DNA Logic-A novel approach to semiconductor based genetics

In the coming years, genetic test results will be increasingly used as indicators that influence medical decision-making. With chronic disease on the rise and the continuing global spread of infectious disease, novel instruments able to detect relevant mutations in a point-of-care setting are being developed to facilitate this increased demand in personalized health care. However, diagnosis for such demand often requires laboratory facilities and skilled personnel, meaning that diagnostic tests are restricted by time and access. This thesis presents a novel configuration for Ion sensitive Field Effect Transistors (ISFETs) to be used as a threshold detector during nucleic acid base pairs match. ISFET-based inverters are used as reaction threshold detectors to convey the chemical reaction level to a logic output once a threshold has been reached. Using this method, novel DNA logic functions are derived for nucleotides allowing local digital computations. The thesis also presents business models that enable such technology to be utilised in point of care applications, and experiment as results and business models given for an HIV point of care example are proposed

Emerging technologies for the non-invasive characterization of physical-mechanical properties of tablets

The density, porosity, breaking force, viscoelastic properties, and the presence or absence of any structural defects or irregularities are important physical-mechanical quality attributes of popular solid dosage forms like tablets. The irregularities associated with these attributes may influence the drug product functionality. Thus, an accurate and efficient characterization of these properties is critical for successful development and manufacturing of a robust tablets. These properties are mainly analyzed and monitored with traditional pharmacopeial and non-pharmacopeial methods. Such methods are associated with several challenges such as lack of spatial resolution, efficiency, or sample-sparing attributes. Recent advances in technology, design, instrumentation, and software have led to the emergence of newer techniques for non-invasive characterization of physical-mechanical properties of tablets. These techniques include near infrared spectroscopy, Raman spectroscopy, X-ray microtomography, nuclear magnetic resonance (NMR) imaging, terahertz pulsed imaging, laser-induced breakdown spectroscopy, and various acoustic- and thermal-based techniques. Such state-of-the-art techniques are currently applied at various stages of development and manufacturing of tablets at industrial scale. Each technique has specific advantages or challenges with respect to operational efficiency and cost, compared to traditional analytical methods. Currently, most of these techniques are used as secondary analytical tools to support the traditional methods in characterizing or monitoring tablet quality attributes. Therefore, further development in the instrumentation and software, and studies on the applications are necessary for their adoption in routine analysis and monitoring of tablet physical-mechanical properties

Integrated Electronics for Molecular Biosensing

This thesis, Integrated electronics for molecular biosensing, focuses on different approaches to sense the presence and activity of a specific analyte by using integrated electronic platforms. The aim of the first platform is to detect the enzyme telomerase. Telomerase causes the elongation of telomeres, which are part of the chromosomes, and determines the lifespan of cells. Telomerase expression is a marker of malignity in tumoral cells and its evaluation can be exploited for early diagnosis of many types of cancer cells. To detect the telomerase enzyme, a CMOS (complementary metal-oxide semiconductor) biosensor based on CMFET (Charge-Modulated Field Effect Transistor) able to measure kinetics of DNA replication and telomerase reaction was developed. The sensor can be functionalized by immobilizing single strands of DNA that contain the telomeric sequence, used as probes. If telomerase is present, the probes will be elongated by the enzyme and the charge on the sensing area will change, which reflects in a variation of the output current or voltage. The chip includes three different readout schemes (voltage, current- and time-based), each of which has different measuring ranges and operating conditions. The measured data is then digitized, stored, and can be sent off-chip through SPI (Serial Peripheral Interface) protocol. A total of 1024 biosensors have been integrated in a single chip with a size of 10x10 mm2. Each sensor can be independently addressed and functionalized by an electrochemical procedure using an integrated potentiostat, thus requiring no external equipment. Although the sensors have been tailored and optimized to perform telomerase detection, the sensing areas can be functionalized to be used with different analytes. This feature turns the chip into a complete bioassay platform. The second part of this work rises from the idea that bacteria, like Escherichia coli, can detect analytes in solution even at extremely low concentrations and change their movement through a process called chemotaxis, to move towards chemical gradients in the solution. E. coli moves by rotating its flagella either clockwise (for random tumbles) or counterclockwise (for straight runs, when it senses a chemical it is attracted to). Therefore, observing bacteria flagellar rotation can give enough information on the presence of a specific analyte in the solution. To electronically detect bacteria movement, an active surface covered in electrodes has been designed. By measuring the impedance between each pair of electrodes through an integrated LIA (lock-in amplifier), it is possible to know how a single bacterium is moving. By that, the presence or absence of the analyte can be deduced, thus effectively turning bacteria into chemical sensors

The development of a nanoscale Coulter counter for rapid genetic sequence recognition

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.Includes bibliographical references (p. 195-205).The goal of this thesis is the development of a nanoscale Coulter counter for the direct electrical detection of specific genetic sequences of deoxyribonucleic acid (DNA); the general approach used to accomplish sequence recognition is a refinement of the resistive pulse technique. Commercial Coulter counters fabricated with sub-micrometer apertures can size particles with roughly twenty nanometers of resolution. The characterization of DNA, which is more than an order of magnitude smaller than this resolution limit, requires the development of a detection system with a two nanometer limiting aperture. To help develop the techniques and instrumentation explored in this thesis, the biological toxin, alpha hemolysin, was implemented as "prototype" limiting aperture. With the practical knowledge gained from using a toxin channel, a general model for the nanopore as a low-noise sensor was developed. With this model, two broad goals were achieved. The first achievement was the development of novel genetic recognition strategies that exploit the properties of the nanopore within the limitations imposed by DNA structure and existing channel geometries. The second achievement was the design and prototyping of novel interface picoammeter for the measurement of the current fluctuations associated with DNA translocation through a nanopore. Although the instrumentation and methods developed in this thesis are limited to genetic sequence recognition, the hope is that elements of this work will be integrated with the development of silicon nanopores to achieve rapid de novo DNA sequencing in the future.by Timothy Allman Denison.Ph.D

Definition of a near real time microbiological monitor for space vehicles

Efforts to identify the ideal candidate to serve as the biological monitor on the space station Freedom are discussed. The literature review, the evaluation scheme, descriptions of candidate monitors, experimental studies, test beds, and culture techniques are discussed. Particular attention is given to descriptions of five candidate monitors or monitoring techniques: laser light scattering, primary fluorescence, secondary fluorescence, the volatile product detector, and the surface acoustic wave detector

Mechanisms of Atrial Arrhythmia: Investigations of the Neuro-Myogenic Interface in the Mouse

Arrhythmia mechanisms rely on multiple factors including structural (myogenic), nervous (neurogenic), and interrelated (the neuro-myogenic interface) factors. I hypothesized that due to this neuro-myogenic interface, the intrinsic cardiac autonomic nervous system (ICANS) is involved in most atrial arrhythmias. This thesis also provides a Threshold Model as a tool to assess the role of different physiological factors influencing arrhythmia. This model allows relative comparison and interpretation of the role of various factors influencing arrhythmogenesis. The mouse allows relatively simple manipulation of genes to determine their role in arrhythmia. This thesis determined what atrial arrhythmias are inducible in the mouse (in vivo) and how to systematically study those arrhythmias. I found that atrial tachycardia/fibrillation (AT/F) and junctional tachycardia (JT) are inducible in the mouse. AF and JT pose significant clinical challenges as many patients do not respond well to current interventions. Neurogenic AF relies on acetylcholine, while myogenic AF relies, in part on gap junctions formed by connexins (Cxs). The atria has muscarinic M2 and M3 receptors. The duration of M2R/M3R G protein signalling is regulated by GTP hydrolysis, a process accelerated by the regulators of G protein signalling (RGS). RGS2 deficient (RGS2-/-) mice had reduced refractory periods that were normalized with a selective M3R blocker (Darifenacin) and increased susceptibility to AT/F induction compared to littermates. For the first time, this showed a role of M3 and RGS in atrial arrhythmia. Cx40 deficient (Cx40-/-) mice were protected from carbachol induced AT/F, while Cx43 G60S mutant (Cx43G60S/+) mice, with an 80% reduction in phospho-Cx43 in the atria were highly susceptible to AT/F that was terminated by darifenacin. This shows a novel neurogenic component to what was previously described as myogenic arrhythmia. Another novel finding was that JT has a neurogenic component, resulting from inappropriate AV nodal pacemaker activation initiated by autonomics. Ivabradine hydrochloride, a selective pacemaker channel blocker, prevented JT and may be useful in patients with JT. In conclusion, this thesis has provided novel findings of the vital role of the neuro-myogenic interface in atrial arrhythmias and has provided the basis for future investigations of potential therapeutic options for patients

SIMULATIONS-GUIDED DESIGN OF PROCESS ANALYTICAL SENSOR USING MOLECULAR FACTOR COMPUTING

Many areas of science now generate huge volumes of data that present visualization, modeling, and interpretation challenges. Methods for effectively representing the original data in a reduced coordinate space are therefore receiving much attention. The purpose of this research is to test the hypothesis that molecular computing of vectors for transformation matrices enables spectra to be represented in any arbitrary coordinate system. New coordinate systems are selected to reduce the dimensionality of the spectral hyperspace and simplify the mechanical/electrical/computational construction of a spectrometer. A novel integrated sensing and processing system, termed Molecular Factor Computing (MFC) based near infrared (NIR) spectrometer, is proposed in this dissertation. In an MFC -based NIR spectrometer, spectral features are encoded by the transmission spectrum of MFC filters which effectively compute the calibration function or the discriminant functions by weighing the signals received from a broad wavelength band. Compared with the conventional spectrometers, the novel NIR analyzer proposed in this work is orders of magnitude faster and more rugged than traditional spectroscopy instruments without sacrificing the accuracy that makes it an ideal analytical tool for process analysis. Two different MFC filter-generating algorithms are developed and tested for searching a near-infrared spectral library to select molecular filters for MFC-based spectroscopy. One using genetic algorithms coupled with predictive modeling methods to select MFC filters from a spectral library for quantitative prediction is firstly described. The second filter-generating algorithm designed to select MFC filters for qualitative classification purpose is then presented. The concept of molecular factor computing (MFC)-based predictive spectroscopy is demonstrated with quantitative analysis of ethanol-in-water mixtures in a MFC-based prototype instrument

NASA Tech Briefs, March 2012

The topics include: 1) Spectral Profiler Probe for In Situ Snow Grain Size and Composition Stratigraphy; 2) Portable Fourier Transform Spectroscopy for Analysis of Surface Contamination and Quality Control; 3) In Situ Geochemical Analysis and Age Dating of Rocks Using Laser Ablation-Miniature Mass Spectrometer; 4) Physics Mining of Multi-Source Data Sets; 5) Photogrammetry Tool for Forensic Analysis; 6) Connect Global Positioning System RF Module; 7) Simple Cell Balance Circuit; 8) Miniature EVA Software Defined Radio; 9) Remotely Accessible Testbed for Software Defined Radio Development; 10) System-of-Systems Technology-Portfolio-Analysis Tool; 11) VESGEN Software for Mapping and Quantification of Vascular Regulators; 12) Constructing a Database From Multiple 2D Images for Camera Pose Estimation and Robot Localization; 13) Adaption of G-TAG Software for Validating Touch and Go Asteroid Sample Return Design Methodology; 14) 3D Visualization for Phoenix Mars Lander Science Operations; 15) RxGen General Optical Model Prescription Generator; 16) Carbon Nanotube Bonding Strength Enhancement Using Metal Wicking Process; 17) Multi-Layer Far-Infrared Component Technology; 18) Germanium Lift-Off Masks for Thin Metal Film Patterning; 19) Sealing Materials for Use in Vacuum at High Temperatures; 20) Radiation Shielding System Using a Composite of Carbon Nanotubes Loaded With Electropolymers; 21) Nano Sponges for Drug Delivery and Medicinal Applications; 22) Molecular Technique to Understand Deep Microbial Diversity; 23) Methods and Compositions Based on Culturing Microorganisms in Low Sedimental Fluid Shear Conditions; 24) Secure Peer-to-Peer Networks for Scientific Information Sharing; 25) Multiplexer/Demultiplexer Loading Tool (MDMLT); 26) High-Rate Data-Capture for an Airborne Lidar System; 27) Wavefront Sensing Analysis of Grazing Incidence Optical Systems; 28) Foam-on-Tile Damage Model; 29) Instrument Package Manipulation Through the Generation and Use of an Attenuated-Fluent Gas Fold; 30) Multicolor Detectors for Ultrasensitive Long-Wave Imaging Cameras; 31) Lunar Reconnaissance Orbiter (LRO) Command and Data Handling Flight Electronics Subsystem; and 32) Electro-Optic Segment-Segment Sensors for Radio and Optical Telescopes

CHEMOMETRICS, SPECTROMETRY, AND SENSORS FOR INTEGRATED SENSING AND PROCESSING: ADVANCING PROCESS ANALYTICAL TECHNOLOGY

The research contained in the following dissertation spans a diverse range of scientific scholarship, including; chemometrics for integrated sensing and processing (ISP), near infrared and acoustic resonance spectrometry for analyte quantification and classification, and an ISP acoustic sensor as an alternative to conventional acoustic spectrometry. These topics may at first seem disjointed; however, closer inspection reveals that chemometrics, spectrometry, and sensors taken together form the umbrella under which applied spectrometry and analytical chemistry fall. The inclusion of each of these three serves to paint the complete portrait of the role of applied spectrometry for the advancement of process analytical technology. To illustrate the totality of this portrait, this research seeks to introduce and substantiate three key claims. (1) When applicable, optical spectrometry and acoustic spectrometry are preferred alternatives to slower and more invasive methods of analysis. (2) Chemometrics can be implemented directly into the physical design of spectrometers, thus sparing the need for computationally demanding post-collection multivariate analyses. (3) Using this principle, ISP sensors can be developed specifically for use in highly applied situations, making possible automatic analyte quantification or classification without the computational burden and extensive data analysis typically associated with conventional spectrometry. More concisely, these three claims can be stated as follows: spectrometry has a broad range of uses, chemometrics for ISP makes spectrometry more efficient, and for all analytical problems with a spectrometric solution, an ISP sensor, specifically tailored to the needs of the experiment, can more effectively solve the same analytical problem