Array biosensor for simultaneous identification of bacterial, viral, and protein analytes

Bacteriophage-based bioassays: an expected paradigm shift in microbial diagnostics

Bacteriophages, as abundant and specific agents, hold significant promise as a solution to combat the growing threat of antimicrobial resistance. Their unique ability to selectively lyse bacterial cells without harming humans makes them a compelling alternative to traditional antibiotics and point-of-care diagnostics. The article reviews the current landscape of diagnostic technologies, identify gaps and highlight emerging possibilities demonstrates a comprehensive approach to advancing clinical diagnosis of microbial pathogens and covers an overview of existing phage-based bioassays. Overall, the provided data in this review effectively communicates the potential of bacteriophages in transforming therapeutic and diagnostic paradigms, offering a holistic perspective on the benefits and opportunities they present in combating microbial infections and enhancing public health.

Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals

Neutralization assays that can measure neutralizing antibodies in serum are vital for large-scale serodiagnosis and vaccine evaluation. Here, we establish multiplexed lab-on-a-chip bioassays for testing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Compared with enzyme-linked immunosorbent assay (ELISA), our method exhibits a low consumption of sample and reagents (10 μL), a low limit of detection (LOD: 0.08 ng/mL), a quick sample-to-answer time (about 70 min), and multiplexed ability (5 targets in each of 7 samples in one assay). We can also increase the throughput as needed. The concentrations of antibodies against RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants after two doses of vaccines are 6.6 ± 3.6, 8.7 ± 4.6, 3.4 ± 2.8, 3.8 ± 2.8, and 2.8 ± 2.3 ng/mL, respectively. This suggests that neutralizing activities against N501Y, E484K, and L452R/E484Q-mutants were less effective than RBD and D614G-mutant. We performed a plaque reduction neutralization test (PRNT) for all volunteers. Compared with PRNT, our assay is fast, accurate, inexpensive, and multiplexed with multiple-sample processing ability, which is good for large-scale serodiagnosis and vaccine evaluation.

New approach in SARS-CoV-2 surveillance using biosensor technology: a review

Biosensors are analytical tools that transform the bio-signal into an observable response. Biosensors are effective for early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection because they target viral antigens to assess clinical development and provide information on the severity and critical trends of infection. The biosensors are capable of being on-site, fast, and extremely sensitive to the target viral antigen, opening the door for early detection of SARS-CoV-2. They can screen individuals in hospitals, airports, and other crowded locations. Microfluidics and nanotechnology are promising cornerstones for the development of biosensor-based techniques. Recently, due to high selectivity, simplicity, low cost, and reliability, the production of biosensor instruments have attracted considerable interest. This review article precisely provides the extensive scientific advancement and intensive look of basic principles and implementation of biosensors in SARS-CoV-2 surveillance, especially for human health. In this review, the importance of biosensors including Optical, Electrochemical, Piezoelectric, Microfluidic, Paper-based biosensors, Immunosensors, and Nano-Biosensors in the detection of SARS-CoV-2 has been underscored. Smartphone biosensors and calorimetric strips that target antibodies or antigens should be developed immediately to combat the rapidly spreading SARS-CoV-2. Wearable biosensors can constantly monitor patients, which is a highly desired feature of biosensors. Finally, we summarized the literature, outlined new approaches and future directions in diagnosing SARS-CoV-2 by biosensor-based techniques.

Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19

Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.

Low-fouling, mixed-charge poly-l-lysine polymers with anionic oligopeptide side-chains

Biosensors and biomedical devices require antifouling surfaces to prevent the non-specific adhesion of proteins or cells, for example, when aiming to detect circulating cancer biomarkers in complex natural media (e.g., in blood plasma or serum). A mixed-charge polymer was prepared by the coupling of a cationic polyelectrolyte and an anionic oligopeptide through a modified "grafting-to" method. The poly-l-lysine (PLL) backbone was modified with different percentages (y%) of maleimide-NHS ester chains (PLL-mal(y%), from 13% to 26%), to produce cationic polymers with specific grafting densities, obtaining a mixed-charge polymer. The anionic oligopeptide structure (CEEEEE) included one cysteine (C) and five glutamic acid (E) units, which were attached to the PLL-mal(y%) polymers, preadsorbed on gold substrates, through the thiol-maleimide Michael-type addition. Contact angle and PM-IRRAS data confirmed monolayer formation of the modified PLLs. Antifouling properties of peptide-PLL surfaces were assessed in adsorption studies using quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance imaging (SPRI) techniques. PLL-mal(26%)-CEEEEE showed the best antifouling performance in single-protein solutions, and the nonspecific adsorption of proteins was 46 ng cm^-2 using diluted human plasma samples. The new PLL-mal(26%)-CEEEEE polymer offers a prominent low-fouling activity in complex media, with rapid and simple procedures for the synthesis and functionalization of the surface compared to conventional non-fouling materials.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

Analytical Protein Microarrays: Advancements Towards Clinical Applications

Protein microarrays represent a powerful technology with the potential to serve as tools for the detection of a broad range of analytes in numerous applications such as diagnostics, drug development, food safety, and environmental monitoring. Key features of analytical protein microarrays include high throughput and relatively low costs due to minimal reagent consumption, multiplexing, fast kinetics and hence measurements, and the possibility of functional integration. So far, especially fundamental studies in molecular and cell biology have been conducted using protein microarrays, while the potential for clinical, notably point-of-care applications is not yet fully utilized. The question arises what features have to be implemented and what improvements have to be made in order to fully exploit the technology. In the past we have identified various obstacles that have to be overcome in order to promote protein microarray technology in the diagnostic field. Issues that need significant improvement to make the technology more attractive for the diagnostic market are for instance: too low sensitivity and deficiency in reproducibility, inadequate analysis time, lack of high-quality antibodies and validated reagents, lack of automation and portable instruments, and cost of instruments necessary for chip production and read-out. The scope of the paper at hand is to review approaches to solve these problems.

Democratization of Nanoscale Imaging and Sensing Tools Using Photonics

Providing means for researchers and citizen scientists in the developing world to perform advanced measurements with nanoscale precision can help to accelerate the rate of discovery and invention as well as improve higher education and the training of the next generation of scientists and engineers worldwide. Here, we review some of the recent progress toward making optical nanoscale measurement tools more cost-effective, field-portable, and accessible to a significantly larger group of researchers and educators. We divide our review into two main sections: label-based nanoscale imaging and sensing tools, which primarily involve fluorescent approaches, and label-free nanoscale measurement tools, which include light scattering sensors, interferometric methods, photonic crystal sensors, and plasmonic sensors. For each of these areas, we have primarily focused on approaches that have either demonstrated operation outside of a traditional laboratory setting, including for example integration with mobile phones, or exhibited the potential for such operation in the near future.

A flow-through holed PDMS membrane as a reusable microarray spotter for biomedical assays

We propose the exploitation of a holed-designed poly(dimethyl)siloxane (PDMS) membrane as an innovative microarray spotter. The membrane is fabricated by a simple technological approach and can be reused several times. A good level of reproducibility is found upon spotting fluorescent proteins at different concentrations over large areas.

Binding, structure, and dynamics of hydrophobic polymers near patterned self-assembled monolayer surfaces

We use molecular dynamics simulations to study the binding, conformations, and dynamics of a flexible 25-mer hydrophobic polymer near well-defined patterned self-assembled monolayers containing a hydrophobic strip (with -CH3 head-groups) having different widths in a hydrophilic (-OH) background. We show that the polymer binds favorably to hydrophobic strips of all widths, including the subnanometer ones comprising 3, 2, or even 1 row of -CH3 head-groups, with the binding strength varying from about 107 to 25 kJ/mol for the widest to the narrowest strip. Near wide hydrophobic patches containing 5 or more -CH3 rows, pancakelike conformations are dominant, whereas hairpinlike structures become preferred ones near the narrower strips. In the vicinity of the narrowest 1-row strip, the polymer folds into semiglobular conformations, thus maintaining sufficient contact with the strip while sequestering its hydrophobic groups away from water. We also show that the confinement makes the translational dynamics of the polymer anisotropic as well as conformational dependent. Our results may help to understand and manipulate the self-assembly and dynamics of soft matter, such as polymers, peptides, and proteins, at inhomogeneous patterned surfaces.

Thousand-fold fluorescent signal amplification for mHealth diagnostics

The low sensitivity of Mobile Health (mHealth) optical detectors, such as those found on mobile phones, is a limiting factor for many mHealth clinical applications. To improve sensitivity, we have combined two approaches for optical signal amplification: (1) a computational approach based on an image stacking algorithm to decrease the image noise and enhance weak signals, and (2) an optical signal amplifier utilizing a capillary tube array. These approaches were used in a detection system which includes multi-wavelength LEDs capable of exciting many fluorophores in multiple wavelengths, a mobile phone or a webcam as a detector, and capillary tube array configured with 36 capillary tubes for signal enhancement. The capillary array enables a ~100× increase in signal sensitivity for fluorescein, reducing the limit of detection (LOD) for mobile phones and webcams from 1000 nM to 10nM. Computational image stacking enables another ~10× increase in signal sensitivity, further reducing the LOD for webcam from 10nM to 1 nM. To demonstrate the feasibility of the device for the detection of disease-related biomarkers, adenovirus DNA labeled with SYBR green or fluorescein was analyzed by both our capillary array and a commercial plate reader. The LOD for the capillary array was 5 ug/mL, and that of the plate reader was 1 ug/mL. Similar results were obtained using DNA stained with fluorescein. The combination of the two signal amplification approaches enables a ~1000× increase in LOD for the webcam platform. This brings it into the range of a conventional plate reader while using a smaller sample volume (10 ul) than the plate reader requires (100 ul). This suggests that such a device could be suitable for biosensing applications where up to 10 fold smaller sample sizes are needed. The simple optical configuration for mHealth described in this paper employing the combined capillary and image processing signal amplification is capable of measuring weak fluorescent signals without the need of dedicated laboratories. It has the potential to be used to increase sensitivity of other optically based mHealth technologies, and may increase mHealth's clinical utility, especially for telemedicine and for resource-poor settings and global health applications.

Capillary Array Waveguide Amplified Fluorescence Detector for mHealth

Mobile Health (mHealth) analytical technologies are potentially useful for carrying out modern medical diagnostics in resource-poor settings. Effective mHealth devices for underserved populations need to be simple, low cost, and portable. Although cell phone cameras have been used for biodetection, their sensitivity is a limiting factor because currently it is too low to be effective for many mHealth applications, which depend on detection of weak fluorescent signals. To improve the sensitivity of portable phones, a capillary tube array was developed to amplify fluorescence signals using their waveguide properties. An array configured with 36 capillary tubes was demonstrated to have a ~100X increase in sensitivity, lowering the limit of detection (LOD) of mobile phones from 1000 nM to 10 nM for fluorescein. To confirm that the amplification was due to waveguide behavior, we coated the external surfaces of the capillaries with silver. The silver coating interfered with the waveguide behavior and diminished the fluorescence signal, thereby proving that the waveguide behavior was the main mechanism for enhancing optical sensitivity. The optical configuration described here is novel in several ways. First, the use of capillaries waveguide properties to improve detection of weak florescence signal is new. Second we describe here a three dimensional illumination system, while conventional angular laser waveguide illumination is spot (or line), which is functionally one-dimensional illumination, can illuminate only a single capillary or a single column (when a line generator is used) of capillaries and thus inherently limits the multiplexing capability of detection. The planar illumination demonstrated in this work enables illumination of a two dimensional capillary array (e.g. x columns and y rows of capillaries). In addition, the waveguide light propagation via the capillary wall provides a third dimension for illumination along the axis of the capillaries. Such an array can potentially be used for sensitive analysis of multiple fluorescent detection assays simultaneously. The simple phone based capillary array approach presented in this paper is capable of amplifying weak fluorescent signals thereby improving the sensitivity of optical detectors based on mobile phones. This may allow sensitive biological assays to be measured with low sensitivity detectors and may make mHealth practical for many diagnostics applications, especially in resource-poor and global health settings.

Recent advances in bacteriophage based biosensors for food-borne pathogen detection

Foodborne diseases are a major health concern that can have severe impact on society and can add tremendous financial burden to our health care systems. Rapid early detection of food contamination is therefore relevant for the containment of food-borne pathogens. Conventional pathogen detection methods, such as microbiological and biochemical identification are time-consuming and laborious, while immunological or nucleic acid-based techniques require extensive sample preparation and are not amenable to miniaturization for on-site detection. Biosensors have shown tremendous promise to overcome these limitations and are being aggressively studied to provide rapid, reliable and sensitive detection platforms for such applications. Novel biological recognition elements are studied to improve the selectivity and facilitate integration on the transduction platform for sensitive detection. Bacteriophages are one such unique biological entity that show excellent host selectivity and have been actively used as recognition probes for pathogen detection. This review summarizes the extensive literature search on the application of bacteriophages (and recently their receptor binding proteins) as probes for sensitive and selective detection of foodborne pathogens, and critically outlines their advantages and disadvantages over other recognition elements.

Recent advances in bacteriophage based biosensors for food-borne pathogen detection

Foodborne diseases are a major health concern that can have severe impact on society and can add tremendous financial burden to our health care systems. Rapid early detection of food contamination is therefore relevant for the containment of food-borne pathogens. Conventional pathogen detection methods, such as microbiological and biochemical identification are time-consuming and laborious, while immunological or nucleic acid-based techniques require extensive sample preparation and are not amenable to miniaturization for on-site detection. Biosensors have shown tremendous promise to overcome these limitations and are being aggressively studied to provide rapid, reliable and sensitive detection platforms for such applications. Novel biological recognition elements are studied to improve the selectivity and facilitate integration on the transduction platform for sensitive detection. Bacteriophages are one such unique biological entity that show excellent host selectivity and have been actively used as recognition probes for pathogen detection. This review summarizes the extensive literature search on the application of bacteriophages (and recently their receptor binding proteins) as probes for sensitive and selective detection of foodborne pathogens, and critically outlines their advantages and disadvantages over other recognition elements.

Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers

We report a top-down approach to the fabrication of oligonucleotide and protein arrays on surfaces coated with ultrathin, amine-reactive polymer multilayers fabricated by the covalent "layer-by-layer" (LbL) assembly of polyethyleneimine (PEI) and the amine-reactive, azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Manual spotting of amine-terminated oligonucleotide probe sequences on planar glass slides coated with PEI/PVDMA multilayers (~35 nm thick) yielded arrays of immobilized probes that hybridized fluorescently labeled complementary sequences with high signal intensities, high signal-to-noise ratios, and high sequence specificity. Treatment of residual azlactone functionality with the nonfouling small-molecule amine d-glucamine resulted in regions between the features of these arrays that resisted adsorption of protein and permitted hybridization in complex media containing up to 10 mg/mL protein. The residual azlactone groups in these films were also exploited to immobilize proteins on film-coated surfaces and fabricate functional arrays of proteins and enzymes. The ability to deposit PEI/PVDMA multilayers on substrates of arbitrary size, shape, and composition permitted the fabrication of arrays of oligonucleotides on the surfaces of multilayer-coated sheets of poly(ethylene terephthalate) and heat-shrinkable polymer film. Arrays fabricated on these flexible plastic substrates can be bent, cut, resized, and manipulated physically in ways that are difficult using more conventional rigid substrates. This approach could thus contribute to the development of new assay formats and new applications of biomolecule arrays. The methods described here are straightforward to implement, do not require access to specialized equipment, and should also be compatible with automated liquid-handling methods used to fabricate higher-density arrays of oligonucleotides and proteins on more traditional surfaces.

Mass Spectrometry and Integrated Virus Detection System Characterization of MS2 Bacteriophage

ABSTRACT In this study, we demonstrate the effect of sample matrix composition of MS2 virus on its characterization by ESI-MS and IVDS. MS2 samples grown and purified using various techniques showed different responses on ESI-MS than that on IVDS. The LC-MS of the specific biomarker of MS2 bacteriophage from an infected Escherichia coli sample was characterized by the presence of E. coli proteins. The significant impact of sample matrix was observed upon identification of MS2 using a database search. Infected E. coli with MS2 showed a matching score indifferent from uninfected ones. Only purified MS2, using CsCl and analyzed by LS-MS, showed a positive match using the database search. However, the variation in MS2 sample matrix had no effect on the deification of MS2.

Battery-free radio frequency identification (RFID) sensors for food quality and safety

Market demands for new sensors for food quality and safety stimulate the development of new sensing technologies that can provide an unobtrusive sensor form, battery-free operation, and minimal sensor cost. Intelligent labeling of food products to indicate and report their freshness and other conditions is one important possible application of such new sensors. This study applied passive (battery-free) radio frequency identification (RFID) sensors for the highly sensitive and selective detection of food freshness and bacterial growth. In these sensors, the electric field generated in the RFID sensor antenna extends from the plane of the RFID sensor and is affected by the ambient environment, providing the opportunity for sensing. This environment may be in the form of a food sample within the electric field of the sensing region or a sensing film deposited onto the sensor antenna. Examples of applications include monitoring of milk freshness, fish freshness, and bacterial growth in a solution. Unlike other food freshness monitoring approaches that require a thin film battery for operation of an RFID sensor and fabrication of custom-made sensors, the passive RFID sensing approach developed here combines the advantages of both battery-free and cost-effective sensor design and offers response selectivity that is impossible to achieve with other individual sensors.

Optical biosensors for food quality and safety assurance-a review

Food quality and safety is a scientific discipline describing handling, preparation and storage of food in ways that prevent food borne illness. Food serves as a growth medium for microorganisms that can be pathogenic or cause food spoilage. Therefore, it is imperative to have stringent laws and standards for the preparation, packaging and transportation of food. The conventional methods for detection of food contamination based on culturing, colony counting, chromatography and immunoassay are tedious and time consuming while biosensors have overcome some of these disadvantages. There is growing interest in biosensors due to high specificity, convenience and quick response. Optical biosensors show greater potential for the detection of pathogens, pesticide and drug residues, hygiene monitoring, heavy metals and other toxic substances in the food to check whether it is safe for consumption or not. This review focuses on optical biosensors, the recent developments in the associated instrumentation with emphasis on fiber optic and surface plasmon resonance (SPR) based biosensors for detecting a range of analytes in food samples, the major advantages and challenges associated with optical biosensors. It also briefly covers the different methods employed for the immobilization of bio-molecules used in developing biosensors.

Highly sensitive diagnostic assay for the detection of protein biomarkers using microresonators and multifunctional nanoparticles

We developed a novel gravimetric immunoassay for sensitive detection of multiple protein biomarkers using silicon microcantilever arrays and multifunctional hybrid nanoparticles. Magnetic-photocatalytic hybrid nanoparticles with a highly crystalline TiO(2) shell were synthesized using a solvothermal reaction without a calcination process. After functionalizing the hybrid nanoparticles and silicon cantilevers with antibodies, the nanoparticles were used to magnetically separate target biomarkers from human serum. Frequency changes of the microcantilevers due to the binding of the nanoparticles were measured using a dip-and-dry method. Frequency changes were further amplified using a photocatalytic silver reduction reaction. Several biomarkers, including interleukin-6, interferon-γ, and alpha-fetoprotein, were selectively detected using arrays of eight silicon microcantilevers. The detection limit of this assay was ∼0.1 pg/mL, which is superior to the clinical threshold of the biomarkers.

Detection of cardiac biomarkers using single polyaniline nanowire-based conductometric biosensors

The detection of myoglobin (Myo), cardiac troponin I (cTnI), creatine kinase-MB (CK-MB), and b-type natriuretic peptide (BNP) plays a vital role in diagnosing cardiovascular diseases. Here we present single site-specific polyaniline (PANI) nanowire biosensors that can detect cardiac biomarkers such as Myo, cTnI, CK-MB, and BNP with ultra-high sensitivity and good specificity. Using single PANI nanowire-based biosensors integrated with microfluidic channels, very low concentrations of Myo (100 pg/mL), cTnI (250 fg/mL), CK-MB (150 fg/mL), and BNP (50 fg/mL) were detected. The single PANI nanowire-based biosensors displayed linear sensing profiles for concentrations ranging from hundreds (fg/mL) to tens (ng/mL). In addition, devices showed a fast (few minutes) response satisfying respective reference conditions for Myo, cTnI, CK-MB, and BNP diagnosis of heart failure and for determining the stage of the disease. This single PANI nanowire-based biosensor demonstrated superior biosensing reliability with the feasibility of label free detection and improved processing cost efficiency due to good biocompatibility of PANI to monoclonal antibodies (mAbs). Therefore, this development of single PANI nanowire-based biosensors can be applied to other biosensors for cancer or other diseases.

Polycrystalline-Diamond MEMS Biosensors Including Neural Microelectrode-Arrays

Diamond is a material of interest due to its unique combination of properties, including its chemical inertness and biocompatibility. Polycrystalline diamond (poly-C) has been used in experimental biosensors that utilize electrochemical methods and antigen-antibody binding for the detection of biological molecules. Boron-doped poly-C electrodes have been found to be very advantageous for electrochemical applications due to their large potential window, low background current and noise, and low detection limits (as low as 500 fM). The biocompatibility of poly-C is found to be comparable, or superior to, other materials commonly used for implants, such as titanium and 316 stainless steel. We have developed a diamond-based, neural microelectrode-array (MEA), due to the desirability of poly-C as a biosensor. These diamond probes have been used for in vivo electrical recording and in vitro electrochemical detection. Poly-C electrodes have been used for electrical recording of neural activity. In vitro studies indicate that the diamond probe can detect norepinephrine at a 5 nM level. We propose a combination of diamond micro-machining and surface functionalization for manufacturing diamond pathogen-microsensors.

PDMS microfluidic capillary systems for patterning proteins on surfaces and performing miniaturized immunoassays

In this chapter, we describe the fabrication and use of microfluidic capillary systems (CSs) made in soft, transparent polydimethylsiloxane (PDMS). Sixteen microfluidic CSs, each containing a loading pad, a microchannel, and a capillary pump are engraved in a single PDMS chip. The CSs are used for two applications, firstly to pattern fibronectin on glass surfaces to locally control the adhesion of cultured cells to the substrate, and secondly to carry out multiplexed miniaturized immunoassays.

Microfluidic DNA microarray analysis: a review

Microarray DNA hybridization techniques have been used widely from basic to applied molecular biology research. Generally, in a DNA microarray, different probe DNA molecules are immobilized on a solid support in groups and form an array of microspots. Then, hybridization to the microarray can be performed by applying sample DNA solutions in either the bulk or the microfluidic manner. Because the immobilized probe DNA binds and retains its complementary target DNA, detection is achieved through the read-out of the tagged markers on the sample target molecules. The recent microfluidic hybridization method shows the advantages of less sample usage and reduced incubation time. Here, sample solutions are confined in microfabricated channels and flow through the probe microarray area. The high surface-to-volume ratio in microchannels of nanolitre volume greatly enhanced the sensitivity as obtained with the bulk solution method. To generate nanolitre flows, different techniques have been developed, and this including electrokinetic control, vacuum suction and syringe pumping. The latter two are pressure-driven methods which are more flexible without the need of considering the physicochemical properties of solutions. Recently, centrifugal force is employed to drive liquid movement in microchannels. This method utilizes the body force from the liquid itself and there are no additional solution interface contacts such as from electrodes or syringes and tubing. Centrifugal force driven flow also features the ease of parallel hybridizations. In this review, we will summarize the recent advances in microfluidic microarray hybridization and compare the applications of various flow methods.

Ligase detection reaction generation of reverse molecular beacons for near real-time analysis of bacterial pathogens using single-pair fluorescence resonance energy transfer and a cyclic olefin copolymer microfluidic chip

Detection of pathogenic bacteria and viruses require strategies that can signal the presence of these targets in near real-time due to the potential threats created by rapid dissemination into water and/or food supplies. In this paper, we report an innovative strategy that can rapidly detect bacterial pathogens using reporter sequences found in their genome without requiring polymerase chain reaction (PCR). A pair of strain-specific primers was designed based on the 16S rRNA gene and were end-labeled with a donor (Cy5) or acceptor (Cy5.5) dye. In the presence of the target bacterium, the primers were joined using a ligase detection reaction (LDR) only when the primers were completely complementary to the target sequence to form a reverse molecular beacon (rMB), thus bringing Cy5 (donor) and Cy5.5 (acceptor) into close proximity to allow fluorescence resonance energy transfer (FRET) to occur. These rMBs were subsequently analyzed using single-molecule detection of the FRET pairs (single-pair FRET; spFRET). The LDR was performed using a continuous flow thermal cycling process configured in a cyclic olefin copolymer (COC) microfluidic device using either 2 or 20 thermal cycles. Single-molecule photon bursts from the resulting rMBs were detected on-chip and registered using a simple laser-induced fluorescence (LIF) instrument. The spFRET signatures from the target pathogens were reported in as little as 2.6 min using spFRET.

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.

Array lead zirconate titanate/glass piezoelectric microcantilevers for real-time detection of Bacillus anthracis with 10 spores/ml sensitivity and 1/1000 selectivity in bacterial mixtures

An array of three identical piezoelectric microcantilever sensors (PEMSs) consisting of a lead zirconate titanate layer bonded to a glass layer was fabricated and examined for simultaneous, in situ, real-time, all-electrical detection of Bacillus anthracis (BA) spores in an aqueous suspension using the first longitudinal extension mode of resonance. With anti-BA antibody immobilized on the sensor surfaces all three PEMS exhibited identical BA detection resonance frequency shifts at all tested concentrations, 10-10(7) spores/ml with a standard deviation of less than 10%. The detection concentration limit of 10 spores/ml was about two orders of magnitude lower than would be permitted by flexural peaks. In blinded-sample testing, the array PEMS detected BA in three samples containing BA: (1) 3.3x10(3) spores/ml, (2) a mixture of 3.3x10(3) spores/ml and 3.3x10(5) S. aureus (SA) and P. aeruginosa (PA) per ml, and (3) a mixture of 3.3x10(3) spores/ml with 3.3x10(6) SA+PA/ml. There was no response to a sample containing only 3.3x10(6) SA+PA/ml. These results illustrate the sensitivity, specificity, reusability, and reliability of array PEMS for in situ, real-time detection of BA spores.

Bacteriophage-modified microarrays for the direct impedimetric detection of bacteria

A novel method is presented for the specific and direct detection of bacteria using bacteriophages as recognition receptors immobilized covalently onto functionalized screen-printed carbon electrode (SPE) microarrays. The SPE networks were functionalized through electrochemical oxidation in acidic media of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) by applying a potential of +2.2 V to the working electrode. Immobilization of T4 bacteriophage onto the SPEs was achieved via EDC by formation of amide bonds between the protein coating of the phage and the electrochemically generated carboxylic groups at the carbon surface. The surface functionalization with EDC, and the binding of phages, was verified by time-of-flight secondary ion mass spectrometry. The immobilized T4 phages were then used to specifically detect E. coli bacteria. The presence of surface-bound bacteria was verified by scanning electron and fluorescence microscopies. Impedance measurements (Nyquist plots) show shifts of the order of 10(4) Omega due to the binding of E. coli bacteria to the T4 phages. No significant change in impedance was observed for control experiments using immobilized T4 phage in the presence of Salmonella. Impedance variations as a function of incubation time show a maximum shift after 20 min, indicating onset of lysis, as also confirmed by fluorescence microscopy. Concentration-response curves yield a detection limit of 10(4) cfu/mL for 50-microL samples.

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.

A highly sensitive and selective diagnostic assay based on virus nanoparticles

Early detection of the protein marker troponin I in patients with a higher risk of acute myocardial infarction can reduce the risk of death from heart attacks. Most troponin assays are currently based on the conventional enzyme linked immunosorbent assay and have detection limits in the nano- and picomolar range. Here, we show that by combining viral nanoparticles, which are engineered to have dual affinity for troponin antibodies and nickel, with three-dimensional nanostructures including nickel nanohairs, we can detect troponin levels in human serum samples that are six to seven orders of magnitude lower than those detectable using conventional enzyme linked immunosorbent assays. The viral nanoparticle helps to orient the antibodies for maximum capture of the troponin markers. High densities of antibodies on the surfaces of the nanoparticles and nanohairs lead to greater binding of the troponin markers, which significantly enhances detection sensitivities. The nickel nanohairs are re-useable and can reproducibly differentiate healthy serum from unhealthy ones. We expect other viral nanoparticles to form similar highly sensitive diagnostic assays for a variety of other protein markers.

A multifunctional thin film Au electrode surface formed by consecutive electrochemical reduction of aryl diazonium salts

A multifunctional thin film surface capable of immobilizing two diverse molecules on a single gold electrode was prepared by consecutive electrodeposition of nitrophenyl and phenylboronic acid pinacol ester (PBA-PE) diazonium salts. Activation of the stacked film toward binding platinum nanoparticles (PtNPs) and yeast cells occurred via chemical deprotection of the pinacol ester followed by electroreduction of nitro to amino groups. FTIR spectral analysis was used to study and verify film composition at each stage of preparation. The affect of electrodeposition protocol over the thickness of the nitrophenyl and PBA-PE layers was explored and had a profound impact on the film properties. Thicker nitrophenyl films led to diminished PBA-PE diazonium reduction currents during assembly and decreased phenylboronic acid (PBA) layer thickness while allowing for higher PtNP loading and catalytic currents from PtNP-mediated peroxide reduction. Multilayer PBA films could be formed over the nitrophenyl film; however, only submonlayer PBA films permitted access to the underlying layer. The sequence of functional group activation toward binding was also shown to be significant, as perchlorate used to remove pinacol ester also converted aminophenyl groups accessible to the solution to nitrophenyl groups, preventing electrostatic PtNP binding. Finally, SEM images show PtNPs immobilized in close proximity (nanometers) to captured yeast cells on the PBA-aminophenyl-Au film. Such multibinding functionality films that maintain conductivity for subsequent electrochemical measurements hold promise for the development of electrochemical and/or optical platforms for fundamental cell studies, genomic and proteomic analysis, and biosensing.