Enzyme Kinetics in Femtoliter Arrays.

Over the last decade, femtoliter arrays have been used as a simple and robust way to encapsulate and monitor the kinetics of single enzyme molecules. Encapsulating individual enzyme molecules within a femtoliter-sized reaction chamber does not require immobilization of the enzyme molecules or fluorescent tagging of the enzyme molecules, which offers the unique advantage of observing unmodified single enzyme molecules free in solution. Several fascinating details about enzyme kinetics have been revealed using these femtoliter arrays, which were unattainable from traditional ensemble experiments. Here, we discuss various considerations to take into account when developing single-molecule enzyme assays in femtoliter arrays and the advantages and disadvantages of various protocols.

Whole-saliva proteolysis and its impact on salivary diagnostics.

There is growing interest in the use of human whole saliva for diagnostics and disease monitoring as an alternative to blood samples. In contrast to blood, whole saliva is a non-sterile body fluid. Proper hand-ling and storage are required to preserve the integrity of potential biomarkers. We investigated salivary autoproteolytic degradation using a variety of approaches. We determined inhibition of protease activities by monitoring the endogenous proteome. In addition, the stability of highly protease-susceptible proteins-histatin 5, statherin, and PRP1-was assessed. Experimental variables included (a) protease inhibitors, (b) salivary pH, (c) incubation temperatures, and (d) sample heating. A cocktail containing AEBSF, aprotinin, pancreatic trypsin inhibitor, leupeptin, antipain, and EDTA could not prevent histatin 5, statherin, or PRP1 degradation in whole saliva. Among the other treatments evaluated, short-term storage of freshly collected samples on ice was effective without interfering with the chemistry of the proteome. In conclusion, whole saliva contains a unique mixture of enzymes as evidenced from their resilience to protease inhibition. Analytical evidence on protein stability is needed to ensure the validity of salivary biomarker study outcomes. Analysis of the data presented will provide help and guidance for the use of saliva samples for diagnostic purposes.

Combined imaging and chemical sensing of L-glutamate release from the foregut plexus of the lepidopteran, Manduca sexta.

A new combined imaging and chemical detection sensor for the measurement of localized L-glutamate release at the insect neuromuscular junction (NMJ) is presented. The sensor is comprised of an L-glutamate-sensitive fluorescent gel, spin-coated onto the tip of an optical imaging fiber. The gel is composed of L-glutamate oxidase (GLOD); a pH-sensitive fluorescent dye, SNAFL; and poly(acrylamide-co-N-acryloxysuccinimide) (PAN). NH(3) is liberated from the interaction of L-glutamate with GLOD, which reversibly reduces the emitted fluorescence signal from SNAFL. This sensor has a spatial resolution of 3-4 micro m, and an L-glutamate detection limit of between 10 and 100 micro M. L-glutamate release and re-uptake from the foregut plexus of Manduca sexta was detected by the sensor in the presence of the L-glutamate re-uptake blocker dihydrokainate, and the post-synaptic L-glutamate receptor antagonist CNQX.

Array-to-array transfer of an artificial nose classifier.

This paper describes the use of a microsphere sensor technology that allows simple fabrication of vapor sensor arrays with reproducible response patterns. Microsphere sensor fabrication protocols are uncomplicated and yield billions of highly reproducible sensors. Microsphere sensor arrays combined with a generalized Whitney-Mann-Wilcoxen (GWMW) classifier were used to discriminate between the presence and absence of nitroaromatic compounds in high background vapor mixtures. The classifier was trained on one sensor array and then used to obtain 98.2 and 93.7% correct classification rates with data collected using two subsequent arrays made up to six months after the initial training was performed. These results represent an advance in the ability to transfer training data between multiple sensor arrays with a fluorescence-based artificial nose.

Field-deployable sniffer for 2,4-dinitrotoluene detection.

A field-deployable instrument has been developed to detect low-level 2,4-dinitrotoluene (2,4-DNT) vapors. The system is based on previously developed artificial nose technology and employs an array of sensory materials attached to the distal tips of an optical fiber bundle. Both semiselective and nonspecific, cross-reactive sensors were employed. Each sensor within the array responds differentially to vapor exposure so the array's fluorescence response patterns are unique for each analyte. The instrument is computationally "trained" to discriminate target response patterns from nontarget and background environments. This detection system has been applied to detect 2,4-DNT, an analyte commonly detected on the soil surface above buried 2,4,6-trinitrotoluene (TNT) land mines, in spiked soil and aqueous and ground samples. The system has been characterized and demonstrated the ability to detect 120 ppb 2,4-DNT vapor in blind (unknown) humidified samples during a supervised field test.

A duplexed microsphere-based fluorescent immunoassay.

Microsphere-based immunoassays are described for the simultaneous measurement of the clinically important drugs digoxin and theophylline. Competitive immunoassays were performed using haptenized microspheres and antibodies labeled with horseradish peroxidase. Enzyme-catalyzed reporter deposition (CARD) resulted in immunofluorescence signal amplification. Two encoding dyes were used to differentiate analytical signals from microspheres containing assays for the two analytes. An epifluorescence microscope and a CCD camera interfaced with a computer were utilized to measure fluorescence signals of individual microspheres. The microspheres from a duplexed assay were mounted on microscope slides as well as inserted into wells etched into the distal ends of optical imaging fibers. Fluorescence images from both formats were captured. In the experiments using microscope slides, the immunoassays were successfully duplexed and only marginal interferences at high analyte concentrations were observed. Preliminary results suggest that simultaneous determination of the two analytes using a fiber-based sensor-array format is feasible, but requires further development before precise quantitative analyses are possible.

Optical multibead arrays for simple and complex odor discrimination.

A fiber optic bead-based sensor array platform has been employed to discriminate between six different odors and air carrier gas. Six different bead sensor types, with over 250 replicates of each, were monitored before, during, and after odor exposure to produce time-dependent fluorescence response patterns that were unique for each sensor-analyte combination. A total of 2,683 sensors were analyzed with respect to changes in their fluorescence, and signals from identical sensor beads were averaged to improve signal-to-noise ratios. Analyte classification rates of 100% were achieved for three complex (coffee bean) odors and three pure (simple) odors (toluene, acetone, 1,3-dinitrotoluene) measured at their highest relative concentrations. When lower odor concentrations were employed, the system exhibited better than 85% classification rates for analyte discrimination. Sensor response repeatability to these odor stimuli has also been quantified statistically, which is vital in defining the detection limit of the overall system. These results demonstrate, for the first time, the utility of our bead array technology for discriminating between different odor types at various dilution levels.

A fiber-optic lactate sensor based on bacterial cytoplasmic membranes.

A new type of fiber-optic biosensor based on bacterial cytoplasmic membranes (CPM) as the biological recognition element and an oxygen sensitive dye layer as the transducer is described for the detection of lactate. CPMs from bacteria with an induced lactate oxidase system are adsorbed onto a cellulose disk. The disk is fixed mechanically over an oxygen sensitive siloxane layer on the distal end of an optical fiber. This system detects lactate with no interference from glucose, fructose or glutamic acid.

High-density fiber-optic DNA random microsphere array.

A high-density fiber-optic DNA microarray sensor was developed to monitor multiple DNA sequences in parallel. Microarrays were prepared by randomly distributing DNA probe-functionalized 3.1-microm-diameter microspheres in an array of wells etched in a 500-microm-diameter optical imaging fiber. Registration of the microspheres was performed using an optical encoding scheme and a custom-built imaging system. Hybridization was visualized using fluorescent-labeled DNA targets with a detection limit of 10 fM. Hybridization times of seconds are required for nanomolar target concentrations, and analysis is performed in minutes.

A fiber-optic microarray biosensor using aptamers as receptors.

A fiber-optic biosensor using an aptamer receptor has been developed for the measurement of thrombin. An antithrombin DNA aptamer was immobilized on the surface of silica microspheres, and these aptamer beads were distributed in microwells on the distal tip of an imaging fiber. A different oligonucleotide bead type prepared using the same method as the aptamer beads was also included in the microwells to measure the degree of nonspecific binding. The imaging fiber was coupled to a modified epifluorescence microscope system, and the distal end of the fiber was incubated with a fluorescein-labeled thrombin (F-thrombin) solution. Nonlabeled thrombin could be detected using a competitive binding assay with F-thrombin. The aptamer beads selectively bound to the target and could be reused without any sensitivity change. The fiber-optic microarray system has a detection limit of 1 nM for nonlabeled thrombin, and each test can be performed in ca. 15 min including the regeneration time.

Application of high-density optical microwell arrays in a live-cell biosensing system.

In this paper, we use optical imaging fibers to fabricate a chemical and biochemical sensor that utilizes the ability of living cells to respond to biologically significant compounds. The sensor is created by randomly dispersing single NIH 3T3 mouse fibroblast cells into an optically addressable fiber-optic microwell array such that each microwell accommodates a single cell. The cells are encoded to identify their location within the array and to correlate changes or manipulations in the local environment to responses of specific cell types. The entire array can be simultaneously measured, yielding a rapid, repetitive, and high-density analysis method.

Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays.

We have developed a randomly ordered fiber-optic gene array for rapid, parallel detection of unlabeled DNA targets with surface immobilized molecular beacons (MB) that undergo a conformational change accompanied by a fluorescence change in the presence of a complementary DNA target. Microarrays are prepared by randomly distributing MB-functionalized 3-microm diameter microspheres in an array of wells etched in a 500-microm diameter optical imaging fiber. Using several MBs, each designed to recognize a different target, we demonstrate the selective detection of genomic cystic fibrosis related targets. Positional registration and fluorescence response monitoring of the microspheres was performed using an optical encoding scheme and an imaging fluorescence microscope system.

Fluorescent excitation transfer immunoassay for the determination of spinosyn A in water.

A fluorescent excitation transfer immunoassay for spinosyn A, a fermentation derived insect control agent, has been developed and applied to the analysis of tap water and wastewater effluent from manufacturing plants. Fluorescein (F) and tetramethylrhodamine (TMR) were chosen as donor and quencher, respectively, for the excitation transfer. Fluorescence quenching was observed from the binding of F-labeled antigen to TMR-labeled antibody. By employing nonlabeled antigen in a competitive immunoassay format, we reversed fluorescence quenching. The assay provides a limit of detection of 0. 01 ppb and a working range of 0.05-1 ppb and allows for the rapid determination of spinosyn A in water with recovery values ranging from 96% to 120%. With the exploitation of the small size of optical fibers, fluorescence from an assay volume of 24 microL could be measured without special vessels.

Combined imaging and chemical sensing of fertilization-induced acid release from single sea urchin eggs.

We demonstrate a microarray sensor capable of obtaining both chemical and visual information on multiple cells simultaneously with single-cell resolution. The array was fabricated by covalently immobilizing a thin, pH-sensitive polymer layer on the distal end of an optical imaging fiber. The sensor's ability to measure localized chemical dynamics in real-time was evaluated using sea urchin fertilization biochemistry as a model system. Following sea urchin fertilization, the Na(+)/H(+) transporter is activated to exchange extracellular sodium ions for intracellular hydrogen ions, causing a release of hydrogen ions at the egg's surface. By placing the pH sensor proximal to the egg and switching between a fluorescence image and a white light image, we were able to observe both localized pH changes following fertilization as well as morphological transformations during cell division.

A far-field-viewing sensor for making analytical measurements in remote locations.

We demonstrate a far-field-viewing GRINscope sensor for making analytical measurements in remote locations. The GRINscope was fabricated by permanently affixing a micro-Gradient index (GRIN) lens on the distal face of a 350-micron-diameter optical imaging fiber. The GRINscope can obtain both chemical and visual information. In one application, a thin, pH-sensitive polymer layer was immobilized on the distal end of the GRINscope. The ability of the GRINscope to visually image its far-field surroundings and concurrently detect pH changes in a flowing stream was demonstrated. In a different application, the GRINscope was used to image pH- and O2-sensitive particles on a remote substrate and simultaneously measure their fluorescence intensity in response to pH or pO2 changes.