Sample preparation of culture medium from Madin-Darby canine kidney cells

A reproducible, standardized and simple sample preparation methodology is the key to successful two-dimensional gel electrophoresis (2-DE). This chapter describes step-by-step the sample preparation of culture medium from Madin-Darby canine kidney (MDCK) cells. Tips and tricks are given to circumvent possible pitfalls.

Determination of carbohydrate-deficient transferrin in human serum with capillary zone electrophoresis. Sample preparation strategies for the removal of interferences caused by increased levels of immunoglobulins

Capillary zone electrophoresis (CZE) in fused-silica capillaries is an effective analytical approach for the separation and determination of the transferrin (Tf) isoforms and thus carbohydrate-deficient transferrin (CDT) in human serum. Sera of patients with progressed liver cirrhosis are prone to interferences in the beta region which prevent the proper determination of CDT by CZE without additional sample preparation. Efforts to identify, reduce or even eliminate these interferences have been undertaken. Data obtained by ultrafiltration, affinity subtraction procedures using protein A, protein L and antibodies against immunoglobulins or Tf, and immunopurification of Tf suggest that the interferences in the patient sera are caused by increased levels of IgA and IgM and are best eliminated by immunopurification. Avian IgY antibody spin column immunocapture of serum Tf followed by CZE analysis of the stripped and concentrated fraction is shown to provide an attractive approach for CDT monitoring in sera with beta region interferences.

14C Analysis and Sample Preparation at the New Bern Laboratory for the Analysis of Radiocarbon with AMS (LARA)

The University of Bern has set up the new Laboratory for the Analysis of Radiocarbon with AMS (LARA) equipped with an accelerator mass spectrometer (AMS) MICADAS (MIni CArbon Dating System) to continue its long history of 14C analysis based on conventional counting. The new laboratory is designated to provide routine 14C dating for archaeology, climate research, and other disciplines at the University of Bern and to develop new analytical systems coupled to the gas ion source for 14C analysis of specific compounds or compound classes with specific physical properties. Measurements of reference standards and wood samples dated by dendrochronology demonstrate the quality of the 14C analyses performed at the new laboratory.

Iodine-129: Sample preparation, quality control and analyses of pre-nuclear materials and of natural waters from Lower Saxony, Germany

Sample preparation procedures for AMS measurements of 129I and 127I in environmental materials and some methodological aspects of quality assurance are discussed. Measurements from analyses of some pre-nuclear soil and thyroid gland samples and of a systematic investigation of natural waters in Lower Saxony, Germany, are described. Although the up-to-now lowest 129I/127I ratios in soils and thyroid glands were observed, they are still suspect to contamination since they are significantly higher than the pre-nuclear equilibrium ratio in the marine hydrosphere. A survey on all available 129I/127I isotopic ratios in precipitation shows a dramatic increase until the middle of the 1980s and a stabilization since 1987 at high isotopic ratios of about (3.6–8.3)×10−7. In surface waters, ratios of (57–380)×10−10 are measured while shallow ground waters show with ratios of (1.3–200)×10−10 significantly lower values with a much larger spread. The data for 129I in soils and in precipitation are used to estimate pre-nuclear and modern 129I deposition densities.

Determination of voriconazole in human serum and plasma by micellar electrokinetic chromatography

The micellar electrokinetic capillary chromatography (MEKC) separation and analysis of voriconazole and UK 115794 (internal standard) were examined and an assay for determination of voriconazole in human plasma and serum was developed. The MEKC medium comprises a 2:15 (v/v) mixture of methanol and a pH 9.3 buffer composed of 5mM Na(2)B(4)O(7), 7 mM Na(2)HPO(4) and 54 mM SDS. Sample preparation is based upon liquid/liquid extraction with ethylacetate and dichloromethane (75%/25%) at physiological pH. Using this approach with 250 microl serum or plasma and reconstitution of the dried extract into 100 microl of a buffer composed of 0.5mM Na(2)B(4)O(7) and 0.7 mM Na(2)HPO(4) (pH 9.3), the detection and quantitation limits were determined to be 0.1 and 0.2 microg/ml, respectively, a sensitivity that is suitable for therapeutic drug monitoring of voriconazole (provisional therapeutic range: 1-6 microg/ml) in human plasma and serum samples. The method was validated and compared to an HPLC method, showing excellent agreement between the two for a set of 91 samples that stemmed from patients being treated with voriconazole. The MEKC assay is also demonstrated to be suitable to explore pharmacokinetic data of voriconazole.

Bioanalysis of new designer drugs

Since the late 1990s the illicit drug market has undergone considerable change: along with the traditional drugs of abuse that still dominate, more than 100 psychotropic substances designed to bypass controlled substances legislation have appeared and led to intoxications and fatalities. Starting from the huge class of phenylalkylamines, containing many subgroups, the spectrum of structures has grown from tryptamines, piperazines, phenylcyclohexyl derivates and pyrrolidinophenones to synthetic cannabinoids and the first synthetic cocaine. Due to the small prevalence and high number of unknown substances, the detection of new designer drugs is a challenge for clinical and forensic toxicologists. Standard screening procedures might fail because a recently discovered or yet unknown substance has not been incorporated in the library used. Nevertheless, many metabolism studies, case reports, screening methods and substance-profiling papers concentrating on single compounds have been published. This review provides an overview of the developed bioanalytical and analytical methods, the matrices used, sample-preparation procedures, concentration of analytes in case of intoxication and also gives a résumé of immunoassay experiences. Additionally, six screening methods for biological matrices with a larger spectrum of analytes are described in more detail.

Tandem mass spectrometry identification and LC-MS quantification of intact cytokinin nucleotides in K-562 human leukemia cells

We describe here a new reversed-phase high-performance liquid chromatography with mass spectrometry detection method for quantifying intact cytokinin nucleotides in human K-562 leukemia cells. Tandem mass spectrometry was used to identify the intracellular metabolites (cytokinin monophosphorylated, diphosphorylated, and triphosphorylated nucleotides) in riboside-treated cells. For the protein precipitation and sample preparation, a trichloroacetic acid extraction method is used. Samples are then back-extracted with diethyl ether, lyophilized, reconstituted, and injected into the LC system. Analytes were quantified in negative selected ion monitoring mode using a single quadrupole mass spectrometer. The method was validated in terms of retention time stabilities, limits of detection, linearity, recovery, and analytical accuracy. The developed method was linear in the range of 1-1,000 pmol for all studied compounds. The limits of detection for the analytes vary from 0.2 to 0.6 pmol.

Contamination of Alpine snow and ice at Colle Gnifetti, Swiss/Italian Alps, from nuclear weapons tests

Plutonium is present in the environment as a consequence of atmospheric nuclear tests, nuclear weapons production and industrial releases over the past 50 years. To study temporal trends, a high resolution Pu record was obtained by analyzing 52 discrete samples of an alpine firn/ice core from Colle Gnifetti (Monte Rosa, 4450 m a.s.l.), dating from 1945 to 1990. The 239Pu signal was recorded directly, without decontamination or preconcentration steps, using an Inductively Coupled Plasma - Sector Field Mass Spectrometer (ICP-SFMS) equipped with an high efficiency sample introduction system, thus requiring much less sample preparation than previously reported methods. The 239Pu profile reflects the three main periods of atmospheric nuclear weapons testing: the earliest peak lasted from 1954/55 to 1958 and was caused by the first testing period reaching a maximum in 1958. Despite a temporary halt of testing in 1959/60, the Pu concentration decreased only by half with respect to the 1958 peak due to long atmospheric residence times. In 1961/62 Pu concentrations rapidly increased reaching a maximum in 1963, which was about 40% more intense than the 1958 peak. After the signing of the "Limited Test Ban Treaty" between USA and USSR in 1964, Pu deposition decreased very sharply reaching a minimum in 1967. The third period (1967-1975) is characterized by irregular Pu concentrations with smaller peaks (about 20-30% of the 1964 peak) which might be related to the deposition of Saharan dust contaminated by the French nuclear tests of the 1960s. The data presented are in very good agreement with Pu profiles previously obtained from the Col du Dome ice core (by multi-collector ICP-MS) and Belukha ice core (by Accelerator Mass Spectrometry, AMS). Although a semi-quantitative method was employed here, the results are quantitatively comparable to previously published results.

Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing

With the advent of high through-put sequencing (HTS), the emerging science of metagenomics is transforming our understanding of the relationships of microbial communities with their environments. While metagenomics aims to catalogue the genes present in a sample through assessing which genes are actively expressed, metatranscriptomics can provide a mechanistic understanding of community inter-relationships. To achieve these goals, several challenges need to be addressed from sample preparation to sequence processing, statistical analysis and functional annotation. Here we use an inbred non-obese diabetic (NOD) mouse model in which germ-free animals were colonized with a defined mixture of eight commensal bacteria, to explore methods of RNA extraction and to develop a pipeline for the generation and analysis of metatranscriptomic data. Applying the Illumina HTS platform, we sequenced 12 NOD cecal samples prepared using multiple RNA-extraction protocols. The absence of a complete set of reference genomes necessitated a peptide-based search strategy. Up to 16% of sequence reads could be matched to a known bacterial gene. Phylogenetic analysis of the mapped ORFs revealed a distribution consistent with ribosomal RNA, the majority from Bacteroides or Clostridium species. To place these HTS data within a systems context, we mapped the relative abundance of corresponding Escherichia coli homologs onto metabolic and protein-protein interaction networks. These maps identified bacterial processes with components that were well-represented in the datasets. In summary this study highlights the potential of exploiting the economy of HTS platforms for metatranscriptomics.

Microgram level radiocarbon (14C) determination on carbonaceous particles in ice

In climate research the interest on carbonaceous particles has increased over the last years because of their influence on the radiation balance of the earth. Nevertheless, there is a paucity of available data regarding their concentrations and sources in the past. Such data would be important for a better understanding of their effects and for estimating their influence on future climate. Here, a technique is described to extract carbonaceous particles from ice core samples with subsequent separation of the two main constituents into organic carbon (OC) and elemental carbon (EC) for analysis of their concentrations in the past. This is combined with further analysis of OC and EC 14C/12C ratios by accelerator mass spectrometry (AMS), what can be used for source apportionment studies of past emissions. We further present how 14C analysis of the OC fraction could be used in the future to date any ice core extracted from a high-elevation glacier. Described sample preparation steps to final analysis include the combustion of micrograms of water–insoluble carbonaceous particles, primary collected by filtration of melted ice samples, the graphitisation of the obtained CO2 to solid AMS target material and final AMS measurements. Possible fractionation processes were investigated for quality assurance. Procedural blanks were reproducible and resulted in carbon masses of 1.3 ± 0.6 μg OC and 0.3 ± 0.1 μg EC per filter. The determined fraction of modern carbon (fM) for the OC blank was 0.61 ± 0.13. The analysis of processed IAEA-C6 and IAEA-C7 reference material resulted in fM = 1.521 ± 0.011 and δ13C = −10.85 ± 0.19‰, and fM = 0.505 ± 0.011 and δ13C = −14.21 ± 0.19‰, respectively, in agreement with consensus values. Initial carbon contents were thereby recovered with an average yield of 93%.

On-chip non-invasive and label-free cell discrimination by impedance spectroscopy

OBJECTIVES: Many flow-cytometric cell characterization methods require costly markers and colour reagents. We present here a novel device for cell discrimination based on impedance measurement of electrical cell properties in a microfluidic chip, without the need of extensive sample preparation steps and the requirement of labelling dyes. MATERIALS AND METHODS, RESULTS: We demonstrate that in-flow single cell measurements in our microchip allow for discrimination of various cell line types, such as undifferentiated mouse fibroblasts 3T3-L1 and adipocytes on the one hand, or human monocytes and in vitro differentiated dendritic cells and macrophages on the other hand. In addition, viability and apoptosis analyses were carried out successfully for Jurkat cell models. Studies on several species, including bacteria or fungi, demonstrate not only the capability to enumerate these cells, but also show that even other microbiological life cycle phases can be visualized. CONCLUSIONS: These results underline the potential of impedance spectroscopy flow cytometry as a valuable complement to other known cytometers and cell detection systems.

Determination of ethyl glucuronide in human serum by capillary zone electrophoresis and an immunoassay

Ethyl glucuronide (EtG) is a marker of recent alcohol consumption. For the optimization of the analysis of EtG by CZE with indirect absorbance detection, the use of capillaries with permanent and dynamic wall coatings, the composition of the BGE, and various sample preparation procedures, including dilution with water, ultrafiltration, protein precipitation, and SPE, were investigated. Two validated screening assays for the determination of EtG in human serum, a CZE-based approach and an enzyme immunoassay (EIA), are described. The CZE assay uses a coated capillary, 2,4-dimethylglutaric acid as an internal standard, and a pH 4.65 BGE comprising 9 mM nicotinic acid, epsilon-aminocaproic acid and 10% v/v ACN. Proteins are removed via precipitation with ACN prior to analysis and the LOQ is 0.50 mg/L. The EIA is based upon commercial reagents which are promoted for the determination of urinary EtG. Krebs-Ringer solution containing 5% BSA is used as a calibration matrix. All samples are ultrafiltered prior to analysis of the ultrafiltrate on a Mira Plus analyzer. Assay calibration ranged between 0 and 2 mg/L and the upper reference limit was determined to be 0.05 mg/L. Both assays proved to be suitable for the analysis of samples from different individuals. For EtG levels above 0.50 mg/L, good agreement was observed for the comparison of the results of the two methods.

Inhibition of 11beta-hydroxysteroid dehydrogenase type 1 by plant extracts used as traditional antidiabetic medicines

Elevated glucocorticoids are a key risk factor for metabolic diseases, and the glucocorticoid-activating enzyme 11beta-hydroxysteroid dehydrogenase 1 (11beta-HSD1) represents a promising therapeutic target. We measured the potential of six traditional antidiabetic medicinal plants extracts to inhibit 11beta-HSD1 activity and glucocorticoid receptor (GR) activation in transfected HEK-293 cells. Leave extracts of Eriobotrya japonica preferentially inhibited 11beta-HSD1 over 11beta-HSD2. Extracts of roasted but not native coffee beans preferentially inhibited 11beta-HSD1 over 11beta-HSD2, emphasizing the importance of sample preparation. Thus, natural compounds inhibiting 11beta-HSD1 may contribute to the antidiabetic effect of the investigated plant extracts.