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Microfluidic assays for in-field pathogen detection


   Biosecurity Innovations

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  Dr CN Meisrimler, Assoc Prof Volker Nock  Applications accepted all year round  Funded PhD Project (Students Worldwide)

About the Project

Deoxyribonucleic acid (DNA)- and Ribonucleic acid (RNA)-based techniques provide a powerful toolkit for the early detection, identification and tracking of biosecurity related pathogens and invasive species. Loop-mediated isothermal amplification (LAMP) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) are relatively new low-cost single-tube techniques for the amplification, and thus detection, of DNA and RNA, respectively. Due to their isothermal nature and ruggedness, LAMP and RT-LAMP could provide major advantages as simple screening assay in remote locations such as native forests and wilderness areas.

 This Ph.D. project will develop DNA- and RNA-based microfluidic assays for the rapid detection of Kauri Dieback and Myrtle Rust, two diseases with significant impact on the native New Zealand ecosystem and primary industries. The ability to quickly confirm and localize pathogens prior to, or at an early stage of infection, would considerably improve understanding and management of both diseases. The project will combine recent advances in LAMP technology for the Kauri Dieback pathogen Phytophthora agathidicida [1] and analysis of the Myrtle Rust pathogen Austropuccinia psidii DNA [3] with recombinase polymerase amplification technology (RPA-LFD) [3] and capillary microfluidics [4,5] to demonstrate a simple, rapid, and specific method for the detection of the Kauri Dieback and Myrtle Rust pathogens in resource-limited settings..

 Supervised by Dr Claudia Meisrimler (SBS) and A./Prof. Volker Nock (ECE) and as part of the newly funded UC Biosecurity Innovations research cluster, the project will use state-of-the-art microfabrication techniques available in the UC Nanofabrication Laboratory, and molecular plant biology and plant pathology expertise available in the School of Biological Sciences. Devices will be experimentally characterised and tested in close collaboration with external stakeholders. The ideal candidate would have a background in either Biochemistry or Microsystems Engineering. Engineering candidates should have experience in the fabrication and use of lab-on-a-chip devices, and be keen to apply these to DNA detection assays. Biologists should have prior experience with DNA-based detection technology and be interested in expanding their experimental technique to microfluidic platforms.


Funding Notes

The scholarship will cover living expenses at NZ$28,000k per year for three years and study fees.

References

[1] R. C. Winkworth, et al., PLOS ONE, 2020, 15, e0224007.
[2] P. A. Tobias, et al., bioRxiv, 2020, DOI: 10.1101/2020.03.18.996108
[3] T. Dai, et al., Forests, 2020, 11, 306.
[4] J. Menges, et al., Lab Chip, 2020, 21, 205 - 214.
[5] C. Meffan, et al., 34th International Conference on Micro Electro Mechanical Systems (MEMS), 2021, pp. 218-221.
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