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This article describes a simple and quick in silico method for the prediction of cytochrome P450 (CYP)-mediated hydroxylation of drug-like compounds. Testosterone and progesterone, two known substrates of CYP3A4, are used to test the method. Further, we apply the procedure to predict sites of hydroxylation of isomers of the flame retardant hexabromocyclododecane by CYP3A4. Within the method, the compound is rotated in the binding pocket of the cytochrome, so that each hydrogen under consideration is placed near the active centre. Afterwards, short molecular dynamics simulations are provided for each step of the rotation. All steps of the simulation are compared concerning the distances between the hydrogens and the active centre and the corresponding energies. The computational results correlate well with experimental results.
Two different hair reference materials, one produced from authentic hair displaying an ethyl glucuronide (EtG) content of about 25 pg/mg and one obtained by fortification of blank hair to an EtG level of 85 pg/mg were submitted to accelerated aging between 4 degrees C and 60 degrees C for periods between one and 24 months. Subsequently, the EtG content was determined in the aged samples and untreated reference samples stored at -22 degrees C under repeatability conditions following the so-called isochronous approach. The EtG content remained stable even at 40 degrees C for 24 months and at 60 degrees C over six months. This is in contrast to many organic analytes contained in trace concentrations in diverse matrices. A slight but significant increase of the recovered EtG in case of authentic hair samples having been exposed for 24 months between 4 degrees C and 60 degrees C may be due to a temperature-driven process that allows increased recoveries of the physiologically embedded EtG.
The design and operation of an observational study on the profiles of volatile organic compounds (VOC) in the breath of 37 lung cancer patients and 23 healthy controls of similar age is outlined. The necessity to quantify each VOC considered as potential disease marker on basis of individual calibration is elaborated and the quality control measures required to maintain reproducibility in breath sampling and subsequent instrumental trace VOC analysis using SPME-GC-MS over a study period of 14 months are described. 24 VOC were quantified on basis of their previously suggested potential as cancer markers. The breath concentration levels of aromatic compounds was expectedly increased in smokers while lung cancer patients displayed significantly increased levels of oxygenated VOC such as aldehydes, 2-butanone and 1-butanol. Though sets of selected oxygenated VOC displayed sensitivities and specificities between 80 and 90% using linear discriminant analysis with leave-one-out cross validation the effective selectivity of the breath VOC approach with regard to cancer detection is clearly limited. Results were discussed against the background of the literature on volatile cancer marker investigations and the prospects to link increased VOC levels in patients’ breath with approaches to employ sniffer dogs. Experiences from this study and the literature suggest that the current state of breath VOC based discrimination between cancer patients and healthy controls is hardly improvable. Observational studies tend to observe significant differences mostly in levels of certain oxygenated VOC but without resolution required for practical application. Any step towards practicable exploitation of VOC profile differences for illness detection would have to solve current restrictions set by the low and variable VOC concentrations. Further challenges are the technical complexity of studies involving breath sampling and possibly the limited capability of current analytical procedures to detect instable marker candidates.
Towards the standardization of biochar analysis: the COST action TD1107 interlaboratory comparison
(2016)
Biochar produced by pyrolysis of organic residues is increasingly used for soil amendment and many other applications. However, analytical methods for its physical and chemical characterization are yet far from being specifically adapted, optimized, and standardized. Therefore, COST Action TD1107 conducted an interlaboratory comparison in which 22 laboratories from 12 countries analyzed three different types of biochar for 38 physical–chemical parameters (macro- and microelements, heavy metals, polycyclic aromatic hydrocarbons, pH, electrical conductivity, and specific surface area) with their preferential methods. The data were evaluated in detail using professional interlaboratory testing software. Whereas intralaboratory repeatability was generally good or at least acceptable, interlaboratory reproducibility was mostly not (20% < mean reproducibility standard deviation < 460%). This paper contributes to better comparability of biochar data published already and provides recommendations to improve and harmonize specific methods for biochar analysis in the future.
The key comparison CCQM-K102: Polybrominated diphenyl ethers in sediment was coordinated by the JRC, Directorate F - Health, Consumers & Reference Materials, Geel (Belgium) under the auspices of the Organic Analysis Working Group (OAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM). Thirteen National Metrology institutes or Designated Institutes and the JRC participated. Participants were requested to report the mass fraction (on a dry mass basis) of BDE 47, 99 and 153 in the freshwater sediment study material. The sediment originated from a river in Belgium and contained PBDEs (and other pollutants) at levels commonly found in environmental samples. The comparison was designed to demonstrate participants' capability of analysing non-polar organic molecules in abiotic dried matrices (approximate range of molecular weights: 100 to 800 g/mol, polarity corresponding to pKow < −2, range of mass fraction: 1–1000 μg/kg). All participants (except one using ultrasonic extraction) applied Pressurised Liquid Extraction or Soxhlet, while the instrumental analysis was performed with GC-MS/MS, GC-MS or GC-HRMS. Isotope Dilution Mass Spectrometry approach was used for quantification (except in one case). The assigned Key Comparison Reference Values (KCRVs) were the medians of thirteen results for BDE 47 and eleven results for BDE 99 and 153, respectively. BDE 47 was assigned a KCRV of 15.60 μg/kg with a combined standard uncertainty of 0.41 μg/kg, BDE 99 was assigned a KCRV of 33.69 μg/kg with a combined standard uncertainty of 0.81 μg/kg and BDE 153 was assigned a KCRV of 6.28 μg/kg with a combined standard uncertainty of 0.28 μg/kg. The k-factor for the estimation of the expanded uncertainty of the KCRVs was chosen as k = 2.
Odor Perception by Dogs: Evaluating Two Training Approaches for Odor Learning of Sniffer Dogs
(2017)
In this study, a standardized experimental set-up with various combinations of herbs as odor sources was designed. Two training approaches for sniffer dogs were compared; first, Training with a pure reference odor, and second, training with a variety of odor mixtures with the target odor as a common denominator. The ability of the dogs to identify the target odor in a new context was tested. Six different herbs (basil, St. John’s wort, dandelion, marjoram, parsley, ribwort) were chosen to produce reference materials in various mixtures with (positive) and without (negative)chamomile as the target odor source. The dogs were trained to show 1 of 2 different behaviors, 1 for the positive, and 1 for the negative sample as a yes/no task. Tests were double blind with one sample presented at a time. In both training approaches, dogs were able to detect chamomile as the target odor in any presented mixture with an average sensitivity of 72% and a specificity of 84%. Dogs trained with odor mixture containing the target odor had more correct indications in the transfer task.
In recent years, an increasing trend towards investigating and monitoring the contamination of the environment by microplastics (MP) (plastic pieces < 5 mm) has been observed worldwide. Nonetheless, a reliable methodology that would facilitate and automate the monitoring of MP is still lacking. With the goal of selecting practical and standardized methods, and considering the challenges in microplastics detection, we present here a critical evaluation of two vibrational spectroscopies, Raman and Fourier transform infrared (FTIR) spectroscopy, and two extraction methods: thermal extraction desorption gas chromatography mass spectrometry (TED-GC-MS) and liquid extraction with subsequent size exclusion chromatography (SEC) using a soil with known contents of PE, PP, PS and PET as reference material. The obtained results were compared in terms of measurement time, technique handling, detection limits and requirements for sample preparation. The results showed that in designing and selecting the right methodology, the scientific question that determines what needs to be understood is significant, and should be considered carefully prior to analysis. Depending on whether the object of interest is quantification of the MP particles in the sample, or merely a quick estimate of sample contamination with plastics, the appropriate method must be selected. To obtain overall information about MP in environmental samples, the combination of several parallel approaches should be considered.
Fuel contamination of soils display complex and variable hydrocarbon mixtures with different volatility and toxicity characteristics. A recently suggested headspace procedure for the structure-based quantification of volatile hydrocarbons is evaluated regarding repeatability, reproducibility, and practical robustness. Three aliphatic and three aromatic fractions covering the boiling range between 69 and 216°C were defined as summation parameters by their respective equivalent carbon number ranges. A standard mixture of 35 aliphatic and aromatic hydrocarbons was used for calibration on basis of selected mass fragments specific for the aliphatics and aromatics, respectively. Two standard soils were fortified with the standard mixture or different fuels, respectively, and submitted to the analytical procedure. Limit of detection (LOD) and limit of quantification (LOQ) were for all fractions lower than 0.1 and 0.3 mg/kg, respectively. Analyte recovery was linear up to between 20 and 110 mg hydrocarbons/kg soil depending on the fraction. Hydrocarbon recovery ranged between 80% and 110% depending on the fraction and the repeatability was typically better than 10%. Finally, the impact of extraction solvent variation, column solid-phase polarity, and alternative summation of fractions were investigated. The procedure was applied to liner samples taken from a site contaminated with aviation fuel and its practicability is discussed.
The development of a test to evaluate the degradation of semi-volatile fuels as diesel by microorganisms is presented. This method is based on the principles described in the CEC-L-103 Standard procedure that is exclusively meant for testing the biodegradability of non-volatile lubricants. Therefore, significant modifications involve aseptic conditions for testing specific microorganisms and conducting the test in closed vessels avoiding evaporation losses, while fuel quantification using gas chromatography-flame ionization detection (GC-FID) is retained. It is suggested that the modified procedure should enable routine application for semi-volatile hydrocarbon-based fuels. GC-FID provides additionally valuable information on the alteration of fuel component patterns during biodegradation. The procedure was successfully tested using two bacteria (Pseudomonas aeruginosa and Sphingomonas sp.) and two yeasts (Moesziomyces sp. and Candida sp.) isolated from real diesel contamination cases. All tested microorganisms caused a significant degradation of diesel fuel achieving hydrocarbon degradation percentages ranging from 23% to 35%. Specific aspects on the test modification and prospects for further modification regarding targeted investigations in the field of fuel contamination by microorganisms are briefly discussed.
A Proof of Concept: Are Detection Dogs a Useful Tool to Verify Potential Biomarkers for Lung Cancer?
(2018)
Early and reliable diagnostic test is essential for effective therapy of lung cancer. Volatile organic compounds that are characteristic for cancer could serve as valuable biomarkers in cancer diagnosis. Both trace analytical and detection dog approaches give some evidence for the existence of such biomarkers. In this proof of concept, study dogs and trace analysis were implemented in combination to gain more information concerning cancer biomarkers. Two dogs were trained to distinguish between absorbed breath samples of lung cancer patients and healthy persons and succeeded with correct identification of patients with 9/9 and 8/9 and correct negative indications from of 8/10 and 4/10 samples from healthy individuals. A recent observational study found that breath samples from lung cancer patients showed an increase in 1-butanol, 2-butanone, 2-pentanone, and hexanal. Synthetic air samples were therefore fortified with these compounds and adsorbed to a fleece. Tested against breath samples from healthy probands, on presentation to the dogs these synthetic samples provoked an indication in three out of four samples. We were able to demonstrate that a combination of the natural nose of a dog and a trace analytic technique can be a valuable concept in the search for cancer biomarkers.