A transistor model for the cystic fibrosis transmembrane conductance regulator.

In this paper we present a transistor circuit model for cystic fibrosis transmembrane conductance regulator (CFTR) that seeks to map the functional form of CFTR both in wild type and mutants. The circuit architecture is configured so that the function, and as much as possible the form, faithfully represents what is known about CFTR from cryo-electron microscopy and molecular dynamics. The model is a mixed analog-digital topology with an AND gate receiving the input from two separate ATP-nucleotide-binding domain binding events. The analog portion of the circuit takes the output from the AND gate as its input. The input to the circuit model and its noise characteristics are extracted from single-channel patch-clamp experiments. The chloride current predicted by the model is then compared with single-channel patch-clamp recordings for wild-type CFTR. We also consider the patch-clamp recordings from CFTR with a G551D point mutation, a clinically relevant mutant that is responsive to therapeutic management. Our circuit model approach enables bioengineering approaches to CFTR and allows biophysicists to use efficient circuit simulation tools to analyze its behavior.

Permissive and nonpermissive channel closings in CFTR revealed by a factor graph inference algorithm.

The closing of the gated ion channel in the cystic fibrosis transmembrane conductance regulator can be categorized as nonpermissive to reopening, which involves the unbinding of ADP or ATP, or permissive, which does not. Identifying the type of closing is of interest as interactions with nucleotides can be affected in mutants or by introducing agonists. However, all closings are electrically silent and difficult to differentiate. For single-channel patch-clamp traces, we show that the type of the closing can be accurately determined by an inference algorithm implemented on a factor graph, which we demonstrate using both simulated and lab-obtained patch-clamp traces.

Potential of surface acoustic wave biosensors for early sepsis diagnosis.

Early diagnosis of sepsis is a difficult problem for intensivists and new biomarkers for early diagnosis have been difficult to come by. Here we discuss the potential of adapting a technology from the electronics industry, surface acoustic wave (SAW) sensors, for diagnosis of multiple markers of sepsis in real time, using non-invasive assays of exhaled breath condensate. The principles and advantages of the SAW technology are reviewed as well as a proposed plan for adapting this flexible technology to early sepsis detection.

A new method for wideband characterization of resonator-based sensing platforms.

A new approach to the electronic instrumentation for extracting data from resonator-based sensing devices (e.g., microelectromechanical, piezoelectric, electrochemical, and acoustic) is suggested and demonstrated here. Traditionally, oscillator-based circuitry is employed to monitor shift in the resonance frequency of the resonator. These circuits give a single point measurement at the frequency where the oscillation criterion is met. However, the resonator response itself is broadband and contains much more information than a single point measurement. Here, we present a method for the broadband characterization of a resonator using white noise as an excitation signal. The resonator is used in a two-port filter configuration, and the resonator output is subjected to frequency spectrum analysis. The result is a wideband spectral map analogous to the magnitude of the S21 parameters of a conventional filter. Compared to other sources for broadband excitation (e.g., frequency chirp, multisine, or narrow time domain pulse), the white noise source requires no design of the input signal and is readily available for very wide bandwidths (1 MHz-3 GHz). Moreover, it offers simplicity in circuit design as it does not require precise impedance matching; whereas such requirements are very strict for oscillator-based circuit systems, and can be difficult to fulfill. This results in a measurement system that does not require calibration, which is a significant advantage over oscillator circuits. Simulation results are first presented for verification of the proposed system, followed by measurement results with a prototype implementation. A 434 MHz surface acoustic wave (SAW) resonator and a 5 MHz quartz crystal microbalance (QCM) are measured using the proposed method, and the results are compared to measurements taken by a conventional bench-top network analyzer. Maximum relative differences in the measured resonance frequencies of the SAW and QCM resonators are 0.0004% and 0.002%, respectively. The ability to track a changing sensor response is demonstrated by inducing temperature variations and measuring resonance frequency simultaneously using the proposed technique in parallel with a network analyzer. The relative difference between the two measurements is about 5.53 ppm, highlighting the impressive accuracy of the proposed system. Using commercially available digital signal processors (DSPs), we believe that this technique can be implemented as a system-on-a-chip solution resulting in a very low cost, easy to use, portable, and customizable sensing system. In addition, given the simplicity of the signal and circuit design, and its immunity to other common interface concerns (injection locking, oscillator interference, and drift, etc.), this method is better suited to accommodating array-based systems.

An investigation of antibody immobilization methods employing organosilanes on planar ZnO surfaces for biosensor applications.

One critical aspect for the development of label-free immunosensors is the employment of highly uniform and repeatable antibody immobilization techniques. In this study, we investigated the use of two different silane molecules (3-glycidyloxypropyl)trimethoxysilane (GPS), and (3-mercaptopropyl)trimethoxysilane (MTS) for the immobilization of fluorescently labeled IgG antibodies on planar ZnO surfaces. The chemical modification of the surfaces was investigated using water contact angle measurements, AFM, and fluorescence microscopy. The results of the water contact angle measurements indicate increased surface hydrophobicity after treatment with GPS and MTS as compared to the control. Surface modification was further verified through AFM measurements which demonstrate an increased surface roughness and particle height after treatment with antibodies. The results of the fluorescence studies indicate that the immobilization protocol employing MTS produced 21% higher fluorescence on average with greater uniformity than the GPS-based protocol, which indicates a higher overall density in antibody coverage on the surface of the ZnO. Acoustic sensor tests were employed to confirm the functionality of sensors treated with the MTS protocol. The results indicate that the immobilization protocol imparts sensitivity and specificity to the ZnO-based devices.

Analogies between digital radio and chemical orthogonality as a method for enhanced analysis of molecular recognition events.

Acoustic wave biosensors are a real-time, label-free biosensor technology, which have been exploited for the detection of proteins and cells. One of the conventional biosensor approaches involves the immobilization of a monolayer of antibodies onto the surface of the acoustic wave device for the detection of a specific analyte. The method described within includes at least two immobilizations of two different antibodies onto the surfaces of two separate acoustic wave devices for the detection of several analogous analytes. The chemical specificity of the molecular recognition event is achieved by virtue of the extremely high (nM to pM) binding affinity between the antibody and its antigen. In a standard ELISA (Enzyme-Linked ImmunoSorbent Assay) test, there are multiple steps and the end result is a measure of what is bound so tightly that it does not wash away easily. The fact that this "gold standard" is very much not real time, masks the dance that is the molecular recognition event. X-Ray Crystallographer, Ian Wilson, demonstrated more than a decade ago that antibodies undergo conformational change during a binding event[1, 2]. Further, it is known in the arena of immunochemistry that some antibodies exhibit significant cross-reactivity and this is widely termed antibody promiscuity. A third piece of the puzzle that we will exploit in our system of acoustic wave biosensors is the notion of chemical orthogonality. These three biochemical constructs, the dance, antibody promiscuity and chemical orthogonality will be combined in this paper with the notions of in-phase (I) and quadrature (Q) signals from digital radio to manifest an approach to molecular recognition that allows a level of discrimination and analysis unobtainable without the aggregate. As an example we present experimental data on the detection of TNT, RDX, C4, ammonium nitrate and musk oil from a system of antibody-coated acoustic wave sensors.

Development of a magnetic quartz crystal microbalance.

A new technique for measurement of magnetic properties of materials is demonstrated. It can be used for the measurement of thin magnetic films during their chemical modification. The resonance frequency of a quartz crystal microbalance (QCM) with conducting polymer (polyaniline) suspension in poly(ethylene glycol) was observed to increase with increasing the externally applied uniform dc magnetic field. Slowly sweeping the magnetic field between 0 and 3.1 T results in a frequency-field response curve. Chemical doping was done by exposing the polyaniline-emeraldine base film to HCl vapor. The change in population of free spins is reflected in increased frequency-field curve magnitude after HCl doping. Two working hypotheses explaining this observation are offered to explain how frequency of QCM with deposited magnetic film shifts with increasing intensity of the magnetic field.

Real-time detection of mesothelin in pancreatic cancer cell line supernatant using an acoustic wave immunosensor.

BACKGROUND: An acoustic wave immunosensor was developed to illustrate the viability of such devices in early detection of molecular cancer biomarkers. The methods described here involve a real-time, less invasive technique for detecting mesothelin, a protein that has been linked to pancreatic and ovarian cancer. METHODS: Antibodies were immobilized on the gold surface of the device via a self-assembled alkanethiol monolayer. Supernatant from two different pancreatic cancer cell-lines (PL1 and CAPAN2) containing an unknown concentration of mesothelin was tested for the protein by a flow-through analytical technique in three types of experiments. Binding of the mesothelin to the immobilized antibody layer caused a shift in the device's resonant frequency, which was correlated to the concentration of supernatant. A reference sensor was used to correct for frequency shifts caused by pressure or viscosity effects from the injection of the supernatant solution. RESULTS: Repeated experiments indicate that the sensors are capable of nanogram detection thresholds of mesothelin proteins at room temperature and in complex mixture. CONCLUSIONS: Acoustic wave device biosensors have the potential to become a valuable tool in screening for pancreatic as well as other types of cancers. The main features include real-time detection, high sensitivity, and ease of use.

Determination of ZnO temperature coefficients using thin film bulk acoustic wave resonators.

Thin film bulk acoustic wave (BAW) resonators have been the subject of research in RF microelectronics for some time. Much of the interest lay in utilizing the resonators to design filters for wireless applications. Some of the major advantages BAW devices present over other filter technologies in use today include size reduction and the possibility of on-chip integration. As the technology matures, the necessity to more fully characterize the performance of the devices and to develop more accurate models describing their behavior is apparent. In this investigation, the effects that temperature variations have on 1.8-2.0 GHz zinc oxide (ZnO)-based solidly mounted BAW resonators (SMRs) are studied. The average temperature coefficients of the series and parallel resonant frequencies of the fabricated devices are found to be -31.5 ppm/degrees C and -35.3 ppm/degrees C, respectively. The slight decrease in separation between the two resonant frequencies with temperature implies there is slightly less effective coupling with increased temperature. No definite trend is found describing the behavior of the quality factor (Q) of the resonator with temperature variations. With little temperature coefficient data for thin film ZnO available in the literature, the importance of an accurate model is evident. The resonator device performance is simulated using Ballato's electronic circuit model for acoustic devices on a SPICE-based platform. By virtue of the comparison between the predicted and measured device response, various material parameters are extracted.