A portable quantitative polymerase chain reaction platform (qPCR) for rapid detection of pathogens impacting model organisms in animal facilities
Award last edited on: 2/13/2024

Sponsored Program
Awarding Agency
Total Award Amount
Award Phase
Solicitation Topic Code
Principal Investigator
Scott Franklin Geller

Company Information

Bay Genomics LLC

1440 4th Street Suite C
Berkeley, CA 94710
   (510) 848-8510
Location: Single
Congr. District: 12
County: Alameda

Phase I

Contract Number: 2023
Start Date: ----    Completed: 8/1/2023
Phase I year
Phase I Amount
In recent years there have been growing concerns about the rigor and reliability of data originating from common and critical animal model experimentation. In fact, a core principal of science - reproducibility - has been called into question largely due to challenges in replicating biologically complicated animal experiments. We have developed a fast, portable, quantitative PCR (the current universal "gold standard" method) device for use in a wide variety of diagnostic settings. We believe that our rapid, handheld, battery-powered and wireless device has the potential to empower rapid diagnostics around the world. In this proposal we aim to validate the use of our prototype device using real-world samples for microbial pathogen detection. Regarding our innovative technology, we have taken a fundamentally different approach to heating and cooling the sample being amplified, avoiding the standard Peltier heating block. The heat transfer is so efficient that we are able to perform a heating and cooling cycle in as little as 15 seconds (possibly even faster), resulting in a 40-cycle run finishing in about 11 minutes. In essence, this means you can get a quantitative answer regarding the presence and abundance of your target pathogen with ultimate sensitivity significantly faster than the current state of the art. Looking deeper into the root causes of animal-derived data variability is pointing to several possible environmental and biological causes. In terms of the biology, microbes that live inside or outside of the body are proving to have clear and present effects on experimental outcomes, yielding data that is inconsistent and questionable. In particular, when the studies of interest are translational by design, and therefore intended to benefit / improve human health, there is even greater cause for concern. We are poised to test our device to identify and quantify the presence (or absence) of pathogens in an fully operating academic animal facility at UC Berkeley. Together with the Office of Laboratory Animal Care, we have identified two important and tractable pathogens as good candidates for initial proof of principle studies: Helicobacter species (bacteria) in mice and B. dendrobatidis, a fungus affecting amphibians.

Public Health Relevance Statement:
Pathogens infecting or invading commonly used model organisms has the potential to negatively impact results, reproducibility, and subsequent success of human clinical trials. It is critical for animal care facilities to monitor to the greatest extent possible the real time presence or absence of such microbes, particularly in rodent facilities, but also in other "barrier" protected areas spanning the gamut of model organisms. Providing simple, fast, easy-to-use, quantitative detection of the most virulent and consequential pathogens helps to ensure the validity and value of the data collected from these essential model organisms, and empowers animal care facilities to quickly respond to and address concerns before they become serious threats.

Project Terms:
Affect; Air; Amphibians; Amphibia; Animal Experimental Use; Animal Research; animal experimentations; Animal Experimentation; Animals; Laboratory Animals; Bacteria; Biological Assay; Assay; Bioassay; Biologic Assays; Biology; Clinical Trials; Electronics; electronic; electronic device; Extravasation; Leakage; Spillage; Fluorescence; fungus; Goals; Health; Health care facility; Health Facilities; Healthcare Facility; care facilities; Heating; Human; Modern Man; Lead; Pb element; heavy metal Pb; heavy metal lead; Manuals; Marketing; Methods; Movement; body movement; Mus; Mice; Mice Mammals; Murine; Noise; Optics; optical; Legal patent; Patents; Polymerase Chain Reaction; Production; Quarantine; isolation/quarantine; Reagent; Research Personnel; Investigators; Researchers; Rodent; Rodentia; Rodents Mammals; Running; Science; seal; Signal Transduction; Cell Communication and Signaling; Cell Signaling; Intracellular Communication and Signaling; Signal Transduction Systems; Signaling; biological signal transduction; Specificity; Testing; Time; Translations; translation; Work; Helicobacter; DNA Sequence; animal care; improved; specimen collection; sample collection; Site; Area; Clinical; Phase; biologic; Biological; animal experiment; experimental animal; experimental animals; Animal Experiments; Ensure; Veterinarians; Collaborations; instrument; Diagnostic; Hour; System; interest; innovative technologies; success; Animal Model; Animal Models and Related Studies; model of animal; Speed; empowerment; Graph; Devices; Sampling; response; animal facility; portability; Experimental Animal Model; µfluidic; Microfluidics; Address; Data; Detection; Reproducibility; Invaded; Small Business Innovation Research Grant; SBIR; Small Business Innovation Research; Validation; validations; Virulent; Monitor; Preparation; preparations; Process; Development; developmental; Output; rapid detection; designing; design; remediation; Outcome; pathogen; Population; innovate; innovative; innovation; Microbe; Pathogen detection; human disease; usability; prototype; commercialization; product development; experiment; experimental research; experiments; experimental study; microbe pathogen; microbial pathogen; pathogenic microbe; Rapid diagnostics; wireless electronic; wireless device; model organism; manufacture

Phase II

Contract Number: 1R43OD034167-01
Start Date: 1/31/2025    Completed: 00/00/00
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