Brian N. Kim

Detection of Transmitter Release from Single Living Cells Using Conducting Polymer Microelectrodes

The advent of organic electronics has made available a host of materials and devices with unique properties for interfacing with biology.1–2 One example is the use of conducting polymer coatings on metal electrodes that are implanted in the central nervous system and interface electrically with neurons, providing stimulation and recording the neurons electrical activity.3–5 Coating a metal electrode with a conducting polymer has been shown to lower the electrical impedance and decrease the mechanical properties mismatch at the interface with tissue, with beneficial effects on the lifetime of the implant.3, 6 Conducting polymers can also be functionalized with biomolecules that stimulate neural growth and minimize the immune response to the implant.3–5, 7 Other examples are organic electronic ion pumps,8 and ion transistors,9 which are recently invented devices capable of precise delivery of neurotransmitters to neurons. These devices were recently implanted in the ear of a guinea pig and were shown to control its hearing.10 Conducting polymers such as poly(3,4-ethylenedioxythiophene) doped with poly(styrene sulfonate) (PEDOT:PSS), a material that has been shown to be biocompatible with a variety of different cells,1 have been used for these applications. These examples highlight the main advantages that organic electronic materials bring to the interface with biology, including their “soft” nature, which offers better mechanical compatibility with tissue than traditional electronic materials, and natural compatibility with mechanically flexible substrates, which paves the way for the development of implants that better conform to the non-planar shape of organs. Finally, the ability of organics to transport ionic in addition to electronic charge creates the opportunity to interface with electrically active cells in novel ways, as the work on ion pumps indicates.

Parallel recording of neurotransmitters release from chromaffin cells using a 10×10 CMOS IC potentiostat array with on-chip working electrodes.

Neurotransmitter release is modulated by many drugs and molecular manipulations. We present an active CMOS-based electrochemical biosensor array with high throughput capability (100 electrodes) for on-chip amperometric measurement of neurotransmitter release. The high-throughput of the biosensor array will accelerate the data collection needed to determine statistical significance of changes produced under varying conditions, from several weeks to a few hours. The biosensor is designed and fabricated using a combination of CMOS integrated circuit (IC) technology and a photolithography process to incorporate platinum working electrodes on-chip. We demonstrate the operation of an electrode array with integrated high-gain potentiostats and output time-division multiplexing with minimum dead time for readout. The on-chip working electrodes are patterned by conformal deposition of Pt and lift-off photolithography. The conformal deposition method protects the underlying electronic circuits from contact with the electrolyte that covers the electrode array during measurement. The biosensor was validated by simultaneous measurement of amperometric currents from 100 electrodes in response to dopamine injection, which revealed the time course of dopamine diffusion along the surface of the biosensor array. The biosensor simultaneously recorded neurotransmitter release successfully from multiple individual living chromaffin cells. The biosensor was capable of resolving small and fast amperometric spikes reporting release from individual vesicle secretions. We anticipate that this device will accelerate the characterization of the modulation of neurotransmitter secretion from neuronal and endocrine cells by pharmacological and molecular manipulations of the cells.

Transparent electrode materials for simultaneous amperometric detection of exocytosis and fluorescence microscopy.

We have developed and tested transparent microelectrode arrays capable of simultaneous amperometric measurement of oxidizable molecules and fluorescence imaging through the electrodes. Surface patterned microelectrodes were fabricated from three different conducting materials: Indium-tin-oxide (ITO), nitrogen-doped diamond-like carbon (DLC) deposited on top of ITO, or very thin (12-17 nm) gold films on glass substrates. Chromaffin cells loaded with lysotracker green or acridine orange dye were placed atop the electrodes and vesicle fluorescence imaged with total internal reflection fluorescence (TIRF) microscopy while catecholamine release from single vesicles was measured as amperometric spikes with the surface patterned electrodes. Electrodes fabricated from all three materials were capable of detecting amperometric signals with high resolution. Unexpectedly, amperometric spikes recorded with ITO electrodes had only about half the amplitude and about half as much charge as those detected with DLC or gold electrodes, indicating that the ITO electrodes are not as sensitive as gold or DLC electrodes for measurement of quantal catecholamine release. The lower sensitivity of ITO electrodes was confirmed by chronoamperometry measurements comparing the currents in the presence of different analytes with the different electrode materials.

Estimating the Lower Heating Values of Hazardous and Solid Wastes

A new equation is proposed to predict the lower heating value of hazardous and non-hazardous materials. The equation was developed by a statistical correlation of heating value and composition data for a variety of materials as reported in a number of sources. The model takes into account the carbon, hydrogen, oxygen, chlorine, and sulfur content of the material being combusted.

A coarse grained model for a lipid membrane with physiological composition and leaflet asymmetry.

The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD) simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG) membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5)bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.

Positively charged amino acids at the SNAP-25 C terminus determine fusion rates, fusion pore properties, and energetics of tight SNARE complex zippering.

SNAP-25 is a Q-SNARE protein mediating exocytosis of neurosecretory vesicles including chromaffin granules. Previous results with a SNAP-25 construct lacking the nine C terminal residues (SNAP-25Δ9) showed changed fusion pore properties (Fang et al., 2008), suggesting a model for fusion pore mechanics that couple C terminal zipping of the SNARE complex to the opening of the fusion pore. The deleted fragment contains the positively charged residues R198 and K201, adjacent to layers 7 and 8 of the SNARE complex. To determine how fusion pore conductance and dynamics depend on these residues, single exocytotic events in bovine chromaffin cells expressing R198Q, R198E, K201Q, or K201E mutants were investigated by carbon fiber amperometry and cell-attached patch capacitance measurements. Coarse grain molecular dynamics simulations revealed spontaneous transitions between a loose and tightly zippered state at the SNARE complex C terminus. The SNAP-25 K201Q mutant showed no changes compared with SNAP-25 wild-type. However, K201E, R198Q, and R198E displayed reduced release frequencies, slower release kinetics, and prolonged fusion pore duration that were correlated with reduced probability to engage in the tightly zippered state. The results show that the positively charged amino acids at the SNAP-25 C terminus promote tight SNARE complex zippering and are required for high release frequency and rapid release in individual fusion events.

3D printing and milling a real-time PCR device for infectious disease diagnostics

Diagnosing infectious diseases using quantitative polymerase chain reaction (qPCR) offers a conclusive result in determining the infection, the strain or type of pathogen, and the level of infection. However, due to the high-cost instrumentation involved and the complexity in maintenance, it is rarely used in the field to make a quick turnaround diagnosis. In order to provide a higher level of accessibility than current qPCR devices, a set of 3D manufacturing methods is explored as a possible option to fabricate a low-cost and portable qPCR device. The key advantage of this approach is the ability to upload the digital format of the design files on the internet for wide distribution so that people at any location can simply download and feed into their 3D printers for quick manufacturing. The material and design are carefully selected to minimize the number of custom parts that depend on advanced manufacturing processes which lower accessibility. The presented 3D manufactured qPCR device is tested with 20-μL samples that contain various concentrations of lentivirus, the same type as HIV. A reverse-transcription step is a part of the device’s operation, which takes place prior to the qPCR step to reverse transcribe the target RNA from the lentivirus into complementary DNA (cDNA). This is immediately followed by qPCR which quantifies the target sequence molecules in the sample during the PCR amplification process. The entire process of thermal control and time-coordinated fluorescence reading is automated by closed-loop feedback and a microcontroller. The resulting device is portable and battery-operated, with a size of 12 × 7 × 6 cm3 and mass of only 214 g. By uploading and sharing the design files online, the presented low-cost qPCR device may provide easier access to a robust diagnosis protocol for various infectious diseases, such as HIV and malaria.

Handheld battery-operated sample preparation device for qPCR nucleic acid detections using simple contactless pouring

Sample preparation is an essential process that precedes nucleic acid detections which use quantitative polymerase chain reaction (qPCR). However, sample preparation is a labor-intensive process and requires skilled labor, thus limiting the publics access in low-resource settings to many high-quality nucleic acid-based detection mechanisms. In this paper, we present a simple, handheld, battery-operated sample preparation device to minimize users involvement. The device uses a simple pouring method to process the DNA sample without pipetting or using disposable pipette tips. The developed device has a size of 12 × 8 × 8 cm3 and mass of only 364 g. The device is compared to gold standard methods, including magnetic bead-based and silica filter-based DNA extractions. For a short segment DNA target of 68 bp, the presented device captured 8.67× more DNA compared to that of the manual magnetic bead-based method. Because of automation, the measured capture efficiency is more consistent and has a smaller deviation between multiple repetitions than the manual method. To present a comprehensive, portable, battery-operated diagnostic system, the sample preparation device is tested in conjunction with a 3D-manufactured qPCR device. The test using three diluted target DNA samples, each spiked in whole blood (1×, 0.1×, and 0.01×), revealed a quantitative detection with ideal cycle threshold separations between the measurements. The combination of two devices will aid in resource-limited settings to promptly and accurately diagnose infections of patients.