Plant Pathogen Detection

The Challenge

Need to develop a rapid, efficient, and low cost method to detect and identify specific microbial pathogens including bacteria, viruses and fungi.

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

To date, we have demonstrated for the first time that it is possible to measure the conductance of DNA:RNA hybrid molecules, we have explored the change in conductance of these molecules with length so as to understand the charge transport mechanisms, and we have demonstrated that the conductance of short RNA sequences that encode for the STX2 (Shiga-like toxin 2) toxin in E. coli can be measured.

  • Established the equipment and process for producing nanoporous gold electrodes and initiated electrochemical studies. This will serve as the backbone for the future studies and the detection platform.
  • Developed RNA extraction methods for bacterial cells on plants.
  • Determined target pathogen detection limits according to the benchmark real-time PCR technique.
  • Produced target RNAs for molecular conductance measurements.
  • Determined conditions for controlled degradation of viral RNAs to sizes appropriate for further analysis using either electrochemical or molecular conductance measurements.

Team

Bryce Falk Professor of Plant Pathology
Paul Feldstein Project Scientist of Plant Pathology
Josh Hihath Assistant Professor of Electrical and Computer Engineering
Andre Knoesen Professor of Electrical and Computer Engineering
Maria Marco Assistant Professor of Food Science and Technology
Erkin Seker Assistant Professor of Electrical and Computer Engineering
Wenting Ju Postdoc of Food Science & Technology
Juan Manuel Artés Vivancos Postdoc of Electrical & Computer Engineering
Jing Zhou Postdoc of Electrical & Computer Engineering and IBM
Pallavi Daggumati Graduate Student of Electrical & Computer Engineering
Yuanhui Li Graduate Student of Electrical & Computer Engineering
Marc Pollack Graduate Student of Microbiology
Simon Chang Undergraduate Student of Plant Pathology
Gavin Clark Undergraduate Student of Plant Pathology
Cindy Ma Undergraduate Student of Microbiology
Ian Morelan Undergraduate Student of Plant Pathology
Zack Myers Undergraduate Student of Electrical & Computer Engineering
Eric Tran Undergraduate Student of Microbiology
Lynn Whang Undergraduate Student of Microbiology

For more information on this program, please contact Tammi Olineka at tlolineka@ucdavis.edu.