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.

Fabrication of a polycarbonate microdevice and boronic acid-mediated surface modification for on-chip sample purification and amplification of foodborne pathogens.

In this study, we integrated sample purification and genetic amplification in a seamless polycarbonate microdevice to facilitate foodborne pathogen detection. The sample purification process was realized based on the increased affinity of the boronic acid-modified surface toward the cis-diol group present on the bacterial outer membrane. The modification procedure was conducted at room temperature using disposable syringe. The visible color and fluorescence signals of alizarin red sodium were used to confirm the success of the surface modification process. Escherichia coli O157:H7 containing green fluorescence protein (GFP) and Staphylococcus aureus were chosen as the microbial models to demonstrate the nonspecific immobilization using the microdevice. Bacterial solutions of various concentrations were injected into the microdevice at three flow rates to optimize the operation conditions. This microdevice successfully amplified the 384-bp fragment of the eaeA gene of the captured E. coli O157:H7 within 1 h. Its detection limit for E. coli O157:H7 was determined to be 1 × 103 colony-forming units per milliliter (CFU mL-1). The proposed microdevice serves as a monolithic platform for facile and on-site identification of major foodborne pathogens.

Freeze-thaw approach: A practical sample preparation strategy for residue analysis of multi-class veterinary drugs in chicken muscle.

Seven drugs from different classes, namely, fluoroquinolones (enrofloxacin, ciprofloxacin, sarafloxacin), sulfonamides (sulfadimidine, sulfamonomethoxine), and macrolides (tilmicosin, tylosin), were used as test compounds in chickens by oral administration, a simple extraction step after cryogenic freezing might allow the effective extraction of multi-class veterinary drug residues from minced chicken muscles by mix vortexing. On basis of the optimized freeze-thaw approach, a convenient, selective, and reproducible liquid chromatography with tandem mass spectrometry method was developed. At three spiking levels in blank chicken and medicated chicken muscles, average recoveries of the analytes were in the range of 71-106 and 63-119%, respectively. All the relative standard deviations were <20%. The limits of quantification of analytes were 0.2-5.0 ng/g. Regardless of the chicken levels, there were no significant differences (P > 0.05) in the average contents of almost any of the analytes in medicated chickens between this method and specific methods in the literature for the determination of specific analytes. Finally, the developed method was successfully extended to the monitoring of residues of 55 common veterinary drugs in food animal muscles.

Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis.

AIMS: To demonstrate and characterize a portable lysis apparatus for rapid single-step bacterial DNA extraction. METHODS AND RESULTS: Our portable lysis apparatus employed a novel design consisting of an annular piezo-element with perforated diaphragm. Using Bacillus subtilis as target bacteria, our portable lysis apparatus was able to achieve a normalized percent lysis as high as 66% within 30 s. This is comparable to that by microprobe ultrasonication and almost 7 times higher than that by conventional bead beating. The effect from adding glass beads was predictable. However, the results from the addition of sodium dodecyl sulphate (SDS) were counter-intuitive because a further increase from 0·5 to 1% concentration reduced the lysis performance. The portable lysis apparatus is also at least 1·5-5 times more power efficient than microprobe ultrasonication. CONCLUSIONS: Our portable lysis apparatus is capable of rapidly extracting bacterial DNA and is more power efficient than microprobe ultrasonication. The addition of glass beads or SDS concentration (up to 0·5%) improves its performance. SIGNIFICANCE AND IMPACT OF THE STUDY: The portable lysis apparatus provides a standalone, rapid, low cost and power efficient way of obtaining genomic constituents prior to a variety of bioassays used in the field of environmental, biomedical and other applied microbiology.

Comparison of microwave-assisted and heat reflux extraction techniques for the extraction of ten major compounds from Zibu Piyin Recipe using ultra high performance liquid chromatography with tandem mass spectrometry.

Microwave-assisted extraction and efficient ultra-high performance liquid chromatography with triple quadrupole mass spectrometry were previously used to quickly extract and simultaneously quantify ginsenoside Rf, Ro, and Rd, 20(S)-ginsenoside-Rg2 , 20(R)-ginsenoside-Rg2 , tanshinone IIA, cryptotanshinone, dihydrotanshinone I, lithospermic acid, and osthole from Zibu Piyin Recipe. We here showed that heat reflux extraction provides higher extraction efficiency of these target compounds but is more time consuming. Chromatographic separation was achieved on an Agilent ZORBAX RRHD Eclipse Plus C18 column with a gradient mobile phase consisting of water/0.5% formic acid and acetonitrile at a flow rate of 0.2 mL/min, and detection was performed by positive and negative ion multiple-reaction monitoring mode. All analytes showed good linearity (r, 0.9989-0.9999) within the test range, with a limit of detection of 0.002-0.180 µg/mL. The overall intra- and interday variations of the ten compounds were ≤2.9%, and the accuracy was evaluated using a recovery test at three concentrations and was in the range 97.61-103.18% (RSD ≤ 4.25%). The analytical results showed remarkable differences in the concentrations of the ten compounds extracted from Zibu Piyin Recipe by microwave-assisted extraction and heat reflux extraction. These findings provide important information for determining the quality of Zibu Piyin Recipe.

Is "dried stool spots on filter paper method (DSSFP)" more sensitive and effective for detecting Blastocystis spp. and their subtypes by PCR and sequencing?

PCR and DNA sequencing are currently the diagnostic methods of choice for detection of Blastocystis spp. and their suptypes. Fresh or frozen stool samples have disadvantages in terms of several aspects such as transportation, storage, and existence of PCR inhibitors. Filter paper technology may provide a solution to these issues. The aim of the present study was to detect Blastocystis spp. and their subtypes by employing two different preservation methods: conventional frozen stool (FS) and dried stool spots on filter paper (DSSFP). Concentration and purity of DNA, sensitivity of PCR, and DNA sequencing results obtained from the two methods were also compared. A total of 230 fecal samples were included and separated into two parts: one part of the fecal samples were directly frozen and stored at -20 °C. The remaining portion of the specimens were homogenized with saline and spread onto the filter papers as thin layer with a diameter of approximately 3 cm. After air-dried, the filter papers were stored at room temperature. DSSFP samples were collected by scraping from the filter papers. DNA were extracted by EURx Stool DNA Extraction Kit from both samples. Concentration and purity were measured with Nano-Drop, then PCR and sequencing were conducted for detection of Blastocystis spp. and its genotypes. Pure DNA was obtained with a A260/A280 ratio of 1.7-2.2 in both methods. DNA yield from FS was 25-405 ng/µl and average DNA concentration was 151 ng/µl, while these were 7-339 and 122 ng/µl for DSSFP, respectively. No PCR inhibition was observed in two methods. DNA from DSSFP were found to be stable and PCR were reproducible for at least 1 year. FS-PCR- and DSSFP-PCR-positive samples were 49 (21.3 %) and 58 (25.3 %), respectively (p = 0.078). The 43 specimens were concordantly positive by both FS-PCR and DSSFP-PCR. When the microscopy was taken as the gold standard, sensitivity of DSSFP-PCR and FS-PCR was 95.5 and 86.4 %, while specificity of both tests was 99.4 and 98.3 %, respectively. DNA sequencing results of 19 microscopically confirmed cases were strictly identical (concordance 100 %) in both methods, and ST2:6, ST3:8, ST4:3, and ST6:2 were the detected subtypes. Among the 230 fecal samples, the most predominant subtypes were ST3, ST2, ST4, and ST1 by both FS and DSSFP methods. Concordance of DNA sequencing results obtained from the two methods was noted to be 90.7 %. To our knowledge, this is the first study that demonstrates DNA extraction from DSSFP is more sensitive and effective than the FS method for diagnosis of Blastocystis spp. and their subtypes by PCR and DNA sequencing.

Electrokinetic preconcentration of particles and cells in microfluidic reservoirs.

Preconcentrating samples of dilute particles or cells to a detectable level is required in many chemical, environmental and biomedical applications. A variety of force fields have thus far been demonstrated to capture and accumulate particles and cells in microfluidic devices, which, however, all take place within the region of microchannels and may potentially cause channel clogging. This work presents a new method for the electrokinetic preconcentration of 1 µm-diameter polystyrene particles and E. coli cells in a very-low-conductivity medium inside a microfluidic reservoir. The entire microchannel can hence be saved for a post-concentration analysis. This method exploits the strong recirculating flows of induced-charge electroosmosis to concentrate particles and cells near the corners of the reservoir-microchannel interface. Positive dielectrophoresis is found to also play a role when small microchannels are used at high electric fields. Such an in-reservoir electrokinetic preconcentration method can be easily implemented in a parallel mode to increase the flow throughput, which may potentially be used to preconcentrate bacterial pathogens in water.

[Instrumentation and Application of a Portable Pretreating System for a Speedy Plasmon-Enhanced Raman Spectroscopy Detection Towards Food Safety].

The present paper developed a portable and fast sample pretreatment apparatus. It has many virtues like being portable, low power consumption and convenient operation, short extraction time and sound repeatability. Therefore, it can meet the requirements of on-site rapid detection pretreatment. The apparatus consists of four functional modules: ultrasonic extraction unit, heating unit, exhaust gas evaporation and absorption unit and control system. In addition, LED control panel and alarm device were designed. The whole treatment process needs three steps: ultrasonic extraction, liquid-liquid extraction and solvent evaporation by heating and pumping. For test of this apparatus performance, three real samples (pepper powder, pepper oil, bean sauce) containing banned additive Rhodamine B were taken as experiment objects. Compared with conventional laboratory pretreatment method, the PERS spectra achieved by two methods were little changed, but the experiment time was halved. In addition, the test results showed relative standard deviation less than ±5%.

Development of an adapted version of polar organic chemical integrative samplers (POCIS-Nylon).

POCIS (polar organic chemical integrative samplers) are increasingly used for sampling polar compounds. Although very efficient for a wide range of pollutants, the classic configuration of the device has a number of limitations, in particular for the sampling of highly polar analytes and hydrophobic compounds. This study presents a new version of the POCIS passive sampler which uses a highly porous Nylon membrane of 30 µm pore size, enabling the sampling of hydrophobic pollutants and improving the accumulation rate of other pollutants. This newly designed tool and the classic POCIS were both tested during a laboratory experiment to evaluate the accumulation kinetics of a selection of pesticides and pharmaceuticals. The observed results show unexpected accumulation kinetics for the new version of POCIS. To explain the data, the use of an intraparticulate diffusion model was required, which also enabled us to propose another explanation of the burst effect observed with the classic POCIS, primarily related to the potential wetting of the device as the first step in the accumulation of compounds.

Development of the performance reference compound approach for the calibration of "polar organic chemical integrative sampler" (POCIS).

The purpose of the Water Framework Directive is to ensure the quality of the natural water across Europe. In this context, passive samplers have shown interesting capacities for the monitoring of contaminants in aqueous ecosystems. They allow the measurement of time-weighted average concentrations, overcoming many drawbacks of the spot-sampling techniques known to be expensive and time consuming. However, application of passive samplers such as polar organic chemical integrative samplers (POCIS) for the monitoring of hydrophilic contaminants requires calibration to define compound sampling rates; key parameters to deduce the pollutant water concentrations from the amounts of pollutants accumulated by the device. Unfortunately, sampling rates are influenced by a range of environmental factors; in that respect, a question remains: is it not evident to know to what extent the sampling rates obtained in laboratory experiments can be used in field conditions? The problem can be solved for hydrophobic samplers by using performance reference compounds (PRCs), and an ongoing challenge for POCIS is focused on the improvement of the quantitative aspect of this family of samplers. In this study, potential PRCs have been selected during a specific experiment and their performance was tested in the laboratory under two hydrodynamic conditions. Results revealed a good proportionality between elimination rates of PRCs and sampling rates of chemicals. Afterwards, the application of the approach under environmental conditions was assessed by deploying POCIS in the Arcachon Bay (France) where POCIS-PRC-derived water concentrations appear to be close to the simultaneous grab-sampling results.

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.

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.

A high-throughput sample preparation method for cellular proteomics using 96-well filter plates.

A high-throughput sample preparation protocol based on the use of 96-well molecular weight cutoff (MWCO) filter plates was developed for shotgun proteomics of cell lysates. All sample preparation steps, including cell lysis, buffer exchange, protein denaturation, reduction, alkylation and proteolytic digestion are performed in a 96-well plate format, making the platform extremely well suited for processing large numbers of samples and directly compatible with functional assays for cellular proteomics. In addition, the usage of a single plate for all sample preparation steps following cell lysis reduces potential samples losses and allows for automation. The MWCO filter also enables sample concentration, thereby increasing the overall sensitivity, and implementation of washing steps involving organic solvents, for example, to remove cell membranes constituents. The optimized protocol allowed for higher throughput with improved sensitivity in terms of the number of identified cellular proteins when compared to an established protocol employing gel-filtration columns.

Comparison of six commercial DNA extraction kits for detection of Brucella neotomae in Mexican and Central American-style cheese and other milk products.

Raw or inadequately pasteurized milk from infected animals and cheese made with such milk are a frequent vehicle for human brucellosis infection. Also, biological terrorism is a concern with certain Brucella spp. Due to matrix-associated real-time polymerase chain reaction (qPCR) inhibitors, robust sample preparations are crucial. We compared six commercial nucleic acid extraction kits using nine Mexican and Central American-style soft cheeses or creams and three liquid milk products inoculated with Brucella neotomae, a surrogate for pathogenic Brucella spp. Kits were evaluated by purity and quantity of DNA as determined by qPCR Ct values, reproducibility across cheese and milk types, and cost. At 10(7) CFU/g in four different cheeses, Qiagen statistically outperformed all other kits. When two cheese styles were inoculated at dual levels, Qiagen and High Pure kit extracted samples at 1.5 × 10(5) CFU/g produced average Ct values of 34-39, while PrepSEQ and MagMAX kit extracted samples exhibited higher or no Ct values. High Pure and Qiagen kits excelled also with liquid milk products. Considering matrices, inoculation levels, and kits evaluated, High Pure and Qiagen products produced Brucella DNA of high quality and quantity indicated by the lowest Ct values and were the least expensive.

A simple separation method with a microfluidic channel based on alternating current potential modulation.

A simple separation and detection system based on an electrochemical potential modulated microchannel (EPMM) device was developed for the first time. The application of alternating current (AC) potential to the microfluidic separation channel walls, which were composed of screen printed carbon electrodes, resulted in the oscillation and fluctuation of analytes and in the formation of a perfect flat flow front. These events resulted in an increase in the effective concentration and in the fine separation of samples. The performance of the EPMM device was examined through the analysis of endocrine disruptors (EDs) and heavy metal ions (HMIs) as model compounds. The analytical parameters that affected the separation and detection of EDs and HMIs were studied in terms of AC amplitude, AC frequency, flow rate, buffer concentration, pH, detection potential, and temperature. The separation efficiency was evaluated through measurements of the theoretical plate number (N), the retention time, and the half-peak width. Linear calibration plots for the detection of EDs and HMIs were obtained between 0.15 and 250.0 nM (detection limit 86.4 ± 2.9 pM) and between 0.01 and 10.0 nM (detection limit 9.5 ± 0.3 pM), respectively. The new device was successfully demonstrated with authentic and real samples.

A membrane microcontactor as a tool for integrated sample preparation.

A membrane microcontactor suitable to perform liquid-liquid extraction as well as evaporation in order to conduct enrichment steps in sample preparation of organ samples has been designed, fabricated, and characterized. Spacers of 100- or 200-µm high were constructed in a metal substrate with a channel width of 13 mm and the extraction kinetics in these channels was evaluated. The spacers were designed such that at the entrance and exit region a uniform flow distribution could take place and that a uniform flow profile could be guaranteed along the channel, hence allowing a large freedom in sample volume to be processed. The extraction and evaporation kinetic behavior of the device was first evaluated by extraction of a drug candidate (4-(2,5-dimethyl-pyrrol-1-y1)-2-hydroxybenzoic acid). To evaluate the device under more challenging working conditions, a homogenized mice kidney sample containing the drug candidate that was administered in life condition was cleaned and enriched with the extraction and evaporation modules and characterized by high-performance liquid chromatography, yielding an overall analysis time of 15-20 min per sample only. The system has the potential to be operated in a continuous fashion, making it appealing to be implemented in screening or high-throughput applications.

Homogeneous immunosubtraction integrated with sample preparation enabled by a microfluidic format.

Immunosubtraction is a powerful and resource-intensive laboratory medicine assay that reports both protein mobility and binding specificity. To expedite and automate this electrophoretic assay, we report on advances to the electrophoretic immunosubtraction assay by introducing a homogeneous, not heterogeneous, format with integrated sample preparation. To accomplish homogeneous immunosubtraction, a step-decrease in separation matrix pore-size at the head of a polyacrylamide gel electrophoresis (PAGE) separation channel enables "subtraction" of target analyte when capture antibody is present (as the large immune-complex is excluded from PAGE), but no subtraction when capture antibody is absent. Inclusion of sample preparation functionality via small pore size polyacrylamide membranes is also key to automated operation (i.e., sample enrichment, fluorescence sample labeling, and mixing of sample with free capture antibody). Homogeneous sample preparation and assay operation allows on-the-fly, integrated subtraction of one to multiple protein targets and reuse of each device. Optimization of the assay is detailed which allowed for ~95% subtraction of target with 20% non-specific extraction of large species at the optimal antibody-antigen ratio, providing conditions needed for selective target identification. We demonstrate the assay on putative markers of injury and inflammation in cerebrospinal fluid (CSF), an emerging area of diagnostics research, by rapidly reporting protein mobility and binding specificity within the sample matrix. We simultaneously detect S100B and C-reactive protein, suspected biomarkers for traumatic brain injury (TBI), in ~2 min. Lastly, we demonstrate S100B detection (65 nM) in raw human CSF with an estimated lower limit of detection of 3.25 nM, within the clinically relevant concentration range for detecting TBI in CSF. Beyond the novel CSF assay introduced here, a fully automated immunosubtraction assay would impact a spectrum of routine but labor and time-intensive laboratory medicine assays.

Quality assurance and quality control for thermal/optical analysis of aerosol samples for organic and elemental carbon.

Accurate, precise, and valid organic and elemental carbon (OC and EC, respectively) measurements require more effort than the routine analysis of ambient aerosol and source samples. This paper documents the quality assurance (QA) and quality control (QC) procedures that should be implemented to ensure consistency of OC and EC measurements. Prior to field sampling, the appropriate filter substrate must be selected and tested for sampling effectiveness. Unexposed filters are pre-fired to remove contaminants and acceptance tested. After sampling, filters must be stored in the laboratory in clean, labeled containers under refrigeration (<4 °C) to minimize loss of semi-volatile OC. QA activities include participation in laboratory accreditation programs, external system audits, and interlaboratory comparisons. For thermal/optical carbon analyses, periodic QC tests include calibration of the flame ionization detector with different types of carbon standards, thermogram inspection, replicate analyses, quantification of trace oxygen concentrations (<100 ppmv) in the helium atmosphere, and calibration of the sample temperature sensor. These established QA/QC procedures are applicable to aerosol sampling and analysis for carbon and other chemical components.