Planar waveguides for ultra-high sensitivity of the analysis of nucleic acids

Optical Whispering-Gallery-Mode Microbubble Sensors

Whispering-gallery-mode (WGM) microbubble resonators are ideal optical sensors due to their high quality factor, small mode volume, high optical energy density, and geometry/design/structure (i.e., hollow microfluidic channels). When used in combination with microfluidic technologies, WGM microbubble resonators can be applied in chemical and biological sensing due to strong light–matter interactions. The detection of ultra-low concentrations over a large dynamic range is possible due to their high sensitivity, which has significance for environmental monitoring and applications in life-science. Furthermore, WGM microbubble resonators have also been widely used for physical sensing, such as to detect changes in temperature, stress, pressure, flow rate, magnetic field and ultrasound. In this article, we systematically review and summarize the sensing mechanisms, fabrication and packing methods, and various applications of optofluidic WGM microbubble resonators. The challenges of rapid production and practical applications of WGM microbubble resonators are also discussed.

Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures

Proteins in biological fluids (blood, urine, cerebrospinal fluid) are important biomarkers of various pathological conditions. Protein biomarkers detection and quantification have been proven to be an indispensable diagnostic tool in clinical practice. There is a growing tendency towards using portable diagnostic biosensor devices for point-of-care (POC) analysis based on microfluidic technology as an alternative to conventional laboratory protein assays. In contrast to universally accepted analytical methods involving protein labeling, label-free approaches often allow the development of biosensors with minimal requirements for sample preparation by omitting expensive labelling reagents. The aim of the present work is to review the variety of physical label-free techniques of protein detection and characterization which are suitable for application in micro-fluidic structures and analyze the technological and material aspects of label-free biosensors that implement these methods. The most widely used optical and impedance spectroscopy techniques: absorption, fluorescence, surface plasmon resonance, Raman scattering, and interferometry, as well as new trends in photonics are reviewed. The challenges of materials selection, surfaces tailoring in microfluidic structures, and enhancement of the sensitivity and miniaturization of biosensor systems are discussed. The review provides an overview for current advances and future trends in microfluidics integrated technologies for label-free protein biomarkers detection and discusses existing challenges and a way towards novel solutions.

Waveguide-based total internal reflection fluorescence microscope enabling cellular imaging under cryogenic conditions

Total internal reflection fluorescence (TIRF) microscopy is an important imaging tool for the investigation of biological structures, especially the study on cellular events near the plasma membrane. Imaging at cryogenic temperatures not only enables observing structures in a near-native and fixed state but also suppresses irreversible photo-bleaching rates, resulting in increased photo-stability of fluorophores. Traditional TIRF microscopes produce an evanescent field based on high numerical aperture immersion objective lenses with high magnification, which results in a limited field of view and is incompatible with cryogenic conditions. Here, we present a waveguide-based TIRF microscope, which is able to generate a uniform evanescent field using high refractive index waveguides on photonic chips and to obtain cellular observation at cryogenic temperatures. Our method provides an inexpensive way to achieve total-internal-reflection fluorescence imaging under cryogenic conditions.

Waveguide-based absorption measurement system for visible wavelength applications

We present a miniaturized waveguide-based absorption measurement system operating at a wavelength of 635 nm, based on a silicon nitride integrated photonic platform, suitable for lab-on-chip applications. We experimentally demonstrate a high correlation between the bulk dye concentration and the measured absorption loss levels in the waveguides. We explain a photonic design process for choosing the ideal waveguide to minimize the coefficient of variation on the analyte concentration. The approach is designed for camera readout, allowing multiple readouts and easy integration for lab-on chip cartridge approach.

Total internal reflection fluorescence quantification of receptor pharmacology

Total internal reflection fluorescence (TIRF) microscopy has been widely used as a single molecule imaging technique to study various fundamental aspects of cell biology, owing to its ability to selectively excite a very thin fluorescent volume immediately above the substrate on which the cells are grown. However, TIRF microscopy has found little use in high content screening due to its complexity in instrumental setup and experimental procedures. Inspired by the recent demonstration of label-free evanescent wave biosensors for cell phenotypic profiling and drug screening with high throughput, we had hypothesized and demonstrated that TIRF imaging is also amenable to receptor pharmacology profiling. This paper reviews key considerations and recent applications of TIRF imaging for pharmacology profiling.

Methods for Detection of Aflatoxins in Agricultural Food Crops

Aflatoxins are toxic carcinogenic secondary metabolites produced predominantly by two fungal species: Aspergillus flavus and Aspergillus parasiticus. These fungal species are contaminants of foodstuff as well as feeds and are responsible for aflatoxin contamination of these agro products. The toxicity and potency of aflatoxins make them the primary health hazard as well as responsible for losses associated with contaminations of processed foods and feeds. Determination of aflatoxins concentration in food stuff and feeds is thus very important. However, due to their low concentration in foods and feedstuff, analytical methods for detection and quantification of aflatoxins have to be specific, sensitive, and simple to carry out. Several methods including thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC), mass spectroscopy, enzyme-linked immune-sorbent assay (ELISA), and electrochemical immunosensor, among others, have been described for detecting and quantifying aflatoxins in foods. Each of these methods has advantages and limitations in aflatoxins analysis. This review critically examines each of the methods used for detection of aflatoxins in foodstuff, highlighting the advantages and limitations of each method. Finally, a way forward for overcoming such obstacles is suggested.

Simultaneous measurement of liquid absorbance and refractive index using a compact optofluidic probe

We present a novel optical technique for simultaneously measuring the absorbance and the refractive index of a thin film using an infrared optofluidic probe. Experiments were carried on two different liquids and the results agree with the bibliographical data. The ultimate goal is to achieve a multi-functional micro-optical device for analytical applications.

Using complementary acoustic and optical techniques for quantitative monitoring of biomolecular adsorption at interfaces

The great wealth of different surface sensitive techniques used in biosensing, most of which claim to measure adsorbed mass, can at first glance look unnecessary. However, with each technique relying on a different transducer principle there is something to be gained from a comparison. In this tutorial review, different optical and acoustic evanescent techniques are used to illustrate how an understanding of the transducer principle of each technique can be exploited for further interpretation of hydrated and extended polymer and biological films. Some of the most commonly used surface sensitive biosensor techniques (quartz crystal microbalance, optical waveguide spectroscopy and surface plasmon resonance) are briefly described and five case studies are presented to illustrate how different biosensing techniques can and often should be combined. The case studies deal with representative examples of adsorption of protein films, polymer brushes and lipid membranes, and describe e.g., how to deal with strongly vs. weakly hydrated films, large conformational changes and ordered layers of biomolecules. The presented systems and methods are compared to other representative examples from the increasing literature on the subject.

Counting cells with a low-cost integrated microfluidics-waveguide sensor

The capability to count cells from biofluids at low cost has important diagnostic implications in resource-poor settings. Many approaches have been developed to address this important need, and while most envision a low per-test cost, the detector instrument can be quite expensive. In this report, we present a novel device that enables low-cost and rapid counting of cells from a drop of blood. We demonstrate a shallow, buried, planar waveguide fabricated by ion exchange in glass that underlies a microfluidic structure for capturing cells. Laser light transmitted through the waveguide was attenuated by the number of metal nanoparticles tagged to the cells because of the interaction of the metal particles with the evanescent field of the waveguide. Calibration of the sensor using bead-tagged lymphocytes captured from human blood showed that the sensor could semi-quantitatively count as few as 100 cells/µL of blood. This technology enables the enumeration of specifically captured cells, allowing for a point-of-care, hand-held device for fast and affordable cell counting in screening, remote, or resource-poor settings.

Optical planar waveguide for cell counting

Low cost counting of cells has medical applications in screening, military medicine, disaster medicine, and rural healthcare. In this report, we present a shallow, buried, planar waveguide fabricated by potassium ion exchange in glass that enables low-cost and rapid counting of metal-tagged objects that lie in the evanescent field of the waveguide. Laser light transmitted through the waveguide was attenuated proportionately to the presence of metal-coated microstructures fabricated from photoresist. This technology enables the low-cost enumeration of cells from blood, urine, or other biofluids.

Fluorescent vesicles for signal amplification in reverse phase protein microarray assays

Developments in microarray technology promise to lead to great advancements in the biomedical and biological field. However, implementation of these analytical tools often relies on signal amplification strategies that are essential to reach the sensitivity levels required for a variety of biological applications. This is true especially for reverse phase arrays where a complex biological sample is directly immobilized on the chip. We present a simple and generic method for signal amplification based on the use of antibody-tagged fluorescent vesicles as labels for signal generation. To assess the gain in assay sensitivity, we performed a model assay for the detection of rabbit immunoglobulin G (IgG) and compared the limit of detection (LOD) of the vesicle assay with the LOD of a conventional assay performed with fluorescent reporter molecules. We evaluated the improvements for two fluorescence-based transduction setups: a high-sensitivity microarray reader (ZeptoREADER) and a conventional confocal scanner. In all cases, our strategy led to an increase in sensitivity. However, gain in sensitivity widely depended on the type of illumination; whereas an approximately 2-fold increase in sensitivity was observed for readout based on evanescent field illumination, the contribution was as high as more than 200-fold for confocal scanning.

Reverse protein arrays applied to host-pathogen interaction studies

Infection of cells and tissues by pathogenic microorganisms often involves severe reprogramming of host cell signaling. Typically, invasive microorganisms manipulate host cellular pathways seeking advantage for replication and survival within the host, or to evade the immune response. Understanding such subversion of the host cell by intracellular pathogens at a molecular level is the key to possible preventive and therapeutic interventions on infectious diseases. Reverse Protein Arrays (RPAs) have been exploited in other fields, especially in molecular oncology. However, this technology has not been applied yet to the study of infectious diseases. Coupling classic in vitro infection techniques used by cellular microbiologists to proteomic approaches such as RPA analysis should provide a wealth of information about how host cell pathways are manipulated by pathogens. The increasing availability of antibodies specific for phosphorylated epitopes in signaling proteins allows monitoring global changes in phosphorylation through the infection process by utilizing RPA analyses. In our lab, we have shown the potential of RPA technology in this field by devising a microarray consisting of lysates from cell cultures infected by Salmonella typhimurium. The protocols used are described here.

Direct light-coupling to thin-film waveguides using a grating-structured GRIN lens

We present a novel coupling scheme using a collimating gradient-index (GRIN) element provided with a high frequency grating to couple light from a single mode optical fiber directly to planar thin-film waveguides. The waveguide devices are used, for example, for an efficient fluorescence excitation in biosensor applications. The external coupler can be multiply reused and supersedes the conventional internal gratings. FEM simulations and experimental results show that the new technique can provide similar coupling efficiencies as common internal grating couplers.

Biosensors based on surface plasmon-enhanced fluorescence spectroscopy

The implementation of surface plasmon-enhanced fluorescence spectroscopy (SPFS) to surface plasmon resonance (SPR) biosensors enables increasing their sensitivity by several orders of magnitude. In SPR-based biosensors, surface plasmons probe the binding of target molecules contained in a liquid sample by their affinity partners attached to a metallic sensor surface. SPR biosensors relying on the detection of refractive index changes allow for direct observation of the binding of large and medium size molecules that produces sufficiently large refractive index changes. In SPR biosensors exploiting SPFS, the capture of fluorophore-labeled molecules to the sensor surface is observed by the detection of fluorescence light emitted from the surface. This technique takes advantage of the enhanced intensity of electromagnetic field accompanied with the resonant excitation of surface plasmons. The interaction with surface plasmons can greatly increase the measured fluorescence signal through enhancing the excitation rate of fluorophores and by more efficient collecting of fluorescence light. SPFS-based biosensors were shown to enable the analysis of samples with extremely low analyte concentrations and the detection of small molecules. In this review, we describe the fundamental principles, implementations, and current state of the art applications of SPFS biosensors. This review focuses on SPFS-based biosensors employing the excitation of surface plasmons on continuous metal-dielectric interfaces.

Fabrication of a cyclic olefin copolymer planar waveguide embedded in a multi-channel poly(methyl methacrylate) fluidic chip for evanescence excitation

The fabrication and characterization of a novel cyclic olefin copolymer (COC) waveguide embedded in a poly(methyl methacrylate), PMMA, fluidic chip configured in a multi-channel format with an integrated monolithic prism for evanescent fluorescence excitation are reported. The fabrication approach allowed the embedded waveguide to be situated orthogonal to a series of fluidic channels within the PMMA wafer to sample fluorescent solutions in these channels using the evanescence properties of the waveguide. Construction of the device was achieved using several fabrication techniques including high precision micromilling, hot embossing and stenciling of a polymer melt to form the waveguide and coupling prism. A waveguide channel was fabricated in the fluidic chip's cover plate, also made from PMMA, and was loaded with a COC solution using a pre-cast poly(dimethylsiloxane), PDMS, stencil containing a prism-shaped recess. The PMMA substrate contained multiple channels (100 microm wide x 30 microm deep with a pitch of 100 microm) that were situated orthogonal to the waveguide to allow penetration of the evanescent field into the sampling solution. The optical properties of the waveguide in terms of its transmission properties and penetration depth of the evanescent field in the adjacent solution were evaluated. Finally, the device was used for laser-induced fluorescence evanescent excitation of a dye solution hydrodynamically flowing through multiple microfluidic channels in the chip and processed using a microscope equipped with a charge-coupled device (CCD) for parallel readout. The device and optical system were able to image 11 channels simultaneously with a limit-of-detection of 7.1 x 10(-20) mol at a signal-to-noise ratio of 2. The waveguide was simple to manufacture and could be scaled to illuminate much higher channel numbers making it appropriate for high-throughput measurements using evanescent excitation.

A High-Sensitivity, Medium-Density, and Target Amplification–Free Planar Waveguide Microarray System for Gene Expression Analysis of Formalin-Fixed and Paraffin-Embedded Tissue

Background: Many microarray platforms and their associated assay chemistries do not work properly with RNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissue samples, a feature that severely hampers the use of microarrays in oncology applications, for which FFPE tissue is the routine specimen. Furthermore, the limited sensitivity of most microarray platforms requires time-consuming and costly amplification reactions of the target RNA, which negatively affects clinical laboratory work flow.

Methods: We developed an approach for sensitively and reliably measuring mRNA abundances in FFPE tissue samples. This approach involves automated RNA extractions, direct hybridization of extracted RNA to immobilized capture probes, antibody-mediated labeling, and readout with an instrument applying the principle of planar waveguides (PWG). A 14-gene multiplex assay conducted with RNA isolated from 20 FFPE blocks was correlated to an analysis of the same with reverse-transcription quantitative real-time PCR (RT-qPCR).

Results: The assay sensitivity for gene expression analysis obtained for the PWG microarray platform was <10 fmol/L, eliminating the need for target preamplification. We observed a correlation coefficient of 0.87 to state-of-the-art RT-qPCR technology with RNA isolated from FFPE tissue, despite a compressed dynamic range for the PWG system (a 2.9-log dynamic range for PWG in our test system vs 5.0 logs for RT-qPCR). The precision of the PWG platform was comparable to RT-qPCR (Pearson correlation coefficient of 0.9851 for PWG vs 0.9896 for RT-qPCR) for technical replicates.

Conclusions: The presented PWG platform demonstrated excellent sensitivity and precision and is especially well suited for any application for which fast, simple, and robust multiplex assays of RNA in FFPE tissue are required.

Quantification of E. coli DNA on a flow-through chemiluminescence microarray readout system after PCR amplification

We report on a hybridization assay using DNA microarrays for the quantification of amplification products of the uidA gene of E. coli. Using the stopped-PCR strategy, the amplified target DNA was strongly dependent on the applied gene copies. The quantification was carried out by a flow-through chemiluminescence microarray readout system. The DNA microarrays were based on a poly(ethylene glycol)-modified glass substrate. The probes on the surface were 18 or 25 nucleotides long and the quantified PCR product was 60 nucleotides. The amplification was stopped after 25 cycles; at this point amplification was in the middle of the logarithmical phase, and the spread between different DNA starting concentrations reached the maximum. A conjugate of streptavidin and horseradish peroxidase (HRP) bound to the biotinylated strands on the microarray surface and catalyzed the reaction of luminol and hydrogen peroxide. The generated light emission was recorded by a sensitive charge-coupled device (CCD) camera. The detection limit for the gene uidA (beta-galactosidase) of E. coli was 1.1 x 10(5) copies/mL. This system allowed for a sensitive detection and quantification of E. coli in a concentration range from 10(6) to 10(9) copies/mL.

Waveguide-based biosensors for pathogen detection

Optical phenomena such as fluorescence, phosphorescence, polarization, interference and non-linearity have been extensively used for biosensing applications. Optical waveguides (both planar and fiber-optic) are comprised of a material with high permittivity/high refractive index surrounded on all sides by materials with lower refractive indices, such as a substrate and the media to be sensed. This arrangement allows coupled light to propagate through the high refractive index waveguide by total internal reflection and generates an electromagnetic wave-the evanescent field-whose amplitude decreases exponentially as the distance from the surface increases. Excitation of fluorophores within the evanescent wave allows for sensitive detection while minimizing background fluorescence from complex, "dirty" biological samples. In this review, we will describe the basic principles, advantages and disadvantages of planar optical waveguide-based biodetection technologies. This discussion will include already commercialized technologies (e.g., Corning's EPIC(®) Ô, SRU Biosystems' BIND(™), Zeptosense(®), etc.) and new technologies that are under research and development. We will also review differing assay approaches for the detection of various biomolecules, as well as the thin-film coatings that are often required for waveguide functionalization and effective detection. Finally, we will discuss reverse-symmetry waveguides, resonant waveguide grating sensors and metal-clad leaky waveguides as alternative signal transducers in optical biosensing.

G-protein coupled receptor array technologies: site directed immobilisation of liposomes containing the H1-histamine or M2-muscarinic receptors

This paper describes a novel strategy to create a microarray of G-protein coupled receptors (GPCRs), an important group of membrane proteins both physiologically and pharmacologically. The H(1)-histamine receptor and the M(2)-muscarinic receptor were both used as model GPCRs in this study. The receptor proteins were embedded in liposomes created from the cellular membrane extracts of Spodoptera frugiperda (Sf9) insect cell culture line with its accompanying baculovirus protein insert used for overexpression of the receptors. Once captured onto a surface these liposomes provide a favourable lipidic environment for the integral membrane proteins. Site directed immobilisation of these liposomes was achieved by introduction of cholesterol-modified oligonucleotides (oligos). These oligo/cholesterol conjugates incorporate within the lipid bilayer and were captured by the complementary oligo strand exposed on the surface. Sequence specific immobilisation was demonstrated using a quartz crystal microbalance with dissipation (QCM-D). Confirmatory results were also obtained by monitoring fluorescent ligand binding to GPCRs captured on a spotted oligo microarray using Confocal Laser Scanning Microscopy and the Zepto-READER microarray imaging system. Sequence specific immobilisation of such biologically important membrane proteins could lead to the development of a heterogeneous self-sorting liposome array of GPCRs which would underpin a variety of future novel applications.

Multiplexed optical pathogen detection with lab-on-a-chip devices

Infectious diseases are still a main cause of human morbidity and mortality. Advanced diagnostics is considered to be a key driver to improve the respective therapeutic outcome. The main factors influencing the impact of diagnostics include: assay speed, availability, information content, in-vitro diagnostics and cost, for which molecular assays are providing the most promising opportunities. Miniaturisation and integration of assay steps into lab-on-a-chip devices has been described as an appropriate way to speed up assay time and make assays available onsite at competitive costs. As meaningful assays for infectious diseases need to include a whole range of clinical relevant information about the pathogen, multiplexed functionality is often required for which optical transduction is particularly well suited. The aim of this review is to assess existing developments in this field and to give an outlook on future requirements and solutions.

A regenerable immunochip for the rapid determination of 13 different antibiotics in raw milk

Access to high-quality and safe food is a basic need in our community and, consequently, the European Union has defined maximum residue levels (MRLs) for a number of antibacterial compounds. However, despite the obvious demand for quantitative multi-residue detection methods that can be carried out on a routine basis, there is currently a lack in the development of such systems. In particular, an automated multianalyte detection instrument is needed that is capable of quantifying several antibiotics simultaneously within minutes. The newly developed hapten microarrays are designed for the parallel analysis of 13 different antibiotics in milk within six minutes by applying an indirect competitive chemiluminescence microarray immunoassay (CL-MIA). To allow multiple analyses, a regenerable microarray chip was developed based on epoxy-activated PEG chip surfaces, onto which microspotted antibiotic derivatives like sulfonamides, beta-lactams, aminoglycosides, fluorquinolones and polyketides are coupled directly without further use of linking agents. Using the chip reader platform MCR 3, this antigen solid phase is stable for at least 50 consecutive analyses.

Flexible acoustic particle manipulation device with integrated optical waveguide for enhanced microbead assays

Realisation of a device intended for the manipulation and detection of bead-tagged DNA and other bio-molecules is presented. Acoustic radiation forces are used to manipulate polystyrene micro-beads into an optical evanescent field generated by a laser pumped ion-exchanged waveguide. The evanescent field only excites fluorophores brought within approximately 100 nm of the waveguide, allowing the system to differentiate between targets bound to the beads and those unbound and still held in suspension. The radiation forces are generated in a standing-wave chamber that supports multiple acoustic modes, permitting particles to be both attracted to the waveguide surface and also repelled. To provide further control over particle position, a novel method of switching rapidly between different acoustic modes is demonstrated, through which particles are manipulated into an arbitrary position within the chamber. A novel type of assay is presented: a mixture of streptavidin coated and control beads are driven towards a biotin functionalised surface, then a repulsive force is applied, making it possible to determine which beads became bound to the surface. It is shown that the quarter-wave mode can enhance bead to surface interaction, overcoming potential barriers caused by surface charges. It is demonstrated that by measuring the time of flight of a microsphere across the device the bead size can be determined, providing a means of multiplexing the detection, potentially detecting a range of different target molecules, or varying bead mass.

Optical waveguide light-mode spectroscopy immunosensors for environmental monitoring

Coupling the high specificity of the immunoanalytical reaction with the high sensitivity of optical waveguide light-mode spectroscopy (OWLS) detection gives the possibility to develop immunosensors with in most cases a definitely lower detection limit than traditionally used immunoassays. Measurements were performed on the sensitized surface of optical waveguide grating coupler sensors (2400 lines/mm grating). The OWLS technique is based on the precise measurement of the resonance angle of a polarized laser light (632.8 nm), diffracted by a grating and incoupled into a thin waveguide. The effective refractive index, determined from the resonance incoupling angle detected at high accuracy, allows determination of layer thickness and coverage (or mass) of the adsorbed or bound material with ultrahigh sensitivity. OWLS immunosensors were developed as label-free immunosensors with an amino group modified SiO(2)-TiO(2) sensor surface on which the immunoreactants could be anchored. One of the components of the antibody-antigen complex was chemically bound on the sensor surface, allowing noncompetitive or competitive detection of the analytes. To illustrate that the resulting immunosensors are suitable for the determination of small and large molecular weight analytes, OWLS sensor formats were applied for quantitative detection of a herbicide active ingredient trifluralin, a Fusarium mycotoxin zearalenone, and an egg yolk protein of key importance in endocrine regulation, vitellogenin.

Quantitative analysis of enhanced light irradiance in waveguide-based fluorescent microarrays

Probing microarray assays in the presence of a hybridization mix retrieves precious information on hybridization kinetics. However, in common detection schemes, useful surface signals compete with the high supernatant background from labelled targets in the mix. A known solution consists in exciting specifically the microarray surface with evanescent fields. Configurations using planar optical waveguides to produce such fields are shown here to present also a dramatic excitation irradiance enhancement at the guide/surrounding matter interface. We compare theoretically and experimentally a guided excitation with a classical external excitation. A full electromagnetic analysis predicts an irradiance increase higher than 10(4) for adequately tailored waveguides. We deposited high-index TiO(2) sol-gel waveguides on glass substrates according to best simulations. Quantitative enhancement analysis exploiting actual biological fluorescent spots perfectly confirms the irradiance amplification effect of a thin waveguide. The impact of amplification on the design of biochip readers is discussed since it leaves ample margin for simple and low-cost light couplers, advantageous in affordable readers and sensor systems.

Automated analytical microarrays: a critical review

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications.

Evanescent field Sensors Based on Tantalum Pentoxide Waveguides - A Review

Evanescent field sensors based on waveguide surfaces play an important rolewhere high sensitivity is required. Particularly tantalum pentoxide (Ta₂O₅) is a suitablematerial for thin-film waveguides due to its high refractive index and low attenuation.Many label-free biosensor systems such as grating couplers and interferometric sensors aswell as fluorescence-based systems benefit from this waveguide material leading toextremely high sensitivity. Some biosensor systems based on Ta₂O₅ waveguides alreadytook the step into commercialization. This report reviews the various detection systems interms of limit of detection, the applications, and the suitable surface chemistry.

Optofluidic integration for microanalysis

This review describes recent research in the application of optical techniques to microfluidic systems for chemical and biochemical analysis. The "lab-on-a-chip" presents great benefits in terms of reagent and sample consumption, speed, precision, and automation of analysis, and thus cost and ease of use, resulting in rapidly escalating adoption of microfluidic approaches. The use of light for detection of particles and chemical species within these systems is widespread because of the sensitivity and specificity which can be achieved, and optical trapping, manipulation and sorting of particles show significant benefits in terms of discrimination and reconfigurability. Nonetheless, the full integration of optical functions within microfluidic chips is in its infancy, and this review aims to highlight approaches, which may contribute to further miniaturisation and integration.

Red blood cells do not attenuate the SPCE fluorescence in surface assays

We describe the positive effect of surface plasmon-coupled fluorescence emission (SPCE) on the detection of a signal from a surface immunoassay in highly absorbing or/and scattering samples. A model immunoassay using fluorescently labeled anti-rabbit antibodies that bind to rabbit immunoglobulin on a silver surface was performed, and the signal was detected in the presence of various highly absorbing and/or scattering solutions or suspensions, such as hemoglobin solution, plastic beads, and red blood cells. The results showed that a highly absorbing solution consisting of small molecules (dye, hemoglobin) attenuates the SPCE signal approximately 2-3-fold. In contrast, suspensions with the same absorption containing large particles (large beads, red blood cell suspension) attenuate the SPCE signal only slightly, approximately 5-10%. Also, a suspension of large undyed, highly scattering beads does not reduce the SPCE signal. The effects on the immunoassay signal of the sample background absorption and scattering, the size of the background particles, and the geometry of the experimental set-up are discussed. We believe that SPCE is a promising technique in the development of biosensors utilized for surface-based assays, as well as any assays performed directly in highly absorbing and/or scattering solutions without washing or separation procedures. Figure Red blood cells (unlike hemoglobin) do not attenuate the SPCE fluorescence in surface assays.

Tuned graft copolymers as controlled coatings for DNA microarrays

DNA microarrays have become a powerful tool for expression profiling and other genomics applications. A critical factor for their sensitivity is the interfacial coating between the chip substrate and the bound DNA. Such a coating has to embrace the divergent requirements of tightly binding the capture probe DNA during the spotting process and of minimizing the nonspecific binding of target DNA during the hybridization assay. To fulfill these conditions, most coatings require a passivation step. Here we demonstrate how the chain density of a graft copolymer with a polycationic backbone, poly(l-lysine)-graft-poly(ethylene glycol), can be tuned such that the binding capacity during capture probe deposition is maximized while the nonspecific binding during hybridization assays is kept to a minimum, thus alleviating the requirement for a separate passivation procedure. Evidence for the superior performance of such coatings in terms of signal-to-noise ratio and spot quality is presented using an evanescent field-based fluorescent sensing technique (the ZeptoREADER). The surface architecture is further characterized using optical waveguide lightmode spectroscopy and time-of-flight secondary ion mass spectrometry. Finally, in a model assay, we demonstrate that expression changes can be detected from 1 microg of total mRNA sample material with a limit of detectable differential expression of +/-1.5.

Optical technologies for the read out and quality control of DNA and protein microarrays

Microarray formats have become an important tool for parallel (or multiplexed) monitoring of biomolecular interactions. Surface-immobilized probes like oligonucleotides, cDNA, proteins, or antibodies can be used for the screening of their complementary targets, covering different applications like gene or protein expression profiling, analysis of point mutations, or immunodiagnostics. Numerous reviews have appeared on this topic in recent years, documenting the intriguing progress of these miniaturized assay formats. Most of them highlight all aspects of microarray preparation, surface chemistry, and patterning, and try to give a systematic survey of the different kinds of applications of this new technique. This review places the emphasis on optical technologies for microarray analysis. As the fluorescent read out of microarrays is dominating the field, this topic will be the focus of the review. Basic principles of labeling and signal amplification techniques will be introduced. Recent developments in total internal reflection fluorescence, resonance energy transfer assays, and time-resolved imaging are addressed, as well as non-fluorescent imaging methods. Finally, some label-free detection modes are discussed, such as surface plasmon microscopy or ellipsometry, since these are particularly interesting for microarray development and quality control purposes.

Development of immunosensor based on OWLS technique for determining Aflatoxin B1 and Ochratoxin A

Mycotoxins are toxic secondary metabolites produced by a number of different fungi, and can be present in a wide range of food and feed commodities including cereal grains, oil seeds, dried fruits, apple juice, wine and meat products from animals fed contaminated meal. Many mycotoxins are highly resistant, and survive food processing, and therefore enter the food chain and provide a threat to human health. The optical waveguide lightmode spectroscopy (OWLS) technique has been applied to the detection of Aflatoxin and Ochratoxin in both competitive and in direct immunoassays. After immobilizing the antibody or antigen conjugate for the direct or indirect measurement, respectively, the sensor chip was used in flow-injection analyser (FIA) system. When using non-competitive method, sensor responses were obtained first only at analyte concentrations of 5-10 ng ml(-1). In both cases, the responses were very unstable. For competitive sensor investigation with the sensitized chip first the optimal dilution rate of monoclonal antibodies was determined, for the measurement of Ochratoxin A and Aflatoxin B1 the monoclonal antibody stock solution was diluted to 1 microg ml(-1) and to a 1:400 dilution, respectively. During the competitive measurement standard solutions were mixed with monoclonal antibodies at the appropriate concentration, the mixture was incubated for 1 min and injected into the OWLS system. The sensitive detection range of the competitive detection method was between 0.5 and 10 ng ml(-1) in both cases. After the establishment of the indirect method, barley and wheat flour samples were measured, and the results were in good correlation by those measured by enzyme linked immuno-sorbent assay (ELISA). Regression coefficient between the two methods for Ochratoxin and Aflatoxin was determined as 0.96 and 0.89, respectively.

Waveguide excitation fluorescence microscopy: A new tool for sensing and imaging the biointerface

A novel biosensing and imaging technique, the waveguide excitation fluorescence microscope, has been developed for the dynamic and quantitative investigation of bio-interfacial events in situ, ranging from ligand-receptor binding to focal adhesion formation in cell-surface interactions. The technique makes use of the evanescent field created when light travels in a mono-mode, planar optical waveguide to excite fluorescence in the near interface region. Advantages of the technique include high target sensitivity for fluorescence detection (femtomolar range), high surface specificity (ca. 100 nm perpendicular to the waveguide), large area analysis with submicron resolution, 'built-in' calibration of fluorescent light gain, and the capability to perform multi-colour imaging in situ and in real time. In this work, the sensitivity of the system has already been demonstrated through dynamic measurements of the streptavidin-biotin binding event to below 20 pM concentrations, signal to noise comparisons with conventional fluorescence microscopy have shown more than a 10-fold improvement, and surface specificity of the technique has also been illustrated in a comparison of fibroblast focal adhesion images. Thus, this new tool can be used to illuminate processes occurring at the interface between biology and synthetic surfaces in a unique manner.

Comparison of the chondrosarcoma cell line SW1353 with primary human adult articular chondrocytes with regard to their gene expression profile and reactivity to IL-1beta

OBJECTIVE

In this study, the human chondrosarcoma cell line SW1353 was investigated by gene expression analysis in order to validate it as an in vitro model for primary human (adult articular) chondrocytes (PHCs).

METHODS

PHCs and SW1353 cells were cultured as high density monolayer cultures with and without 1ng/ml interleukin-1beta (IL-1beta). RNA was isolated and assayed using a custom-made oligonucleotide microarray representing 312 chondrocyte-relevant genes. The expression levels of selected genes were confirmed by real-time polymerase chain reaction and the gene expression profiles of the two cell types, both with and without IL-1beta treatment, were compared.

RESULTS

Overall, gene expression profiling showed only very limited similarities between SW1353 cells and PHCs at the transcriptional level. Similarities were predominantly seen with respect to catabolic effects after IL-1beta treatment. In both cell systems matrix metalloproteinase-1 (MMP-1), MMP-3 and MMP-13 were strongly induced by IL-1beta, without significant induction of MMP-2. IL-6 was also found to be up-regulated by IL-1beta in both cellular models. On the other hand, intercellular mediators such as leukemia inhibitory factor (LIF) and bone morphogenetic protein-2 (BMP-2) were not induced by IL-1beta in SW1353 cells, but significantly up-regulated in PHCs. Bioinformatical analysis identified nuclear factor kappa-B (NFkappaB) as a common transcriptional regulator of IL-1beta induced genes in both SW1353 cells and PHCs, whereas other transcription factors were only found to be relevant for individual cell systems.

CONCLUSION

Our data characterize SW1353 cells as a cell line with only a very limited potential to mimic PHCs, though SW1353 cells can be of value to study the induction of protease expression within cells, a phenomenon also seen in chondrocytes.

Evanescent wave fluorescence biosensors

Since discovery and first use in the mid-1970s, evanescent wave fluorescence biosensors have developed into a diverse range of instruments, each designed to meet a particular detection need. In this review, we provide a brief synopsis of what evanescent wave fluorescence biosensors are, how they work, and how they are used. In addition, we have summarized the important patents that have impacted the evolution from laboratory curiosities to fully automated commercial products. Finally, we address the critical issues that evanescent wave fluorescence biosensors will face in the coming years.

Determination of Binding Constants on Microarrays with Confocal Fluorescence Detection

Confocal laser scanning microscopy was employed for the determination of binding constants of receptor-ligand interactions in a microarray format. Protocols for a localized immobilization of amine containing substances on glass via GOPTS (3-glycidyloxypropyl)trimethoxysilane) were optimized with respect to the detection of ligand binding by fluorescence. Compatibility with miniaturization by nanopipetting devices was ensured during all steps. The interaction of the tripeptide L-Lys-D-Ala-D-Ala with vancomycin immobilized on glass served as a model. To minimize consumption of ligand, binding constants were determined by stepwise titration of binding sites. The binding constant of the unlabeled ligand was determined by competitive titration with a fluorescently labeled analogue. The determined binding constants agreed well with those determined by other techniques, previously. Labeled ligand bound stronger than the unlabeled one. This difference was dye-dependent. Still, binding was specific for the tripeptide moiety confirming that ligand and fluorescent analogue competed for the same binding sites these results validate the determination of binding constants by competitive titration. The protocols established for confocal fluorescence detection are applicable to axially resolved detection modalities and screening for unlabeled ligands by competitive titration in general.