Optical Leaky Waveguide Sensor for Detection of Bacteria with Ultrasound Attractor Force

Mechanochemical Degradation of Biopolymers

Mechanochemical treatment of various organic molecules is an emerging technology of green processes in biofuel, fine chemicals, or food production. Many biopolymers are involved in isolating, derivating, or modifying molecules of natural origin. Mechanochemistry provides a powerful tool to achieve these goals, but the unintentional modification of biopolymers by mechanochemical manipulation is not always obvious or even detectable. Although modeling molecular changes caused by mechanical stresses in cavitation and grinding processes is feasible in small model compounds, simulation of extrusion processes primarily relies on phenomenological approaches that allow only tool- and material-specific conclusions. The development of analytical and computational techniques allows for the inline and real-time control of parameters in various mechanochemical processes. Using artificial intelligence to analyze process parameters and product characteristics can significantly improve production optimization. We aim to review the processes and consequences of possible chemical, physicochemical, and structural changes.

Review of Label-Free Monitoring of Bacteria: From Challenging Practical Applications to Basic Research Perspectives

Novel biosensors already provide a fast way to detect the adhesion of whole bacteria (or parts of them), biofilm formation, and the effect of antibiotics. Moreover, the detection sensitivities of recent sensor technologies are large enough to investigate molecular-scale biological processes. Usually, these measurements can be performed in real time without using labeling. Despite these excellent capabilities summarized in the present work, the application of novel, label-free sensor technologies in basic biological research is still rare; the literature is dominated by heuristic work, mostly monitoring the presence and amount of a given analyte. The aims of this review are (i) to give an overview of the present status of label-free biosensors in bacteria monitoring, and (ii) to summarize potential novel directions with biological relevancies to initiate future development. Optical, mechanical, and electrical sensing technologies are all discussed with their detailed capabilities in bacteria monitoring. In order to review potential future applications of the outlined techniques in bacteria research, we summarize the most important kinetic processes relevant to the adhesion and survival of bacterial cells. These processes are potential targets of kinetic investigations employing modern label-free technologies in order to reveal new fundamental aspects. Resistance to antibacterials and to other antimicrobial agents, the most important biological mechanisms in bacterial adhesion and strategies to control adhesion, as well as bacteria-mammalian host cell interactions are all discussed with key relevancies to the future development and applications of biosensors.

Development and In-Depth Characterization of Bacteria Repellent and Bacteria Adhesive Antibody-Coated Surfaces Using Optical Waveguide Biosensing

Bacteria repellent surfaces and antibody-based coatings for bacterial assays have shown a growing demand in the field of biosensors, and have crucial importance in the design of biomedical devices. However, in-depth investigations and comparisons of possible solutions are still missing. The optical waveguide lightmode spectroscopy (OWLS) technique offers label-free, non-invasive, in situ characterization of protein and bacterial adsorption. Moreover, it has excellent flexibility for testing various surface coatings. Here, we describe an OWLS-based method supporting the development of bacteria repellent surfaces and characterize the layer structures and affinities of different antibody-based coatings for bacterial assays. In order to test nonspecific binding blocking agents against bacteria, OWLS chips were coated with bovine serum albumin (BSA), I-block, PAcrAM-g-(PMOXA, NH₂, Si), (PAcrAM-P) and PLL-g-PEG (PP) (with different coating temperatures), and subsequent Escherichia coli adhesion was monitored. We found that the best performing blocking agents could inhibit bacterial adhesion from samples with bacteria concentrations of up to 10⁷ cells/mL. Various immobilization methods were applied to graft a wide range of selected antibodies onto the biosensor's surface. Simple physisorption, Mix&Go (AnteoBind) (MG) films, covalently immobilized protein A and avidin-biotin based surface chemistries were all fabricated and tested. The surface adsorbed mass densities of deposited antibodies were determined, and the biosensor;s kinetic data were evaluated to divine the possible orientations of the bacteria-capturing antibodies and determine the rate constants and footprints of the binding events. The development of affinity layers was supported by enzyme-linked immunosorbent assay (ELISA) measurements in order to test the bacteria binding capabilities of the antibodies. The best performance in the biosensor measurements was achieved by employing a polyclonal antibody in combination with protein A-based immobilization and PAcrAM-P blocking of nonspecific binding. Using this setting, a surface sensitivity of 70 cells/mm² was demonstrated.

Advances in Ultrasound-Responsive Hydrogels for Biomedical Applications

Various intelligent hydrogels have been developed for biomedical applications because they can achieve multiple, variable, controllable and reversible changes in their shape and properties in a spatial and temporal manner,...

Acoustofluidic device for acoustic capture of Bacillus anthracis spore analogues at low concentration

A portable device for the rapid concentration of Bacillus subtilis var niger spores, also known as Bacillus globigii (BG), using a thin-reflector acoustofluidic configuration is described. BG spores form an important laboratory analog for the Bacillus anthracis spores, a serious health and bioterrorism risk. Existing systems for spore detection have limitations on detection time and detection that will benefit from the combination with this technology. Thin-reflector acoustofluidic devices can be cheaply and robustly manufactured and provide a more reliable acoustic force than previously explored quarter-wave resonator systems. The system uses the acoustic forces to drive spores carried in sample flows of 30 ml/h toward an antibody functionalized surface, which captures and immobilizes them. In this implementation, spores were fluorescently labeled and imaged. Detection at concentrations of 100 CFU/ml were demonstrated in an assay time of 10 min with 60% capture. We envisage future systems to incorporate more advanced detection of the concentrated spores, leading to rapid, sensitive detection in the presence of significant noise.

Highly sensitive and label-free digital detection of whole cell E. coli with Interferometric Reflectance Imaging

Bacterial infectious diseases are a major threat to human health. Timely and sensitive pathogenic bacteria detection is crucial in bacterial contaminations identification and preventing the spread of infectious diseases. Due to limitations of conventional bacteria detection techniques there have been concerted research efforts towards developing new biosensors. Biosensors offering label-free, whole bacteria detection are highly desirable over those relying on label-based or pathogenic molecular components detection. The major advantage is eliminating the additional time and cost required for labeling or extracting the desired bacterial components. Here, we demonstrate rapid, sensitive and label-free Escherichia coli (E. coli) detection utilizing interferometric reflectance imaging enhancement allowing visualizing individual pathogens captured on the surface. Enabled by our ability to count individual bacteria on a large sensor surface, we demonstrate an extrapolated limit of detection of 2.2 CFU/ml from experimental data in buffer solution with no sample preparation. To the best of our knowledge, this level of sensitivity for whole E. coli detection is unprecedented in label-free biosensing. The specificity of our biosensor is validated by comparing the response to target bacteria E. coli and non-target bacteria S. aureus, K. pneumonia and P. aeruginosa. The biosensor's performance in tap water proves that its detection capability is unaffected by the sample complexity. Furthermore, our sensor platform provides high optical magnification imaging and thus validation of recorded detection events as the target bacteria based on morphological characterization. Therefore, our sensitive and label-free detection method offers new perspectives for direct bacterial detection in real matrices and clinical samples.

On the Behaviour of Living Cells under the Influence of Ultrasound

Medical ultrasound technology is available, affordable, and non-invasive. It is used to detect, quantify, and heat tissue structures. This review article gives a concise overview of the types of behaviour that biological cells experience under the influence of ultrasound only, i.e., without the presence of microbubbles. The phenomena are discussed from a physics and engineering perspective. They include proliferation, translation, apoptosis, lysis, transient membrane permeation, and oscillation. The ultimate goal of cellular acoustics is the detection, quantification, manipulation and eradication of individual cells.

Giant Magnetoresistance: Basic Concepts, Microstructure, Magnetic Interactions and Applications

The giant magnetoresistance (GMR) effect is a very basic phenomenon that occurs in magnetic materials ranging from nanoparticles over multilayered thin films to permanent magnets. In this contribution, we first focus on the links between effect characteristic and underlying microstructure. Thereafter, we discuss design criteria for GMR-sensor applications covering automotive, biosensors as well as nanoparticular sensors.

Optical nano antennas: state of the art, scope and challenges as a biosensor along with human exposure to nano-toxicology

The concept of optical antennas in physical optics is still evolving. Like the antennas used in the radio frequency (RF) regime, the aspiration of optical antennas is to localize the free propagating radiation energy, and vice versa. For this purpose, optical antennas utilize the distinctive properties of metal nanostructures, which are strong plasmonic coupling elements at the optical regime. The concept of optical antennas is being advanced technologically and they are projected to be substitute devices for detection in the millimeter, infrared, and visible regimes. At present, their potential benefits in light detection, which include polarization dependency, tunability, and quick response times have been successfully demonstrated. Optical antennas also can be seen as directionally responsive elements for point detectors. This review provides an overview of the historical background of the topic, along with the basic concepts and parameters of optical antennas. One of the major parts of this review covers the use of optical antennas in biosensing, presenting biosensing applications with a broad description using different types of data. We have also mentioned the basic challenges in the path of the universal use of optical biosensors, where we have also discussed some legal matters.

Focusing of sub-micrometer particles and bacteria enabled by two-dimensional acoustophoresis

Handling of sub-micrometer bioparticles such as bacteria are becoming increasingly important in the biomedical field and in environmental and food analysis. As a result, there is an increased need for less labor-intensive and time-consuming handling methods. Here, an acoustophoresis-based microfluidic chip that uses ultrasound to focus sub-micrometer particles and bacteria, is presented. The ability to focus sub-micrometer bioparticles in a standing one-dimensional acoustic wave is generally limited by the acoustic-streaming-induced drag force, which becomes increasingly significant the smaller the particles are. By using two-dimensional acoustic focusing, i.e. focusing of the sub-micrometer particles both horizontally and vertically in the cross section of a microchannel, the acoustic streaming velocity field can be altered to allow focusing. Here, the focusability of E. coli and polystyrene particles as small as 0.5 μm in diameter in microchannels of square or rectangular cross sections, is demonstrated. Numerical analysis was used to determine generic transverse particle trajectories in the channels, which revealed spiral-shaped trajectories of the sub-micrometer particles towards the center of the microchannel; this was also confirmed by experimental observations. The ability to focus and enrich bacteria and other sub-micrometer bioparticles using acoustophoresis opens the research field to new microbiological applications.

Integrated sorting, concentration and real time PCR based detection system for sensitive detection of microorganisms

The extremely low limit of detection (LOD) posed by global food and water safety standards necessitates the need to perform a rapid process of integrated detection with high specificity, sensitivity and repeatability. The work reported in this article shows a microchip platform which carries out an ensemble of protocols which are otherwise carried in a molecular biology laboratory to achieve the global safety standards. The various steps in the microchip include pre-concentration of specific microorganisms from samples and a highly specific real time molecular identification utilizing a q-PCR process. The microchip process utilizes a high sensitivity antibody based recognition and an electric field mediated capture enabling an overall low LOD. The whole process of counting, sorting and molecular identification is performed in less than 4 hours for highly dilute samples.

Lab-on-a-Chip Magneto-Immunoassays: How to Ensure Contact between Superparamagnetic Beads and the Sensor Surface

Lab-on-a-chip immuno assays utilizing superparamagnetic beads as labels suffer from the fact that the majority of beads pass the sensing area without contacting the sensor surface. Different solutions, employing magnetic forces, ultrasonic standing waves, or hydrodynamic effects have been found over the past decades. The first category uses magnetic forces, created by on-chip conducting lines to attract beads towards the sensor surface. Modifications of the magnetic landscape allow for additional transport and separation of different bead species. The hydrodynamic approach uses changes in the channel geometry to enhance the capture volume. In acoustofluidics, ultrasonic standing waves force µm-sized particles onto a surface through radiation forces. As these approaches have their disadvantages, a new sensor concept that circumvents these problems is suggested. This concept is based on the granular giant magnetoresistance (GMR) effect that can be found in gels containing magnetic nanoparticles. The proposed design could be realized in the shape of paper-based test strips printed with gel-based GMR sensors.

Photonic wire biosensor microarray chip and instrumentation with application to serotyping of Escherichia coli isolates

A complete photonic wire molecular biosensor microarray chip architecture and supporting instrumentation is described. Chip layouts with 16 and 128 independent sensors have been fabricated and tested, where each sensor can provide an independent molecular binding curve. Each sensor is 50 μm in diameter, and consists of a millimeter long silicon photonic wire waveguide folded into a spiral ring resonator. An array of 128 sensors occupies a 2 × 2 mm2 area on a 6 × 9 mm2 chip. Microfluidic sample delivery channels are fabricated monolithically on the chip. The size and layout of the sensor array is fully compatible with commercial spotting tools designed to independently functionalize fluorescence based biochips. The sensor chips are interrogated using an instrument that delivers sample fluid to the chip and is capable of acquiring up to 128 optical sensor outputs simultaneously and in real time. Coupling light from the sensor chip is accomplished through arrays of sub-wavelength surface grating couplers, and the signals are collected by a fixed two-dimensional detector array. The chip and instrument are designed so that connection of the fluid delivery system and optical alignment are automated, and can be completed in a few seconds with no active user input. This microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria using serospecific polyclonal antibody probe molecules.

Acoustofluidics 21: ultrasound-enhanced immunoassays and particle sensors

In part 21 of the tutorial series "Acoustofluidics--exploiting ultrasonic standing wave forces and acoustic streaming in microfluidic systems for cell and particle manipulation", we review applications of ultrasonic standing waves used for enhancing immunoassays and particle sensors. The paper covers ultrasonic enhancement of bead-based immuno-agglutination assays, bead-based immuno-fluorescence assays, vibrational spectroscopy sensors and cell deposition on a sensor surface.

Sensitivity Comparison of Surface Plasmon Resonance and Plasmon-Waveguide Resonance Biosensors

Plasmon-waveguide resonance (PWR) sensors are particularly useful for investigation of biomolecular interactions with or within lipid bilayer membranes. Many studies demonstrated their ability to provide unique qualitative information, but the evaluation of their sensitivity as compared to other surface plasmon resonance (SPR) sensors has not been broadly investigated. We report here a comprehensive sensitivity comparison of SPR and PWR biosensors for the p-polarized light component. The sensitivity of five different biosensor designs to changes in refractive index, thickness and mass are determined and discussed. Although numerical simulations show an increase of the electric field intensity by 30-35 % and the penetration depth by four times in PWR, the waveguide-based method is 0.5 to 8 fold less sensitive than conventional SPR in all considered analytical parameters. The experimental results also suggest that the increase in the penetration depth in PWR is made at the expense of the surface sensitivity. The physical and structural reasons for PWR sensor limitations are discussed and a general viewpoint for designing more efficient SPR sensors based on dielectric slab waveguides is provided.

Peptide functionalized polydiacetylene liposomes act as a fluorescent turn-on sensor for bacterial lipopolysaccharide

Mixed polydiacetylene (PDA) liposomes functionalized on their surface with a fluorescent pentalysine peptide derivative and histidine in a ratio of 1:9 can identify bacterial lipopolysaccharide (LPS). Upon photopolymerization of the self-assembled liposomes the initial fluorescence of the peptide-diacetylene amphiphiles is quenched. Interaction with LPS in aqueous solution or on the surface of E. coli DH5α restores the fluorescence. This increase in fluorescence is selective for LPS relative to other negatively charged analytes including nucleotides and ctDNA. This simple turn-on fluorescent sensor allows detecting LPS even at low micromolar concentrations.

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.

An overview of recent strategies in pathogen sensing

Pathogenic bacteria are one of the major concerns in food industries and water treatment facilities because of their rapid growth and deleterious effects on human health. The development of fast and accurate detection and identification systems for bacterial strains has long been an important issue to researchers. Although confirmative for the identification of bacteria, conventional methods require time-consuming process involving either the test of characteristic metabolites or cellular reproductive cycles. In this paper, we review recent sensing strategies based on micro- and nano-fabrication technology. These technologies allow for a great improvement of detection limit, therefore, reduce the time required for sample preparation. The paper will be focused on newly developed nano- and micro-scaled biosensors, novel sensing modalities utilizing microfluidic lab-on-a-chip, and array technology for the detection of pathogenic bacteria.

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.

Low-frequency ultrasound in biotechnology: state of the art

The use of low-frequency (10-60 kHz) ultrasound for enhancement of various biotechnological processes has received increased attention over the last decade as a rapid and reagentless method. Recent breakthroughs in sonochemistry have made the ultrasound irradiation procedure more feasible for a broader range of applications. By varying the sonication parameters, various physical, chemical and biological effects can be achieved that can enhance the target processes in accordance with the applied conditions. However, the conditions that have provided beneficial effects of ultrasound on bioprocesses are case-specific and are therefore not widely available in the literature. This review summarizes the current state of the art in areas where sonochemistry could be successfully combined with biotechnology with the aim of enhancing the efficiency of bioprocesses, including biofuel production, bioprocess monitoring, enzyme biocatalysts, biosensors and biosludge treatment.

Graphene-based single-bacterium resolution biodevice and DNA transistor: interfacing graphene derivatives with nanoscale and microscale biocomponents

Establishing "large-contact-area" interfaces of sensitive nanostructures with microbes and mammalian cells will lead to the development of valuable tools and devices for biodiagnostics and biomedicine. Chemically modified graphene (CMG) nanostructures with their microscale area, sensitive electrical properties, and modifiable chemical functionality are excellent candidates for such biodevices at both biocellular and biomolecular scale. Here, we report on the fabrication and functioning of a novel CMG-based (i) single-bacterium biodevice, (ii) label-free DNA sensor, and (iii) bacterial DNA/protein and polyelectrolyte chemical transistor. The bacteria biodevice was highly sensitive with a single-bacterium attachment generating approximately 1400 charge carriers in a p-type CMG. Similarly, single-stranded DNA tethered on graphene hybridizes with its complementary DNA strand to reversibly increase the hole density by 5.61 x 1012 cm(-2). We further demonstrate (a) a control on the device sensitivity by manipulating surface groups, (b) switching of polarity specificity by changing surface polarity, and (c) a preferential attachment of DNA on thicker CMG surfaces and sharp CMG wrinkles.