Miss Anya Kardailsky1, Dr Eddy Dowle1, Dr Christoph Matthaei1, Dr Neil Gemmell1, Dr Gert-Jan Jeunen1
1University Of Otago, Dunedin, New Zealand
Freshwater quality in many New Zealand catchments is declining due to increased agricultural use, urban development and other anthropogenic effects. Traditional methods of biomonitoring of freshwater stream health uses microscopic analyses that are biased, costly, slow and require a high degree of specialist taxonomic knowledge, all of which limits its use and effectiveness. In this study, bulk eDNA samples of freshwater macroinvertebrates collected from local streams are used to assess the application of CRISPR-Cas enrichment approaches to generate biomass estimates, increase the sensitivity of rare species identification, and decrease biomonitoring costs. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) is a bacterial immune system that has been adapted for both DNA editing and enrichment due to its highly specific DNA targeting ability. I assess if this technology can overcome the biases that have limited genomic biomonitoring in the past and prevented quantitative measures of stream health. This method is compared to traditional metabarcoding approaches to assess accuracy, sensitivity and opportunities for the application of the CRISPR technique in molecular biomonitoring. This study presents an exciting opportunity to expand the field of genomic-based biomonitoring techniques and allow for faster, cheaper, more accurate measures of stream health.
Biography:
My name is Anya Kardailsky. I’m currently a Masters student at the University of Otago in New Zealand due to graduate by May 2023. I have always been passionate about conservation, and I want to use my skills developed during my bachelor’s degree in genetics, and various eDNA focused summer projects, to develop better methods of conserving the environment.
I am working across the Zoology and Anatomy departments with supervisors in both, which has allowed me to learn an ecology focused approach using molecular genetic techniques and skills.
Skills like:
– Field work collecting many different eDNA sample types on land and in a boat for several weeks
– Microscopy analysis of freshwater macroinvertebrates
– Lab work in PCR free environments
– Sequencing and library preparations and subsequent bioinformatic analysis
– Reference mitochondrial genome sequencing and assembly
– CRISPR-Cas enrichment techniques; sgRNA design, troubleshooting, analysis
My current Masters project allows me to do exactly what I’ve wanted to in the conservation or biomonitoring sphere, by attempting to create a DNA-based water health monitoring technique of freshwater rivers using CRISPR-Cas enrichment. This will allow for real-time information about the current health of our waterways and brings us a step further in creating an eDNA based method of freshwater monitoring.
Poster presentations from the Queenstown Molecular Biology meeting and postgrad symposia hosted at my university, links to a radio interview discussing my research and a paper I was a co-author of, and my 3MT can be found on my LinkedIn page: https://www.linkedin.com/in/anya-kardailsky/