Development and evaluation of a microdevice for amino acid biomarker detection and analysis on Mars

The Urey instrument: an advanced in situ organic and oxidant detector for Mars exploration

The Urey organic and oxidant detector consists of a suite of instruments designed to search for several classes of organic molecules in the martian regolith and ascertain whether these compounds were produced by biotic or abiotic processes using chirality measurements. These experiments will also determine the chemical stability of organic molecules within the host regolith based on the presence and chemical reactivity of surface and atmospheric oxidants. Urey has been selected for the Pasteur payload on the European Space Agency's (ESA's) upcoming 2013 ExoMars rover mission. The diverse and effective capabilities of Urey make it an integral part of the payload and will help to achieve a large portion of the mission's primary scientific objective: "to search for signs of past and present life on Mars." This instrument is named in honor of Harold Urey for his seminal contributions to the fields of cosmochemistry and the origin of life.

Glycine identification in natural jarosites using laser desorption Fourier transform mass spectrometry: implications for the search for life on Mars

The jarosite group minerals have received increasing attention since the discovery of jarosite on the martian surface by the Mars Exploration Rover Opportunity. Given that jarosite can incorporate foreign ions within its structure, we have investigated the use of jarosite as an indicator of aqueous and biological processes on Earth and Mars. The use of laser desorption Fourier transform mass spectrometry has revealed the presence of organic matter in several jarosite samples from various locations worldwide. One of the ions from the natural jarosites has been attributed to glycine because it was systematically observed in combinations of glycine with synthetic ammonium and potassium jarosites, Na(2)SO(4) and K(2)SO(4). The ability to observe these organic signatures in jarosite samples with an in situ instrumental technique, such as the one employed in this study, furthers the goals of planetary geologists to determine whether signs of life (e.g., the presence of biomolecules or biomolecule precursors) can be detected in the rock record of terrestrial and extraterrestrial samples.

Electrophoretic separations on microfluidic chips

This review presents a brief outline and novel developments of electrophoretic separation in microfluidic chips. Distinct characteristics of microchip electrophoresis (MCE) are discussed first, in which sample injection plug, joule heat, channel turn, surface adsorption and modification are introduced, and some successful strategies and recognized conclusions are also included. Important achievements of microfluidic electrophoresis separation in small molecules, DNA and protein are then summarized. This review is aimed at researchers, who are interested in MCE and want to adopt MCE as a functional unit in their integrated microsystems.

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require approximately 70 min to deliver approximately 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between repeating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.

Monolithic Teflon membrane valves and pumps for harsh chemical and low-temperature use

Microfluidic diaphragm valves and pumps capable of surviving conditions required for unmanned spaceflight applications have been developed. The Pasteur payload of the European ExoMars Rover is expected to experience temperatures ranging between -100 degrees C and +50 degrees C during its transit to Mars and on the Martian surface. As such, the Urey instrument package, which contains at its core a lab-on-a-chip capillary electrophoresis analysis system first demonstrated by Mathies et al., requires valving and pumping systems that are robust under these conditions before and after exposure to liquid samples, which are to be analyzed for chemical signatures of past or present living processes. The microfluidic system developed to meet this requirement uses membranes consisting of Teflon and Teflon AF as a deformable material in the valve seat region between etched Borofloat glass wafers. Pneumatic pressure and vacuum, delivered via off-chip solenoid valves, are used to actuate individual on-chip valves. Valve sealing properties of Teflon diaphragm valves, as well as pumping properties from collections of valves, are characterized. Secondary processing for embossing the membrane against the valve seats after fabrication is performed to optimize single valve sealing characteristics. A variety of different material solutions are found to produce robust devices. The optimal valve system utilizes a membrane of mechanically cut Teflon sandwiched between two thin spun films of Teflon AF-1600 as a composite "laminated" diaphragm. Pump rates up to 1600 nL s(-1) are achieved with pumps of this kind. These high pumping rates are possible because of the very fast response of the membranes to applied pressure, enabling extremely fast pump cycling with relatively small liquid volumes, compared to analogous diaphragm pumps. The developed technologies are robust over extremes of temperature cycling and are applicable in a wide range of chemical environments.

Analysis of Neuroactive Amines in Fermented Beverages Using a Portable Microchip Capillary Electrophoresis System

A portable microfabricated capillary electrophoresis (CE) instrument is used for the determination of neurologically active biogenic amines, especially tyramine and histamine, in fermented beverages. The target molecules are labeled on their primary amino groups with fluorescamine in a 10-min reaction, and the samples analyzed directly, producing a detailed electropherogram in only 120 s on a microfabricated glass CE device containing 21.4-cm-long separation channels. Tyramine was found mainly in red wines at <1-3.4 mg/L, while the histamine content of these samples ranged from 1.8 to 19 mg/L. The highest levels of histamine (20-40 mg/L) were found in sake. The analysis of samples drawn from grape crush through malolactic fermentation in four varieties of zinfandel red wines revealed that histamine and tyramine are produced during yeast and malolactic fermentation, respectively. Following malolactic fermentation, the histamine content in these samples ranged from 3.3 to 30 mg/L, and the tyramine content ranged from 1.0 to 3.0 mg/L. This highly sensitive and rapid lab-on-a-chip analysis method establishes the feasibility of monitoring neurologically active amine content and potentially other chemically and allergenically important molecules in our food supply.

Fully integrated microfluidic separations systems for biochemical analysis

Over the past decade a tremendous amount of research has been performed using microfluidic analytical devices to detect over 200 different chemical species. Most of this work has involved substantial integration of fluid manipulation components such as separation channels, valves, and filters. This level of integration has enabled complex sample processing on miniscule sample volumes. Such devices have also demonstrated high throughput, sensitivity, and separation performance. Although the miniaturization of fluidics has been highly valuable, these devices typically rely on conventional ancillary equipment such as power supplies, detection systems, and pumps for operation. This auxiliary equipment prevents the full realization of a "lab-on-a-chip" device with complete portability, autonomous operation, and low cost. Integration and/or miniaturization of ancillary components would dramatically increase the capability and impact of microfluidic separations systems. This review describes recent efforts to incorporate auxiliary equipment either as miniaturized plug-in modules or directly fabricated into the microfluidic device.

Microfabricated Two-Dimensional Electrophoresis Device for Differential Protein Expression Profiling

A microfluidic separation system is developed to perform two-dimensional differential gel electrophoretic (DIGE) separations of complex, cellular protein mixtures produced by induced protein expression in E. coli. The micro-DIGE analyzer is a two-layer borosilicate glass microdevice consisting of a single 3.75 cm long channel for isoelectric focusing, which is sampled in parallel by 20 channels effecting a second-dimension separation by native electrophoresis. The connection between the orthogonal separation systems is accomplished by smaller channels comprising a microfluidic interface (MFI) that prevents media leakage between the two dimensions and enables facile loading of discontinuous gel systems in each dimension. Proteins are covalently labeled with Cy2 and Cy3 DIGE and detected simultaneously with a rotary confocal fluorescence scanner. Reproducible two-dimensional separations of both purified proteins and complex protein mixtures are performed with minimal run-to-run variation by including 7 M urea in the second-dimension separation matrix. The capabilities of the micro-DIGE analyzer are demonstrated by following the induced expression of maltose binding protein in E. coli. Although the absence of sodium dodecyl sulfate (SDS) in the second-dimension sizing separation limits the orthogonality and peak capacity of the separation, this analyzer is a significant first step toward the reproducible two-dimensional analysis of complex protein samples in microfabricated devices. Furthermore, the microchannel interface structures developed here will facilitate other multidimensional separations in microdevices.

Microfluidic large-scale integration: the evolution of design rules for biological automation

Microfluidic large-scale integration (mLSI) refers to the development of microfluidic chips with thousands of integrated micromechanical valves and control components. This technology is utilized in many areas of biology and chemistry and is a candidate to replace today's conventional automation paradigm, which consists of fluid-handling robots. We review the basic development of mLSI and then discuss design principles of mLSI to assess the capabilities and limitations of the current state of the art and to facilitate the application of mLSI to areas of biology. Many design and practical issues, including economies of scale, parallelization strategies, multiplexing, and multistep biochemical processing, are discussed. Several microfluidic components used as building blocks to create effective, complex, and highly integrated microfluidic networks are also highlighted.

Autonomous Microfluidic Sample Preparation System for Protein Profile-Based Detection of Aerosolized Bacterial Cells and Spores

For domestic and military security, an autonomous system capable of continuously monitoring for airborne biothreat agents is necessary. At present, no system meets the requirements for size, speed, sensitivity, and selectivity to warn against and lead to the prevention of infection in field settings. We present a fully automated system for the detection of aerosolized bacterial biothreat agents such as Bacillus subtilis (surrogate for Bacillus anthracis) based on protein profiling by chip gel electrophoresis coupled with a microfluidic sample preparation system. Protein profiling has previously been demonstrated to differentiate between bacterial organisms. With the goal of reducing response time, multiple microfluidic component modules, including aerosol collection via a commercially available collector, concentration, thermochemical lysis, size exclusion chromatography, fluorescent labeling, and chip gel electrophoresis were integrated together to create an autonomous collection/sample preparation/analysis system. The cycle time for sample preparation was approximately 5 min, while total cycle time, including chip gel electrophoresis, was approximately 10 min. Sensitivity of the coupled system for the detection of B. subtilis spores was 16 agent-containing particles per liter of air, based on samples that were prepared to simulate those collected by wetted cyclone aerosol collector of approximately 80% efficiency operating for 7 min.

Microfluidics in amino acid analysis

Microfluidic devices have been widely used to derivatize, separate, and detect amino acids employing many different strategies. Virtually zero-dead volume interconnections and fast mass transfer in small volume microchannels enable dramatic increases in on-chip derivatization reaction speed, while only minute amounts of sample and reagent are needed. Due to short channel path, fast subsecond separations can be carried out. With sophisticated miniaturized detectors, the whole analytical process can be integrated on one platform. This article reviews developments of lab-on-chip technology in amino acid analysis, it shows important design features such as sample preconcentration, precolumn and postcolumn amino acid derivatization, and unlabeled and labeled amino acid detection with focus on advanced designs. The review also describes important biomedical and space exploration applications of amino acid analysis on microfluidic devices.

Integration of continuous-flow sampling with microchip electrophoresis using poly(dimethylsiloxane)-based valves in a reversibly sealed device

Here we describe a reversibly sealed microchip device that incorporates poly(dimethylsiloxane) (PDMS)-based valves for the rapid injection of analytes from a continuously flowing stream into a channel network for analysis with microchip electrophoresis. The microchip was reversibly sealed to a PDMS-coated glass substrate and microbore tubing was used for the introduction of gas and fluids to the microchip device. Two pneumatic valves were incorporated into the design and actuated on the order of hundreds of milliseconds, allowing analyte from a continuously flowing sampling stream to be injected into an electrophoresis separation channel. The device was characterized in terms of the valve actuation time and pushback voltage. It was also found that the addition of sodium dodecyl sulfate (SDS) to the buffer system greatly increased the reproducibility of the injection scheme and enabled the analysis of amino acids derivatized with naphthalene-2,3-dicarboxaldehyde/cyanide. Results from continuous injections of a 0.39 nL fluorescein plug into the optimized system showed that the injection process was reproducible (RSD of 0.7%, n = 10). Studies also showed that the device was capable of monitoring off-chip changes in concentration with a device lag time of 90 s. Finally, the ability of the device to rapidly monitor on-chip concentration changes was demonstrated by continually sampling from an analyte plug that was derivatized upstream from the electrophoresis/continuous flow interface. A reversibly sealed device of this type will be useful for the continuous monitoring and analysis of processes that occur either off-chip (such as microdialysis sampling) or on-chip from other integrated functions.

Microchip separations in reduced-gravity and hypergravity environments

Microfabricated fluidics technology, e.g., lab-on-a-chip devices, offers many attractive features for performing chemistry and biochemistry on space-based platforms. We have constructed a portable, battery-operated microfluidic platform that was tested under reduced gravity and hypergravity conditions that would be experienced in space flight and launch. This device consisted of a microchip, microchip holder, two 0-8-kV high-voltage power supplies, a high-voltage switch, a solid-state diode-pumped green laser, an optical train, a channel photomultiplier, and an inertial mass measurement unit all under the control of a laptop computer and powered by 10 D-cell alkaline batteries. The unit was tested on NASA's reduced gravity research aircraft at gravity levels that are relevant to NASA's intended use of bioreporter-based microchips for environmental monitoring of space and planetary environments on manned and unmanned spacecraft. Over the course of two flights, 834 fast electrophoretic separations of four amino acids were performed under a variety of gravitational environments including zero-g, Martian-g, lunar-g, and approximately 1.8-g. All separations were performed in less than 12 s and automatically analyzed. After correction with an internal migration standard, the migration time reproducibilities were all <1% relative standard deviation.

Development of a universal serial bus-powered mini-high-voltage power supply for microchip electrophoresis

We describe a miniature high-voltage power supply (HVPS) with dimensions of 4.7 x 5.6 x 2.5 cm (W x L x H) powered by universal serial bus (USB) ports. Two strategies were adopted to ensure its efficient power usage. (i) Only two high-voltage converters (one positive and one negative) and two relays were used for power saving, while keeping the sample plug stable and well-defined and avoiding sample leakage for microchip electrophoresis. (ii) The components and their running modes were specially designed to decrease power waste according to the feature of different periods of the microchip electrophoresis process. Performance of this USB-based mini-HVPS was demonstrated using sodium fluorescein analyte with microchip electrophoresis/LIF detection.

Microbial life in glacial ice and implications for a cold origin of life

Application of physical and chemical concepts, complemented by studies of prokaryotes in ice cores and permafrost, has led to the present understanding of how microorganisms can metabolize at subfreezing temperatures on Earth and possibly on Mars and other cold planetary bodies. The habitats for life at subfreezing temperatures benefit from two unusual properties of ice. First, almost all ionic impurities are insoluble in the crystal structure of ice, which leads to a network of micron-diameter veins in which microorganisms may utilize ions for metabolism. Second, ice in contact with mineral surfaces develops a nanometre-thick film of unfrozen water that provides a second habitat that may allow microorganisms to extract energy from redox reactions with ions in the water film or ions in the mineral structure. On the early Earth and on icy planets, prebiotic molecules in veins in ice may have polymerized to RNA and polypeptides by virtue of the low water activity and high rate of encounter with each other in nearly one-dimensional trajectories in the veins. Prebiotic molecules may also have utilized grain surfaces to increase the rate of encounter and to exploit other physicochemical features of the surfaces.

An astrophysically-relevant mechanism for amino acid enantiomer enrichment

The sublimation of low ee amino acids was examined while exploring simple mechanisms by which high ee amino acids can be generated under conditions that exist in space; significant enantioenrichment of a variety of amino acids by sublimation was achieved.

Evaluation of enantioselective gas chromatography for the determination of minute deviations from racemic composition of α-amino acids with emphasis on tyrosine: Accuracy and precision of the method

Whereas the determination of high enantiomeric fractions (EF) of chiral compounds is very well established, the accurate determination of small deviations from racemic compositions has not yet received much attention despite its relevance to studies dealing with the origin of homochirality, where only small initial enantiomeric bias is expected. Racemic samples of representative alpha-amino acids were derivatized as N-(O,S)-trifluoroacetyl/ethylesters and analyzed by enantioselective gas chromatography (GC) on fused silica capillaries coated with the chiral stationary phases (CSPs) Chirasil-D-Val, Chirasil-L-Val, and Lipodex E with GC/FID and GC/MS detection. The validation (accuracy and precision) of the determination of the enantiomeric fraction EF of the D-enantiomer in racemic or near-racemic compositions for 10 DL-alpha-amino acids obtained from commercial sources has been carried out. Emphasis is given to DL-tyrosine, the enantiomers of which have recently been claimed to show different crystallization properties. Values of EF obtained from GC measurements using CSPs were compared with those from CE using chiral mobile phase additives. While the precision of the GC method is generally better than 0.08% for all DL-alpha-amino acids studied, accuracy (trueness) of determination of amino acids with polar side chains is poorer than expected from the precision as a result of systematic errors. The accuracy determined relied on measurements on two oppositely configurated CSPs.

FISH and chips: chromosomal analysis on microfluidic platforms

Interphase fluorescence in situ hybridisation (FISH) is a sensitive diagnostic tool used for the detection of alterations in the genome on cell-by-cell basis. However, the cost-per-test and the technical complexity of current FISH protocols have slowed its widespread utilisation in clinical settings. For many cancers, the lack of a cost-effective and informative diagnostic method has compromised the quality of life for patients. We present the first demonstration of a microchip-based FISH protocol, coupled with a novel method to immobilise peripheral blood mononuclear cells inside microfluidic channels. These first on-chip implementations of FISH allow several chromosomal abnormalities associated with multiple myeloma to be detected with a ten-fold higher throughput and 1/10-th the reagent consumption of the traditional slide-based method. Moreover, the chip test is performed within hours whereas the conventional protocol required days. In addition, two on-chip methods to enhance the hybridisation aspects of FISH have been examined: mechanical and electrokinetic pumping. Similar agitation methods have led to significant improvements in hybridisation efficiency with DNA microarray work, but with this cell-based method the benefits were moderate. On-chip FISH technology holds promise for sophisticated and cost-effective screening of cancer patients at every clinic visit.

On-chip pumping for pressure mobilization of the focused zones following microchip isoelectric focusing

Isoelectric focusing (IEF), traditionally accomplished in slab or tube gels, has also been performed extensively in capillary and, more recently, in microchip formats. IEF separations performed in microchips typically use electroosmotic flow (EOF) or chemical treatment to mobilize the focused zones past the detection point. This report describes the development and optimization of a microchip IEF method in a hybrid PDMS-glass device capable of controlling the mobilization of the focused zones past the detector using on-chip diaphragm pumping. The microchip design consisted of a glass fluid layer (separation channels), a PDMS layer and a glass valve layer (pressure connections and valve seats). Pressure mobilization was achieved on-chip using a diaphragm pump consisting of a series of reversible elastomeric valves, where a central diaphragm valve determined the volume of solution displaced while the gate valves on either side imparted directionality. The pumping rate could be adjusted to control the mobilization flow rate by varying the actuation times and pressure applied to the PDMS to actuate the valves. In order to compare the separation obtained using the chip with that obtained in a capillary, a serpentine channel design was used to match the separation length of the capillary, thereby evaluating the effect of diaphragm pumping itself on the overall separation quality. The optimized mIEF method was applied to the separation of labeled amino acids.

Lab-on-a-chip devices for global health: past studies and future opportunities

A rapidly emerging field in lab-on-a-chip (LOC) research is the development of devices to improve the health of people in developing countries. In this review, we identify diseases that are most in need of new health technologies, discuss special design criteria for LOC devices to be deployed in a variety of resource-poor settings, and review past research into LOC devices for global health. We focus mainly on diagnostics, the nearest-term application in this field.

A fully integrated microfluidic genetic analysis system with sample-in-answer-out capability

We describe a microfluidic genetic analysis system that represents a previously undescribed integrated microfluidic device capable of accepting whole blood as a crude biological sample with the endpoint generation of a genetic profile. Upon loading the sample, the glass microfluidic genetic analysis system device carries out on-chip DNA purification and PCR-based amplification, followed by separation and detection in a manner that allows for microliter samples to be screened for infectious pathogens with sample-in-answer-out results in < 30 min. A single syringe pump delivers sample/reagents to the chip for nucleic acid purification from a biological sample. Elastomeric membrane valving isolates each distinct functional region of the device and, together with resistive flow, directs purified DNA and PCR reagents from the extraction domain into a 550-nl chamber for rapid target sequence PCR amplification. Repeated pressure-based injections of nanoliter aliquots of amplicon (along with the DNA sizing standard) allow electrophoretic separation and detection to provide DNA fragment size information. The presence of Bacillus anthracis (anthrax) in 750 nl of whole blood from living asymptomatic infected mice and of Bordetella pertussis in 1 microl of nasal aspirate from a patient suspected of having whooping cough are confirmed by the resultant genetic profile.

Biochemistry of amino acid racemization and clinical application to musculoskeletal disease

During aging, proteins are subject to numerous forms of damage. Several types of non-enzymatic post-translational modifications have been described in aging proteins, including oxidation, nitration, glycation, and racemization. Racemization of amino acids is the spontaneous conversion of L-enantiomers to the D-form, which is dependent on temperature, pH, and time. Because of the time-dependent nature of racemization, it can be used to determine the relative age and turnover rates of long-lived proteins. There are many such long-lived proteins within the body; they are found in the brain, eye, and heart, but are particularly abundant in proteins found in musculoskeletal tissues such as bone and cartilage. During disease, musculoskeletal tissues have pathologically altered turnover rates. Because turnover rates can be estimated from levels of racemization, racemized musculoskeletal protein fragments may serve as useful biomarkers of disease. This review discusses the biochemistry of amino acid racemization in proteins and its clinical application to musculoskeletal disease.

Application of the Mars Organic Analyzer to nucleobase and amine biomarker detection

The Mars Organic Analyzer (MOA), a portable microfabricated capillary electrophoresis instrument being developed for planetary exploration, is used to analyze a wide variety of fluorescamine-labeled amine-containing biomarker compounds, including amino acids, mono and diaminoalkanes, amino sugars, nucleobases, and nucleobase degradation products. The nucleobases cytosine and adenine, which contain an exocyclic primary amine, were effectively labeled, separated, and detected at concentrations <500 nM. To test the general applicability of the MOA for biomarker detection, amino acids and mono- and diamines were extracted from bacterial cells using both hydrolysis and sublimation followed by analysis. The extrapolated limit of detection provided by the valine biomarker was approximately 4 x 10(3) cells per sample. Products of an NH(4)CN polymerization that simulate a prebiotic synthesis were also successfully isolated via sublimation and analyzed. Adenine and alanine/serine were detected with no additional sample cleanup at 120 +/- 13 microM and 4.1 +/- 1 microM, respectively, corresponding to a reaction yield of 0.04% and 0.0003%, respectively. This study demonstrates that the MOA provides sensitive detection and analysis of low levels of a wide variety of amine-containing organic compounds from both biological and abiotic sources.

The limitations on organic detection in Mars-like soils by thermal volatilization-gas chromatography-MS and their implications for the Viking results

The failure of Viking Lander thermal volatilization (TV) (without or with thermal degradation)-gas chromatography (GC)-MS experiments to detect organics suggests chemical rather than biological interpretations for the reactivity of the martian soil. Here, we report that TV-GC-MS may be blind to low levels of organics on Mars. A comparison between TV-GC-MS and total organics has been conducted for a variety of Mars analog soils. In the Antarctic Dry Valleys and the Atacama and Libyan Deserts we find 10-90 mug of refractory or graphitic carbon per gram of soil, which would have been undetectable by the Viking TV-GC-MS. In iron-containing soils (jarosites from Rio Tinto and Panoche Valley) and the Mars simulant (palogonite), oxidation of the organic material to carbon dioxide (CO(2)) by iron oxides and/or their salts drastically attenuates the detection of organics. The release of 50-700 ppm of CO(2) by TV-GC-MS in the Viking analysis may indicate that an oxidation of organic material took place. Therefore, the martian surface could have several orders of magnitude more organics than the stated Viking detection limit. Because of the simplicity of sample handling, TV-GC-MS is still considered the standard method for organic detection on future Mars missions. We suggest that the design of future organic instruments for Mars should include other methods to be able to detect extinct and/or extant life.

Multichannel Reverse Transcription-Polymerase Chain Reaction Microdevice for Rapid Gene Expression and Biomarker Analysis

A microdevice is developed for RNA analysis that integrates one-step reverse transcription and 30 cycles of PCR (RT-PCR) amplification with capillary electrophoresis (CE) separation and fluorescence detection of the amplicons. The four-layer glass-PDMS-glass-glass hybrid microdevice integrates microvalves, on-chip heaters and temperature sensors, nanoliter reaction chambers (380 nL), and 5-cm-long CE separation channels. The direct integration of these processes results in attomolar detection sensitivity (<11 template RNA molecules or approximately 0.1 cellular equiv) and rapid 45-min analysis, while minimizing sample waste and eliminating contamination. Size-based electrophoretic product analysis provides definitive amplicon-size verification and multiplex analysis. Multiplexed differential gene expression analysis is demonstrated on mdh and gyrB E. coli transcripts. RNA splice variant analysis of the RBBP8 gene is used to identify tumorigenic tissue. RT-PCR microdevice analysis of normal breast tissue RNA generates the expected 202-bp normal splice isoform; tumor breast tissue RNA samples generate a 151-bp amplicon signifying the presence of the tumorigenic splice variant. The ability to perform RNA transcript and splice variant biomarker analysis establishes our RT-PCR microdevice as a versatile gene expression platform.

Rapid on-column analysis of glucosamine and its mutarotation by microchip capillary electrophoresis

A novel electrophoretic microchip method for analyzing alpha- and beta-d-glucosamine and their interconversion in solution is presented. d-Glucosamine is labeled with fluorescamine and analyzed by capillary electrophoresis in under 2 min revealing its pH-dependent mutarotation between the alpha- and beta-anomers. The forward interconversion rates for the labeled sugars, based on an iterative analysis of the plateau heights between the peaks, are 0.72+/-0.09, 1.3+/-0.1, and 2.2+/-0.3 x 10(-3)s(-1) at pH 8.99, 9.51 and 10.01, respectively. In a separate experiment, the mutarotation of the unlabeled alpha-d-anomer was followed; the relative intensities of the alpha- and beta-peaks as a function of reaction time at pH 9.51 give a forward rate constant of 0.6+/-0.1 x 10(-3)s(-1). These results demonstrate that fast microchip separations, previously exploited for amine, amino acid, and nucleobase analysis, can also be used to analyze amino sugars and their mutarotation.

Survival and germinability of Bacillus subtilis spores exposed to simulated Mars solar radiation: implications for life detection and planetary protection

Bacterial spores have been considered as microbial life that could survive interplanetary transport by natural impact processes or human spaceflight activity. Deposition of terrestrial microbes or their biosignature molecules onto the surface of Mars could negatively impact life detection experiments and planetary protection measures. Simulated Mars solar radiation, particularly the ultraviolet component, has been shown to reduce spore viability, but its effect on spore germination and resulting production of biosignature molecules has not been explored. We examined the survival and germinability of Bacillus subtilis spores exposed to simulated martian conditions that include solar radiation. Spores of B. subtilis that contain luciferase resulting from expression of an sspB-luxAB gene fusion were deposited on aluminum coupons to simulate deposition on spacecraft surfaces and exposed to simulated Mars atmosphere and solar radiation. The equivalent of 42 min of simulated Mars solar radiation exposure reduced spore viability by nearly 3 logs, while germination-induced bioluminescence, a measure of germination metabolism, was reduced by less than 1 log. The data indicate that spores can retain the potential to initiate germination-associated metabolic processes and produce biological signature molecules after being rendered nonviable by exposure to Mars solar radiation.

Rapid and High-Throughput Forensic Short Tandem Repeat Typing Using a 96-Lane Microfabricated Capillary Array Electrophoresis Microdevice*

A 96-channel microfabricated capillary array electrophoresis (muCAE) device was evaluated for forensic short tandem repeat (STR) typing using PowerPlex 16 and AmpFlSTR Profiler Plus multiplex PCR systems. The high-throughput muCAE system produced high-speed <30-min parallel sample separations with single-base resolution. Forty-eight previously analyzed single-source samples were accurately typed, as confirmed on an ABI Prism 310 and/or the Hitachi FMBIO II. Minor alleles in 3:1 mixture samples containing female and male DNA were reliably typed as well. The instrument produced full profiles from sample DNA down to 0.17 ng, a threshold similar to that found for the ABI 310. Seventeen nonprobative samples from various evidentiary biological stains were also correctly typed. The successful application of the muCAE device to actual forensic STR typing samples is a significant step toward the development of a completely integrated STR analysis microdevice.

Combining the Enantioselectivities of l-Valine Diamide and Permethylated β-Cyclodextrin in One Gas Chromatographic Chiral Stationary Phase

An L-valine diamide chiral selector was attached to a polysiloxane through a long hydrocarbon spacer giving rise to a chiral stationary phase (CSP), Chirasil-Val-C11. The enantioselective properties of this readily accessible diamide CSP under gas chromatographic conditions were found to be similar to that of the commercially available Chirasil-Val CSP prepared by a polymer-analogous route. A new binary CSP, Chirasil-DexVal-C11, was synthesized by means of simultaneous attachment of both the L-valine diamide and permethylated beta-cyclodextrin selectors to a polysiloxane using platinum-catalyzed hydrosilylation, thereby overcoming the immiscibility problem known for Chirasil-Val and Chirasil-Dex. This binary CSP retained both the enantioselectivity of Chirasil-Val-C11 toward alpha-amino acid derivatives and the unsurpassed enantioselectivity of Chirasil-Dex toward underivatized chiral alcohols, ketones, and hydrocarbons. Furthermore, it was shown that the presence of the cyclodextrin selector in Chirasil-Val-C11 significantly improved the enantioseparation of proline, which represented a problematic amino acid on diamide CSPs.

On-chip pressure injection for integration of infrared-mediated DNA amplification with electrophoretic separation

Poly(dimethylsiloxane) (PDMS) membrane valves were utilized for diaphragm pumping on a PDMS-glass hybrid microdevice in order to couple infrared-mediated DNA amplification with electrophoretic separation of the products in a single device. Specific amplification products created during non-contact, infrared (IR) mediated polymerase chain reaction (PCR) were injected via chip-based diaphragm pumping into an electrophoretic separation channel. Channel dimensions were designed for injection plug shaping via preferential flow paths, which aided in minimizing the plug widths. Unbiased injection of sample could be achieved in as little as 190 ms, decreasing the time required with electrokinetic injection by two orders of magnitude. Additionally, sample stacking was promoted using laminar or biased-laminar loading to co-inject either water or low ionic strength DNA marker solution along with the PCR-amplified sample. Complete baseline resolution (Res = 2.11) of the 80- and 102-bp fragments of pUC-18 DNA marker solution was achieved, with partially resolved 257- and 267-bp fragments (Res = 0.56), in a separation channel having an effective length of only 3.0 cm. This resolution was deemed adequate for many PCR amplicon separations, with the added advantage of short separation time-typically complete in <120 s. Decreasing the amount of glass surrounding the PCR chamber reduced the DNA amplification time, yielding a further enhancement in analysis speed, with heating and cooling rates as high as 13.4 and -6.4 degrees C s(-1), respectively. With the time requirements greatly reduced for each step, it was possible to seamlessly couple IR-mediated amplification, sample injection, and separation/detection of a 278-bp fragment from the invA gene of <1000 starting copies of Salmonella typhimurium DNA in approximately 12 min on a single device, representing the fastest PCR-ME integration achieved to date.

Development and multiplexed control of latching pneumatic valves using microfluidic logical structures

Novel latching microfluidic valve structures are developed, characterized, and controlled independently using an on-chip pneumatic demultiplexer. These structures are based on pneumatic monolithic membrane valves and depend upon their normally-closed nature. Latching valves consisting of both three- and four-valve circuits are demonstrated. Vacuum or pressure pulses as short as 120 ms are adequate to hold these latching valves open or closed for several minutes. In addition, an on-chip demultiplexer is demonstrated that requires only n pneumatic inputs to control 2(n-1) independent latching valves. These structures can reduce the size, power consumption, and cost of microfluidic analysis devices by decreasing the number of off-chip controllers. Since these valve assemblies can form the standard logic gates familiar in electronic circuit design, they should be useful in developing complex pneumatic circuits.

Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing

An efficient, nanoliter-scale microfabricated bioprocessor integrating all three Sanger sequencing steps, thermal cycling, sample purification, and capillary electrophoresis, has been developed and evaluated. Hybrid glass-polydimethylsiloxane (PDMS) wafer-scale construction is used to combine 250-nl reactors, affinity-capture purification chambers, high-performance capillary electrophoresis channels, and pneumatic valves and pumps onto a single microfabricated device. Lab-on-a-chip-level integration enables complete Sanger sequencing from only 1 fmol of DNA template. Up to 556 continuous bases were sequenced with 99% accuracy, demonstrating read lengths required for de novo sequencing of human and other complex genomes. The performance of this miniaturized DNA sequencer provides a benchmark for predicting the ultimate cost and efficiency limits of Sanger sequencing.

Point-of-care biosensor systems for cancer diagnostics/prognostics

With the growing number of fatalities resulting from the 100 or so cancer-related diseases, new enabling tools are required to provide extensive molecular profiles of patients to guide the clinician in making viable diagnosis and prognosis. Unfortunately with cancer-related diseases, there is not one molecular marker that can provide sufficient information to assist the clinician in making effective prognoses or even diagnoses. Indeed, large panels of markers must typically be evaluated that cut across several different classes (mutations in certain gene fragments--DNA; over/under-expression of gene activity as monitored by messenger RNAs; the amount of proteins present in serum or circulating tumor cells). The classical biosensor format (dipstick approach for monitoring the presence of a single element) is viewed as a valuable tool in many bioassays, but possesses numerous limitations in cancer due primarily to the single element nature of these sensing platforms. As such, if biosensors are to become valuable tools in the arsenal of the clinician to manage cancer patients, new formats are required. This review seeks to provide an overview of the current thinking on molecular profiling for diagnosis and prognosis of cancers and also, provide insight into the current state-of-the-art in the biosensor field and new strategies that must be considered to bring this important technology into the cancer field.

Atomic and Molecular Parity Nonconservation and Sum Frequency Generation Solutions to the Ozma Problem

Two Ozma problems are defined. Parity nonconservation is necessary for their solutions. Both problems may be solved by beta decay or atomic optical activity. Atomic and molecular sum frequency generation is chosen, as it supplies rich methods of effecting "gedanken" solutions to the Ozma problems. A new method of measuring a parameter manifesting molecular parity violations is advanced.

Design and Characterization of Poly(dimethylsiloxane)-Based Valves for Interfacing Continuous-Flow Sampling to Microchip Electrophoresis

This work describes the fabrication and evaluation of a poly(dimethyl)siloxane (PDMS)-based device that enables the discrete injection of a sample plug from a continuous-flow stream into a microchannel for subsequent analysis by electrophoresis. Devices were fabricated by aligning valving and flow channel layers followed by plasma sealing the combined layers onto a glass plate that contained fittings for the introduction of liquid sample and nitrogen gas. The design incorporates a reduced-volume pneumatic valve that actuates (on the order of hundreds of milliseconds) to allow analyte from a continuously flowing sampling channel to be injected into a separation channel for electrophoresis. The injector design was optimized to include a pushback channel to flush away stagnant sample associated with the injector dead volume. The effect of the valve actuation time, the pushback voltage, and the sampling stream flow rate on the performance of the device was characterized. Using the optimized design and an injection frequency of 0.64 Hz showed that the injection process is reproducible (RSD of 1.77%, n = 15). Concentration change experiments using fluorescein as the analyte showed that the device could achieve a lag time as small as 14 s. Finally, to demonstrate the potential uses of this device, the microchip was coupled to a microdialysis probe to monitor a concentration change and sample a fluorescein dye mixture.

Surface-Enhanced Raman Optical Activity on Adenine in Silver Colloidal Solution

We report the collection of Raman optical activity (ROA) spectra of adenine in silver colloidal solution, that is, surface-enhanced Raman optical activity (SEROA) using considerably shorter data acquisition times, reduced excitation power, and lower concentration, as compared to classical ROA measurements on molecules of biological interest so far reported in the literature. These improvements in experimental parameters for ROA measurements can be explained by enhanced Raman signals in the local optical fields of the silver nanoparticles and by at least 1 order of magnitude higher values for circular intensity differences (CIDs), as compared to classical ROA that has been suggested before and theoretically discussed in terms of large field gradients near a metal surface. The measured ROA effect for adenine can be understood in terms of adsorption-induced chirality in the prochiral molecules on the silver nanoparticles. Surface-enhanced Raman optical activity offers potential capabilities for sensitive, rapid, stereochemical characterization of basic building blocks of biopolymers, such as amino acids and nucleosides, as well as biologically active molecules, in particular, also for probing organization and self-assembling of such molecules on metal surfaces.

Recent advances in amino acid analysis by capillary electrophoresis

This paper describes a number of articles that have been published on amino acid analysis using CE during the period from June 2003 to May 2005. This review article follows the previous ones of Smith (Electrophoresis 1999, 20, 3078-3083), Prata et al. (Electrophoresis 2001, 22, 4129-4138), and Poinsot et al. (Electrophoresis 2003, 24, 4047-4062). Several new developments in amino acid analysis with CE are reported concerning UV detection, LIF, MS, and NMR. In addition, we describe articles concerning clinical and pharmaceutical studies, neuroclinical applications, and agricultural and food analysis.