A microfluidic bioreactor with in situ SERS imaging for the study of controlled flow patterns of biofilm precursor materials

Laminar Flow Infrared Spectroelectrochemistry

In this work, we advance lab-on-chip electrochemistry and spectroscopy by combining these capabilities onto a single platform, thereby achieving mid-infrared spectroelectrochemistry (SEC) for the first time. The key feature of this technique is the use of deterministic laminar flow patterns to precisely transport a reacted solution from upstream electrodes to a downstream spectral detection region. Laminar flow spectroelectrochemistry (LF-SEC) is therefore a completely new approach, which derives its distinction and advantage over traditional SEC by physically separating electrode and attenuated total reflection (ATR) elements. As such, these functional elements retain optimal properties, such as inert, highly conductive electrodes and a bare ATR element for sensitive Fourier transform infrared (FTIR) spectroscopy. By combining ATR-FTIR with a scanning aperture system, LF-SEC provides the additional advantage of spectroscopically monitoring reactions at individual electrodes. The LF-SEC system design is first optimized through a series of targeted experiments using a ferricyanide/ferrocyanide redox pair to validate electrochemical functionality, undertake spectroscopic calibration, optimize experimental parameters, and finally validate the quantitative relationship between FTIR results and the reaction rate under galvanostatic control. After optimization, we demonstrate the technique by monitoring the oxidation of the therapeutic compound ascorbic acid (vitamin C) in the presence of biomolecular interference from a molecule with an overlapping oxidation potential. We find that molecular availability causes the reaction to switch between reaction pathways, which we could finely monitor using LF-SEC. This work opens the door to future developments that take advantage of the microfluidic reactor setup, with benefits ranging from portability to high-throughput studies under precise reaction conditions.

SpectIR-fluidics: completely customizable microfluidic cartridges for high sensitivity on-chip infrared spectroscopy with point-of-application studies on bacterial biofilms

We present a generalizable fabrication method for a new class of analytical devices that merges virtually any microfluidic design with high-sensitivity on-chip attenuated total reflection (ATR) sampling using any standard Fourier transform infrared (FTIR) spectrometer. Termed "spectIR-fluidics", a major design feature is the integration of a multi-groove silicon ATR crystal into a microfluidic device, compared with previous approaches in which the ATR surface served as a structural support for the entire device. This was accomplished by the design, fabrication, and aligned bonding of a highly engineered ATR sensing layer, which con```tains a seamlessly embedded ATR crystal on the channel side and an optical access port that matched the spectrometer light path characteristics at the device exterior. The refocused role of the ATR crystal as a dedicated analytical element, combined with optimized light coupling to the spectrometer, results in limits of detection as low as 540 nM for a D-glucose solution, arbitrarily complex channel features that are fully enclosed, and up to 18 world-to-chip connections. Three purpose-built spectIR-fluidic cartridges are used in a series of validation experiments followed by several point-of-application studies on biofilms from the gut microbiota of plastic-consuming insects using a small portable spectrometer.

In Situ Spatiotemporal SERS Measurements and Multivariate Analysis of Virally Infected Bacterial Biofilms Using Nanolaminated Plasmonic Crystals

In situ spatiotemporal biochemical characterization of the activity of living multicellular biofilms under external stimuli remains a significant challenge. Surface-enhanced Raman spectroscopy (SERS), combining the molecular fingerprint specificity of vibrational spectroscopy with the hotspot sensitivity of plasmonic nanostructures, has emerged as a promising noninvasive bioanalysis technique for living systems. However, most SERS devices do not allow reliable long-term spatiotemporal SERS measurements of multicellular systems because of challenges in producing spatially uniform and mechanically stable SERS hotspot arrays to interface with large cellular networks. Furthermore, very few studies have been conducted for multivariable analysis of spatiotemporal SERS datasets to extract spatially and temporally correlated biological information from multicellular systems. Here, we demonstrate in situ label-free spatiotemporal SERS measurements and multivariate analysis of Pseudomonas syringae biofilms during development and upon infection by bacteriophage virus Phi6 by employing nanolaminate plasmonic crystal SERS devices to interface mechanically stable, uniform, and spatially dense hotspot arrays with the P. syringae biofilms. We exploited unsupervised multivariate machine learning methods, including principal component analysis (PCA) and hierarchical cluster analysis (HCA), to resolve the spatiotemporal evolution and Phi6 dose-dependent changes of major Raman peaks originating from biochemical components in P. syringae biofilms, including cellular components, extracellular polymeric substances (EPS), metabolite molecules, and cell lysate-enriched extracellular media. We then employed supervised multivariate analysis using linear discriminant analysis (LDA) for the multiclass classification of Phi6 dose-dependent biofilm responses, demonstrating the potential for viral infection diagnosis. We envision extending the in situ spatiotemporal SERS method to monitor dynamic, heterogeneous interactions between viruses and bacterial networks for applications such as phage-based anti-biofilm therapy development and continuous pathogenic virus detection.

Scanning Aperture Approach for Spatially Selective ATR-FTIR Spectroscopy: Application to Microfluidics

We present a novel spectroscopy accessory that can easily convert any Fourier transform infrared (FTIR) spectrometer into a fully automated mapping and assaying system. The accessory uses a multiridge attenuated total reflection (ATR) wafer as the sensing element coupled with a moving aperture that is used to select the regions of interest on the wafer. In this demonstration, the accessory is combined with a series of parallel micropatterned channels, which are positioned co-linear with the light-coupling ridges on the opposite side of the ATR wafer. The ATR spectroscopy microfluidic assay accessory (ASMAA) was used in continuous mapping mode to scan perpendicular to the ATR ridges, revealing complex but repeatable oscillations in the spectral intensities. To understand this behavior, the light path through the optical components was simulated with consideration of the aperture position, ridge-to-channel alignment, and excitation beam profile. With this approach, the simulation reproduced the experimental mapping results and provided evidence that the measurement position and area changed with the aperture position. To demonstrate the assay mode, we obtained spectra along the centerline of individual microchannels and determined noise baselines and limits of detection.

Coral-like plasmonic probes for tip-enhanced Raman spectroscopy

Tip-enhanced Raman spectroscopy is a powerful tool for the analysis of system interfaces, enabling access to chemical information with nanometric spatial resolution and sensitivity up to the single molecule level. Such features are due to the presence of proper metallic nanostructures at the TERS probe apex, which, via the excitation of a plasmonic field, confine light to a nanometric region. The nano-sized characteristic of such metallic structures intrinsically renders the fabrication of high performing and reproducible TERS probes still a challenge. In this paper, we present a facile, rapid and effective approach to prepare Ag-based TERS probes. The fabrication process proposed herein is based on spinodal dewetting of Ag-coated AFM-probes through a RF plasma treatment. The obtained probes appear covered with a coral-like silver nanotexture, endowed with an excellent plasmonic activity. Intriguingly, such a texture can be easily tuned by changing some process parameters, such as Ag film thickness and exposure time to the plasma. The as-prepared TERS probes show a high TERS enhancement, reaching 107, and allow a good spatial resolution, down to 10 nm. Finally, we suggest an easy and effective procedure to restore oxidized TERS tips following exposure to ambient air, which can be applied to all types of Ag-based TERS tips.

Microfluidic bioanalytical flow cells for biofilm studies: a review

Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive experimental results include time-varying biofilm properties, structural and chemical heterogeneity, and especially their strong sensitivity to environmental cues. Therefore, in addition to judicious choice of measurement tools, a well-designed biofilm study requires strict control over experimental conditions, more so than most chemical studies. Due to excellent control over a host of physiochemical parameters, microfluidic flow cells have become indispensable in microbiological studies. Not surprisingly, the number of lab-on-chip studies focusing on biofilms and other microbiological systems with expanded analytical capabilities has expanded rapidly in the past decade. In this paper, we comprehensively review the current state of microfluidic bioanalytical research applied to bacterial biofilms and offer a perspective on new approaches that are expected to drive continued advances in this field.

Hydrodynamic Effects on Biofilms at the Biointerface Using a Microfluidic Electrochemical Cell: Case Study of Pseudomonas sp

The anchoring biofilm layer is expected to exhibit a different response to environmental stresses than for portions in the bulk, due to the protection from other strata and the proximity to the attachment surface. The effect of hydrodynamic stress on surface-adhered biofilm layers was tested using a specially designed microfluidic bio flow cell with an embedded three-electrode detection system. In situ electrochemical impedance spectroscopy (EIS) measurements of biocapacitance and bioresistance of Pseudomonas sp. biofilms were conducted during the growth phase and under different shear flow conditions with verification by other surface sensitive techniques. Distinct, but reversible changes to the amount of biofilm and its structure at the attachment surface were observed during the application of elevated shear stress. In contrast, regular microscopy revealed permanent distortion to the biofilm bulk, in the form of streamers and ripples. Following the application of extreme shear stresses, complete removal of significant portions of biofilm outer layers occurred, but this did not change the measured quantity of biofilm at the electrode attachment surface. The structure of the remaining biofilm, however, appeared to be modified and susceptible to further changes following application of shear stress directly to the unprotected biofilm layers at the attachment surface.

Analytical characterization using surface-enhanced Raman scattering (SERS) and microfluidic sampling

With the rapid development of analytical techniques, it has become much easier to detect chemical and biological analytes, even at very low detection limits. In recent years, techniques based on vibrational spectroscopy, such as surface enhanced Raman spectroscopy (SERS), have been developed for non-destructive detection of pathogenic microorganisms. SERS is a highly sensitive analytical tool that can be used to characterize chemical and biological analytes interacting with SERS-active substrates. However, it has always been a challenge to obtain consistent and reproducible SERS spectroscopic results at complicated experimental conditions. Microfluidics, a tool for highly precise manipulation of small volume liquid samples, can be used to overcome the major drawbacks of SERS-based techniques. High reproducibility of SERS measurement could be obtained in continuous flow generated inside microfluidic devices. This article provides a thorough review of the principles, concepts and methods of SERS-microfluidic platforms, and the applications of such platforms in trace analysis of chemical and biological analytes.

Development and calibration of a microfluidic biofilm growth cell with flow-templating and multi-modal characterization

We report the development of a microfluidic flow-templating platform with multi-modal characterization for studies of biofilms and their precursor materials. A key feature is a special three inlet flow-template compartment, which confines and controls the location of biofilm growth against a template wall. Characterization compartments include Raman imaging to study the localization of the nutrient solutions, optical microscopy to quantify biofilm biomass and localization, and cyclic voltammetry for flow velocity measurements. Each compartment is tested and then utilized to make preliminary measurements.

A microfluidic chip for high resolution Raman imaging of biological cells

A microfluidic chip was designed, prepared and tested for integration with a confocal Raman imaging spectrometer with the specific purpose of enabling studies of individual biological cells.

Micropatterned biofilm formations by laminar flow-templating

We present a microfluidic device capable of patterning linear biofilm formations using a flow templating approach. We describe the design considerations and fabrication methodology of a two level flow-templating micro-bioreactor (FT-μBR), which generates a biofilm growth stream surrounded on 3 sides by a growth inhibiting confinement stream. Through a combination of experiments and simulations we comprehensively evaluate and exploit control parameters to manipulate the biofilm growth template stream dimensions. The FT-μBR is then used to grow biofilm patterns with controllable dimensions. A proof-of-principle study using the device demonstrates its utility in conducting biofilm growth rate measurements under different shear stress environments. This opens the way for quantitative studies into the effects of the local shear environment on biofilm properties and for the synthesis of a new generation of functional biomaterials with controllable properties.