Development of a murre (<Emphasis Type="Italic">Uria</Emphasis> spp.) egg control material

The Seabird Tissue Archival and Monitoring Project (STAMP) is a collaborative Alaska-wide effort by the US Fish and Wildlife Service’s Alaska Maritime National Wildlife Refuge (USFWS/AMNWR), the US Geological Survey’s Biological Resources Division (USGS/BRD), the Bureau of Indian Affairs Alaska Region Subsistence Branch (BIA/ARSB), and the National Institute of Standards and Technology (NIST) to monitor long-term (decadal) trends in environmental contaminants using seabird eggs. To support this effort, a matrix- (seabird egg) and concentration-specific control material was needed to ensure quality during analytical work. Although a herring gull egg quality assurance (HGQA) material is available from Environment Canada (EC), contaminant concentrations in this material tended to be higher than those observed in Alaskan murre (Uria spp.) eggs. Therefore, to prepare a more appropriate control material, a total of 12 common murre (U. aalge) and thick-billed murre (U. lomvia) eggs from four Bering Sea and Gulf of Alaska nesting locations were cryohomogenized to create 190 aliquots each containing approximately 6 g. This new control material was analyzed by different methods at NIST and EC facilities for the determination of concentrations and value assignment of 63 polychlorinated biphenyl (PCB) congeners, 20 organochlorine pesticides, and 11 polybrominated diphenyl ether (PBDE) congeners. The total PCB concentration is approximately 58 ng g⁻¹ wet mass. Results obtained for analytes not listed on the certificates of analysis of the previously used control materials, HGQA and NIST’s Standard Reference Material (SRM) 1946 Lake Superior Fish Tissue, are also presented.      

Laser ablation inductively coupled plasma mass spectrometry for direct analysis of the spatial distribution of trace elements in metallurgical-grade silicon

The spatial distribution and concentration of impurities in metallurgical-grade silicon (MG-Si) samples (97–99% w/w Si) were investigated by use of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The spatial resolution (120 μm) and low limits of detection (mg kg⁻¹) for quality assurance of such materials were studied in detail. The volume-dependent precision and accuracy of non-matrix-matched calibration for quantification of minor elements, using NIST SRM 610 (silicate standard), indicates that LA-ICP-MS is well suited to rapid process control of such materials. Quantitative results from LA-ICP-MS were compared with previously reported literature data obtained by use of ICP-OES and rf-GD-OES. In particular, the distribution of element impurities and their relationship to their different segregation coefficients in silicon is demonstrated. Dedicated to Professor Klaus G. Heumann     

Comparison of five extraction methods for measuring PCBs,PBDEs, organochlorine pesticides,and lipid content in serum

An increasing number of studies use blood obtained noninvasively to monitor organohalogen contaminants; however, blood can be difficult to analyze because of its aqueous nature and high protein content. We compared five methods for extracting polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), organochlorine pesticides, and lipids from serum using National Institute of Standards and Technology Standard Reference Material 1589a PCBs, Pesticides, PBDEs, and Dioxins/Furans in Human Serum. Liquid:liquid (LLE), cavity-dispersed microwave-assisted (MAE), focused microwave-assisted (FME), solid-phase (SPE), and pressurized fluid (PFE) extraction techniques were compared. FME extraction yielded the optimal recovery of internal standards (IS). All methods resulted in similar contaminant concentrations that also agreed with the certified values for SRM 1589a, except for only a few compounds measured by methods other than FME. Based on these findings, the FME method was determined to be the best overall extraction method. One procedural factor was found to affect contaminant concentrations; use of IS carrier solvents that were immiscible with serum (or when the serum was not directly physically mixed with IS) resulted in a 30% underestimation of organohalogen concentrations. This study offers valid, novel extraction alternatives beyond traditional methods (e.g., LLE) for blood contaminant measurements. Figure       

Evaluation of solid-phase microextraction conditions for the determination of polycyclic aromatic hydrocarbons in aquatic species using gas chromatography

This paper describes a headspace solid-phase microextraction (HS-SPME) procedure coupled to gas chromatography with mass spectrometric detection (GC–MS) for the determination of eight PAHs in aquatic species. The influence of various parameters on the PAH extraction efficiency was carefully examined. At 75 °C and for an extraction time of 60 min, a polydimethylsiloxane–divinylbenzene (PDMS/DVB) fiber coating was found to be most suitable. Under the optimized conditions, detection limits ranged from 8 to 450 pg g⁻¹, depending on the compound and the sample matrix. The repeatability varied between 7 and 15% (RSD). Accuracy was tested using the NIST SRM 1974b reference material. The method was successfully applied to different samples, and the studied PAHs were detected in several of the samples. Figure Headspace SPME sampling followed by GC–MS facilitates routine monitoring of PAHs in aquatic species     

Rapid and quantitative DNA analysis of genetic mutations for polycystic kidney disease (PKD) using magnetic/luminescent nanoparticles

Rapid and accurate detection of genetic mutations based on nanotechnology would provide substantial advances in detection of polycystic kidney disease (PKD), a disease whose current methods of detection are cumbersome due to the large size and duplication of the mutated gene. In this study, a nanotechnology-based DNA assay was developed for detection of SNPs (single nucleotide polymorphisms) in a feline autosomal dominant PKD (ADPKD) model which can readily be adapted to diagnosis of human ADPKD type 1. Europium and terbium phosphors were doped into gadolinium crystal hosts with a magnetic core, providing stable luminescence and the possibility of magnetic manipulations in a solution-based assay. A hybridization-in-solution DNA assay was optimized for feline PKD gene SNP detection using genomic DNA extracted from feline kidney tissue and blood. This assay showed a substantial differentiation between PKD and control specimens. The nanotechnology-based DNA assay is attractive from the viewpoint of rapid availability, simple methodology, and cost reduction for clinical use to detect mutations involved in human ADPKD and other genetic diseases. Figure Schematic diagram of PKD (Polycystic Kidney Disease) SNPs detection assay using feline genomic DNA in magnetic/luminescent nanoparticle-based DNA hybridization     

Calibration possibilities and modifier use in ETV ICP OES determination of trace and minor elements in plant materials

The possibilities for universal calibration based on multi-element aqueous standard solutions and graphite laboratory reference materials (graphite standards) for the electrothermal vaporization inductively coupled plasma optical emission spectrometric (ETV ICP OES) determination of Al, B, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, P, Pb, S, Sr, Ti, V, and Zn in plant materials were investigated. A commercially available state-of-the-art ETV device was coupled with an Echelle ICP spectrometer equipped with a charge-injection-device (CID) camera for spectral detection. The transition area between transport tube and ETV graphite tube and the gas streams for inner gas, bypass gas, and modifier gas were optimized to achieve best transport efficiencies. The influence of four gaseous modifiers (CCl₄, CHCl₃, CCl₂F₂, and C₃H₈) added to the inner gas was studied. Five reference materials (RM P-Alfalfa, Lucerne; NIES CRM No.9 “Sargasso”; CTA-VTL-2 Virginia Tobacco Leaves; NIST SRM 1515 Apple Leaves; IAEA-V-10 Hay Powder) were used for method validation. If certified reference materials are not available, calibration against graphite standards or dried aqueous standard solutions is possible. Three carbonization procedures as sample pretreatment for the plant materials were investigated. Figure Picture of the ETV system (sample changer and graphite-tube furbace) used in this work Presented at the European Symposium on Atomic Spectrometry (ESAS) September 28-October 1, 2008, Weimar, Germany.     

Study of thiazole orange in aptamer-based dye-displacement assays

We screened a series of RNA and DNA aptamers for their ability to serve in the dye displacement assays in which analytes compete with TO dye. We conclude that, while the performance of the TO dye displacement approach is not always predictable, it is still a simple and sensitive assay to detect binding between RNA aptamers and small molecules. In particular, we describe efficient assays for tobramycin and theophylline, with up to 90% displacement of TO observed, and we describe the first aptameric assay for cAMP. Figure An RNA or DNA aptamer against a molecule (circle) binds TO dye, resulting in a fluorescent complex. Presence of free molecule in solution results in the displacement of TO from the complex and a reduction in fluorescence Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Determination of cadmium in grains by isotope dilution ICP–MS and coprecipitation using sample constituents as carrier precipitants

A coprecipitation method using sample constituents as carrier precipitants was developed that can remove molybdenum, which interferes with the determination of cadmium in grain samples via isotope dilution inductively coupled plasma mass spectrometry (ID-ICPMS). Samples were digested with HNO₃, HF, and HClO₄, and then purified 6 M sodium hydroxide solution was added to generate colloidal hydrolysis compounds, mainly magnesium hydroxide. Cadmium can be effectively separated from molybdenum because the cadmium forms hydroxides and adsorbs onto and/or is occluded in the colloid, while the molybdenum does not form hydroxides or adsorb onto the hydrolysis colloid. The colloid was separated by centrifugation and then dissolved with 0.2 M HNO₃ solution to recover the cadmium. The recovery of Cd achieved using the coprecipitation was >97%, and the removal efficiency of Mo was approximately 99.9%. An extremely low procedural blank (below the detection limit of ICPMS) was achieved by purifying the 6 M sodium hydroxide solution via Mg coprecipitation using Mg(NO₃)₂ solution. The proposed method was applied to two certified reference materials (NIST SRM 1567a wheat flour and SRM 1568a rice flour) and CCQM-P64 soybean powder. Good analytical results with small uncertainties were obtained for all samples. This method is simple and reliable for the determination of Cd in grain samples by ID-ICPMS. Figure Overview of a coprecipitation method using sample constituents     

Several concerns about the primer design in the universal molecular beacon real-time PCR assay and its application in HBV DNA detection

A universal hepatitis B virus (HBV) DNA detection kit is appealing for the worldwide diagnosis and monitoring of the treatment of different mutant types of hepatitis B virus. A sensitive and reproducible real-time PCR assay based on the universal molecular beacon (U-MB) technique was developed for the detection of HBV DNA in serum. The U-MB probe used in the assay has no interaction with the HBV DNA sequence. The U-MB technique not only reduced the cost of HBV detection but also had the potential for the development of a universal detection kit for different mutant HBV types and other DNA systems. To demonstrate its clinical utility, 90 serum samples were analyzed using the U-MB real-time PCR method. In the experiments we found that several crucial factors needed to be considered in the primer design, such as the avoidance of formation of severe primer–dimer and primer self-hairpin structure. With the optimized primer sets, satisfactory results were obtained for all the tested samples. We concluded that this assay would be an excellent candidate for a universal HBV DNA detection method. Principle of the U-MB real-time PCR method for HBV DNAdetection     

Fluoroquinolones in soil—risks and challenges

Fluoroquinolones (FQs) are among the most important antibacterial agents used in human and veterinary medicine. Because of the growing practice of adding manure and sewage sludge to agricultural fields these drugs end up in soils, where they can accumulate and have adverse effects on organisms. This paper presents an overview of recent developments in the determination of FQs in solid environmental matrices and describes the risks and challenges (persistence, fate, effects, and remediation) which result from their presence in soil. Figure Pathways into the environment for FQs     

A review of the DNA standard reference materials developed by the National Institute of Standards and Technology

The Standard Reference Materials Program at the US National Institute of Standards and Technology (NIST) has three human DNA standard reference materials (SRM 2390, SRM 2391a, and SRM 2392) currently available¹ (Orders and requests for information concerning these SRMs should be directed to the Standard Reference Materials Program, National Institute of Standards and Technology, 100 Bureau Drive, Stop 2321, Gaithersburg, MD 20899-2321, Telephone (301) 975-6776, FAX: (301) 948-3730.) [1, 2]. Both the DNA profiling SRM 2390 and the polymerase chain reaction (PCR)-based DNA profiling SRM 2391a are intended for use in forensic and paternity identifications, for instructional law enforcement, or for non-clinical research purposes and are not intended for clinical diagnostics. The mitochondrial DNA (mtDNA) SRM 2392 is to provide standardization and quality control when performing PCR and sequencing any segment or the entire 16,569 base pairs that comprise human mitochondrial DNA. SRM 2392 is designed for use by the forensic, medical, and toxicological communities for human identification, disease diagnosis or mutation detection.     

Playing tag with quantitative proteomics

There is steady need for new proteomic strategies on quantitative measurements that provide essential components for detailing dynamic changes in many cellular functions and processes. Stable isotope labeling is a rapidly evolving field, which can be used either after protein extraction with chemical labeling, or in cell culture with metabolic incorporation. In this review, we explore the most frequently utilized quantitation techniques with particular attention paid to chemical labeling using different isotopic tags, including a recent labeling strategy—soluble polymer-based isotopic labeling (SoPIL)—that achieves efficient labeling in homogeneous conditions. Special care should be devoted to the selection of appropriate quantitation approaches according to the needs of the sample and overall experimental design. We evaluate recent advances in quantitative proteomics using stable isotope labeling and their applications to current insightful biological inquiries. Figure Chemical modules of isotopic tags for quantitative proteomics.     

A novel approach for the detection of DNA using immobilized peptide nucleic acid (PNA) probes and signal enhancement by real-time immuno-polymerase chain reaction (RT-iPCR)

A new approach for the detection of DNA target molecules is described, using capture probes and subsequent signal enhancement by a uniform polymerase chain reaction (PCR). Peptide nucleic acid probes were immobilized in real-time PCR-compatible microtiter plates. After hybridization of biotinylated DNA targets, detection was performed by real-time immuno-PCR, a method formerly used for protein detection. We demonstrate the feasibility of this strategy for the qualitative detection of DNA oligonucleotides with a detection limit (LOD) of 6 attomol. Furthermore, the method was applied to PCR-amplified samples from genetically modified maize DNA (Mon810). A 483-bp DNA fragment was detected in mixture with 99.9% of noncomplementary DNA with a sensitivity down to the level of attomole. Figure       

Characterization of cellular chemical dynamics using combined microfluidic and Raman techniques

The integration of a range of technologies including microfluidics, surface-enhanced Raman scattering and confocal microspectroscopy has been successfully used to characterize in situ single living CHO (Chinese hamster ovary) cells with a high degree of spatial (in three dimensions) and temporal (1 s per spectrum) resolution. Following the introduction of a continuous flow of ionomycin, the real time spectral response from the cell was monitored during the agonist-evoked Ca²⁺ flux process. The methodology described has the potential to be used for the study of the cellular dynamics of a range of signalling processes. Figure Spectral mapping of a single CHO cell     

Nuclear magnetic resonance of mass-limited samples using small RF coils

Figure Schematic diagram of a typical arrangement used for hyphenating chemical microseparations (e.g. capillary HPLC, CE, or CEC) with microcoil NMR detection     

Bienzyme sensors based on novel polymethylferrocenyl dendrimers

Amperometric bienzyme electrodes with horseradish peroxidase (HRP) and glucose oxidase (GOx) co-immobilized on polymethylferrocenyl dendrimers deposited onto platinum electrodes have been used for determination of the hydrogen peroxide produced by the oxidase during the enzymatic reaction. The redox dendrimers consist of flexible poly(propylenimine) dendrimer cores functionalised with octamethylferrocenyl units. The effects of dendrimer generation, the thickness of the dendrimer layer, substrate concentration, interferences, and reproducibility on the response of the sensors were investigated. The new bienzyme biosensors respond to substrate at work potential values between 200 and 50 mV (vs. SCE), have good sensitivity, and are resistant to interferences. Figure     

Impedimetric genosensors for the detection of DNA hybridization

Impedance spectroscopy is proposed as the transduction principle for detecting the hybridization of DNA complementary strands. In our experiments, different DNA oligonucleotides were used as model gene substances. The gene probe is first immobilized on a graphite-epoxy composite working electrode based genosensor. Detection principle is based on changes of impedance spectra of a redox marker, the ferro/ferricyanide couple, after hybridization with target DNA. Resistance offered to the electrochemical reaction serves as the working signal, allowing for an unlabelled gene assay.      

A review of the DNA standard reference materials developed by the National Institute of Standards and Technology

The Standard Reference Materials Program at the US National Institute of Standards and Technology (NIST) has three human DNA standard reference materials (SRM 2390, SRM 2391a, and SRM 2392) currently available [1, 2]. Both the DNA profiling SRM 2390 and the polymerase chain reaction (PCR)-based DNA profiling SRM 2391a are intended for use in forensic and paternity identifications, for instructional law enforcement, or for non-clinical research purposes and are not intended for clinical diagnostics. The mitochondrial DNA (mtDNA) SRM 2392 is to provide standardization and quality control when performing PCR and sequencing any segment or the entire 16,569 base pairs that comprise human mitochondrial DNA. SRM 2392 is designed for use by the forensic, medical, and toxicological communities for human identification, disease diagnosis or mutation detection.     

Highly sensitive restriction enzyme assay and analysis: a review

Biological assays at the single molecule level are crucial to fundamental studies of DNA-protein mechanisms. In order to cater for high throughput applications, one area of immense research potential is single-molecule bioassays where miniaturized devices are developed to perform rapid and effective biological reactions and analyses. With the success of various emerging technologies for engineering miniaturized structures down to the nanoscale level, supported by specialized equipment for detection, many investigations in the field of life science that were once thought impossible can now be actively explored. In this review, the significance of downscaling to the single-molecule level is firstly presented in selected examples, with the focus placed on restriction enzyme assays. To determine the effectiveness of single-molecule restriction enzyme reactions, simple and direct analytical methods based on DNA stretching have often been reliably employed. DNA stretching can be realized based on a number of working principles related to the physical forces exerted on the DNA samples. We then discuss two examples of a nanochannel system and a microchamber system where single-molecule restriction enzyme digestion and DNA stretching have been integrated, which possess prospective capabilities of developing into highly sensitive and high-throughput restriction enzyme assays. Finally, we take a brief look at the general trends in technological development in this field by comparing the advantages and disadvantages of performing assays at bulk, microscale and single-molecule levels. Figure Minaturization of Restriction Enzyme Assays and DNA Stretching     

Gradient HPLC separation of dehydroepiandrosterone (DHEA) from its metabolites and biological congeners: role of tetrahydrofuran in the chromatographic mechanism

A three-step gradient reversed-phase high-performance liquid chromatography (RP-HPLC) method was developed for the separation of dehydroepiandrosterone (DHEA), its sulfate ester (DHEA-S), its three C7-oxidized metabolites (7αOH-DHEA, 7βOH-DHEA, 7-keto-DHEA), and its biosynthetic congeners (androstenedione, testosterone, estradiol, pregnenolone). This new method allows the quantitative characterization of DHEA metabolism and biosynthetic transformation under given physiological, pathological, or therapeutically influenced circumstances. Tetrahydrofuran probably acts as a proton acceptor coadsorbent, while isopropanol behaves as a proton donor during the separation of testosterone, estradiol, and the stereoisomers of 7-OH-DHEA. Figure Optimized gradient RP-HPLC results in full separation of DHEA from its biosynthetic congeners and metabolites