Improving molecular detection of Candida DNA in whole blood:comparison of seven fungal DNA extraction protocols using real-time PCR

The limitations of classical diagnostic methods for invasive Candida infections have led to the development of molecular techniques such as real-time PCR to improve diagnosis. However, the detection of low titres of Candida DNA in blood from patients with candidaemia requires the use of extraction methods that efficiently lyse yeast cells and recover small amounts of DNA suitable for amplification. In this study, a Candida-specific real-time PCR assay was used to detect Candida albicans DNA in inoculated whole blood specimens extracted using seven different extraction protocols. The yield and quality of total nucleic acids were estimated using UV absorbance, and specific recovery of C. albicans genomic DNA was estimated quantitatively in comparison with a reference (Qiagen kit/lyticase) method currently in use in our laboratory. The extraction protocols were also compared with respect to sensitivity, cost and time required for completion. The TaqMan PCR assay used to amplify the DNA extracts achieved high levels of specificity, sensitivity and reproducibility. Of the seven extraction protocols evaluated, only the MasterPure yeast DNA extraction reagent kit gave significantly higher total nucleic acid yields than the reference method, although nucleic acid purity was highest using either the reference or YeaStar genomic DNA kit methods. More importantly, the YeaStar method enabled C. albicans DNA to be detected with highest sensitivity over the entire range of copy numbers evaluated, and appears to be an optimal method for extracting Candida DNA from whole blood.

High Percentage Inorganic Arsenic Content of Mining Impacted and Nonimpacted Chinese Rice

Two approaches were undertaken to characterize the arsenic (As) content of Chinese rice. First, a national market basket survey (n = 240) was conducted in provincial capitals, sourcing grain from China's premier rice production areas. Second, to reflect rural diets, paddy rice (n = 195) directly from farmers fields were collected from three regions in Hunan, a key rice producing province located in southern China. Two of the sites were within mining and smeltery districts, and the third was devoid of large-scale metal processing industries. Arsenic levels were determined in all the samples while a subset (n = 33) were characterized for As species, using a new simple and rapid extraction method suitable for use with Hamilton PRP-X100 anion exchange columns and HPLC-ICP-MS. The vast majority (85%) of the market rice grains possessed total As levels <150 ng g(-1). The rice collected from mine-impacted regions, however, were found to be highly enriched in As, reaching concentrations of up to 624 ng g(-1). Inorganic As (As(i)) was the predominant species detected in all of the speciated grain, with As(i) levels in some samples exceeding 300 ng g(-1). The As(i) concentration in polished and unpolished Chinese rice was successfully predicted from total As levels. The mean baseline concentrations for As(i) in Chinese market rice based on this survey were estimated to be 96 ng g(-1) while levels in mine-impacted areas were higher with ca. 50% of the rice in one region predicted to fail the national standard.

Water-compatible imprinted polymers for selective depletion of riboflavine from beverages

Artificial riboflavin receptors adapted to aqueous environments were studied for their ability to selectively extract riboflavine (Rf) from three types of beverages i.e. milk, beer and a multivitamin mixture. The basic receptor was first prepared by molecular imprinting in nonaqueous medium using a hydrogen-bond donor-acceptor-donor functional monomer (2,6-bis(acrylamido)pyridine), complementary to the imide motif of the template, riboflavin tetra-acetate as template and pentaerythritol triacrylate (PETA) as a hydrophilic cross-linking monomer. The polymer was then packed in columns and used for extraction of riboflavine from beverages. Riboflavine (Rf) was selectively removed from milk and an artificial vitamin mixture but the nonspecific binding was still significant, as judged from the binding of Rf to a control nonimprinted polymer. In order to suppress this nonspecific binding, attempts to hydrolytically hydrophilize the polymer matrix were performed. The preferred approach consisted in a controlled base hydrolysis of pendent unreacted acrylate groups, using hydroxides with differently sized counterions as reagents. This resulted in a decreased binding of Rf to both polymers, but to an equal extent implying a preferential suppression of the nonspecific contribution to the binding. The hydrophilized polymers, when subjected to beer, showed larger imprinting factors at lower phase ratios compared to the nontreated polymers and a maximum removal of 86% compared to 47% for the nonimprinted control polymer.

Synthesis of caffeic acid and p-hydroxybenzoic acid molecularly imprinted polymers and their application for the selective extraction of polyphenols from olive mill waste waters

Using caffeic acid and p-hydroxybenzoic acid as templates, two molecularly imprinted polymers (MIPs) were prepared that were used for isolation of polyphenols from olive mill waste water samples (OMWWs) without previous pre-treatment. For the preparation of the caffeic acid MIPs 4-vinylpyridine, allylurea, allylaniline and methacrylic acid were tested as functional monomers, ethylene glycol dimethylacrylate (EDMA), pentaerythritol trimethylacrylate (PETRA) and divinylbenzene 80 (DVB80) as cross-linkers and tetrahydrofuran as porogen. For p-hydroxybenzoic acid 4-vinylpyridine, allylurea and allylaniline were tested as functional monomers, EDMA and PETRA as cross-linkers and acetonitrile as porogen. The performance of the synthesized polymers was evaluated against seven structurally related compounds by means of polymer-based HPLC. The two polymers that presented the most interesting properties were further evaluated by batch rebinding and from the derived isotherms their capacity and binding strength were determined. Using solid-phase extraction (SPE), their ability to recognize and bind the template molecule from an aqueous solution as well as the pH dependence of the binding strength were explored. After establishing the best SPE protocol, an aqueous model mixture of compounds and a raw OMWWs sample were loaded on the two best polymers. The result of the consecutive use of the two polymers on the same sample was explored. It was concluded that acidic conditions favour the recognition abilities of both polymers and that they can be used for a quick and efficient isolation of the polyphenol fraction directly from raw OMWW.

Selective solid-phase extraction sorbent for caffeine made by molecular imprinting

A molecularly imprinted polymer (MIP) was prepared with caffeine as the template molecule. Thermal polymerisation (60°C) was optimised, varying ratios of monomer, cross linker and template. The polymer was used as a solid-phase extraction (SPE) sorbent, for selective trapping and pre-concentration of caffeine. Caffeine was loaded on the MIP-SPE cartridge using different loading conditions (solvents, pH value). Washing and elution of the caffeine bound to the MIP was studied utilising different protocols. The extraction protocol was successfully applied to the direct extraction of caffeine from beverages and spiked human plasma.

Preparation of a molecularly imprinted polymer for the solid-phase extraction of scopolamine with hyoscyamine as a dummy template molecule

Molecularly imprinted polymers (MIPs) selective for scopolamine were produced using hyoscyamine (a close structural analogue) as template molecule. The produced polymers were used as media for solid-phase extraction, exhibiting selective binding properties for the analyte from biological samples. Human and calf urine and serum were processed on the MIP under various extraction protocols. The best performance was observed after loading the analyte in aqueous environment facilitating retention on the MIP by non-selective hydrophobic interactions. The MIPs were subsequently washed using an optimised solvent system to enable selective desorption of the analyte. Other related and non-related compounds were accessed to evaluate molecular recognition properties. Recoveries of up to 79% were achieved for the analyte of interest from biological samples.

Dioxouranium(VI) extraction in microchannels using ionic liquids

The extraction of uranium(VI) from aqueous nitric acid solutions by tributylphosphate {TBP; 30%(v/v)} dissolved in the ionic liquid 1-butyl-3-methylimidazolium bis{(trifluoromethyl)sulfonyl}amide was investigated. The experiments were performed in a Teflon microchannel of 0.5 mm internal diameter, while the dioxouranium(VI) concentrations in the aqueous and the ionic liquid phases were determined by UV-Vis spectroscopy. The effects of initial nitric acid concentration (0.01-3 M), residence time, and phase flow rate ratio were studied. It was found that, with increasing nitric acid concentration, the percentage of dioxouranium(VI) extracted decreased and then increased again, while the extraction efficiency followed a slightly different trend. Overall mass transfer coefficients varied between 0.049 s and 0.312 s . © 2012 Elsevier B.V. All rights reserved.

Optimisation and scaling of interfacial GeO2 layers for high-k gate stacks on germanium and extraction of dielectric constant of GeO2

Germanium is an attractive channel material for MOSFETs because of its higher mobility than silicon. In this paper, GeO2 has been investigated as an interfacial layer for high-kappa gate stacks on germanium. Thermally grown GeO2 layers have been prepared at 550 degrees C to minimise GeO volatilisation. GeO2 growth has been performed in both pure O-2 ambient and O-2 diluted with N-2. GeO2 thickness has been scaled down to approximately 3 nm. MOS capacitors have been fabricated using different GeO2 thicknesses with a standard high-kappa dielectric on top. Electrical properties and thermal stability have been tested up to at least 350 degrees C. The K value of GeO2 was experimentally determined to be 4.5. Interface state densities (D-it) of less than 10(12) CM-2 eV(-1) have been extracted for all devices using the conductance method.

Molecularly imprinted polymers for the extraction of imiquimod from biological samples using a template analogue strategy

Molecularly Imprinted Polymers (MIPs) against imiquimod, a highly potent immune response modifier used in the treatment of skin cancer, were synthesised using a template analogue strategy and were compared with imprints of the drug itself. An investigation of the complexation between the functional monomer and the template analogue revealed an association constant of 1,376 ± 122 M-1, significantly higher than previously reported values for similar systems. The binding characteristics of the synthesised imprinted polymers were evaluated and extremely strong binding for imiquimod was observed while imprinting factors as high as 17 were calculated. When applied as sorbents in solid-phase extraction of imiquimod from aqueous, urine and blood serum samples, clean extracts and recoveries up to 95% were achieved, and it is concluded that while imiquimod imprints exhibited higher capacity for the drug, template analogue imprints are more selective. The results obtained suggest potential applications of imiquimod imprints as sorbents in rapid extraction and monitoring of undesirable systemic release of the drug.