Showing papers by "Paul W. Bohn published in 2016"

Ion Accumulation and Migration Effects on Redox Cycling in Nanopore Electrode Arrays at Low Ionic Strength

Abstract: Ion permselectivity can lead to accumulation in zero-dimensional nanopores, producing a significant increase in ion concentration, an effect which may be combined with unscreened ion migration to improve sensitivity in electrochemical measurements, as demonstrated by the enormous current amplification (∼2000-fold) previously observed in nanopore electrode arrays (NEA) in the absence of supporting electrolyte. Ionic strength is a key experimental factor that governs the magnitude of the additional current amplification (AFad) beyond simple redox cycling through both ion accumulation and ion migration effects. Separate contributions from ion accumulation and ion migration to the overall AFad were identified by studying NEAs with varying geometries, with larger AFad values being achieved in NEAs with smaller pores. In addition, larger AFad values were observed for Ru(NH3)63/2+ than for ferrocenium/ferrocene (Fc+/Fc) in aqueous solution, indicating that coupling efficiency in redox cycling can significantly a...

A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization

Abstract: The complex interactions between plants and their microbiome can have a profound effect on the health and productivity of the plant host. A better understanding of the microbial mechanisms that promote plant health and stress tolerance will enable strategies for improving the productivity of economically-important plants. Pantoea sp. YR343 is a motile, rod-shaped bacterium isolated from the roots of Populus deltoides that possesses the ability to solubilize phosphate and produce the phytohormone indole-3-acetic acid. Pantoea sp. YR343 readily colonizes plant roots and does not appear to be pathogenic when applied to the leaves or roots of selected plant hosts. To better understand the molecular mechanisms involved in plant association and rhizosphere survival by Pantoea sp. YR343, we constructed a mutant in which the crtB gene encoding phytoene synthase was deleted. Phytoene synthase is responsible for converting geranylgeranyl pyrophosphate to phytoene, an important precursor to the production of carotenoids. As predicted, the ΔcrtB mutant is defective in carotenoid production, and shows increased sensitivity to oxidative stress. Moreover, we find that the ΔcrtB mutant is impaired in biofilm formation and production of indole-3-acetic acid. Finally we demonstrate that the ΔcrtB mutant shows reduced colonization of plant roots. Taken together, these data suggest that carotenoids are important for plant association and/or rhizosphere survival in Pantoea sp. YR343.

Redox Cycling in Nanopore-Confined Recessed Dual-Ring Electrode Arrays

Abstract: A redox cycling geometry based on an array of nanopore-confined recessed dual-ring electrodes (RDREs) has been devised to amplify electrochemical signals and enhance the sensitivity of electroanalytical measurements. The RDRE arrays were fabricated using layer-by-layer deposition followed by focused ion beam milling. A characteristic feature of the nanoscale dual-ring geometry is that electrochemical reactions occurring at the bottom-ring electrode can be tuned by modulating the potential at the top-ring electrode. Thus, the resulting device was operated in generator–collector mode by holding the top-ring electrodes at a constant potential and performing cyclic voltammetry by sweeping the bottom-ring potential in aqueous Fe(CN)63–/4–. The enhanced (∼23×) limiting current, achieved by cycling the redox couple between top- and bottom-ring electrodes with high collection efficiency, was compared with that obtained in the absence of self-induced redox cycling (SIRC). Measured shifts in Fe(CN)63–/4– concentrat...

Coupling of Independent Electrochemical Reactions and Fluorescence at Closed Bipolar Interdigitated Electrode Arrays

Abstract: Electrochemical reactions occurring at the opposite ends of bipolar electrodes (BPEs) are necessarily coupled, enabling electron transfer events at one end to be read out optically, for example, by coupling to fluorogenic reactions at the other end. To explore the potential of this technique for studying multiple redox events, arrays of parallel BPE interdigitated electrode arrays (IDEAs) were fabricated and integrated with separate analytical and reporter microfluidic channels, respectively, in a closed BPE configuration. The apparatus was initially evaluated employing Fe(CN)63/4− in the analytical channel coupled to weakly emissive resazurin and strongly emissive resorufin as the fluorogenic redox reporter pair. The device was then used to investigate a proton-coupled electron transfer reaction, hydroquinone (QH2) oxidation, in structures with an integrated pH modulation electrode (PME). A pH-sensitive dye, fluorescein, was co-introduced into the analytical channel to monitor PME modulation of solution pH, and its coupling to QH2 oxidation, thereby permitting changes in solution pH, and consequently QH2 oxidation rate, to be monitored directly in the analytical channel and compared to the fluorescence in the reporter channel. In addition, diffusion of OH− generated at the PME produced a spatial pH profile that was visualized via fluorescein emission, and, because the oxidation of QH2 at each BPE is strongly dependent on the local pH, via the coupled fluorogenic reaction at the opposite pole of the corresponding BPE digit in the reporter channel. Thus, BPE IDEAs support the coupling of independent redox reactions and the use of fluorescence imaging to explore a diverse set of spatially varying electrochemical phenomena realized in a variety of electrochemical geometries.

Electrochemistry at single molecule occupancy in nanopore-confined recessed ring-disk electrode arrays.

Abstract: Electrochemical reactions at nanoscale structures possess unique characteristics, e.g. fast mass transport, high signal-to-noise ratio at low concentration, and insignificant ohmic losses even at low electrolyte concentrations. These properties motivate the fabrication of high density, laterally ordered arrays of nanopores, embedding vertically stacked metal–insulator–metal electrode structures and exhibiting precisely controlled pore size and interpore spacing for use in redox cycling. These nanoscale recessed ring-disk electrode (RRDE) arrays exhibit current amplification factors, AFRC, as large as 55-fold with Ru(NH3)62/3+, indicative of capture efficiencies at the top and bottom electrodes, Φt,b, exceeding 99%. Finite element simulations performed to investigate the concentration distribution of redox species and to assess operating characteristics are in excellent agreement with experiment. AFRC increases as the pore diameter, at constant pore spacing, increases in the range 200–500 nm and as the pore spacing, at constant pore diameter, decreases in the range 1000–460 nm. Optimized nanoscale RRDE arrays exhibit a linear current response with concentration ranging from 0.1 μM to 10 mM and a small capacitive current with scan rate up to 100 V s−1. At the lowest concentrations, the average pore occupancy is 〈n〉 ∼ 0.13 molecule establishing productive electrochemical signals at occupancies at and below the single molecule level in these nanoscale RRDE arrays.

Closed bipolar electrode-enabled dual-cell electrochromic detectors for chemical sensing

Abstract: Bipolar electrodes (BPE) are electrically floating metallic elements placed in electrified fluids that enable the coupling of anodic and cathodic redox reactions at the opposite ends by electron transfer through the electrode. One particularly compelling application allows electron transfer reactions at one end of a closed BPE to be read out optically by inducing a redox-initiated change in the optical response function of a reporter system at the other end. Here, a BPE-enabled method for electrochemical sensing based on the electrochromic response of a methyl viologen (MV) reporter is developed, characterized, and rendered in a field-deployable format. BPE-enabled devices based on two thin-layer-cells of ITO and Pt were fabricated to couple an analytical reaction in one cell with an MV reporter reaction, producing a color change in the complementary cell. Using Fe(CN)63/4- as a model analyte, the electrochemically induced color change of MV was determined initially by measuring its absorbance via a CCD camera coupled to a microscope. Then, smartphone-based detection and RGB analysis were employed to further simplify the sensing scheme. Both methods produced a linear relationship between the analyte concentration, the quantity of MV generated, and the colorimetric response, yielding a limit of detection of 1.0 μM. Similar responses were observed in the detection of dopamine and acetaminophen. Further evolution of the device replaced the potentiostat with batteries to control potential, demonstrating the simplicity and portability of the device. Finally, the physical separation of the reporter and analytical cells renders the device competent to detect analytes in different (e.g. non-aqueous) phases, as demonstrated by using the electrochromic behavior of aqueous MV to detect ferrocene in acetonitrile in the analytical cell.

Raman chemical imaging of the rhizosphere bacterium Pantoea sp. YR343 and its co-culture with Arabidopsis thaliana

Abstract: Chemical imaging of plant-bacteria co-cultures makes it possible to characterize bacterial populations and behaviors and their interactions with proximal organisms, under conditions closest to the environment in the rhizosphere. Here Raman micro-spectroscopy and confocal Raman imaging are used as minimally invasive probes to study the rhizosphere bacterial isolate, Pantoea sp. YR343, and its co-culture with model plant Arabidopsis thaliana by combining enhanced Raman spectroscopies with electron microscopy and principal component analysis (PCA). The presence of carotenoid pigments in the wild type Pantoea sp. YR343 was characterized using resonance Raman scattering, which was also used to confirm successful disruption of the crtB gene in an engineered carotenoid mutant strain. Other components of the Pantoea sp. YR343 cells were imaged in the presence of resonantly enhanced pigments using a combination of surface enhanced Raman imaging and PCA. Pantoea sp. YR343 cells decorated with Ag colloid synthesized ex situ gave spectra dominated by carotenoid scattering, whereas colloids synthesized in situ produced spectral signatures characteristic of flavins in the cell membrane. Scanning electron microscopy (SEM) of whole cells and transmission electron microscopy (TEM) images of thinly sliced cross-sections were used to assess structural integrity of the coated cells and to establish the origin of spectral signatures based on the position of Ag nanoparticles in the cells. Raman imaging was also used to characterize senescent green Arabidopsis thaliana plant roots inoculated with Pantoea sp. YR343, and PCA was used to distinguish spectral contributions from plant and bacterial cells, thereby establishing the potential of Raman imaging to visualize the distribution of rhizobacteria on plant roots.

Nanopore-enabled electrode arrays and ensembles

Abstract: This review (with 116 refs.) addresses recent developments in nanoelectrode arrays and ensembles with particular attention to nanopore-enabled arrays and ensembles. Nanoelectrode-based arrays exhibit unique mass transport and ion transfer properties, which can be exploited for electroanalytical measurements with enhanced figures-of-merit with respect to microscale and larger components. Following an introduction into the topic, we cover (a) methods for fabrication of solid-state nanopore electrodes, (b) chemical and biochemical sensors, (c) nanochannel arrays with embedded nanoelectrodes; (d) recessed nanodisk electrode arrays; (e) redox cycling in nanopore electrode arrays, (f) finally discuss novel nanoarrays for electrochemistry, and then give a future outlook. A wide variety of nanoelectrode array-based chemical and biochemical sensors properties are discussed in addition to faradaic, ion transfer and spectroelectrochemical applications.

Metal-assisted polyatomic SIMS and laser desorption/ionization for enhanced small molecule imaging of bacterial biofilms

Abstract: Mass spectrometry imaging (MSI) has become an important analytical tool for many sectors of science and medicine. As the application of MSI expands into new areas of inquiry, existing methodologies must be adapted and improved to meet emerging challenges. Particularly salient is the need for small molecule imaging methods that are compatible with complex multicomponent systems, a challenge that is amplified by the effects of analyte migration and matrix interference. With a focus on microbial biofilms from the opportunistic pathogen Pseudomonas aeruginosa, the relative advantages of two established microprobe-based MSI techniques-polyatomic secondary ion mass spectrometry (SIMS) and laser desorption/ionization-are compared, with emphasis on exploring the effect of surface metallization on small molecule imaging. A combination of qualitative image comparison and multivariate statistical analysis demonstrates that sputtering microbial biofilms with a 2.5 nm layer of gold selectively enhances C60-SIMS ionization for several molecular classes including rhamnolipids and 2-alkyl-quinolones. Metallization also leads to the reduction of in-source fragmentation and subsequent ionization of media-specific background polymers, which improves spectral purity and image quality. These findings show that the influence of metallization upon ionization is strongly dependent on both the surface architecture and the analyte class, and further demonstrate that metal-assisted C60-SIMS is a viable method for small molecule imaging of intact molecular ions in complex biological systems.

Label-free molecular imaging of bacterial communities of the opportunistic pathogen Pseudomonas aeruginosa.

Abstract: Biofilms, such as those formed by the opportunistic human pathogen Pseudomonas aeruginosa are complex, matrix enclosed, and surface-associated communities of cells. Bacteria that are part of a biofilm community are much more resistant to antibiotics and the host immune response than their free-floating counterparts. P. aeruginosa biofilms are associated with persistent and chronic infections in diseases such as cystic fibrosis and HIV-AIDS. P. aeruginosa synthesizes and secretes signaling molecules such as the Pseudomonas quinolone signal (PQS) which are implicated in quorum sensing (QS), where bacteria regulate gene expression based on population density. Processes such as biofilms formation and virulence are regulated by QS. This manuscript describes the powerful molecular imaging capabilities of confocal Raman microscopy (CRM) and surface enhanced Raman spectroscopy (SERS) in conjunction with multivariate statistical tools such as principal component analysis (PCA) for studying the spatiotemporal distribution of signaling molecules, secondary metabolites and virulence factors in biofilm communities of P. aeruginosa. Our observations reveal that the laboratory strain PAO1C synthesizes and secretes 2-alkyl-4-hydroxyquinoline N-oxides and 2-alkyl-4-hydroxyquinolones in high abundance, while the isogenic acyl homoserine lactone QS-deficient mutant (ΔlasIΔrhlI) strain produces predominantly 2-alkyl-quinolones during biofilm formation. This study underscores the use of CRM, along with traditional biological tools such as genetics, for studying the behavior of microbial communities at the molecular level.

Effects of molecular confinement and crowding on horseradish peroxidase kinetics using a nanofluidic gradient mixer

Abstract: The effects of molecular confinement and crowding on enzyme kinetics were studied at length scales and under conditions similar to those found in biological cells. These experiments were carried out using a nanofluidic network of channels constituting a nanofluidic gradient mixer, providing the basis for measuring multiple experimental conditions simultaneously. The 100 nm × 40 μm nanochannels were wet etched directly into borosilicate glass, then annealed and characterized with fluorescein emission prior to kinetic measurements. The nanofluidic gradient mixer was then used to measure the kinetics of the conversion of the horseradish peroxidase (HRP)-catalyzed conversion of non-fluorescent Amplex Red (AR) to the fluorescent product resorufin in the presence of hydrogen peroxide (H2O2). The design of the gradient mixer allows reaction kinetics to be studied under multiple (five) unique solution compositions in a single experiment. To characterize the efficiency of the device the effects of confinement on HRP-catalyzed AR conversion kinetics were studied by varying the starting ratio of AR:H2O2. Equimolar concentrations of Amplex Red and H2O2 yielded the highest reaction rates followed by 2:1, 1:2, 5:1, and finally 1:5 [AR]:[H2O2]. Under all conditions, initial reaction velocities were decreased by excess H2O2. Crowding effects on kinetics were studied by increasing solution viscosity in the nanochannels in the range 1.0–1.6 cP with sucrose. Increasing the solution viscosities in these confined geometries decreases the initial reaction velocity at the highest concentration from 3.79 μM min−1 at 1.00 cP to 0.192 μM min−1 at 1.59 cP. Variations in reaction velocity are interpreted in the context of models for HRP catalysis and for molecular crowding.

Microchannel Voltammetry in the Presence of Large External Voltages and Electric Fields

Abstract: The ability to perform electrochemistry in the presence of large voltages and electric field magnitudes without concern for the local potential has many possible applications in micro/nanofluidic assays and in capillary electrophoresis. Traditionally, electrochemistry in the presence of significant external electric fields has been dominated by end-channel detection for capillary and microchip electrophoresis detection. We describe novel instrumentation for potentiostatically controlled voltammetry that can be applied in the presence of high external voltages and electric fields. Cyclic voltammetry is demonstrated without significant shifts in the half-wave potential at working electrodes at local potentials of up to ∼1500 V and field strengths of up to 3000 V/cm, using a standard Ag/AgCl reference electrode.

From single cells to single molecules: general discussion

Abstract: General information Publication status: Published Organisations: Department of Chemistry, NanoChemistry Contributors: Gooding, J., Magnussen, O., Fermin, D., Crooks, R., Kanoufi, F., Schuhmann, W., Nichols, R., Schmickler, W., Tao, N., Chen, S., Actis, P., Page, A., Tschulik, K., Faez, S., Edwards, M., Johnson, R., Nogala, W., Kranz, C., Eikerling, M., Unwin, P., Thomas, B., Prabhakaran, V., Clausmeyer, J., Vincent, K., Koper, M., Tian, Z., Mount, A., Alpuche-Aviles, M. A., White, H., Ewing, A., Higgins, S., Baker, L., Zhan, D., Ulstrup, J., Bohn, P. W., Lemay, S. Number of pages: 30 Pages: 141-170 Publication date: 2016 Peer-reviewed: Yes

Feasibility study of mid-infrared absorption spectroscopy using electrospray ionization

Abstract: Precise detection of trace amount of molecules, such as the disease biomarkers present in biofluids or explosive residues, requires high sensitivity detection. electrospray ionization–mass spectrometry (ESI-MS) is a common and effective technique for sensitive trace molecular detection in small-volume liquid samples. In ESI-MS, nano-liter volume samples are ionized and aerosolized by ESI, and fed into MS for mass analysis. ESI-MS has proven to be a reliable ionization technique for coupling liquid phase separations like liquid chromatography (LC) and capillary zone electrophoresis (CE) with the highly specific resolving power of MS. While CE and ESI can be performed on a microfluidic chip having a footprint of a few cm 2 , MS is typically at least 100 times bigger in size than a micro-chip. A reduced size, weight, and power profile would enable semi-portable applications in forensics, environmental monitoring, defense, and biological/pharmaceutical applications. To achieve this goal, we present an initial study evaluating the use of mid-infrared absorption spectroscopy (MIRAS) in place of MS to create a ESI-MIRAS system. To establish feasibility, we perform ESI-MIRAS on phospholipid samples, which have been previously demonstrated to be separable by CE. Phospholipids are biomarkers of degenerative neurological, kidney, and bone diseases and can be found in biofluids such as blood, urine and cerebrospinal fluid. To establish sensitivity limits, calibration samples of 100 μM concentration are electrospray deposited on to a grounded Si wafer for different times (1 minutes to 4 minutes with a 1 minute step). The minimum detectable concentration-time product, where a FTIR globar is used as the MIR source, is found ~200 μM·s.