A versatile cryo-transfer system, connecting cryogenic focused ion beam sample preparation to atom probe microscopy

Atom probe tomography (APT) is a powerful technique to obtain 3D chemical and structural information, however the 'standard' atom probe experimental workflow involves transfer of specimens at ambient conditions. The ability to transfer air- or thermally-sensitive samples between instruments while maintaining environmental control is critical to prevent chemical or morphological changes prior to analysis for a variety of interesting sample materials. In this article, we describe a versatile transfer system that enables cryogenic- or room-temperature transfer of specimens in vacuum or atmospheric conditions between sample preparation stations, a focused ion beam system (Zeiss Crossbeam 540) and a widely used commercial atom probe system (CAMECA LEAP 4000X HR). As an example for the use of this transfer system, we present atom probe data of gallium- (Ga)-free grain boundaries in an aluminum (Al) alloy specimen prepared with a Ga-based FIB.

Lab-on-a-Filter Techniques for Economical, Effective, and Flexible Proteome Analysis

Effective and reliable protease digestion of biological samples is critical to the success in bottom-up proteomics analysis. Various filter-based approaches using different types of membranes have been developed in the past several years and largely implemented in sample preparations for modern proteomics. However, these approaches rely heavily on commercial filter products, which are not only costly but also limited in membrane options. Here, we present a plug-and-play device for filter assembly and protease digestion. The device can accommodate a variety of membrane types, can be packed in-house with minimal difficulty, and is extremely cost-effective and reliable. Our protocol offers a versatile platform for general proteome analyses and clinical mass spectrometry.

Glass Fiber-Supported Hybrid Monolithic Spin Tip for Enrichment of Phosphopeptides from Urinary Extracellular Vesicles

Extracellular vesicles (EVs) are attracting increasing interest with their intriguing role in intercellular communications. Protein phosphorylation in EVs is of great importance for understanding intercellular signaling processes. However, the study of EV phosphoproteomics is impeded by their relatively low amount in limited clinical sample volumes, and it is necessary to have a sensitive and efficient enrichment method for EV phosphopeptides. Herein, a novel Ti(IV)-functionalized and glass fiber-supported hybrid monolithic spin tip, termed PhosTip, was prepared for enriching phosphopeptides from urinary EVs. Glass fiber as the stationary phase positions the hybrid monolith in a standard pipet tip and prevents the monolith from distortion during experiments. The preparation procedure for the new PhosTip is simple and time-saving. The hybrid monolithic PhosTip provides excellent enrichment efficiency of low-abundance phosphopeptides from cell digests and urinary EVs with minimum contamination and sample loss. Using the PhosTip, we demonstrate that 5373 and 336 unique phosphopeptides were identified from 100 and 1 μg of cell lysates, while 3919 and 217 unique phosphopeptides were successfully identified from 10 and 1 mL of urinary samples, respectively. The PhosTip was finally applied to enrich phosphopeptides in urine EVs from prostate cancer patients and healthy controls and quantify 118 up-regulated proteins with phosphosites in prostate cancer samples. These results demonstrated that the PhosTip could be a simple and convenient tool for enriching phosphopeptides from clinical samples and for broader applications in biomarker discovery.

Comparison of extraction techniques for polycyclic aromatic hydrocarbons from lichen biomonitors

Lichens are useful biomonitors for atmospheric polycyclic aromatic hydrocarbons (PAHs). Different sample preparation techniques were explored in this regard, including ultrasound-assisted solvent extraction, microwave-assisted extraction, Soxhlet, and the quick, easy, cheap, effective, rugged, and safe (QuEChERS) technique. It was found that a QuEChERS technique using hexane:acetone (1:1, v/v), never reported before for application to lichens, provided the best recoveries of internal standards, the highest total peak area for all PAHs of interest, and %RSDs comparable with the other preparation techniques tested. The optimized sample preparation technique was found to be a comparatively fast method (45 min), with good recoveries (96%), using less solvents and minimal energy consumption. Strong matrix effects were found: both strong enhancement (for the lighter PAHs) and strong suppression (for the heavier PAHs). The use of matrix-matched standards is thus imperative for the accurate determination of PAH concentrations in the lichen samples. Graphical abstract "Note: This data is mandatory. Please provide."

Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications

The demand for understanding the roles genes play in biological systems has steered the biosciences into the direction the metabolome, as it closely reflects the metabolic activities within a cell. The importance of the metabolome is further highlighted by its ability to influence the genome, transcriptome, and proteome. Consequently, metabolomic information is being used to understand microbial metabolic networks. At the forefront of this work is mass spectrometry, the most popular metabolomics measurement technique. Mass spectrometry-based metabolomic analyses have made significant contributions to microbiological research in the environment and human disease. In this chapter, we break down the technical aspects of mass spectrometry-based metabolomics and discuss its application to microbiological research.

Untargeted Soil Metabolomics Using Liquid Chromatography-Mass Spectrometry and Gas Chromatography-Mass Spectrometry

The molecular composition of soil organic matter (SOM) sets the foundation for terrestrial microbial community structures and carbon cycling dynamics. However, the specific chemical constituents of SOM are underexplored. In this chapter we present a protocol for the extraction of small molecule metabolites from soil followed by compound detection and identification using liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. There are options within the protocol to assess either the extracellular pool of metabolites or the total pool (including intracellular) and either polar or nonpolar metabolites, depending on the reader's research interests. These methods can be followed individually for a more targeted analysis or all methods can be combined to obtain a more comprehensive understanding of SOM metabolite composition (such as amino acids, nucleobases, organic acids, fatty acids, carbohydrates, secondary metabolites, and antibiotics).

Integration of sample preparation and analysis into an optofluidic chip for multi-target disease detection

Detection of molecular biomarkers with high specificity and sensitivity from biological samples requires both sophisticated sample preparation and subsequent analysis. These tasks are often carried out on separate platforms which increases required sample volumes and the risk of errors, sample loss, and contamination. Here, we present an optofluidic platform which combines an optical detection section with single nucleic acid strand sensitivity, and a sample processing unit capable of on-chip, specific extraction and labeling of nucleic acid and protein targets in complex biological matrices. First, on-chip labeling and detection of individual lambda DNA molecules down to concentrations of 8 fM is demonstrated. Subsequently, we demonstrate the simultaneous capture, fluorescence tagging and detection of both Zika specific nucleic acid and NS-1 protein targets in both buffer and human serum. We show that the dual DNA and protein assay allows for successful differentiation and diagnosis of Zika against cross-reacting species like dengue.

A radial calibration window for analytical ultracentrifugation

Analytical ultracentrifugation (AUC) is a first-principles based method for studying macromolecules and particles in solution by monitoring the evolution of their radial concentration distribution as a function of time in the presence of a high centrifugal field. In sedimentation velocity experiments, hydrodynamic properties relating to size, shape, density, and solvation of particles can be measured, at a high hydrodynamic resolution, on polydisperse samples. In a recent multilaboratory benchmark study including data from commercial analytical ultracentrifuges in 67 laboratories, the calibration accuracy of the radial dimension was found to be one of the dominant factors limiting the accuracy of AUC. In the present work, we develop an artifact consisting of an accurately calibrated reflective pattern lithographically deposited onto an AUC window. It serves as a reticle when scanned in AUC control experiments for absolute calibration of radial magnification. After analysis of the pitch between landmarks in scans using different optical systems, we estimate that the residual uncertainty in radial magnification after external calibration with the radial scale artifact is ≈0.2 %, of similar magnitude to other important contributions after external calibration such as the uncertainty in temperature and time. The previous multilaboratory study had found many instruments with errors in radial measurements of 1 % to 2 %, and a few instruments with errors in excess of 15 %, meaning that the use of the artifact developed here could reduce errors by 5-to 10-fold or more. Adoption of external radial calibration is thus an important factor for assuring accuracy in studies related to molecular hydrodynamics and particle size measurements by AUC.

Critical Assessment of Analytical Techniques in the Search for Biomarkers on Mars: A Mummified Microbial Mat from Antarctica as a Best-Case Scenario

The search for biomarkers of present or past life is one of the major challenges for in situ planetary exploration. Multiple constraints limit the performance and sensitivity of remote in situ instrumentation. In addition, the structure, chemical, and mineralogical composition of the sample may complicate the analysis and interpretation of the results. The aim of this work is to highlight the main constraints, performance, and complementarity of several techniques that have already been implemented or are planned to be implemented on Mars for detection of organic and molecular biomarkers on a best-case sample scenario. We analyzed a 1000-year-old desiccated and mummified microbial mat from Antarctica by Raman and IR (infrared) spectroscopies (near- and mid-IR), thermogravimetry (TG), differential thermal analysis, mass spectrometry (MS), and immunological detection with a life detector chip. In spite of the high organic content (ca. 20% wt/wt) of the sample, the Raman spectra only showed the characteristic spectral peaks of the remaining beta-carotene biomarker and faint peaks of phyllosilicates over a strong fluorescence background. IR spectra complemented the mineralogical information from Raman spectra and showed the main molecular vibrations of the humic acid functional groups. The TG-MS system showed the release of several volatile compounds attributed to biopolymers. An antibody microarray for detecting cyanobacteria (CYANOCHIP) detected biomarkers from Chroococcales, Nostocales, and Oscillatoriales orders. The results highlight limitations of each technique and suggest the necessity of complementary approaches in the search for biomarkers because some analytical techniques might be impaired by sample composition, presentation, or processing. Key Words: Planetary exploration-Life detection-Microbial mat-Life detector chip-Thermogravimetry-Raman spectroscopy-NIR-DRIFTS. Astrobiology 17, 984-996.

Laboratory to pilot scale: Microwave extraction for polyphenols lettuce

Microwave hydrodiffusion and gravity (MHG) technique has been applied to pilot-scale solvent-free microwave extraction (SFME) of polyphenols from Lettuce sativa. Following the dictates of green extraction and with the aim to save time and energy, the lab-scale knowledge on SFME was exploited for the development of a pilot-scale process. The investigation entailed the optimization of all main parameters (temperature, time, extracted water volume, etc.) and we showed that the polyphenols composition profile under SFME was similar to the classic methods though a bit lower in total content. The energy consumption in the optimized procedure (30min) was 1W/g of fresh matrix.

A lab-on-a-chip system integrating tissue sample preparation and multiplex RT-qPCR for gene expression analysis in point-of-care hepatotoxicity assessment

A truly practical lab-on-a-chip (LOC) system for point-of-care testing (POCT) hepatotoxicity assessment necessitates the embodiment of full-automation, ease-of-use and "sample-in-answer-out" diagnostic capabilities. To date, the reported microfluidic devices for POCT hepatotoxicity assessment remain rudimentary as they largely embody only semi-quantitative or single sample/gene detection capabilities. In this paper, we describe, for the first time, an integrated LOC system that is somewhat close to a practical POCT hepatotoxicity assessment device - it embodies both tissue sample preparation and multiplex real-time RT-PCR. It features semi-automation, is relatively easy to use, and has "sample-in-answer-out" capabilities for multiplex gene expression analysis. Our tissue sample preparation module incorporating both a microhomogenizer and surface-treated paramagnetic microbeads yielded high purity mRNA extracts, considerably better than manual means of extraction. A primer preloading surface treatment procedure and the single-loading inlet on our multiplex real-time RT-PCR module simplify off-chip handling procedures for ease-of-use. To demonstrate the efficacy of our LOC system for POCT hepatotoxicity assessment, we perform a preclinical animal study with the administration of cyclophosphamide, followed by gene expression analysis of two critical protein biomarkers for liver function tests, aspartate transaminase (AST) and alanine transaminase (ALT). Our experimental results depict normalized fold changes of 1.62 and 1.31 for AST and ALT, respectively, illustrating up-regulations in their expression levels and hence validating their selection as critical genes of interest. In short, we illustrate the feasibility of multiplex gene expression analysis in an integrated LOC system as a viable POCT means for hepatotoxicity assessment.

Evaluation of different parameters in the extraction of incurred pesticides and environmental contaminants in fish

Sample processing is often ignored during analytical method development and validation, but accurate results for real samples depend on all aspects of the analytical process. Also, validation is often conducted using only spiked samples, but extraction yields may be lower in incurred samples. In this study, different variables in extraction for incurred pesticides and environmental contaminants in fish were investigated. Among 207 analytes screened using low-pressure gas chromatography-tandem mass spectrometry, consisting of 150 pesticides, 15 polycyclic aromatic hydrocarbons (PAHs), 14 polychlorinated biphenyls (PCBs), 6 polybrominated diphenyl ethers (PBDEs), and 22 other flame retardants (FRs), 35 (16 pesticides, 9 PCBs, 5 PBDEs, and 5 PAHs) were identified for quantification in samples of salmon, croaker, and NIST Standard Reference Material 1947 (Lake Michigan Fish Tissue). Extraction efficiencies using different extraction devices (blending, vortexing, and vibrating) versus time, sample size, and sample/solvent ratio were determined. In comparison to blending results, use of a pulsed-vortexer for 1 min with 1/1 (g/mL) sample/acetonitrile ratio was generally sufficient to extract the incurred contaminants in the homogenized fish tissues. Conversely, extraction with a prototype vibration shaker often took 60 min to achieve 100% extraction efficiency. A main conclusion from this study is that accurate results for real samples can be obtained using batch extraction with a pulsed-vortexer in a simple and efficient method that achieves high sample throughput.

Electromechanical cell lysis using a portable audio device: enabling challenging sample preparation at the point-of-care

Audio sources are ubiquitously available on portable electronic devices, including cell phones. Here we demonstrate lysis of Mycobacterium marinum and Staphylococcus epidermidis bacteria utilizing a portable audio device coupled with a simple and inexpensive electromagnetic coil. The resulting alternating magnetic field rotates a magnet in a tube with the sample and glass beads, lysing the cells and enabling sample preparation for these bacteria anywhere there is a cell phone, mp3 player, laptop, or other device with a headphone jack.

A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples

Foodborne disease is a major public health threat worldwide. Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture or molecular-based methods are time consuming and usually take a few hours to days to complete. In response to the demand for rapid on line or on site detection of pathogens, in this study, we describe for the first time an eight-chamber lab-on-a-chip (LOC) system with integrated magnetic bead-based sample preparation and loop-mediated isothermal amplification (LAMP) for rapid and quantitative detection of Salmonella spp. in food samples. The whole diagnostic procedures including DNA isolation, isothermal amplification, and real-time detection were accomplished in a single chamber. Up to eight samples could be handled simultaneously and the system was capable to detect Salmonella at concentration of 50 cells per test within 40 min. The simple design, together with high level of integration, isothermal amplification, and quantitative analysis of multiple samples in short time, will greatly enhance the practical applicability of the LOC system for rapid on-site screening of Salmonella for applications in food safety control, environmental surveillance, and clinical diagnostics.

On-chip sample preparation for complete blood count from raw blood

This paper describes a monolithic microfluidic device capable of on-chip sample preparation for both RBC and WBC measurements from whole blood. For the first time, on-chip sample processing (e.g. dilution, lysis, and filtration) and downstream single cell measurement were fully integrated to enable sample preparation and single cell analysis from whole blood on a single device. The device consists of two parallel sub-systems that perform sample processing and electrical measurements for measuring RBC and WBC parameters. The system provides a modular environment capable of handling solutions of various viscosities by adjusting the length of channels and precisely controlling mixing ratios, and features a new 'offset' filter configuration for increased duration of device operation. RBC concentration, mean corpuscular volume (MCV), cell distribution width, WBC concentration and differential are determined by electrical impedance measurement. Experimental characterization of over 100,000 cells from 10 patient blood samples validated the system's capability for performing on-chip raw blood processing and measurement.

Capacitive deionization on-chip as a method for microfluidic sample preparation

Desalination as a sample preparation step is essential for noise reduction and reproducibility of mass spectrometry measurements. A specific example is the analysis of proteins for medical research and clinical applications. Salts and buffers that are present in samples need to be removed before analysis to improve the signal-to-noise ratio. Capacitive deionization is an electrostatic desalination (CDI) technique which uses two porous electrodes facing each other to remove ions from a solution. Upon the application of a potential of 0.5 V ions migrate to the electrodes and are stored in the electrical double layer. In this article we demonstrate CDI on a chip, and desalinate a solution by the removal of 23% of Na(+) and Cl(-) ions, while the concentration of a larger molecule (FITC-dextran) remains unchanged. For the first time impedance spectroscopy is introduced to monitor the salt concentration in situ in real-time in between the two desalination electrodes.

Combining electrochemical sensors with miniaturized sample preparation for rapid detection in clinical samples

Clinical analyses benefit world-wide from rapid and reliable diagnostics tests. New tests are sought with greatest demand not only for new analytes, but also to reduce costs, complexity and lengthy analysis times of current techniques. Among the myriad of possibilities available today to develop new test systems, amperometric biosensors are prominent players-best represented by the ubiquitous amperometric-based glucose sensors. Electrochemical approaches in general require little and often enough only simple hardware components, are rugged and yet provide low limits of detection. They thus offer many of the desirable attributes for point-of-care/point-of-need tests. This review focuses on investigating the important integration of sample preparation with (primarily electrochemical) biosensors. Sample clean up requirements, miniaturized sample preparation strategies, and their potential integration with sensors will be discussed, focusing on clinical sample analyses.

Microfluidic in-reservoir pre-concentration using a buffer drain technique

Pre-concentration methods are essential for detecting low concentrations of influenza virus in biological samples from patients. Here, we describe a new method for draining buffer from solution in the reservoir of a microfluidic device to increase the concentration of virus in the reservoir. Viruses were captured in the reservoir by an ion depletion barrier from connected ion selective microfluidic channels. 75 μl of buffer was successfully drained from a 100 μl sample, resulting in a 4-fold increase in influenza hemagglutinin concentration in the reservoir. The volume of the final concentrated sample was suitable for detection of influenza hemagglutinin by the enzyme-linked immunosorbent assay, demonstrating the usefulness of the developed platform for enhanced sensitivity of virus detection in a conventional analysis.

Cannabinoids in oral fluid by on-site immunoassay and by GC-MS using two different oral fluid collection devices

Oral fluid (OF) enables non-invasive sample collection for on-site drug testing, but performance of on-site tests with occasional and frequent smokers' OF to identify cannabinoid intake requires further evaluation. Furthermore, as far as we are aware, no studies have evaluated differences between cannabinoid disposition among OF collection devices with authentic OF samples after controlled cannabis administration. Fourteen frequent (≥4 times per week) and 10 occasional (less than twice a week) adult cannabis smokers smoked one 6.8% ∆(9)-tetrahydrocannabinol (THC) cigarette ad libitum over 10 min. OF was collected with the StatSure Saliva Sampler, Oral-Eze, and Draeger DrugTest 5000 test cassette before and up to 30 h after cannabis smoking. Test cassettes were analyzed within 15 min and gas chromatography-mass spectrometry cannabinoid results were obtained within 24 h. Cannabinoid concentrations with the StatSure and Oral-Eze devices were compared and times of last cannabinoid detection (t(last)) and DrugTest 5000 test performance were assessed for different cannabinoid cutoffs. 11-nor-9-Carboxy-THC (THCCOOH) and cannabinol concentrations were significantly higher in Oral-Eze samples than in Stat-Sure samples. DrugTest 5000 t(last) for a positive cannabinoid test were median (range) 12 h (4-24 h) and 21 h (1- ≥ 30 h) for occasional and frequent smokers, respectively. Detection windows in screening and confirmatory tests were usually shorter for occasional than for frequent smokers, especially when including THCCOOH ≥20 ng L(-1) in confirmation criteria. No differences in t(last) were observed between collection devices, except for THC ≥2 μg L(-1). We thus report significantly different THCCOOH and cannabinol, but not THC, concentrations between OF collection devices, which may affect OF data interpretation. The DrugTest 5000 on-site device had high diagnostic sensitivity, specificity, and efficiency for cannabinoids.

Influence of amount of starting material for DNA extraction on detection of low-level presence of genetically engineered traits

Two laboratories independently examined how the amount of starting material influences DNA extraction efficiency and, ultimately, the detection of low-level presence of genetically engineered (GE) traits in commercialized grains. GE traits from one maize, two canola, and two soybean samples were used as prototypical models in the study design as well as two commonly used DNA extraction methods, a small scale (0.1 and 0.2 g samples) and a large scale (1.0 and 2.0 g samples). The DNA samples were fortified (spiked) at 0.1 and 0.01% (w/w) levels. The amount of DNA recovery varied between the two laboratories, although a sufficient amount of DNA was obtained to perform replicate PCR analysis by both laboratories. Reliable detection of all five events was achieved by both laboratories at 0.1% level using either small-scale or large-scale DNA extractions. Reliable detection of the GE events was achieved at 0.01% level for soybean and canola but not for maize. Variability was observed among the two laboratories in terms of the Ct values generated. There was no difference between small-scale and large-scale DNA extraction methods for qualitative PCR detections of all five GE events.

Improvement in day zero recoveries in field soil dissipation studies using larger diameter soil samples

Obtaining acceptable recovery of the applied test substance at zero time in field soil dissipation studies has been a subject of considerable interest among scientists conducting regulatory field studies. In particular, achieving recoveries of ≥90% in soil samples collected immediately after applications in most studies has been elusive. This study investigated a modified soil sampling method, which could be used not only on day zero but for the entire study duration, to see if the recoveries in soil samples, especially in the early stages, can be improved. The modified sampling system has demonstrated that recoveries averaging 90% are possible and can be routinely obtained on day zero. Description of this modified sampling procedure and statistical analysis of the data collected for day zero samples are discussed.

Innovative assistant extraction of flavonoids from pine (Larix olgensis Henry) needles by high-density steam flash-explosion

High-density steam flash-explosion (HDSF) was first employed to extract flavonoids from pine needles. The HDSF treatment was performed at a steam pressure of 0.5-2.0 MPa for 20-120 s. Scanning electron microscopy and high-performance liquid chromatography combined with photodiode-array detection and electrospray ionization mass spectrometry (HPLC-DAD-ESI-MS) were used to characterize the morphological changes and analyze flavonoids of pine needles before and after HDSF treatment. Our results indicated that, after steam explosion at 1.5 MPa for 60 s, the flavonoids extracted reached 50.8 rutin equivalents mg/g dry weight, which was 2.54-fold as that of the untreated sample. HDSF pretreatment caused the formation of large micropores on the pine needles and production of particles, as well as the removal of wax layers. Compared to microwave-assisted, ultrasound-assisted, and solvent extraction, HDSF pretreatment took only 30 min to reach a maximum yield of 47.0 rutin equivalents mg/g flavonoids extract after pine needles were treated at 1.5 MPa for 80 s. In addition, after HDSF treatment, the aglycones were 3.17 times higher than that of untreated pine needles, while glycosides were lower by 57% (in HPLC-DAD individuals' sum) due to hydrolysis of flavonoids glycosides. It can be concluded that HDSF is a practical pretreatment for extraction of flavonoids and conversion in the healthy food and pharmaceutical industries.

A microbead-incorporated centrifugal sample pretreatment microdevice

In this study, we present a novel bead-incorporated centrifugal sample pretreatment microdevice to purify influenza A H3N2 viral RNA. Simple revolution per minute (RPM) control can lead to RNA capture on a bead-bed, and the sequential loading of a washing solution and an elution solution. Tetraethoxy orthosilicate (TEOS)-treated glass microbeads were utilized as a capture matrix. The sample pretreatment microdevice consists of four reservoirs for storing an RNA sample, a washing solution, an elution solution, and a collected sample, and they were merged at the microbead-bed microchannel. The washing solution reservoir and the elution solution reservoir were connected to the bead-bed microchannel through a capillary valve and a siphon channel, respectively. An RNA sample (a lysed influenza A H3N2 virus), a washing solution (70% ethanol) and an elution solution (water or a reverse transcription-polymerase chain reaction (RT-PCR) cocktail) were loaded into the designated reservoirs, and they were successively transported to the bead-bed by RPM control owing to the optimized channel design. Purified RNAs could be obtained in 440 s. Then, a target H3 gene was amplified by an off-chip based real-time RT-PCR to evaluate the capture efficiency of RNA on our proposed microdevice. 81% of RNAs were successfully captured and purified. Interestingly, the use of the RT-PCR cocktail itself as an elution solution resulted in a 76% capture yield. Furthermore, we successfully performed RNA purification from the clinical nasopharyngeal swabs to identify the subtype of the influenza A virus. This platform provides high potential for the direct integration of the sample pretreatment microdevice into the downstream micro-PCR unit to create a total genetic analysis microsystem.

10,000-fold concentration increase of the biomarker cardiac troponin I in a reducing union microfluidic chip using cationic isotachophoresis

This paper describes the preconcentration of the biomarker cardiac troponin I (cTnI) and a fluorescent protein (R-phycoerythrin) using cationic isotachophoresis (ITP) in a 3.9 cm long poly(methyl methacrylate) (PMMA) microfluidic chip. The microfluidic chip includes a channel with a 5× reduction in depth and a 10× reduction in width. Thus, the overall cross-sectional area decreases by 50× from inlet (anode) to outlet (cathode). The concentration is inversely proportional to the cross-sectional area so that as proteins migrate through the reductions, the concentrations increase proportionally. In addition, the proteins gain additional concentration by ITP. We observe that by performing ITP in a cross-sectional area reducing microfluidic chip we can attain concentration factors greater than 10,000. The starting concentration of cTnI was 2.3 μg mL⁻¹ and the final concentration after ITP concentration in the microfluidic chip was 25.52 ± 1.25 mg mL⁻¹. To the author's knowledge this is the first attempt at concentrating the cardiac biomarker cTnI by ITP. This experimental approach could be coupled to an immunoassay based technique and has the potential to lower limits of detection, increase sensitivity, and quantify different isolated cTnI phosphorylation states.

Rapid microscale in-gel processing and digestion of proteins using surface acoustic waves

A new method for in-gel sample processing and tryptic digestion of proteins is described. Sample preparation, rehydration, in situ digestion and peptide extraction from gel slices are dramatically accelerated by treating the gel slice with surface acoustic waves (SAWs). Only 30 minutes total workflow time is required for this new method to produce base peak chromatograms (BPCs) of similar coverage and intensity to those observed for traditional processing and overnight digestion. Simple set up, good reproducibility, excellent peptide recoveries, rapid turnover of samples and high confidence protein identifications put this technology at the fore-front of the next generation of proteomics sample processing tools.

Rapid protein depletion from complex samples using a bead-based microfluidic device for the point of care

Translation of sample preparation methods to point-of-care formats has remained a challenge. We present a plastic laminate microfluidic device for protein depletion from human plasma using ligand immobilized porous beads stored dry within a novel, pneumatically-driven mixer. The card design accelerated the protein depletion process from hours to minutes. Using immunoglobulin G as a model protein, we have successfully shown protein removal efficiency from spiked buffer between 70-80% and from diluted human plasma samples between 66-77%. Low non-specific binding of our downstream target ligand, immunoglobulin M, was observed with the spiked buffer and diluted human plasma samples. For future device optimization, the physical limitations to rapid protein removal on card were also explored. Bench-top experiments with improved mixing efficiency and a lower sample dilution factor achieved 99% IgG removal using the same amount of mixing time. This design can easily be adapted for depletion of other high abundance or interfering proteins by inclusion of other ligand immobilized beads.

Novel sampling methods for atmospheric semi-volatile organic compounds (SOCs) in a high altitude alpine environment

High- and low-volume active air samplers as well as bulk deposition samplers were developed to sample atmospheric SOCs under the adverse conditions of a mountain environment. Active sampling employed separate filters for different European source regions. Filters were switched depending on daily trajectory forecasts, whose accuracy was evaluated post hoc. The sampling continued on three alpine summits over five periods of four months. The prevailing trajectories varied stronger between sampling periods than between stations. The sampling equipment (active and bulk deposition) proved dependable for operation in a mountain environment, with idle times being mainly due to non-routine manipulations and connectivity.

Long-term air monitoring of organochlorine pesticides using Semi Permeable Membrane Devices (SPMDs) in the Alps

Atmospheric sampling of organochlorine pesticides (OCPs) was conducted using Semi Permeable Membrane Devices (SPMDs) deployed in the Alps at different altitudinal transects for two consecutive exposure periods of half a year and a third simultaneous year-long period. Along all the altitude profiles, the sequestered amounts of OCPs increased in general with altitude. SPMDs were still working as kinetic samplers after half a year for the majority of the OCPs. However, compounds with the lowest octanol-air partition coefficient (K(oa)), reached equilibrium within six months. This change in the SPMD uptake was determined for the temperature gradient along the altitude profile influencing K(oa), OCPs availability in the gaseous phase, and SPMD performance. In sum, it seems two effects are working in parallel along the altitude profiles: the change in SPMD performance and the different availability of OCPs along the altitudinal transects determined by their compound properties and concentrations in air.

Modification of a reaction vessel for the determination of total mercury in hair by cold vapor atomic absorption spectrometry

A classical cold vapor atomic absorption spectrometric (CVAAS) method for the determination of total mercury in blood has been previously adapted for application to samples of human hair. The reaction vessel specified in the original adaptation was, however, large and difficult to use with small hair samples. In the present study, the reaction vessel has been modified and reduced in size and the protocols have been optimized in order to provide an analytical method that is more efficient, less time-consuming, and gives lower blank values than the original adaptation. The optimized method was validated by multiple, independent, replicated assays of certified reference hair samples, and the mean recovery obtained (98.7%) indicated an efficient performance of the digestion and detection processes. The method was applied to the assay of 144 hair samples derived from populations that had or had not been exposed to mercury from environmental sources. The results from all of the samples analyzed were consistent with those published previously for similar samples.

Validation of high-throughput measurement system with microwave-assisted extraction, fully automated sample preparation device, and gas chromatography-electron capture detector for determination of polychlorinated biphenyls in whale blubber

Validation of a high-throughput measurement system with microwave-assisted extraction (MAE), fully automated sample preparation device (SPD), and gas chromatography-electron capture detector (GC-ECD) for the determination of polychlorinated biphenyls (PCBs) in minke whale blubber was performed. PCB congeners accounting for > 95% of the total PCBs burden in blubber were efficiently extracted with a small volume (20 mL) of n-hexane using MAE due to simultaneous saponification and extraction. Further, the crude extract obtained by MAE was rapidly purified and automatically substituted to a small volume (1 mL) of toluene using SPD without using concentrators. Furthermore, the concentration of PCBs in the purified and concentrated solution was accurately determined by GC-ECD. Moreover, the result of accuracy test using a certified material (SRM 1588b; Cod liver oil) showed good agreement with the NIST certified concentration values. In addition, the method quantification limit of total-PCB in whale blubbers was 41 ng g(-1). This new measurement system for PCBs takes only four hours. Consequently, it indicated this method is the most suitable for the monitoring and screening of PCBs in the conservation of the marine ecosystem and safe distribution of foods.

Optimization of sample transfer in two-dimensional microfluidic separation systems

Multidimensional microfluidic separation systems combining a first dimension microchannel with an array of parallel second dimension microchannels can suffer from non-uniform sample transfer between the dimensions, sample leakage, and injection plug tailing within the second dimension array. These factors can significantly reduce overall two-dimensional separation performance. In this paper, numerical and analytical models reveal an optimized chip design which combines multidimensional backbiasing and an angled channel geometry to ensure leakage-free and uniform interdimensional sample transfer, while also minimizing injected sample plug lengths. The optimized design is validated experimentally using a multidimensional chip containing five second dimension channels.

Development of a simple hollow fibre supported liquid membrane extraction method to extract and preconcentrate dinitrophenols in environmental samples at ngL−1 level by liquid chromatography

An easy and rapid hollow-fibre supported liquid membrane method (HFSLM) has been developed to extract and determinate the total concentration of four dinitrophenols in environmental water at ng L(-1) level. This extraction method provides a high selectivity, short extraction time and very low cost for real samples. It is a three-phase system, aqueous-organic-aqueous, where the organic solvent is held into the fibre pores, being in contact with the two other phases. The organic phase is formed by two different organic solvents, with two different polarities, n-undecane and toluene (1:1). The optimization step was performed using a three-variable Doehler design, involving three factors, stirring speed, fibre length and sample volume. The organic phase composition, as well as the pH of the acceptor and donor phases was also optimized. The extraction equilibrium was reached after 30 min, after which essentially the total amount (90-80%) of the four dinitrophenolic compounds were extracted from the sample. Better repeatability and reproducibility at the expense of lower enrichment factors was obtained compared with other methods, employing incomplete extraction during a fixed time. The matrix effect was tested by performing extractions from leachate water and river water. This method is linear in the range 0.1-100 microgL(-1) in different matrices, with detection limit around 100 ng L(-1), after extraction of 6 mL of sample and using high performance liquid chromatography for final analysis.

Principles, developments and applications of on-line coupling of extraction with chromatography

On-line coupling of extraction and chromatographic separation allows the whole analysis to be performed in a closed system. On-line systems are particularly useful when the analytes are labile, the amount of sample is limited, or very high sensitivity is required. Many on-line systems have been developed both for liquid and for solid samples. This review discusses the different instruments that have been constructed and the factors that need to be considered in the coupling. Selected illustrative applications are described to illustrate the potential of the on-line systems.

Automated, on-line membrane extraction

Over the last few years, membranes have been used to develop new approaches in analytical extraction, concentration and cleanup. An important advantage of membrane processes is that the sample and the extraction phase can be continuously brought into contact without physical mixing, and may be directly interfaced to an analytical instrument. This provides the basis for automated, real-time monitoring. Membrane extraction has been applied to a wide range of organic and inorganic analytes, and has been directly interfaced with chromatography, spectroscopy and mass spectrometry. Implementations of membrane extraction are diverse, encompassing different types of membranes, module designs and configurations. This review highlights some of these, and particularly the unique capabilities in automated, and on-line measurements.

Terpene degradation and extraction from basil and oregano leaves using subcritical water

In the first part of this study, the stability of five terpenes (alpha-pinene, limonene, camphor, citronellol, and carvacrol) under subcritical water conditions was investigated. The stability studies were carried out at four different temperatures (100, 150, 200, and 250 degrees C) with two different heating times (30 and 300 min). When water temperature was increased, the degradation of terpenes became more serious. Prolonged exposure time to each heating temperature also caused decreased terpene stability. The terpene recoveries were determined by conducting subcritical water extraction of sand spiked with terpenes. The recoveries are typically around 70 to 80% for extractions at 100 degrees C. Terpene recoveries were decreased with increasing water temperature due to poorer stability of terpenes. After the degradation and recovery studies, basil and oregano leaves were extracted using water at both 100 and 150 degrees C. The concentrations of each individual terpene in the water extract generally ranged from trace quantity to 65 microg terpene/g herb. However, the concentration of carvacrol in the oregano-water extract at 150 degrees C was found to be as high as 4270 microg carvacrol/g oregano.

Ultrasound in analytical chemistry

Ultrasound is a type of energy which can help analytical chemists in almost all their laboratory tasks, from cleaning to detection. A generic view of the different steps which can be assisted by ultrasound is given here. These steps include preliminary operations usually not considered in most analytical methods (e.g. cleaning, degassing, and atomization), sample preparation being the main area of application. In sample preparation ultrasound is used to assist solid-sample treatment (e.g. digestion, leaching, slurry formation) and liquid-sample preparation (e.g. liquid-liquid extraction, emulsification, homogenization) or to promote heterogeneous sample treatment (e.g. filtration, aggregation, dissolution of solids, crystallization, precipitation, defoaming, degassing). Detection techniques based on use of ultrasonic radiation, the principles on which they are based, responses, and the quantities measured are also discussed.

Recent developments in methods and technology for analysis of biological samples by MALDI-TOF-MS

Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) is widely used in a variety of fields because it has the characteristics of speed, ease of use, high sensitivity, and wide detectable mass range for obtaining molecular weights and for structural characterization of macromolecules. In this article we summarize recent developments in matrix additives, new matrices, and sample-pretreatment methods using off-probe or on-probe techniques or nanomaterials for MALDI-TOF-MS analysis of biological samples.