Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Protein-ligand binding sensors have enormous potential for biosensing, but achieving accuracy in complex solutions is a major challenge. There is a need for simple post hoc analytical tools that are not computationally expensive, yet provide near real time feedback on data derived from impedance spectra. Here, we show the use of a simple, open source support vector machine learning algorithm for analyzing impedimetric data in lieu of using equivalent circuit analysis. We demonstrate two different protein-based biosensors to show that the tool can be used for various applications. We conclude with a mobile phone-based demonstration focused on the measurement of acetone, an important biomarker related to the onset of diabetic ketoacidosis. In all conditions tested, the open source classifier was capable of performing as well as, or better, than the equivalent circuit analysis for characterizing weak/transient interactions between a model ligand (acetone) and a small chemosensory protein derived from the tsetse fly. In addition, the tool has a low computational requirement, facilitating use for mobile acquisition systems such as mobile phones. The protocol is deployed through Jupyter notebook (an open source computing environment available for mobile phone, tablet or computer use) and the code was written in Python. For each of the applications, we provide step-by-step instructions in English, Spanish, Mandarin and Portuguese to facilitate widespread use. All codes were based on scikit-learn, an open source software machine learning library in the Python language, and were processed in Jupyter notebook, an open-source web application for Python. The tool can easily be integrated with the mobile biosensor equipment for rapid detection, facilitating use by a broad range of impedimetric biosensor users. This post hoc analysis tool can serve as a launchpad for the convergence of nanobiosensors in planetary health monitoring applications based on mobile phone hardware.

Cryoconcentration of flavonoid extract for enhanced biophotovoltaics and pH sensitive thin films.

Flavonoids are important value added products for dye sensitized solar cells biosensors, functional foods, medicinal supplements, nanomaterial synthesis, and other applications. Brassica oleracea contains high levels of anthocyanins in leaf sap vacuoles, and there are many viable extraction techniques that vary in terms of simplicity, environmental impact, cost, and extract photochemical/electrochemical properties. The efficiency of value added biotechnologies from flavonoid is a function of anthocyanin activity/concentration and molecule stability (i.e., ability to retain molecular resonance under a wide range of conditions). In this paper, we show that block cryoconcentration and partial thawing of anthocyanin from B. oleracea is a green, facile, and highly efficient technique that does not require any special equipment or protocols for producing enhanced value added products. Cryoconcentration increased anthocyanin activity and total phenol content approximately 10 times compared with common extraction techniques. Cryoconcentrated extract had enhanced electrochemical properties (higher oxidation potential), improved chroma, and higher UV absorbance than extract produced with other methods for a pH range of 2-12, with minimal effect on the diffusion coefficient of the extract. As a proof of concept for energy harvesting and sensor applications, dye sensitized solar cells and pH-sensitive thin films were prepared and tested. These devices were comparable with other recently published biotechnologies in terms of efficacy, but did not require expensive/environmentally detrimental extraction or concentration methods. This low cost, biorenewable, and simple method can be used for development of a variety of value added products. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:206-217, 2018.

A paper based graphene-nanocauliflower hybrid composite for point of care biosensing.

We demonstrate the first report of graphene paper functionalized with fractal platinum nanocauliflower for use in electrochemical biosensing of small molecules (glucose) or detection of pathogenic bacteria (Escherichia coli O157:H7). Raman spectroscopy, scanning electron microscopy and energy dispersive spectroscopy show that graphene oxide-coated nanocellulose was partially reduced by both thermal treatment, and further reduced by chemical treatment (ascorbic acid). Fractal nanoplatinum with cauliflower-like morphology was formed on the reduced graphene oxide paper using pulsed sonoelectrodeposition, producing a conductive paper with an extremely high electroactive surface area (0.29±0.13cm(2)), confirmed by cyclic voltammetry and electrochemical impedance spectroscopy. The platinum surface was functionalized with either glucose oxidase (via chitosan encapsulation) or a RNA aptamer (via covalent linking) for demonstration as a point of care biosensor. The detection limit for both glucose (0.08±0.02µM) and E. coli O157:H7 (≈4 CFUmL(-1)) were competitive with, or superior to, previously reported devices in the biosensing literature. The response time (6s for glucose and 12min for E. coli) were also similar to silicon biochip and commercial electrode sensors. The results demonstrate that the nanocellulose-graphene-nanoplatinum material is an excellent paper-based platform for development of electrochemical biosensors targeting small molecules or whole cells for use in point of care biosensing.

pulSED: pulsed sonoelectrodeposition of fractal nanoplatinum for enhancing amperometric biosensor performance.

For the first time, we combine pulsed electrodeposition with out-of-phase pulsed sonication for controlled synthesis of fractal nanoplatinum structures as the transducer layer in electrochemical sensing. We develop and test this technique, called bimodal pulsed sonoelectrodeposition (pulSED), as a simple approach for creating highly conductive transducer nanometals for use in sensing and biosensing. We first compared the efficiency of pulSED nanoplatinum to other pulsed electrodeposition techniques, and then explored the effect of duty cycle and plating time on electroactive surface area and nanoparticle size/morphology. The developed pulSED nanoplatinum displayed fractal features with a relatively homogenous size distribution (26.31 ± 1.3 nm) and extremely high electroactive surface (0.28 ± 0.04 cm(2)) relative to other electroplating techniques (up to one order of magnitude higher). A high duty cycle (900 mHz) promotes formation of stable nanostructures (including fractal nanostructures) and reduces amorphous structure formation due to bubble cavitation and enhanced mass transport of metal ions to the electrode surface. To demonstrate the applicability of the pulSED technique, non-enzymatic and enzymatic sensors were developed for measuring hydrogen peroxide and glucose. The sensitivity for non-enzymatic peroxide sensing (3335 ± 305 µA cm(-2) mM(-1)), non-enzymatic glucose sensing (73 ± 14 µA cm(-2) mM(-1)) and enzymatic glucose biosensing (155 ± 25 µA cm(-2) mM(-1)) was higher than, or similar to, other nanomaterial-mediated amperometric sensors reported in the literature. The pulSED technique is a one pot method for tunable synthesis of nanometal structures as a transducer layer in electrochemical sensing and biosensing that requires no precursors or capping agents, and can be carried out at room temperature with inexpensive hardware.

A comparative study of graphene-hydrogel hybrid bionanocomposites for biosensing.

Hydrogels have become increasingly popular as immobilization materials for cells, enzymes and proteins for biosensing applications. Enzymatic biosensors that utilize hydrogel as an encapsulant have shown improvements over other immobilization techniques such as cross linking and covalent bonding. However, to date there are no studies which directly compare multiple hydrogel-graphene nanocomposites using the same enzyme and test conditions. This study compares the performance of four different hydrogels used as protein encapsulants in a mediator-free biosensor based on graphene-nanometal-enzyme composites. Alcohol oxidase (AOx) was encapsulated in chitosan poly-N-isopropylacrylamide (PNIPAAM), silk fibroin or cellulose nanocrystals (CNC) hydrogels, and then spin coated onto a nanoplatinum-graphene modified electrode. The transduction mechanism for the biosensor was based on AOx-catalyzed oxidation of methanol to produce hydrogen peroxide. To isolate the effect(s) of stimulus response on biosensor behavior, all experiments were conducted at 25 °C and pH 7.10. Electroactive surface area (ESA), electrochemical impedance spectroscopy (EIS), sensitivity to methanol, response time, limit of detection, and shelf life were measured for each bionanocomposite. Chitosan and PNIPAAM had the highest sensitivity (0.46 ± 0.2 and 0.3 ± 0.1 µA mM(-1), respectively) and electroactive surface area (0.2 ± 0.06 and 0.2 ± 0.02 cm(2), respectively), as well as the fastest response time (4.3 ± 0.8 and 4.8 ± 1.1 s, respectively). Silk and CNC demonstrated lower sensitivity (0.09 ± 0.02 and 0.15 ± 0.03 µA mM(-1), respectively), lower electroactive surface area (0.12 ± 0.02 and 0.09 ± 0.03 cm(2), respectively), and longer response time (8.9 ± 2.1 and 6.3 ± 0.8 s, respectively). The high porosity of chitosan, PNIPAAM, and silk gels led to excellent transport, which was significantly better than CNC bionanocomposites. Electrochemical performance of CNC bionanocomposites were relatively poor, which may be linked to poor gel stability. The differences between the Chitosan/PNIPAAM group and the Silk/CNC group were statistically significant (p < 0.05) based on ANOVA. Each of these composites was within the range of other published devices in the literature, while some attributes were significantly improved (namely response time and shelf life). The main advantages of these hydrogel composites over other devices is that only one enzyme is required, all materials are non-toxic, the sensor does not require mediators/cofactors, and the shelf life and response time are significantly improved over other devices.

A nanoceria-platinum-graphene nanocomposite for electrochemical biosensing.

Most graphene-metal nanocomposites for biosensing are formed using noble metals. Recently, development of nanocomposites using rare earth metals has gained much attention. This paper reports on the development of a nanoceria-nanoplatinum-graphene hybrid nanocomposite as a base transducing layer for mediator-free enzymatic biosensors. The hybrid nanocomposite was shown to improve detection of superoxide or hydrogen peroxide when compared to other carbon-metal hybrid nanocomposites. Based on this finding, the nanocomposite was applied for biosensing by adding either a peroxide-producing oxidase (glucose oxidase), or a superoxide-producing oxidase (xanthine oxidase). Material analysis indicated that nanoceria and nanoplatinum were equally distributed along the surface of the hybrid material, ensuring detection of either superoxide or hydrogen peroxide produced by oxidase activity. Glucose biosensors demonstrated a sensitivity (66.2±2.6µAmM(-1)cm(-2)), response time (6.3±3.4s), and limit of detection (1.3±0.6µM) that were comparable to other graphene-mediated electrodes in the current literature. Remarkably, XOD biosensor sensitivity (1164±332µAmM(-1)), response time (5.0±1.5s), and limit of detection (0.2±0.1µM) were higher than any reported biosensors using similar metal-decorated carbon nanomaterials. This material is the first demonstration of a highly efficient, diverse nanoceria/nanoplatinum/graphene hybrid nanocomposite for biosensing.

Development and validation of an open source O2-sensitive gel for physiological profiling of soil microbial communities.

Community level physiological profiling is a simple, high-throughput technique for assessing microbial community physiology. Initial methods relying on redox-dye based detection of respiration were subject to strong enrichment bias, but subsequent development of a microtiter assay using an oxygen-quenched dye reduced this bias and improved the versatility of the approach. Commercial production of the oxygen microplates recently stopped, which led to the present effort to develop and validate a system using a luminophore dye (platinum tetrakis pentafluorophenyl) immobilized at the bottom of wells within a 96 well microtiter plate. The technique was used to analyze three well-characterized Florida soils: oak saw palmetto scrub, coastal mixed hardwood, and soil from an agricultural field used to grow corn silage. Substrate induced respiration was monitored by measuring respiration rates in soils under basal conditions and comparing to soils supplemented with nitrogen and various carbon sources (mannose, casein, asparagine, coumaric acid). All data was compared to a previously available commercial assay. There were no significant differences in the maximum peak intensity or the time to peak response for all soils tested (p<0.001, α=0.05). The experimental assay plates can be reused on soils up to four times (based on a deviation of less than 5%), where the commercial assay should not be reused. The results indicate that the new oxygen-based bioassay is a cost effective, open source tool for functional profiling of microbial communities.

Emerging technologies for non-invasive quantification of physiological oxygen transport in plants.

Oxygen plays a critical role in plant metabolism, stress response/signaling, and adaptation to environmental changes (Lambers and Colmer, Plant Soil 274:7-15, 2005; Pitzschke et al., Antioxid Redox Signal 8:1757-1764, 2006; Van Breusegem et al., Plant Sci 161:405-414, 2001). Reactive oxygen species (ROS), by-products of various metabolic pathways in which oxygen is a key molecule, are produced during adaptation responses to environmental stress. While much is known about plant adaptation to stress (e.g., detoxifying enzymes, antioxidant production), the link between ROS metabolism, O2 transport, and stress response mechanisms is unknown. Thus, non-invasive technologies for measuring O2 are critical for understanding the link between physiological O2 transport and ROS signaling. New non-invasive technologies allow real-time measurement of O2 at the single cell and even organelle levels. This review briefly summarizes currently available (i.e., mainstream) technologies for measuring O2 and then introduces emerging technologies for measuring O2. Advanced techniques that provide the ability to non-invasively (i.e., non-destructively) measure O2 are highlighted. In the near future, these non-invasive sensors will facilitate novel experimentation that will allow plant physiologists to ask new hypothesis-driven research questions aimed at improving our understanding of physiological O2 transport.

Shear-induced detachment of biofilms from hollow fiber silicone membranes.

A suite of techniques was utilized to evaluate the correlation between biofilm physiology, fluid-induced shear stress, and detachment in hollow fiber membrane aerated bioreactors. Two monoculture species biofilms were grown on silicone fibers in a hollow fiber membrane aerated bioreactors (HfMBR) to assess detachment under laminar fluid flow conditions. Both physiology (biofilm thickness and roughness) and nutrient mass transport data indicated the presence of a steady state mature biofilm after 3 weeks of development. Surface shear stress proved to be an important parameter for predicting passive detachment for the two biofilms. The average shear stress at the surface of Nitrosomonas europaea biofilms (54.5 ± 3.2 mPa) was approximately 20% higher than for Pseudomonas aeruginosa biofilms (45.8 ± 7.7 mPa), resulting in higher biomass detachment. No significant difference in shear stress was measured between immature and mature biofilms of the same species. There was a significant difference in detached biomass for immature vs. mature biofilms in both species. However, there was no difference in detachment rate between the two species.

A self referencing platinum nanoparticle decorated enzyme-based microbiosensor for real time measurement of physiological glucose transport.

Glucose is the central molecule in many biochemical pathways, and numerous approaches have been developed for fabricating micro biosensors designed to measure glucose concentration in/near cells and/or tissues. An inherent problem for microsensors used in physiological studies is a low signal-to-noise ratio, which is further complicated by concentration drift due to the metabolic activity of cells. A microsensor technique designed to filter extraneous electrical noise and provide direct quantification of active membrane transport is known as self-referencing. Self-referencing involves oscillation of a single microsensor via computer-controlled stepper motors within a stable gradient formed near cells/tissues (i.e., within the concentration boundary layer). The non-invasive technique provides direct measurement of trans-membrane (or trans-tissue) analyte flux. A glucose micro biosensor was fabricated using deposition of nanomaterials (platinum black, multiwalled carbon nanotubes, Nafion) and glucose oxidase on a platinum/iridium microelectrode. The highly sensitive/selective biosensor was used in the self-referencing modality for cell/tissue physiological transport studies. Detailed analysis of signal drift/noise filtering via phase sensitive detection (including a post-measurement analytical technique) are provided. Using this highly sensitive technique, physiological glucose uptake is demonstrated in a wide range of metabolic and pharmacological studies. Use of this technique is demonstrated for cancer cell physiology, bioenergetics, diabetes, and microbial biofilm physiology. This robust and versatile biosensor technique will provide much insight into biological transport in biomedical, environmental, and agricultural research applications.

Membrane-aerated biofilm proton and oxygen flux during chemical toxin exposure.

Bioreactors containing sessile bacteria (biofilms) grown on hollow fiber membranes have been used for treatment of many wastestreams. Real time operational control of bioreactor performance requires detailed knowledge of the relationship between bulk liquid water quality and physiological transport at the biofilm-liquid interface. Although large data sets exist describing membrane-aerated bioreactor effluent quality, very little real time data is available characterizing boundary layer transport under physiological conditions. A noninvasive, microsensor technique was used to quantify real time (≈1.5 s) changes in oxygen and proton flux for mature Nitrosomonas europaea and Pseudomonas aeruginosa biofilms in membrane-aerated bioreactors following exposure to environmental toxins. Stress response was characterized during exposure to toxins with known mode of action (chlorocarbonyl cyanide phenyl-hydrazone and potassium cyanide), and four environmental toxins (rotenone, 2,4-dinitrophenol, cadmium chloride, and pentachlorophenol). Exposure to sublethal concentrations of all environmental toxins caused significant increases in O(2) and/or H(+) flux (depending on the mode of action). These real time microscale signatures (i.e., fingerprints) of O(2) and H(+) flux can be coupled with bulk liquid analysis to improve our understanding of physiology in counter-diffusion biofilms found within membrane aerated bioreactors; leading to enhanced monitoring/modeling strategies for bioreactor control.

A self-referencing glutamate biosensor for measuring real time neuronal glutamate flux.

Quantification of neurotransmitter transport dynamics is hindered by a lack of sufficient tools to directly monitor bioactive flux under physiological conditions. Traditional techniques for studying neurotransmitter release/uptake require inferences from non-selective electrical recordings, are invasive/destructive, and/or suffer from poor temporal resolution. Recent advances in electrochemical biosensors have enhanced in vitro and in vivo detection of neurotransmitter concentration under physiological/pathophysiological conditions. The use of enzymatic biosensors with performance enhancing materials (e.g., carbon nanotubes) has been a major focus for many of these advances. However, these techniques are not used as mainstream neuroscience research tools, due to relatively low sensitivity, excessive drift/noise, low signal-to-noise ratio, and inability to quantify rapid neurochemical kinetics during synaptic transmission. A sensing technique known as self-referencing overcomes many of these problems, and allows non-invasive quantification of biophysical transport. This work presents a self-referencing CNT modified glutamate oxidase biosensor for monitoring glutamate flux near neural/neuronal cells. Concentration of basal glutamate was similar to other in vivo and in vitro measurements. The biosensor was used in self-referencing (oscillating) mode to measure net glutamate flux near neural cells during electrical stimulation. Prior to stimulation, the average influx was 33.9+/-6.4 fmol cm(-2)s(-1)). Glutamate efflux took place immediately following stimulation, and was always followed by uptake in the 50-150 fmol cm(-2)s(-1) range. Uptake was inhibited using threo-beta-benzyloxyaspartate, and average surface flux in replicate cells (1.1+/-7.4 fmol cm(-2)s(-1)) was significantly lower than uninhibited cells. The technique is extremely valuable for studying neuropathological conditions related to neurotransmission under dynamic physiological conditions.

Non-invasive self-referencing electrochemical sensors for quantifying real-time biofilm analyte flux.

Current techniques for characterizing biofilm physiology lack the signal filtering capability required for quantifying signals associated with real time biologically active transport. Though a great deal was learned from previous investigations, no results have been reported on the characterization of in vivo, real time biofilm flux using non-invasive (non-destructive) techniques. This article introduces the self-referencing technique for applications in biofilm physiology. Self-referencing is a non-invasive sensing modality which is capable of sensing changes in biologically active analyte flux as small as 10 fmol cm(-2) s(-1). Studies directly characterizing flux, as opposed to concentration, have the advantage of quantifying real time changes in biologically active transport which are otherwise lost to background noise. The use of this modality for characterizing biofilm physiology is validated with a reversible enzyme inhibition study. The experiment used self-referencing potentiometric sensors for quantifying real time ammonium and nitrite flux. Amperometric and optical sensing methods, though not presented herein, are also powerful sensing tools which benefit from operation in self-referencing mode. Reversible ammonia monooxygenase inhibition by a copper chelator (thiourea), and subsequent relief by excess copper addition was successfully demonstrated using self-referencing ion-selective microelectrodes for a mature Nitrosomonas europaea biofilm.