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Molecular Recognition, Biosensors and Bioassays
Angelika Niemz Research in Professor Niemz's lab is focused primarily on technologies for identification of clinical pathogens and biothreat agents in point of care settings, through rapid isothermal DNA amplification coupled with visual or electronic detection. The lab is developing methods for fabrication of nanostructured surfaces based on self-assembly and biomolecular recognition. There are several projects in progress: - Isothermal DNA Amplification with Colorimetric Detection: Specific DNA sequences can be easily and rapidly detected by combining a novel isothermal amplification method for short oligonucleotides (EXPAR) with colorimetric detection through aggregation of DNA-functionalized gold nanospheres. The assay is sequence-specific, and permits detection of 100 fM trigger (oligonucleotides generated in the amplification reaction) in under 10 minutes. Triggers from genomic DNA of Herpes Simplex Virus have successfully been detected using the assay. Because of its simplicity, versatility and speed, the assay holds great potential for point-of-care applications.
- Impedance-based Electronic DNA Detection on Silicon: The Niemz lab has developed biosensors for label-free electronic DNA detection, suitable for direct interfacing with microelectronic devices. DNA hybridization to probe DNA-functionalized silicon biosensor electrodes leads to a change in surface charge density, which in turn causes a shift in the semiconductor's impedance response through the field effect. To increase the sensitivity of detection, they have combined electronic DNA detection with isothermal DNA amplification through the EXPAR reaction. To enable miniaturized multiplexed detection, an array of individually addressable microsensor electrodes was fabricated. They are further investigating how co-immobilizing DNA functionalized gold nanospheres affects the observed shift in impedance response. These sensors are expected to facilitate rapid, specific, and sensitive detection of clinical pathogens and biothreat agents in point of care settings.
- DNA Nanoarrays: The lab is also developing a method for depositing DNA-conjugated gold nanospheres into arrays of surface nanopores obtained from hexagonally ordered thin PS-PMMA diblock copolymer films on silicon. The deposition occurs spontaneously from solution and is driven by either electrostatic interactions or specific DNA hybridization events between the DNA nanospheres and the surface nanopores. To mitigate this spontaneous deposition, the nanopores have been chemically modified with either positively charged aminosilanes or oligonucleotide probe sequences. Deposition of biofunctionalized nanoparticles into nanostructured surfaces based on intrinsic molecular interactions, in particular of bio-inspired, specific self-assembly, is expected to facilitate the fabrication of complex surface structures and enable the development of biosensor surfaces.
- Functional Enzyme Immobilization in Hydrogel Microarrays: A microarray-based technology platform to enable experimental investigation of enzyme activities in a high throughput format is also under development. The enzymes being used are protein phosphatases, which play an important role in regulatory networks. Functional microarrays are obtained through a combination of affinity capture and copolymerization of proteins within hydrogel pad microarrays on glass slides. Quantification of enzymatic activities involves the correlation of experimental data obtained from fluorogenic assays with simulations of the reaction-diffusion system.
Medical Device Machine Learning
Gail Baura Physiologic signals provide a wealth of information that can be used to develop new medical devices. These signals can be harnessed, through machine learning, to enable diagnosis and monitoring of various conditions. If a signal is continuous, such as the traditional electrocardiogram, various noise minimization, pattern recognition, classification, and prediction strategies may be employed. For metabolic signals such as hormones, compartmental modeling and other approaches are appropriate. Research in the Baura lab is focused on a new sensor and detection algorithm for drowsiness monitoring, and on efficient methodologies for identifying candidate biomarkers of obesity. Microfluidics and Microfabrication
Jim Sterling
Ali Nadim There is a need to miniaturize, automate and simplify nucleic acid tests, immunoassays, and other bio-molecular assays in order to achieve desired levels of specificity, sensitivity, detection speed, and long-term stability. The Microfluidics Research Lab is exploring the use of electrostatically actuated motion of sub-micro-liter droplets, i.e. electrowetting, to develop biosensors and to automate laboratory processes that have traditionally been performed using liquid-handling robots, micro-titer plates, and translation stages. The lab is equipped with state-of-the-art microfabrication instruments to make electrowetting and microfluidic chips for performing biological and chemical protocols with the aim of incorporating them into compact handheld systems, small footprint laboratory instruments, and lab automation-compatible systems. In addition, miniaturized systems are being engineered to perform sample preparation steps for nucleic acid analysis including lysis, purification, amplification and detection. Engineering of Compact, Automated Systems for Biothreat Analysis
Robert Doebler
Jim Sterling
Ali Nadim
Robert Doebler
Jim Sterling
Ali Nadim Biothreat detection research at KGI is being conducted in several multi-disciplinary, multi-team efforts. With funding from DHS, NIH and DARPA, the focus of the research is on bioanalytical methods and engineering instrument/device development for nucleic acid diagnostics. The projects are focused mainly on: (1) sample preparation methods including electrical and mechanical sample lysis and nucleic acid purification components, (2) thermally-controlled DNA amplification systems integrated with compact optical fluorescence systems, and (3) chip-based free-solution capillary electrophoresis of short oligonucleotides. The efforts address primarily the ability to detect-to-protect by diagnosing the presence of bacterial and viral pathogens in swab or air-filtered samples.
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