Efficiency of DNA extraction methods on the evaluation of soil microeukaryotic diversity

The evaluation of microbial molecular diversity has been mainly based on the extraction of total DNA from environmental samples. The indirect extraction methods, which have been used for prokaryotes, have never been used to recover soil microeukaryotic DNA. We evaluated the efficiency of an improved indirect DNA extraction protocol developed herein and the direct lysis (the sodium dodecyl sulfate (SDS)-based method and commercial DNA extraction kit) on estimating the molecular diversity of soil microbial eukaryotes. DNA quality and quantity as well as denaturing gradient gel electrophoresis (DGGE) profiles were determined using three soil samples from different stations. The indirect method detected the highest DGGE bands in spite of the low DNA yield. The commercial kit detected a lower number of DGGE bands than the indirect method. The SDS-based method produced the lowest DGGE bands and DNA purity but the highest yield. Using the indirect method, we further evaluated the effect of freezing and air-dried preservations on estimating the microeukaryotic diversity. In spite of the low DNA yield obtained from the air-dried preservation, no significant differences were found in either the number of DGGE bands or the DNA purity between two manners. Our results indicate that the improved indirect method could obtain a high purity of intracellular DNA and high efficiency in the estimation of molecular diversity of soil microbial eukaryotes.     

A method for the solvent extraction of low-boiling-point plant volatiles

A new method has been developed for the extraction of volatiles from plant materials and tested on seedling tissue and mature leaves of Arabidopsis thaliana, pine needles and commercial mixtures of plant volatiles. Volatiles were extracted with n-pentane and then subjected to quick distillation at a moderate temperature. Under these conditions, compounds such as pigments, waxes and non-volatile compounds remained undistilled, while short-chain volatile compounds were distilled into a receiving flask using a high-efficiency condenser. Removal of the n-pentane and concentration of the volatiles in the receiving flask was carried out using a Vigreux column condenser prior to GC-MS. The method is ideal for the rapid extraction of low-boiling-point volatiles from small amounts of plant material, such as is required when conducting metabolic profiling or defining biological properties of volatile components from large numbers of mutant lines.     

RNA extraction from plant tissues

Several protocols and commercial kits are used for the extraction of nucleic acids from different plant tissues. Although there are several procedures available to remove sugars, which hinder the extraction of clean genomic DNA, there are few to assist with extraction of RNA. Those presently used include precipitations with ethylene glycol monobutyl ether or lithium chloride (LiCl), or centrifugation in cesium chloride (CsCl) gradients, but these generally either do not allow high recovery of RNA, are time consuming, rely on hazardous chemicals or need special equipment. Here we present the use of the simple cation, Ca²⁺, which has been tested and shown to be very efficient for the precipitation of high molecular weight pectic sugars during RNA extraction. Results are presented for different plant tissues, especially tissues of peach and apple fruits at varying ripening stages.     

Mixed substrate solid state fermentation for production and extraction of lipase from Aspergillus niger MTCC 2594

A novel mixed substrate solid-state fermentation (SSF) process has been developed for Aspergillus niger MTCC 2594 using wheat bran (WB) and gingelly oil cake (GOC) and the results showed that addition of GOC to WB (WB : GOC, 3 : 1, w/w) increased the lipase activity by 36.0% and the activity was 384.3+/-4.5 U/g dry substrate at 30 degrees C and 72 h. Scale up of lipase production to 100 g and 1 kg tray-level batch fermentation resulted in 95.0% and 84.0% of enzyme activities respectively at 72 h. A three-stage multiple contact counter-current extraction yielded 97% enzyme recovery with a contact time of 60 min. However, extraction by simple percolation and plug-flow methods resulted in decreased enzyme recoveries. The mixed substrate SSF process has resulted in a significant increase in specific activity (58.9%) when compared to a submerged fermentation (SmF) system. Furthermore, an efficient process of extraction has been standardized with this process. Use of GOC along with WB as potential raw materials for enzyme production could be of great commercial significance. This is the first report on the production and extraction of lipase from Aspergillus niger using mixed solid substrates, WB and GOC, which are potential raw materials for the production of enzymes and other value-added products.     

An integrated biosensor platform for extraction and detection of nucleic acids

The development of portable systems for analysis of nucleic acids (NAs) is crucial for the evolution of biosensing in the context of future healthcare technologies. The integration of NA extraction, purification, and detection modules, properly actuated by microfluidics technologies, is a key point for the development of portable diagnostic systems. In this paper, we describe an integrated biosensor platform based on a silicon–plastic hybrid lab-on-disk technology capable of managing NA extraction, purification, and detection processes in an integrated format. The sample preparation process is performed by solid-phase extraction technology using magnetic beads on a plastic disk, while detection is done through quantitative real-time polymerase chain reaction (qRT-PCR) on a miniaturized silicon device. The movement of sample and reagents is actuated by a centrifugal force induced by a disk actuator instrument. The assessment of the NA extraction and detection performance has been carried out by using hepatitis B virus (HBV) DNA genome as a biological target. The quantification of the qRT-PCR chip in the hybrid disk showed an improvement in sensitivity with respect to the qRT-PCR commercial platforms, which means an optimization of time and cost. Limit of detection and limit of quantification values of about 8 cps/reaction and 26 cps/reaction, respectively, were found by using analytical samples (synthetic clone), while the results with real samples (serum with spiked HBV genome) indicate that the system performs as well as the standard methods.     

Reactive extraction of lactic acid using alamine 336 in MIBK: equilibria and kinetics

Lactic acid is an important commercial product and extracting it out of aqueous solution is a growing requirement in fermentation based industries and recovery from waste streams. The design of an amine extraction process requires (i) equilibrium and (ii) kinetic data for the acid-amine (solvent) system used. Equilibria for lactic acid extraction by alamine 336 in methyl-iso-butyl-ketone (MIBK) as a diluent have been determined. The extent to which the organic phase (amine +MIBK) may be loaded with lactic acid is expressed as a loading ratio, z=[HL](o)/[B](i,o). Calculations based on the stoichiometry of the reactive extraction and the equilibria involved indicated that more lactic acid is transferred to the organic phase than would be expected from the (1:1) stoichiometry of the reaction. The extraction equilibrium was interpreted as a result of consecutive formation of two acid-amine species with stoichiometries of 1:1 and 2:1. Equilibrium complexation constant for (1:1) and (2:1) has been estimated. Kinetics of extraction of lactic acid by alamine 336 in MIBK has also been determined. In a first study of its kind, the theory of extraction accompanied by a chemical reaction has been used to obtain the kinetics of extraction of lactic acid by alamine 336 in MIBK. The reaction between lactic acid and alamine 336 in MIBK in a stirred cell falls in Regime 3, extraction accompanied by a fast chemical reaction occurring in the diffusion film. The reaction has been found to be zero order in alamine 336 and first order in lactic acid with a rate constant of 1.38 s(-1). These data will be useful in the design of extraction processes.     

Metaproteomics: Evaluation of protein extraction from activated sludge

Metaproteomic studies of full‐scale activated sludge systems require reproducible protein extraction methods. A systematic evaluation of three different extractions protocols, each in combination with three different methods of cell lysis, and a commercial kit were evaluated. Criteria used for comparison of each method included the extracted protein concentration and the number of identified proteins and peptides as well as their phylogenetic, cell localization and functional distribution and quantitative reproducibility. Furthermore, the advantage of using specific metagenomes and a 2‐step database approach was illustrated. The results recommend a protocol for protein extraction from activated sludge based on the protein extraction reagent B‐Per and bead beating. The data have been deposited to the ProteomeXchange with identifier PXD000862 ( http://proteomecentral.proteomexchange.org/dataset/PXD000862 ).     

Cryptococcus spp. DNA extraction from environmental samples

The genus Cryptococcus encompasses 38 species, but only 3 are associated with disease in humans and animals, Cryptococcus laurentii, Cryptococcus albidus and Cryptococcus neoformans. The last one is the most frequently reported. The disease is acquired by the inhalation of infectious propagules present in the environment. The habitat has been established using extraction techniques with buffer supplemented with antibiotics and plating in selective media. The aim of this work was to evaluate several DNA extraction techniques for Cryptocococus spp. from environmental samples. The control isolates were C. neoformans, C. albidus, C. laurentii and Paracoccidiodes brasiliensis. We also used vermiculita and soil samples contaminated with different yeast concentrations (10 to 10(6) cells/g) and samples naturally contaminated with C. neoformans. DNA was extracted with physical and chemical methods and with a commercial kit, and the DNA was purified with agarose blocks and silica columns. For the PCR amplification we used the CN4-CN5 primers, which are specific for C. neoformans. Only the commercial kit allowed DNA extraction and amplification from contaminated soil samples up to a concentration of 10 cells/g and from one sample naturally colonized. With this work we extracted and amplified DNA from Cryptococcus spp. from environmental samples with appropriate PCR specificity, it will be a tool to establish the ecological areas of C. neoformans in our country.     

Recent extraction techniques for natural products: microwave-assisted extraction and pressurised solvent extraction

In the last 10 years there has been an increased interest in using techniques involving microwave-assisted extraction and pressurised solvent extraction in analytical laboratories. This review gives a brief overview of both methods, and reports on their application to the extraction of natural products. The influence of parameters such as the nature of the solvent and volume, temperature, time and particle size of the matrix is discussed. Through numerous examples, it is demonstrated that both techniques allow reduced solvent consumption and shorter extraction times, while the extraction yields of the analytes are equivalent to or even higher than those obtained with conventional methods.     

Liquid-liquid extraction of commercial glucose oxidase by reversed micelles

Aim of this work was to establish the optimum operating conditions for the extraction and recovery by cationic reversed micelles of commercial glucose oxidase (GOX) from Aspergillus niger, in view of possible application to raw cell homogenates. The influence of pH, temperature, electric conductivity and solvent/co-solvents ratio on the extraction was investigated by a fractional factorial design of 2(3-1) type, conjugated with a mixture experimental design, using the residual enzyme activity to evaluate the results. The best conditions for GOX extraction were ensured using isooctane as solvent and hexanol and butanol as co-solvents at 76/6/18 volume ratio, pH 6.0, 0.2 M cetyl trimethylammonium bromide (CTAB) as cationic surfactant, and electrical conductivity (kappa) of 4.8 mS cm-1. The highest yield of GOX activity recovery (about 90%) was in fair accordance with the value predicted by the model.     

Data extraction from proteomics raw data: an evaluation of nine tandem MS tools using a large Orbitrap data set

In shot-gun proteomics raw tandem MS data are processed with extraction tools to produce condensed peak lists that can be uploaded to database search engines. Many extraction tools are available but to our knowledge, a systematic comparison of such tools has not yet been carried out. Using raw data containing more than 400,000 tandem MS spectra acquired using an Orbitrap Velos we compared 9 tandem MS extraction tools, freely available as well as commercial. We compared the tools with respect to number of extracted MS/MS events, fragment ion information, number of matches, precursor mass accuracies and agreement in-between tools. Processing a primary data set with 9 different tandem MS extraction tools resulted in a low overlap of identified peptides. The tools differ by assigned charge states of precursors, precursor and fragment ion masses, and we show that peptides identified very confidently using one extraction tool might not be matched when using another tool. We also found a bias towards peptides of lower charge state when extracting fragment ion data from higher resolution raw data without deconvolution. Collecting and comparing the extracted data from the same raw data allow adjusting parameters and expectations and selecting the right tool for extraction of tandem MS data.     

Measurement of tooth extraction forces in upper incisors

A new method, applied for the first time in this research, was used for measurement of tooth extraction forces. The research has been done in a group of 50 examinees to whom the tooth extraction has been done with lower premolar forceps - forceps "13" and in the control group of 54 examinees in whom the tooth extraction has been done with upper incisive forceps - forceps "1". The measurement instrument registered the extraction forces values in both types of forceps. There was no difference in any parameters in these two groups except in used pressure. While using the forceps "13", a significantly lower tooth extraction force was measured than the force measured while using the forceps "1" (p < 0.001). This means that in clinical work we can already apply noticeably less force using the lower premolar forceps for the extraction of the upper incisors (in the moments of rotation up to 70%). These results are meaningful, because they lead to better and improved instrument solutions and working techniques.     

A novel process for extraction of edible oils: Enzyme assisted three phase partitioning (EATPP)

Three phase partitioning (TPP), a technique used in protein purification has been evaluated, for extraction of oil from three different plant sources viz: mango kernel, soybean and rice bran. The process consists of simultaneous addition of t-butanol (1:1,v/v) and ammonium sulphate (w/v) to a crude preparation/slurry. Under optimized condition, the protein appears as an interfacial precipitate between upper t-butanol containing oil and lower aqueous phase. Pretreatment of the slurries with a commercial enzyme preparation of proteases, Protizyme, followed by three phase partitioning resulted in 98%, 86% and 79% (w/w) oil yields in case of soybean, rice bran and mango kernel, respectively. The efficiency of the present technique is comparable to solvent extraction with an added advantage of being less time consuming and using t-butanol which is a safer solvent as compared to n-hexane used in conventional oil extraction process.     

Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures

The quality and yield of extracted DNA are critical for the majority of downstream applications in molecular biology. Moreover, molecular techniques such as quantitative real-time PCR (qPCR) are becoming increasingly widespread; thus, validation and cross-laboratory comparison of data require standardization of upstream experimental procedures. DNA extraction methods depend on the type and size of starting material(s) used. As such, the extraction of template DNA is arguably the most significant variable when cross-comparing data from different laboratories. Here, we describe a reliable, inexpensive and rapid method of DNA purification that is equally applicable to small or large scale or high-throughput purification of DNA. The protocol relies on a CTAB-based buffer for cell lysis and further purification of DNA with phenol : chloroform : isoamyl alcohol. The protocol has been used successfully for DNA purification from rumen fluid and plant cells. Moreover, after slight alterations, the same protocol was used for large-scale extraction of DNA from pure cultures of Gram-positive and Gram-negative bacteria. The yield of the DNA obtained with this method exceeded that from the same samples using commercial kits, and the quality was confirmed by successful qPCR applications.     

Emulsion liquid membranes for chiral separations: Selective extraction of rac-phenylalanine enantiomers

We describe the use of emulsion liquid membrane technology to perform chiral separations on low molecular weight species. We have reviewed liquid membrane technology in the context of existing process scale chiral separations. We illustrate the potential of this new technique by presenting our results on the selective extraction of phenylalanine enantiomers, using copper (II) N-decyl-(L)-hydroxyproline as a chiral selector in an emulsion liquid membrane configuration. This is compared with an analogous batch solvent extraction system. Initial batch enantiomeric excesses of greater than 40% were observed with the emulsion liquid membrane system compared with around 25% for the solvent extraction system. It was also noted that the system is not limited by the equilibrium capacity constraints of the solvent extraction system. We have shown that kinetic chiral liquid membrane technology offers high productivity and flexibility compared with analogous process scale chiral technologies. Recent transfer of highly specific chiral reversed-phase high-performance liquid chromatographic chemistries have shown that “one-stop” enantiomeric excesses of commercial interest (>95%) are achievable using kinetic chiral liquid membrane systems. Solvent and temperature selection strategies also have been outlined as means of increasing the enantioselectivity of existing liquid membrane extraction chemistries. Chirality 9:261–267, 1997. © 1997 Wiley-Liss, Inc.     

Comparison of five commercial extraction kits for subsequent membrane protein profiling

Membrane proteins account for 70–80% of all pharmaceutical targets emphasizing their clinical relevance. Identification of new, differentially expressed membrane proteins reflecting distinct disease properties is thus of high importance. Unfortunately, isolation and analysis of membrane-bound proteins is hampered by their relative low abundance in total cell lysates, their frequently large size and their hydrophobic properties. We thus aimed to identify protocols that allow for highly efficient isolation and purification of membrane-bound proteins for subsequent protein profiling. We present a comparative study of different membrane protein extraction methods that vary in total protein yield between 0.02 and 4.8 mg using constant cell pellets of the colorectal carcinoma cell line SW620. We also demonstrate by means of polyacrylamide gel electrophoresis (SDS–PAGE) and Western blot analysis that the majority of commercial membrane extraction kits harbor a substantial cytosolic contamination of their membranous fraction. Based on purity of membranous fraction, protein yield, time and costs, we show superiority of two commercial extraction kits for downstream proteome analyses of membrane proteins.     

Influence of various dust sampling and extraction methods on the measurement of airborne endotoxin.

The influence of various filter types and extraction conditions on the quantitation of airborne endotoxin with the Limulus amebocyte lysate test was studied by using airborne dusts sampled in a potato processing plant. Samples were collected with an apparatus designed to provide parallel samples. Data from the parallel-sampling experiment were statistically evaluated by using analysis of variance. In addition, the influence of storage conditions on the detectable endotoxin concentration was investigated by using commercially available lipopolysaccharides (LPS) and endotoxin-containing house dust extracts. The endotoxin extraction efficiency of 0.05% Tween 20 in pyrogen-free water was seven times higher than that of pyrogen-free water only. Two-times-greater amounts of endotoxin were extracted from glass fiber, Teflon, and polycarbonate filters than from cellulose ester filters. The temperature and shaking intensity during extraction were not related to the extraction efficiency. Repeated freeze (-20 degrees C)-and-thaw cycles with commercial LPS reconstituted in pyrogen-free water had a dramatic effect on the detectable endotoxin level. A 25% loss in endotoxin activity per freeze-thaw cycle was observed. Storage of LPS samples for a period of 1 year at 7 degrees C had no effect on the endotoxin level. House dust extracts showed a decrease of about 20% in the endotoxin level after they had been frozen and thawed for a second time. The use of different container materials (borosilicate glass, "soft" glass, and polypropylene) did not result in different endotoxin levels. This study indicates that the assessment of endotoxin exposure may differ considerably between groups when different sampling, extraction, and storage procedures are employed.     

Production, extraction and purificationof violacein: an antibiotic pigment producedby Chromobacterium violaceum

A procedure for the production, extraction, and purification of violacein was developed using Chromobacterium violaceum (CCT 3496) cultivated on cotton, in modified 1 litre Roux bottles. A surface tray bioreactor was built to perform these experiments. Violacein was extracted with commercial ethanol, and purified by filtration, Soxhlet extraction, crystallization and high performance liquid chromatography. The violacein was analysed and identified by proton and carbon-13 NMR spectroscopies, thermogravimetric analysis, mass spectrometry, UV-VIS spectroscopy and infrared spectroscopy. It was concluded that the product was highly purified violacein.     

Separation of lactic acid from fermented broth by reactive extraction

The separation of lactic acid from complex fermentation broth was examined. Liquid–liquid extraction using reversible chemical complexation for reactive extraction was chosen to be the separation method. Over 50% yield of lactic acid was obtained from fermented broth in a single extraction step, when using the tertiary amine as the extractant, 1-dekanol as the diluent and trimethylamine (TMA) as the stripping solution. The effect of complex media on the extraction behaviour has hardly been examined previously.     

Application of magnetic hydroxyapatite nanoparticles for solid phase extraction of plasmid DNA

We developed a facile method for plasmid DNA (pDNA) extraction from crude Escherichia coli lysate using magnetic hydroxyapatite nanoparticles (MHapNPs) in the presence of polyethylene glycol (PEG)/NaCl. DNA condensation induced by PEG/NaCl is a prerequisite for achieving pronounced DNA recovery. The quality and quantity of MHapNP-purified pDNA under optimal binding buffer conditions (0.5 volume of 20% PEG 8000/2M NaCl) were comparable to those obtained using organic solvents or commercial kits. This MHapNP technique is rapid, simple, cost-effective, and environmentally friendly and has the potential to extract DNA from other cell lysates.