Why It Is Important

Current technologies for pathogen detection, such as real-time qPCR, require a relatively large amount of target and rely on specific assays to identify distinct pathogens. Multiple independent assays drastically increase the amount of template required as well as the cost. There is a clear and evident need to develop new technologies that can quickly, efficiently, and inexpensively identify pathogens of plants and humans based on genetic markers.

Our Approach

The team’s  approach is founded on recent advances in nanotechnology, electrical engineering, genomics and biotechnology, and our vision is to utilize expertise from these distinct disciplines to solve the problem described above: rapid, low cost identification of microbes. We will use our combined expertise to synthesize, characterize, and micro-fabricate, electrochemical and conductance electrodes for DNA-based detection schemes are crucial for achieving pathogen identification. We place particular emphasis on fundamental mechanisms including how electrode morphology influences detection processes, and how to couple genomic information and bioinformatics to achieve our goals. Our long term output is intended for cell-phone sized devices which are field-ready for agriculture and food industries. Fundamental to our approach is the use of the rapidly increasing number of genome sequences available for a wide range of microbes, including those which are pathogens of plants and/or animals. Even closely related variants of a given pathogen species, which may have important differences in host range and/or pathogenicity, differ in their genome sequences. In the proposed project, this information is exploited to detect specific pathogens. Our vision is to directly detect genetic information at the molecular level with electronic detection methods.

Impacts & Highlights

• Revealed how nanostructure dictates biofouling sensitivity in porous electrodes and how the electrically-conductive porous network can be employed for electrophoretic release of captured targets
• Demonstrated techniques to modify the nanostructure of electrodes and include multiple electrodes with different nanostructure on a single-chip for a high throughput study of electrochemical biosensing
• Illustrated the utility of conductance measurements in multiplexed identification of sequence mismatches
• Filed a provisional patent on the detection-purification platform, titled “Nanoporous Gold Electrodes for Integrated Electrochemical Detection and Purification of Nucleic Acids”
• The established start-up, Astrona Biotechnologies, received IndieBio funding for intensive training on commercialization.

Team

Bryce Falk	Professor of Plant Pathology
Erkin Seker	Assistant Professor of Electrical & Computer Engineering
Maria L. Marco	Associate Professor of Food Science & Technology
Josh Hihath	Assistant Professor of Electrical & Computer Engineering
Andre Knoesen	Professor of Electrical & Computer Engineering
Paul A. Feldstein	Project Scientist of Plant Pathology
Zimple Matharu	Postdoc of Electrical & Computer Engineering
Pallavi Daggumati	Graduate Student of Electrical & Computer Engineering
Marc Pollack	Graduate Student of Microbiology
Yuanhui Li	Graduate Student of Electrical & Computer Engineering
Jovana Veselinovic	Graduate Student of Chemical Engineering
Cindy Ma	Undergraduate Student of Microbiology
Eric Tran	Undergraduate Student of Microbiology
Lynn Whang	Undergraduate Student of Microbiology

For more information on this program, please contact Christine Parks ceparks@ucdavis.edu.