Integrated Sample Preparation Research Articles

Numerical modeling and experimental validation of uniform microchamber filling in centrifugal microfluidics

In this paper, a comprehensive approach to numerical and experimental analysis of microchamber filling in centrifugal microfluidics is presented. In the development of micro total analysis systems, it is often necessary to achieve complete, uniform filling of relatively large microchambers, such as those needed for nucleic acid amplification or detection. With centrifugal devices, these large microchambers must often be orientated perpendicularly to the direction of centrifugal force and are usually bounded by materials with varying surface properties. The resulting fluidic flow in such systems can be complex and is not well characterized. To gain further insight into complex fluidic behavior on centrifugal microfluidic platforms, numerical modeling using the Volume of Fluids method is performed to simulate microchamber filling in a centrifugal microfluidic device with integrated sample preparation, amplification, and detection capabilities. Parametric analyses are performed using numerical models to predict microchamber filling behavior for a range of pressure conditions. High-speed flow visualization techniques are used to track the liquid meniscus during filling of the microchambers, and comparison to the numerical predictions for experimental validation is achieved by analyzing the liquid volume fraction as a function of the non-dimensional temporal profile during filling. When channel filling profiles are compared, the numerical model predictions utilizing static conditions are in strong agreement with the experimental data. When dynamic modeling conditions are used, the numerical predictions are extremely accurate as compared to the experimental data.

Sample preparation: the forgotten beginning.

Advances in molecular technologies and automated instrumentation have provided many opportunities for improved detection and identification of microorganisms; however, the upstream sample preparation steps needed to apply these advances to foods have not been adequately researched or developed. Thus, the extent to which these advances have improved food microbiology has been limited. The purpose of this review is to present the current state of sample preparation, to identify knowledge gaps and opportunities for improvement, and to recognize the need to support greater research and development efforts on preparative methods in food microbiology. The discussion focuses on the need to push technological developments toward methods that do not rely on enrichment culture. Among the four functional components of microbiological analysis (i.e., sampling, separation, concentration, detection), the separation and concentration components need to be researched more extensively to achieve rapid, direct, and quantitative methods. The usefulness of borrowing concepts of separation and concentration from other disciplines and the need to regard the microorganism as a physicochemical analyte that may be directly extracted from the food matrix are discussed. The development of next-generation systems that holistically integrate sample preparation with rapid, automated detection will require interdisciplinary collaboration and substantially increased funding.

Microchips for CE: Breakthroughs in real‐world food analysis

The well-known complexity of food matrices is approached using CE microchips with different strategies to improve the selectivity and sensitivity of the analysis by avoiding and/or making the sample preparation as simple as possible: (i) enhancing the peak capacity in order to perform direct injection, (ii) using the microchip platform to measure one target analyte/group of analytes with or without separating other related interferences, (iii) integrating sample preparation steps on the microchip platform, and (iv) integrating new analytical tools from nanotechnology in the detection stage. New analyte separations of food significance involving DNA probes, biogenic amines, vanilla flavors, and dyes have been reported as successfully breaking new barriers in areas of high impact in the market, such as transgenic food analysis, as well as the detection of frauds and toxins. Simple microchip layouts are still the most common designs used, though sophisticated new ones are emerging. In contrast to other application areas, electrochemical detection continues to be the most common detection route, followed by LIF, though non-conventional detection routes are also emerging, such as chemiluminescence or UV. In terms of analytical performance, the integration of calibration and quality control on a microchip platform, and remarkable accuracy and precision are being obtained using creative analytical methodologies that enhance the analytical potency of microfluidic chips for their future commercialization. This review critically states the most important advances derived from work done in the field over the past 2-3 years.

Development of an On-site Measurement System for Salivary Stress-related Substances Based on Microchip Capillary Electrophoresis Technology

Psychological stress is of major importance to all age groups in recent years, and may lead to mental disorder and various diseases. An objective and quantitative method for measuring salivary stress-related substances is highly desired because saliva collection is easy, stress free and noninvasive. We have developed a rapid and easy-to-use analytical tool for the measurement of cortisol and secretory immunoglobulin A (sIgA) based on microchip technology, immunoselectivity and electrophoretic separation technique. Performing immunoreaction and capillary electrophoresis (CE) separation on microchips is a promising technique for on-site determination of biogenic substances, and has a few advantages over conventional immunoassay methods: reduced sample size, shortening analysis times, high separation efficiency, reduced cost, and downsizing of analytical system. At this stage of our research, some preliminary prototypes of a high-sensitive microchip CE instrument were constructed to determine the stress-related substances in real saliva samples. However, there is not enough detection sensitivity for cortisol analysis. On the other hand, sIgA was successfully analyzed using a laboratory-built microchip CE system and optimal analytical conditions. The sIgA determination is rapid compared with a conventional immunoassay method, and provides an acceptable degree of repeatability and recovery. In the future, microchip technologies will enable total automation and integration of sample preparation. This research has widespread future potential for monitoring multiple stress-related markers within minutes from a trace of saliva, and can contribute to disease prevention and overall good health.

Synergistic Design of Electric Field and Membrane in Facilitating Continuous Adsorption for Cleanup and Enrichment of Proteins in Direct ESI-MS Analysis

We designed and fabricated a novel microdevice to facilitate continuous adsorption phenomena for biological sample preparation. Using the device, we also developed an online, highly integrated, multifunctional strategy, with a promise of accepting a large volume of crude tissue extracts with the end point generation of a reliable MS identification within 20 min. Under an external electric field, charged membranes can adsorb multiple layers of proteins, which exceed the capacity limit of common resins or membranes. It enlarges sample loading and trapping efficiency, thus bypasses the tradeoff between sample capacity and downstream detection sensitivity. This integrated approach, formed by synergistic utilization among electric field, membrane, and fluidic handling at the microscale, reduces the overall complexity of crude samples in one step for direct MS analysis. The sample preparation goals, including enrichment, desalting, removal of noncharged contaminants, and initial fractionation, can be rapidly performed in a single device. The strategy facilitates reproducible MS quantification by circumventing traditional laborious and time-consuming sample preparation steps. In addition, MEPD extended the ion trap linear dynamic range from 2 to at least 4 orders of magnitude by eliminating ion suppression effect, enriching target analyte(s), and decreasing sample loss during integrated sample preparation.

Development of a digital microfluidic platform for point of care testing

Point of care testing is playing an increasingly important role in improving the clinical outcome in health care management. The salient features of a point of care device are rapid results, integrated sample preparation and processing, small sample volumes, portability, multifunctionality and low cost. In this paper, we demonstrate some of these salient features utilizing an electrowetting-based Digital Microfluidic platform. We demonstrate the performance of magnetic bead-based immunoassays (cardiac troponin I) on a digital microfluidic cartridge in less than 8 minutes using whole blood samples. Using the same microfluidic cartridge, a 40-cycle real-time polymerase chain reaction was performed within 12 minutes by shuttling a droplet between two thermal zones. We further demonstrate, on the same cartridge, the capability to perform sample preparation for bacterial infectious disease pathogen, methicillin-resistant Staphylococcus aureus and for human genomic DNA using magnetic beads. In addition to rapid results and integrated sample preparation, electrowetting-based digital microfluidic instruments are highly portable because fluid pumping is performed electronically. All the digital microfluidic chips presented here were fabricated on printed circuit boards utilizing mass production techniques that keep the cost of the chip low. Due to the modularity and scalability afforded by digital microfluidics, multifunctional testing capability, such as combinations within and between immunoassays, DNA amplification, and enzymatic assays, can be brought to the point of care at a relatively low cost because a single chip can be configured in software for different assays required along the path of care.

Microfluidic Chips for Detecting the t(4;14) Translocation and Monitoring Disease during Treatment Using Reverse Transcriptase-Polymerase Chain Reaction Analysis of IgH-MMSET Hybrid Transcripts

Diagnosis platforms incorporating low-cost microfluidic chips enable sensitive, rapid, and accurate genetic analysis that could facilitate customized therapies tailored to match the vulnerabilities of any types of cancer. Using ex vivo cancer cells, we have detected the unique molecular signature and a chromosomal translocation in multiple myeloma. Multiple myeloma is characterized by IgH rearrangements and translocations that enable unequivocal identification of malignant cells, detected here with integrated microfluidic chips incorporating genetic amplification via reverse transcriptase-polymerase chain reaction and capillary electrophoresis. On microfluidic chips, we demonstrated accurate and versatile detection of molecular signatures in individual cancer cells, with value for monitoring response to therapy, detecting residual cancer cells that mediate relapse, and evaluating prognosis. Thus, testing for two clinically important molecular biomarkers, the IgH VDJ signature and hybrid transcripts signaling the t(4;14) chro-mosomal translocation, with predictive value in diagnosis, treatment decisions, and monitoring has been efficiently implemented on a miniaturized microfluidic system.

An integrated sample preparation to determine coccidiostats and emerging Fusarium‐mycotoxins in various poultry tissues with LC‐MS/MS

The usefulness of an existing sample preparation technique used for ionophoric coccidiostats (lasalocid, monensin, salinomycin and narasin) was applied in the analysis of emerging Fusarium-mycotoxins beauvericin (BEA) and enniatins (ENNs) in poultry tissues (liver and meat). Also, maduramicin and liver as a new sample matrix was introduced. The developed methods were validated and applied for the determination of coccidiostats and BEA/ENNs in Finnish poultry tissues in 2004-2005. The validation parameters demonstrated that the integrated sample preparation technique is applicable to the parallel determination of these contaminants in poultry tissues. Of the samples analysed (276 meat and 43 liver), only trace levels of LAS, MON, SAL, NAR and MAD were detected in 7, 3, 5, 6 and 4% of the samples, respectively. Interestingly, for the first time, traces of BEA and ENNs could also be detected in animal tissues. BEA and ENNs A, A1, B and B1 were found in 2, 0.3, 0.6, 4 and 3% of the samples, respectively. The simultaneous presence of coccidiostats and mycotoxins was detected in three turkey samples in 2004.

LTCC-based microchips for the electrochemical detection of phenolic compounds

The low temperature co-fired ceramic (LTCC) technology can be defined as the fabrication of multilayer applications with the aid of single tapes, which are to be used to integrate passive elements like resistors, capacitors and inductors into the substrate. Using modern manufacturing processes, a large-scale cost-effective production is possible. The ceramic is chemical inert with a good thermal conductivity and just cause excellent properties for the development of “lab-on-a-chip” systems. These devices are described as small, portable and large-scale analytical tools, which includes a number of steps for an automatic analysis. Such systems are typically manufactured out of silicon, glass or polymers. However, devices made from silicon or glass are relatively expensive. Polymers allow low production costs but surface properties of materials are often crucial. A promising alternative seems to be the here presented LTCC-technique. The aim of this study is the development of a “lab-on-a-chip” device based on a LTCC multilayer chip including integrated sample preparation, capillary electrophoresis and electrochemical detection (ECD) as well as all required electrodes and contacts. The separation and detection of numerous phenolic compounds were investigated. Samples were injected by an electrokinetic method and were detected amperometrically. Detection limits were found to be between 12.5 and 250 μmol. The migration velocity was found to be between 0.018 and 0.038 cm s −1 applying a field strength of 86.5 V cm −1. A polyphenol mixture of dopamine, pyrogallol and gallic acid could be separated and detected amperometrically on LTCC-microchips.

Integrated Sample Preparation, Reaction, and Detection on a High-Frequency Centrifugal Microfluidic Platform

We extend the toolbox of lab procedures in life sciences by development of centrifugal microfluidics for high-level process integration. This is accomplished by implementing novel functional principles for sedimentation, batch-mode mixing, frequency-dependent online flow control, and optical read-out, which can be integrated into a process chain. The modular centrifugal setup comprises a microstructured disposable polymer disk as well as a reusable spinning and detection unit. We successfully developed centrifugal microfluidic technologies, which are suitable for sample preparation, process engineering, personalized diagnostics, and hematology, on this platform.

Recent developments in electrochemical detection for microchip capillary electrophoresis

Significant progress in the development of miniaturized microfluidic systems has occurred since their inception over a decade ago. This is primarily due to the numerous advantages of microchip analysis, including the ability to analyze minute samples, speed of analysis, reduced cost and waste, and portability. This review focuses on recent developments in integrating electrochemical (EC) detection with microchip capillary electrophoresis (CE). These detection modes include amperometry, conductimetry, and potentiometry. EC detection is ideal for use with microchip CE systems because it can be easily miniaturized with no diminution in analytical performance. Advances in microchip format, electrode material and design, decoupling of the detector from the separation field, and integration of sample preparation, separation, and detection on-chip are discussed. Microchip CEEC applications for enzyme/immunoassays, clinical and environmental assays, as well as the detection of neurotransmitters are also described.

Human genomic DNA analysis using a semi-automated sample preparation, amplification, and electrophoresis separation platform.

The growing importance of analyzing the human genome to detect hereditary and infectious diseases associated with specific DNA sequences has motivated us to develop automated devices to integrate sample preparation, real-time PCR, and microchannel electrophoresis (MCE). In this report, we present results from an optimized compact system capable of processing a raw sample of blood, extracting the DNA, and performing a multiplexed PCR reaction. Finally, an innovative electrophoretic separation was performed on the post-PCR products using a unique MCE system. The sample preparation system extracted and lysed white blood cells (WBC) from whole blood, producing DNA of sufficient quantity and quality for a polymerase chain reaction (PCR). Separation of multiple amplicons was achieved in a microfabricated channel 30 microm x 100 microm in cross section and 85 mm in length filled with a replaceable methyl cellulose matrix operated under denaturing conditions at 50 degrees C. By incorporating fluorescent-labeled primers in the PCR, the amplicons were identified by a two-color (multiplexed) fluorescence detection system. Two base-pair resolution of single-stranded DNA (PCR products) was achieved. We believe that this integrated system provides a unique solution for DNA analysis.

Solid-phase microextraction combined with surface-enhanced laser desorption/ionization introduction for ion mobility spectrometry and mass spectrometry using polypyrrole coatings.

The successful application of polypyrrole (PPY) solid-phase microextraction (SPME) coatings as both an extraction phase and a surface to enhance laser desorption/ionization (SELDI) of analytes is reported. This SPME/SELDI fiber integrates sample preparation and sample introduction on the tip of a coated optical fiber, as well as acting as the transmission medium for the UV laser light. Using ion mobility spectrometry (IMS) detection, the signal intensity was examined as a function of extraction surface area and concentration of analyte. The linear relationship between concentration and signal intensity shows potential applicability of this detection method for quantitative analysis. Extraction time profiles for the fiber, using tetraoctylammonium bromide as test analyte, illustrated that equilibrium can be reached in less than one minute. To investigate the performance of the PPY coating, the laser desorption profile was studied. The fiber was also tested using a quadrupole time-of-flight (Q-TOF) mass spectrometer with leucine enkephalin as test analyte. Since no matrix was used, mass spectra free from matrix background were obtained. This novel SPME/SELDI fiber is easy to manufacture, and is suitable for studying low-mass analytes because of the intrinsic low background. These findings suggest that other types of conductive polymers could also be used as an extraction phase and surface to enhance laser desorption/ionization in mass spectrometry.

Integrated sample preparation and MALDI mass spectrometry on a microfluidic compact disk.

High-throughput microfluidic processing of protein digests integrated with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry on a compact disk (CD) is described. Centrifugal force moves liquid through multiple microstructures, each containing a 10-nL reversed-phase chromatography column. The CD enables parallel preparation of 96 samples with volumes ranging from one to several microliters. The peptides in the digests are concentrated, desalted, and subsequently eluted from the columns directly into MALDI target areas (200 x 400 microm) on the CD using a solvent containing the MALDI matrix. After crystallization, the CD is inserted into the MALDI instrument for peptide mass fingerprinting and database identification at a routine sensitivity down to the 200-amol level. Detection of proteolytic peptides down to the 50-amol level is demonstrated. The success rate of the CD technology in protein identification is about twice that of the C(18) ZipTips and standard MALDI steel targets. The CDs are operated using robotics to transfer samples and reagents from microcontainers to the processing inlets on the disposable CD and spinning to control the movement of liquid through the microstructures.

Nucleic acid approaches for detection and identification of biological warfare and infectious disease agents

Biological warfare agents are the most problematic of the weapons of mass destruction and terror. Both civilian and military sources predict that over the next decade the threat from proliferation of these agents will increase significantly. In this review we summarize the state of the art in detection and identification of biological threat agents based on PCR technology with emphasis on the new technology of microarrays. The advantages and limitations of real-time PCR technology and a review of the literature as it applies to pathogen and virus detection are presented. The paper covers a number of issues related to the challenges facing biological threat agent detection technologies and identifies critical components that must be overcome for the emergence of reliable PCR-based DNA technologies as bioterrorism countermeasures and for environmental applications. The review evaluates various system components developed for an integrated DNA microchip and the potential applications of the next generation of fully automated DNA analyzers with integrated sample preparation and biosensing elements. The article also reviews promising devices and technologies that are near to being, or have been, commercialized.

Simulation of microfluidic pumping in a genomic DNA blood-processing cassette

Microfluidic cassettes that perform integrated biological sample preparation and DNA analysis require fluidic control and transport mechanisms built into the device. In this study, pneumatically actuated diaphragm pumps and valves were employed to achieve precise fluidic manipulation and enabled the execution of several sample-processing steps within a single cassette. However, the design of the microfluidic cassette to accomplish this multi-step fluidic protocol required a complex three-dimensional fluid path through valves, bends, various sized passageways and a porous filter for cell capture. In order to understand the fluidic behavior in such a device, measurements were taken of the pneumatic pressure delivered to the diaphragm pump as it pushed sample through the complicated fluidic pathway. Simultaneously monitored were the resulting volumetric flow rate, and the corresponding pre- and post-filter fluid pressures. The data enabled the construction of a model that simulated the fluidic action through the device using established fluid mechanics theory that closely matched flow rate and pressure data. The ability to simulate the behavior of diaphragm pumping and resulting fluidic movements in complex microfluidic devices provides a greater comprehension of this phenomenon and a useful tool in the application to future devices for biochemical analysis.

An automated on-line multidimensional HPLC system for protein and peptide mapping with integrated sample preparation.

A comprehensive on-line two-dimensional 2D-HPLC system with integrated sample preparation was developed for the analysis of proteins and peptides with a molecular weight below 20 kDa. The system setup provided fast separations and high resolving power and is considered to be a complementary technique to 2D gel electrophoresis in proteomics. The on-line system reproducibly resolved approximately 1000 peaks within the total analysis time of 96 min and avoided sample losses by off-line sample handling. The low-molecular-weight target analytes were separated from the matrix using novel silica-based restricted access materials (RAM) with ion exchange functionalities. The size-selective sample fractionation step was followed by anion or cation exchange chromatography as the first dimension. The separation mechanism in the subsequent second dimension employed hydrophobic interactions using short reversed-phase (RP) columns. A new column-switching technique, including four parallel reversed-phase columns, was employed in the second dimension for on-line fractionation and separation. Gradient elution and UV detection of two columns were performed simultaneously while loading the third and regenerating the fourth column. The total integrated workstation was operated in an unattended mode. Selected peaks were collected and analyzed off-line by MALDI-TOF mass spectrometry. The system was applied to protein mapping of biological samples of human hemofiltrate as well as of cell lysates originating from a human fetal fibroblast cell line, demonstrating it to be a viable alternative to 2D gel electrophoresis for mapping peptides and small proteins.

High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor.

High throughput DNA sequencing has been performed by using a microfabricated 96-channel radial capillary array electrophoresis (microCAE) microchannel plate detected by a 4-color rotary confocal fluorescence scanner. The microchannel plate features a novel injector for uniform sieving matrix loading as well as high resolution, tapered turns that provide an effective separation length of 15.9 cm on a compact 150-mm diameter wafer. Expanded common buffer chambers for the cathode, anode, and waste reservoirs are used to simplify electrode addressing and to counteract buffering capacity depletion arising from the high electrophoretic current. DNA sequencing data from 95 successful lanes out of 96 lanes run in parallel were batch-processed with basefinder, producing an average read length of 430 bp (phred q > or = 20). Phred quality values were found to exceed 40 (0.01% probability of incorrectly calling a base) for over 80% of the read length. The microCAE system demonstrated here produces sequencing data at a rate of 1.7 kbp/min, a 5-fold increase over current commercial capillary array electrophoresis technology. Additionally, this system permits lower reagent volumes and lower sample concentrations, and it presents numerous possibilities for integrated sample preparation and handling. The unique capabilities of microCAE technology should make it the next generation, high performance DNA sequencing platform.

Miniaturized electrophoresis: an evolving role in laboratory medicine.

The promise of capillary electrophoresis (CE) for supplanting conventional methods in the clinical laboratory led to intense interest in this analytical tool a decade ago. Since then, a number of clinical applications have been defined along with those that have impacted the pharmaceutical, environmental, and forensic arenas. Concurrent with the development of CE applications was the emergence of electrophoresis in the microchip format. The main attraction of this platform, the ability to execute high-resolution separations in a few hundred seconds, was not its only attribute. The capability for parallel processing of separations was complemented by the potentialfor integrating sample preparation into the same device. This Review highlights recent progress towards CE and microchip electrophoresis as clinical diagnostic tools, with literature coverage from 1996 to 2000.

Renewable microcolumns for automated DNA purification and flow-through amplification: from sediment samples through polymerase chain reaction

There is an increasing need for field-portable systems for the detection and characterization of microorganisms in the environment. Nucleic acids analysis is frequently the method of choice for discriminating between bacteria in complex systems, but standard protocols are difficult to automate and current microfluidic devices are not configured specifically for environmental sample analysis. In this report, we describe the development of an integrated DNA purification and polymerase chain reaction (PCR) amplification system and demonstrate its use for the automated purification and amplification of Geobacter chapellei DNA (genomic DNA or plasmid targets) from sediments. The system includes renewable separation columns for the automated capture and release of microparticle purification matrices, and can be easily reprogrammed for new separation chemistries and sample types. The DNA extraction efficiency for the automated system ranged from 3 to 25%, depending on the length and concentration of the DNA target. The system was more efficient than batch capture methods for the recovery of dilute genomic DNA even though the reagent volumes were smaller than required for the batch procedure. The automated DNA concentration and purification module was coupled to a flow-through, Peltier-controlled DNA amplification chamber, and used to successfully purify and amplify genomic and plasmid DNA from sediment extracts. Cleaning protocols were also developed to allow reuse of the integrated sample preparation system, including the flow-through PCR tube.