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PubMed2006

Overview of DNA purification for nucleic acid-based diagnostics from environmental and clinical samples.

Direct deoxyribonucleic acid (DNA)-based detection methods are crucial for future environmental monitoring and clinical diagnosis. In this chapter, we provide an overview of the various sample preparation approaches for bacteria for direct analyses (i.e., without culturing) in environmental and clinical samples. The issues of sampling, sample preservation, separation of the microorganisms from the environmental or clinical matrix, and DNA purification are covered. This chapter will focus on the advantages and the disadvantages of the methods available.

Animals↗

PubMedDate not supplied

Determination of self-absorption corrections for gamma analysis of environmental samples: comparing gamma-absorption curves and spiked matrix-matched samples.

Accurate determination of the massic activity of gamma-emitting radionuclides in environmental samples, particularly sediments and soils, cannot be achieved without taking into account sample self-absorption. The extent of self-absorption in the sample will depend on a number of factors including sample composition, density, sample size and gamma-ray energy. The preferred method for correcting for this effect is to use spiked or natural matrix reference materials that match each sample type to be analysed. However, for laboratories that must measure a wide variety of sample matrices this method is too costly and time-consuming. Another technique commonly used is to make direct gamma-ray transmission measurements for each sample. This method, while more practical, still requires a minimum of three measurements to be made for each sample analysed. A more convenient method is to prepare sets of gamma-absorption curves. This approach involves making a series of direct transmission measurements for samples of varying densities but similar type. Sets of matching samples, both spiked and unspiked, were prepared and density correction factors determined using the direct transmission method and the spiked sample approach. It was found that, for soil and sediment samples, these two methods typically differed by 5-9% for higher energy gamma rays and by 12-15% for the 59.54 keV 241Am peak. Gamma-absorption curves were also derived and, for the admittedly limited dataset, 95% confidence intervals of +/-7% for the curve generated using the spiked samples method were obtained.

Calibration↗

PubMed2006

Determination of sulfonamide antibiotics in wastewater: a comparison of solid phase microextraction and solid phase extraction methods.

In recent years, pharmaceutical and personal care products (PPCPs) have been detected in diverse environments (including groundwater, river water, and municipal wastewater). In order to evaluate their environmental impact, PPCPs must first be accurately determined. In this study, we focused on developing methods to accurately determine 10 sulfonamide antibiotics: sulfaguanidine, sulfacetamide, sulfadiazine, sulfathiazine, sulfapyridine, sulfamerazine, sulfamethazine, sulfamethoxazole, sulfadimethoxine, and sulfasalazine. While sulfonamides can easily be determined in pure water, wastewater influent and effluent collected from sewage treatment plants in Burlington and Toronto (Ontario) were found to generate confounding matrix effects. In an effort to overcome these matrix effects, we developed a solid phase microextraction (SPME) method to determine sulfonamides. Of the five different fiber assemblies investigated, the carbowax/divinylbenzene (CW/DVB) fiber produced the optimal response to sulfonamides. The SPME method was further optimized for sorption time (20min), solution salinity (10%, w/v, KCl), pH (4.5), and static desorption time (30min). When compared to solid phase extraction (SPE) using MCX cartridges, we observed that despite having higher MDLs and poorer sensitivity, SPME possessed the advantage of speed and reduced solvent usage. Most importantly, in contrast to SPE, when we applied the SPME method to fortified wastewater samples, we were generally able to accurately determine (i.e., recover) those sulfonamides that were present. Therefore, we conclude that SPME is a viable method for overcoming matrix effects in environmental samples.

Anti-Bacterial Agents↗

PubMed1996

Integrin signaling.

Integrins are a family of adhesion receptors used by cells to interact with their extracellular matrix. Integrins also function as signaling receptors, integrating information from the extracellular matrix and other environmental cues including growth factors and hormones. Signals triggered by integrins direct cell adhesion and regulate other aspects of cell behavior including cell proliferation and differentiation, and determine cell survival. The biochemical pathways initiated by integrin engagement are now being identified.

Animals↗

PubMed1999

[Application of supercritical fluid extraction (SFE) on environmental analysis].

In this paper, publications from 1993 are classified according to the type of matrix from which the environmental analytes are extracted. Although the most applications of SFE are used for the solid, some analysts have concerned with aqueous and gaseous media. Various aspects of investigation of environmental potential carcinogen, such as, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, dioxins, pesticides, phenols and other hazardous and toxic pollutants in environmental samples have been reviewed with 55 references. The coupled techniques of SFE have also been introduced in this paper.

Air Pollutants↗

PubMed2006

Tackling matrix effects during development of a liquid chromatographic-electrospray ionisation tandem mass spectrometric analysis of nine basic pharmaceuticals in aqueous environmental samples.

When developing an LC-MS/MS-method matrix effects are a major issue. The effect of co-eluting compounds arising from the matrix can result in signal enhancement or suppression. During method development much attention should be paid to diminish matrix effects as much as possible. The present work evaluates matrix effects from aqueous environmental samples in the simultaneous analysis of a group of nine specific pharmaceuticals with LC-ESI/MS/MS: flubendazole, propiconazole, pipamperone, cinnarizine, ketoconazole, miconazole, rabeprazole, itraconazole and domperidone. Solutions to diminish signal suppression were examined: optimisation of the sample preparation, decrease of the flow rate, and the use of appropriate internal standards. Several SPE-stationary phases were tested in view of retention of the analytes: Oasis HLB, C8, Phenyl, Strata X-polymer RP sorbent and Strata X-polymeric SCX/RP sorbent. Oasis HLB showed the best retention for all analytes. The Oasis HLB SPE-method was optimised, but analyses showed high matrix suppression. Therefore, a second SPE-method, on a phenyl stationary phase (the second best option), was also optimised. A comparison of the matrix effect was made between the two procedures: the phenyl-method was less subject to matrix effects, however, the average matrix effect (ME%) of 46% indicated that matrix effects where still present. Several optimisation options for the phenyl-method were evaluated: addition of a ferric nitrate solution before extraction, application of an alkaline wash step, and use of a second SPE-cartridge, either a NH2-column or a florisil column. A more efficient sample clean-up was achieved by applying the extract after extraction on the phenyl column and after dilution with chloroform, onto a NH2-column (average ME%: 53%). In addition, applying a post-column split (1:5), further reduced matrix effects (average ME%: 65%). Labelled internal standards are the best way to tackle matrix effects, but no such internal standards were commercially available for the analytes of interest. The thorough search and application of four internal standards (structural analogues) was beneficial and compensates the matrix effect partially (average ME%: 83%). In an attempt to reduce the analysis time Speedisk phenyl columns were applied. Under these conditions matrix effects decreased even more while recoveries were between 91 and 109%. Different kinds of surface water samples were analyzed, and different matrix effects were observed. For this reason, standard addition will be used to perform quantitative analysis.

Chromatography, Liquid↗

PubMed1999

Determination of 3,3'-dichlorobenzidine and its degradation products in environmental samples with a small low-field Fourier transform ion cyclotron resonance mass spectrometer.

3,3'-Dichlorobenzidine (DCB) and its degradation products, 3-chlorobenzidine (MCB) and benzidine, are of environmental concern because of their carcinogenic nature. The suitability of a small Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer for the analysis of these environmental contaminants in different types of matrices was explored. All the measurements were carried out by depositing the sample solution directly on a disk that was introduced into the mass spectrometer. This approach is very fast and simple because it requires no prior chromatographic separation or derivatization. Calibration curves determined by collecting 70-eV electron ionization mass spectra of neat samples yielded lower limits of detection of 29 and 17 pg (total amount on the solids probe) for DCB and benzidine, respectively (based on a signal to noise ratio of > or = 2:1), while chemical ionization with ammonia resulted in lower limits of detection of 21 pg for DCB and 9 pg for benzidine (total amount on the solids probe). FT-ICR analysis of sediments collected from Lake Macatawa (Holland, MI) verified the presence of DCB in this complex, environmentally significant sample matrix. Laboratory experiments designed to probe biodegradation and photodegradation pathways showed that DCB undergoes sequential dehalogenation to yield MCB and then benzidine under exposure to microorganisms and under simulated tropospheric solar radiation. The ability of the FT-ICR to determine elemental compositions of compounds introduced as described above was demonstrated for one of the degradation products.

3,3'-Dichlorobenzidine↗

PubMed2000

Comparisons of soxhlet extraction, pressurized liquid extraction, supercritical fluid extraction and subcritical water extraction for environmental solids: recovery, selectivity and effects on sample matrix.

Extractions of a polycyclic aromatic hydrocarbon (PAH)-contaminated soil from a former manufactured gas plant site were performed with a Soxhlet apparatus (18 h), by pressurized liquid extraction (PLE) (50 min at 100 degrees C), supercritical fluid extraction (SFE) (1 h at 150 degrees C with pure CO2), and subcritical water (1 h at 250 degrees C, or 30 min at 300 degrees C). Although minor differences in recoveries for some PAHs resulted from the different methods, quantitative agreement between all of the methods was generally good. However, the extract quality differed greatly. The organic solvent extracts (Soxhlet and PLE) were much darker, while the extracts from subcritical water (collected in toluene) were orange, and the extracts from SFE (collected in CH2Cl2) were light yellow. The organic solvent extracts also yielded more artifact peaks in the gas chromatography (GC)-mass spectrometry and GC-flame ionization detection chromatograms, especially compared to supercritical CO2. Based on elemental analysis (carbon and nitrogen) of the soil residues after each extraction, subcritical water, PLE, and Soxhlet extraction had poor selectivity for PAHs versus bulk soil organic matter (approximately 1/4 to 1/3 of the bulk soil organic matter was extracted along with the PAHs), while SFE with pure CO2 removed only 8% of the bulk organic matrix. Selectivities for different compound classes also vary with extraction method. Extraction of urban air particulate matter with organic solvents yields very high concentrations of n- and branched alkanes (approximately C18 to C30) from diesel exhaust as well as lower levels of PAHs, and no selectivity between the bulk alkanes and PAHs is obtained during organic solvent extraction. Some moderate selectivity with supercritical CO2 can be achieved by first extracting the bulk alkanes at mild conditions, followed by stronger conditions to extract the remaining PAHs, i.e., the least polar organics are the easiest organics to extract with pure CO2. In direct contrast, subcritical water prefers the more polar analytes, i.e., PAHs were efficiently extracted from urban air particulates at 250 degrees C, with little or no extraction of the alkanes. Finally, recent work has demonstrated that many pollutant molecules become "sequestered" as they age for decades in the environment (i.e., more tightly bound to soil particles and less available to organisms or transport). Therefore, it may be more important for an extraction method to only recover pollutant molecules that are environmentally-relevant, rather than the conventional attempts to extract all pollutant molecules regardless of how tightly bound they are to the soil or sediment matrix. Initial work comparing SFE extraction behavior using mild to strong conditions with bioremediation behavior of PAHs shows great promise to develop extraction methodology to measure environmentally-relevant concentrations of pollutants in addition to their total concentrations.

Chromatography↗

PubMed2003

Determination of polychlorinated biphenyl congeners and chlorinated pesticides in a fish tissue standard reference material.

The concentrations of a wide range of polychlorinated biphenyl congeners (PCBs) and chlorinated pesticides in a fish tissue Standard Reference Material (SRM) have been determined using multiple methods of analysis. This material, SRM 1946, Lake Superior Fish Tissue, was recently issued by the National Institute of Standards and Technology (NIST) and complements a suite of marine environmental natural-matrix SRMs that are currently available from NIST for the determination of organic contaminants such as aliphatic hydrocarbons, polycyclic aromatic hydrocarbons (PAHs), PCBs, and chlorinated pesticides. SRM 1946 is a fresh tissue homogenate (frozen) prepared from filleted adult lake trout (Salvelinus namaycush namaycush) collected from the Apostle Islands region of Lake Superior. SRM 1946 has certified and reference concentrations for PCB congeners, including the three non- ortho PCB congeners, and chlorinated pesticides. Certified concentrations are available for 30 PCB congeners and 15 chlorinated pesticides. Reference concentrations are available for 12 PCB congeners and 2 chlorinated pesticides. In addition, SRM 1946 is characterized for additional chemical constituents and properties: fatty acids, extractable fat, methylmercury, total mercury, selected trace elements, proximates, and caloric content. The characterization of chlorinated compounds is described in this paper with an emphasis on the approach used for the certification of the concentrations of PCB congeners and chlorinated pesticides. The PCB congener and chlorinated pesticide data are also compared to concentrations in other marine natural-matrix reference materials available from NIST (fish oil, mussel tissue, whale blubber, and a second fresh frozen fish tissue homogenate prepared from filleted adult lake trout collected from Lake Michigan) and from other organizations such as the National Research Council Canada (ground whole carp), the International Atomic Energy Agency (fish homogenate), and the European Commission Joint Research Centre [fish oils (cod and mackerel) and mussel tissue].

Animals↗

PubMed2006

Highly selective micro-sequential injection lab-on-valve (muSI-LOV) method for the determination of ultra-trace concentrations of nickel in saline matrices using detection by electrothermal atomic absorption spectrometry.

A highly selective procedure is proposed for the determination of ultra-trace level concentrations of nickel in saline aqueous matrices exploiting a micro-sequential injection Lab-On-Valve (muSI-LOV) sample pretreatment protocol comprising bead injection separation/pre-concentration and detection by electrothermal atomic absorption spectrometry (ETAAS). Based on the dimethylglyoxime (DMG) reaction used for nickel analysis, the sample, as contained in a pH 9.0 buffer, is, after on-line merging with the chelating reagent, transported to a reaction coil attached to one of the external ports of the LOV to assure sufficient reaction time for the formation of Ni(DMG)(2) chelate. The non-ionic coordination compound is then collected in a renewable micro-column packed with a reversed-phase copolymeric sorbent [namely, poly(divinylbenzene-co-N-vinylpyrrolidone)] containing a balanced ratio of hydrophilic and lipophilic monomers. Following elution by a 50-muL methanol plug in an air-segmented modality, the nickel is finally quantified by ETAAS. Under the optimized conditions and for a sample volume of 1.8 mL, a retention efficiency of 70 % and an enrichment factor of 25 were obtained. The proposed methodology showed a high tolerance to the commonly encountered alkaline earth matrix elements in environmental waters, that is, calcium and magnesium, and was successfully applied for the determination of nickel in an NIST standard reference material (NIST 1640-Trace elements in natural water), household tap water of high hardness and local seawater. Satisfying recoveries were achieved for all spiked environmental water samples with maximum deviations of 6 %. The experimental results for the standard reference material were not statistically different to the certified value at a significance level of 0.05.

Journal Article↗

PubMed2006

Analysis of bioavailable phenols from natural samples by recombinant luminescent bacterial sensors.

A whole-cell recombinant bacterial sensor for the detection of phenolic compounds was constructed and used for the analysis of bioavailable phenols in natural samples. The sensor Pseudomonas fluorescens OS8(pDNdmpRlux) contains luxCDABE operon as a reporter under the control of phenol-inducible Po promoter from Pseudomonas sp. CF600. Expression of lux genes from the Po promoter, and thus the production of bioluminescence is controlled by the transcriptional activator DmpR, which initiates transcription in the presence of phenolic compounds. To take into account possible quenching (turbidity, toxicity) and/or stimulating effects of the environmental samples on the bacterial luminescence, control bacteria comparable to the sensors but lacking the phenol recognising elements were constructed and used in parallel in assays. The sensor bacteria were inducible with phenol, methylphenols, 2,3-, 2,4-, 2,6- and 3,4-dimethylphenol, resorcinol and 5-methylresorcinol but not with 2,5-dimethylresorcinol. The detection limits for different phenols varied from 0.03 mg/l (2-methylphenol) to 42.7 mg/l (5-methylresorcinol), being 0.08 mg/l for phenol, the most abundant phenolic contaminant in the environment. Different phenolic compounds had an additive effect on the inducibility of the sensor. The constructed sensor bacteria were applied on groundwaters and semi-coke leachates to estimate the bioavailable fraction of phenols. The sensor-determined amount of phenols in different samples varied from 6% to 95% of total phenol content depending on the nature of the sample. As the phenol-recognising unit in the sensor originates from a natural phenol biodegradation pathway, the sensor-determined amount of phenols corresponds to the biodegradable amount of phenolic pollutants in the samples and therefore this sensor could be used to estimate the natural biodegradation potential of phenolic compounds in the complex environmental mixtures and matrixes.

Biological Availability↗

PubMed2006

Occurrence of ionophore antibiotics in water and sediments of a mixed-landscape watershed.

Analytical methods for quantifying three ionophore antibiotics, monensin, salinomycin, and narasin, were developed for water and sediment matrices. Sample preparation was based on solid-phase extraction (SPE) and high-performance liquid chromatography (HPLC) tandem mass spectrometry (MS/MS) was used to separate and detect the compounds. Recoveries ranged from 83% to 117% for water and from 51% to 105% for sediment in three different concentrations with less than 10% of relative standard deviation. The statistical detection limit was 0.001-0.003 microg/L for water and 0.4-3.6 microg/kg for sediment. Ionophore antibiotics are only used to treat coccidiostats for broilers or turkeys, and to increase growth and feed efficiency for beef and dairy cattle. Since they are not used for human purposes, these compounds can act as markers for the transport of animal pharmaceuticals to the watershed. The occurrence of three ionophore compounds was determined at five sampling sites along the Cache la Poudre River in Northern Colorado representing pristine, urban, and agriculture landscapes. Statistical analysis demonstrates that the measured concentration was significantly different among sampling sites in different sampling events for both water and sediment. In addition, significant differences were observed among different sampling times at each sampling site. Furthermore, all three ionophores were found in the sediments at much higher concentrations than in water indicating the importance of this matrix when determining environmental impacts.

Agrochemicals↗

PubMed2002

Internal response correction for fluorescent whole-cell biosensors.

Whole-cell biosensors based on reporter genes are finding a variety of applications in analytical chemistry. Despite their ability to selectively recognize the analyte in a complex mixture, few applications of such sensing devices to real sample analysis are reported. This is mainly due to nonspecific effects on the biosensor response caused by components of the sample matrix and by environmental changes. To overcome this problem, a bacterial biosensor with an internal correction mechanism of the analytical response was developed by introducing an additional reporter gene that provides a reference signal of the analytical performance of the biosensor. The first reporter (GFPuv), expressed in response to the concentration of L-arabinose, provides the analytical signal; the second reporter (EYFP), constitutively expressed if a constant amount of IPTG is added to each sample, was used as an internal reference. By inducing the biosensor with varying amounts of L-arabinose and a constant amount of IPTG, it was possible to obtain a dose-response curve for L-arabinose, together with a constant production of EYFP, which allowed for a dynamic evaluation of the metabolic activity of the cell. When tested in nonoptimal conditions (e.g., in the presence of either ethanol or deoxycholic acid at toxic concentrations), the presence of the internal reference system corrected the analytical response due to nonspecific interferences.

Arabinose↗

PubMed2001

Multiresidue method for the analysis of pesticide residues in fruits and vegetables by accelerated solvent extraction and capillary gas chromatography.

An analytical procedure using accelerated solvent extraction and capillary gas chromatography with electron capture and flame photometric detections was developed to simultaneously determine residues of different pesticides in fruits and vegetables. Single laboratory validation of the method was carried out for 28 compounds selected from eight pesticide classes, in blank and fortified samples of fresh pear, cantaloupe, white potato, and cabbage. The method had to meet specific established validation criteria for regulatory purposes applicable to our laboratory. At each of the two fortification levels studied, 24 of the 28 pesticides gave recoveries of more than 70% with a coefficient of variation of less than 10%. With respect to existing procedures, the method showed acceptable limits of detection (from 0.0019 to 0.14 microg/g depending on the pesticide and matrix) while minimizing environmental concerns, time, and labor.

Chromatography, Gas↗

PubMed2006

Surface precipitation of highly porous hydrotalcite-like film on Al from a zinc aqueous solution.

A hydrotalcite-like film has been successfully deposited on an Al-bearing glass substrate based on an interface reaction between an Al layer and a zinc aqueous solution. The film selectively grew on the Al surface but not on the glass surface. The film on Al was composed of layered nanosheets of a hydrotalcite-like compound containing Al and Zn. Comparably, deposits on the plastic surface and precipitates in solution were wurzite-type ZnO with various morphologies depending upon the preparation conditions. At low supersaturation degrees, single crystals and superstructures of Zn-Al hydrotalcite were also obtained. This porous hydrotalcite film has a potential application as catalyst supports, environmental materials, or matrixes for hydrotalcite-based nanocomposite films. Using Al as a reaction interface makes it easy to coat porous hydrotalcites on a series of matrix materials varying in shapes and properties, which is important for achieving practical applications. In addition, the method developed should be widely applicable to other systems for the preparation of porous or oriented hydrotalcite-like thin films by an appropriate combination of divalent/trivalent solution-substrate systems.

Journal Article↗

PubMed2003

Comprehensive two-dimensional high-performance liquid chromatography for the separation of polycyclic aromatic hydrocarbons.

A comprehensive two-dimensional HPLC system for the separation of polycyclic aromatic hydrocarbons was developed using a pentabromobenzyl column as the first dimension and two short monolithic C18 columns as the second dimension. The primary column and two secondary columns were coupled by a 10-port 2-position valve. The effluent from the first dimension was repetitively injected into the second dimension every 12 s. Due to its resolution, this technique is a powerful tool for the separation of polycyclic aromatic hydrocarbons in a complex matrix such as environmental samples.

Chromatography, High Pressure Liquid↗

PubMed1999

Microspatial genetic structure in the land snail helix aspersa (Gastropoda: helicidae)

The microspatial genetic structure of allele frequencies at seven isozyme loci was examined for 15 populations of the land snail Helix aspersa sampled in a village from Brittany (north-western France). Spatial heterogeneity of allele frequencies was highly significant (P < 0.001). Fixation indices reflected nonrandom mating within neighbourhoods and a slight but consistent differentiation between colonies (FST=0.044; P < 0.01). Analyses of gene flow or genetic distances failed to reveal a significant relationship with geographical distance, probably because of the complexity of environmental heterogeneity. However, matrix comparisons between genetic distances and connectivity networks among adjacent colonies (Gabriel-connected graph) yielded a significant correlation in every case, indicating a 'step-by-step' relationship between neighbouring localities. Moreover, most of the allozymes were spatially structured and showed (i) a gradual isolation of colonies with increasing geographical distances, and (ii), for some correlogram profiles, a circular gradient illustrating a multidirectional colonization of the village. The probable existence of disperser individuals allowed us to suggest a metapopulation model which would explain the maintenance of such animals in fragmented habitats where anthropogenic disturbances and extinction/recolonization events are commonly observed.

Journal Article↗

PubMed1997

Influence of the cosmetic treatment of hair on drug testing.

An important issue of concern for drug analysis in hair is the change in the drug concentration induced by the cosmetic treatment of hair. The products used for this treatment are strong bases and they are expected to cause hair damage. As a result drugs may be lost from the hair matrix or, under conditions of environmental contamination, be more easily incorporated into the hair matrix. We investigated the effects of cosmetic treatment in vivo by analysing hair samples selected from people who had treated their hair by bleaching or dyeing before sample collection. All of the subjects admitted a similar drug consumption during the time period for which the strands were analysed. Samples were viewed under a microscope to establish the degree of hair damage. Treated and untreated portions from each lock of hair were then selected, separated and analysed by standard detection procedures for cocaine, opiates, cannabinoids and nicotine. In all cases the drug content in hair that had undergone cosmetic treatment decreased in comparison to untreated hair. The majority of the mean differences were in the range of 40%-60% (cocaine, benzoylecgonine, codeine, 6-acetylmorphine and THC-COOH). For morphine the mean difference was higher than 60%, and two cases (THC and nicotine) differed by approx. 30%. These differences depended not only on the type of cosmetic treatment, as bleaching produced higher decreases than dyeing, but also on the degree of hair damage i.e. the more damaged the hair, the larger the differences in the concentration levels of drugs.

Hair↗