obtention of mangiferin and lupeol from mango fruit (Mangifera indica L.) of autochthonous and Ataulfo varieties grown in Nayarit, using emerging extraction techniques. Five extraction techniques were evaluated: maceration, Soxhlet, sonication (UAE), microwave (MAE) and high hydrostatic pressures (HHP). Two maturity stages (physiological and consumption) as well as peel and fruit pulp were evaluated for preparative scale implementation. Peels from Ataulfo mango at consumption maturity stage can be considered as a source of mangiferin and lupeol using the UEA method as it improves extraction efficiency by increasing yield and shortening time.

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Comparar efectividad del polietilenglicol y manitol en la preparación intestinal mediante escala de Boston, pacientes de la consulta externa de gastroenterología, tercer trimestre, 2012. Estudio prospectivo, transversal, experimental. Muestra de 100 pacientes aleatorizados en dos grupos: polietilenglicol y manitol, 50 en cada uno. A todos se les instauró dieta líquida el día previo al estudio e indicación para la ingesta de la solución a evaluar. Se realizó colonoscopia con evaluación endoscópica según escala de Boston. La tolerancia a la preparación fue considerada fácil por 88% en el grupo polietilenglicol vs 100% del grupo manitol (p=0,041). El 98% del grupo manitol consideró que este medicamento tenía sabor agradable en comparación con polietilenglicol (78%) (p=0,002). El efecto adverso más frecuente en ambos grupos fue la náusea. El polietilenglicol alcanzó exploraciones completas con restos en un 82% colon derecho, 56% colon transverso y 72% colon izquierdo, mientras que con manitol prevaleció la exploración completa sin restos en 66%, 90% y 68% respectivamente (p<0,05). La puntuación global de la escala de Boston con polietilenglicol y manitol fue 6 vs 8 (p<0,05). Manitol resultó ser más efectivo que polietilenglicol para la preparación del colon en su totalidad y por segmentos

To compare the effectiveness of polyethyleneglycol and mannitol bowel preparation by Boston scale, in patients from the outpatient gastroenterology in the third quarter of 2012. Prospective, cross, experimental with a sample of 100 patients randomized to group polyethyleneglycol and mannitol group, 50 in each. All were introduced liquid diet the day before the test with the appropriate indication for the intake of the solution to evaluate and colonoscopy was performed endoscopic evaluation scale as Boston. Tolerance was considered easy preparation by 88% in polyethyleneglycol group vs 100% mannitol group (p=0.041). 98% mannitol group had considered that this medicine palatable compared with polyethyleneglycol (78%) (p=0.002). The most common adverse event in both groups was nausea. Polyethyleneglycol reached full scans with remains at 82% right colon, transverse colon 56% and 72% left colon, whereas mannitol prevailed without full exploration remains at 66%, 90% and 68% respectively (p<0,05). The overall rating scale was polyethyleneglycol Boston 6 vs 8 in the mannitol group (p<0,05). Mannitol was more effective for the preparation of polyethyleneglycol entire colon and segments

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This paper reports, for the first time, the development of an analytical method employing modified matrix solid-phase dispersion (MSPD) for the extraction of CH3Hg(+) and Hg(2+) species from fish samples. Separation and determination of mercury species were performed by gas chromatography coupled to mass spectrometry (GC/MS). Important MSPD parameters, such as sample mass, type and mass of solid support, concentration of extraction solution (HCl and NaCl), and stirring time, were investigated by the response surface methodology. The derivatization step and the separation of mercury species were also evaluated for the determination by GC/MS. Quantitative recoveries were obtained with 0.2 g of fish sample, 0.5 g of SiO2 as the solid support, 0.5 mol L(-1) NaCl and 4.2 mol L(-1) HCl as the extraction solution, and 1 min stirring time. The MSPD method showed to be suitable for the extraction and determination of mercury species in certified reference materials of dogfish liver (DOLT-3) and dogfish muscle (DORM-2). It had good agreement (about 99%) with the certified values, and the relative standard deviation was lower than 9.5%. The limits of detection were 0.06 and 0.12 µg g(-1), for CH3Hg(+) and Hg(2+), respectively. A matrix effect was observed, and the quantification was carried out by the matrix-matched calibration. The method was applied to tuna fish ( Thunnus thynnus ), angel shark ( Squatina squatina ), and guitarfish ( Rhinobatos percellens ) samples. The results of the mercury speciation by MPSD and GC/MS were compared to the total mercury concentration determined by flow injection cold vapor generation inductively coupled plasma mass spectrometry, after microwave-assisted digestion. Agreement ranged from 102% to 105%.

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Raw or inadequately pasteurized milk from infected animals and cheese made with such milk are a frequent vehicle for human brucellosis infection. Also, biological terrorism is a concern with certain Brucella spp. Due to matrix-associated real-time polymerase chain reaction (qPCR) inhibitors, robust sample preparations are crucial. We compared six commercial nucleic acid extraction kits using nine Mexican and Central American-style soft cheeses or creams and three liquid milk products inoculated with Brucella neotomae, a surrogate for pathogenic Brucella spp. Kits were evaluated by purity and quantity of DNA as determined by qPCR Ct values, reproducibility across cheese and milk types, and cost. At 10(7) CFU/g in four different cheeses, Qiagen statistically outperformed all other kits. When two cheese styles were inoculated at dual levels, Qiagen and High Pure kit extracted samples at 1.5 × 10(5) CFU/g produced average Ct values of 34-39, while PrepSEQ and MagMAX kit extracted samples exhibited higher or no Ct values. High Pure and Qiagen kits excelled also with liquid milk products. Considering matrices, inoculation levels, and kits evaluated, High Pure and Qiagen products produced Brucella DNA of high quality and quantity indicated by the lowest Ct values and were the least expensive.

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In this work, a silica surface chemically modified with [3-(2,2'-dipyridylamine)propyl] groups, named [3-(2,2'-dipyridylamine)propyl]silica (Si-Pr-DPA) was prepared, characterized, and evaluated for its heavy metal adsorption characteristics from aqueous solution. To our knowledge, we are the first authors who have reported the present modification. The material was characterized using infrared spectroscopy, SEM, and NMR (29) Si and (13) C solid state. Batch and column experiments were conducted to investigate for heavy metal removal from dilute aqueous solution by sorption onto Si-Pr-DPA. From a number of studies the affinity of various metal ions for the Si-Pr-DPA sorbent was determined to follow the order Fe(III) > Cr(III) >> Cu(II) > Cd(II) > Pb(II) > Ni(II). Two standard reference materials were used for checking the accuracy and precision of the method. The proposed method was successfully applied to the analysis of environmental samples. This ligand material has great advantage for adsorption of transition-metal ions from aqueous medium due to its high degree of organofunctionalization associated with the large adsorption capacity, reutilization possibility, and rapidity in reaching the equilibrium.

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The dynamism of microbial populations in the rumen has been studied with molecular methods that analyze single nucleotide polymorphisms of ribosomal RNA gene fragments (rDNA). Therefore DNA of good quality is needed for this kind of analysis. In this work we report the evaluation of four DNA extraction protocols (mechanical lysis or chemical lysis with CTAB, ethylxanthogenate or DNAzol(®)) from ruminal fluid. The suitability of two of these protocols (mechanical lysis and DNAzol(®)) was tested on single-strand conformation polymorphism (SSCP) of rDNA of rumen microbial populations. DNAzol(®) was a simple method that rendered good integrity, yield and purity. With this method, subtle changes in protozoan populations were detected in young bulls fed with slightly different formulations of a supplement of multinutritional blocks of molasses and urea. Sequences related to Eudiplodinium maggi and a non-cultured Entodiniomorphid similar to Entodinium caudatum, were related to major fluctuating populations in an SSCP assay.

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In the present study, a flow injection system using dual mini-columns, SiO(2)/Al(2)O(3)/TiO(2) and silica gel functionalized with [3-(2-aminoethylamino)propyl] trimethoxysilane (SiO(2)/AAPTMS) for the sequential preconcentration of Cr(III) and Cr(VI), respectively, from water samples with FAAS detection was proposed. A two-level full factorial design (2(4)) and desirability function were employed for the optimization of variables related to the system performance. The detection limits of 0.66 and 0.27 µg L(-1) for Cr(III) and Cr(IV), respectively, were obtained under the optimized preconcentration conditions (flow rate of 7.0 mL min(-1)), pH 5.0, buffer concentration (acetate buffer) of 0.01 mol L(-1), and eluent (2.5 mol L(-1) HCl) flow rate of 5.0 mL min(-1). The other parameters including preconcentration factor (PF), consumptive index (CI), and concentration efficiency (CE) were found to be 17.62/32.98, 1.13/0.6 mL, and 6.2/11.54 min(-1) for Cr(III)/Cr(VI), respectively. The developed method was applied to the Cr(III) and Cr(VI) determination in water samples [tap, lake and mineral water, artificial saliva and parenteral solutions (physiological serum, water for injection, and glucose physiological solution)]. The method accuracy was checked by the analysis of standard reference materials (trace elements in water).

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BACKGROUND: The hematocrit effect is a hurdle for successful introduction of the dried blood spot (DBS) in a regulated environment. Recently, attempts were taken to overcome the hematocrit effect by whole-cut DBS analysis. This paper presents the next-generation whole-cut DBS; dried matrix on paper disks (DMPD). RESULTS: DMPD eliminated the hematocrit effect and demonstrated better accuracy and precision than regular DBS with partial punching. Observed accuracy and precision were 6.0 and 2.3% for DMPD, respectively, and -10.4 and 17.1%, for DBS, respectively. CONCLUSION: The DMPD technique performed better than regular DBS by eliminating the hematocrit effect related blood volume bias. Although this effect was not observed with DMPD, a systematic error of 6.0% was detected and further technical development of DMPD could improve the performance.

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A rapid and simple extraction technique based on aqueous two-phase system (ATPS) was developed for separation and enrichment of vitamin B(12) in urine samples. The proposed ATPS-based method involves the application of the hydrophilic ionic liquid (IL) 1-hexyl-3-methylimidazolium chloride and K(2)HPO(4). After the extraction procedure, the vitamin B(12)-enriched IL upper phase was directly injected into the high performance liquid chromatography (HPLC) system for analysis. All variables influencing the IL-based ATPS approach (e.g., the composition of ATPS, pH and temperature values) were evaluated. The average extraction efficiency was 97% under optimum conditions. Only 5.0 mL of sample and a single hydrolysis/deproteinization/extraction step were required, followed by direct injection of the IL-rich upper phase into HPLC system for vitamin B(12) determination. A detection limit of 0.09 µg mL(-1), a relative standard deviation (RSD) of 4.50% (n=10) and a linear range of 0.40-8.00 µg mL(-1) were obtained. The proposed green analytical procedure was satisfactorily applied to the analysis of samples with highly complex matrices, such as urine. Finally, the IL-ATPS technique could be considered as an efficient tool for the water-soluble vitamin B(12) extraction.

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A three-phase hollow-fiber liquid-phase microextraction (HF-LPME) method for the stereoselective determination of bufuralol metabolites 1'-oxobufuralol (1'-Oxo-BF) and 1'-hydroxybufuralol (1'-OH-BF) in microsomal preparations is described for the first time. The HPLC analysis was carried out using a Chiralcel OD-H column with hexane/2-propanol/methanol (97.5:2.0:0.5, v/v/v) plus 0.5% diethylamine as the mobile phase, and UV detection at 248 and 273 nm. The HF-LPME optimized conditions involved: n-octanol as the organic solvent, 0.2 mol/L acetic acid as the acceptor phase, donor phase pH adjusted to 13, sample agitation at 1500 rpm and extraction for 30 min. By using this extraction procedure, the recovery rates were in the range of 63-69%. The method was linear over the concentration range of 100-5000 ng/mL for each enantiomer of 1'-Oxo-BF (r>0.9978) and of 100-2500 ng/mL for each stereoisomer of 1'-OH-BF (r>0.9957). The quantification limits were 100 ng/mL for all analytes. The validated method was used to assess the in vitro biotransformation of bufuralol using rat liver microsomal fraction that demonstrated predominant formation of (S)-1'-Oxo-BF and (R,R)-1'-OH-BF.

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It has been demonstrated that laser induced breakdown spectrometry (LIBS) can be used as an alternative method for the determination of macro (P, K, Ca, Mg) and micronutrients (B, Fe, Cu, Mn, Zn) in pellets of plant materials. However, information is required regarding the sample preparation for plant analysis by LIBS. In this work, methods involving cryogenic grinding and planetary ball milling were evaluated for leaves comminution before pellets preparation. The particle sizes were associated to chemical sample properties such as fiber and cellulose contents, as well as to pellets porosity and density. The pellets were ablated at 30 different sites by applying 25 laser pulses per site (Nd:YAG@1064 nm, 5 ns, 10 Hz, 25J cm(-2)). The plasma emission collected by lenses was directed through an optical fiber towards a high resolution echelle spectrometer equipped with an ICCD. Delay time and integration time gate were fixed at 2.0 and 4.5 µs, respectively. Experiments carried out with pellets of sugarcane, orange tree and soy leaves showed a significant effect of the plant species for choosing the most appropriate grinding conditions. By using ball milling with agate materials, 20 min grinding for orange tree and soy, and 60 min for sugarcane leaves led to particle size distributions generally lower than 75 µm. Cryogenic grinding yielded similar particle size distributions after 10 min for orange tree, 20 min for soy and 30 min for sugarcane leaves. There was up to 50% emission signal enhancement on LIBS measurements for most elements by improving particle size distribution and consequently the pellet porosity.

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This review presents a critical discussion of selected reports dealing with the pretreatment methods of oily samples and the determination of their organic and inorganic constituents using flow systems and spectrometric methods. Special emphasis is given to the on-line couplings with detection systems based on UV-visible spectrophotometry and spectrofluorimetry, atomic absorption spectrometry either with flame or electrothermal atomization as well as inductively coupled plasma optical emission spectrometry or inductively coupled plasma-mass spectrometry. Simple dilution with organic solvents, digestion with concentrated acids under thermal heating, microwave or ultrasound radiation and emulsification procedures are mostly used. The empirical preparation of certain organized assemblies like micelles, emulsions and specially microemulsions added to the confusion of some of the terms, demand a brief description of their characteristics, the correct formulation and some of their applications to the manipulation and treatment of oily samples. The analytical capabilities of combining flow manifolds with spectrometric methods for the determination of specific parameters in oily samples apparently have not been sufficiently exploited yet.

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