May 2021 Webinar: Synthetic Biology in the Environment and Biocontrol Application Domain

July 21st, 2021

Watch the Synthetic Biology Future Science Platform Webinar featuring Dr Nina Pollak and Dr Caitlin Cooper.

This webinar was presented in May 2021 as part of the Synthetic Biology Future Science Platform (SynBio FSP) Seminar Series. This webinar covers work in the Environment and Biocontrol Application Domain.

Regular webinars offer information about the latest work from SynBio FSP including funded projects, the work of CSIRO-University Fellows and SynBioFSP PhD students.

Webinar program

Dr Owain Edwards, Application Domain Leader, Environment and Biocontrol welcomed participants, acknowledged the Traditional Owners and introduced the speakers:

  • Dr Nina Pollak (Research Scientist, University of the Sunshine Coast and CSIRO SynBio FSP Fellow) who spoke about her fellowship research: from biological computation to tissue-engineered pseudo-organisms for bioremediation
  • Dr Caitlin Cooper (Research Scientist, CSIRO Health & Biosecurity) who spoke about successful genome editing in cane toads and further developing CSIRO’s genome engineering capability.

View on CSIRO’s Vimeo channel

View the transcript

Full biographies and abstracts

Dr Nina Pollak, Research Scientist, University of the Sunshine Coast and recent CSIRO SynBio FSP Fellow


Dr Nina Pollak held a CSIRO Synthetic Biology Future Science Fellowship (2017–2021) focusing on smart biosensing and remediation technologies after completing her PhD in Biochemistry and Molecular Biology in Austria. Her research explored the expansion of synthetic biology into the field of tissue engineering, to produce novel multicellular structures, which can move and sense their environment in an organism-like fashion. Currently, Nina is a Research Scientist at the University of the Sunshine Coast developing rapid diagnostics for detecting viruses. This includes novel multiplex diagnostic technology now being applied to arboviral detection.


Biological computation requires in vivo control of molecular behavior to progress development of autonomous devices in the detection and remediation technology sector. miRNA switches represent excellent, easily engineerable synthetic biology tools to achieve user-defined gene regulation. We employed a modular design strategy by engineering toxin-induced control of an enzyme scavenger. The ability to exert control of toxicity demonstrates potential for modular detoxification systems that provide a pathway to new therapeutic, biocomputing and bioremediation applications. Further, we investigated deoxiribozymes (DNAzymes) and aptamers as another biocomputing and biosensing system, due to the enzymatic properties of DNAzymes and the ligand-inducible conformational structures of aptamers. We described a novel method for providing ligand-responsive allosteric control to a DNAzyme using an RNA aptamer.

Out of seven designs, three demonstrated effective toxin-responsive allosteric regulation with the ability to semi-quantitatively determine the toxin concentration. Finally, we sought to develop a novel bioremediation system, exploring the expansion of synthetic biology into the field of tissue engineering, to produce novel multicellular structures, which can move and sense their environment in an organism-like fashion. These “pseudo-organisms”, are constructed from biological and synthetic hybrid components using a 3D bioprinting approach and were designed to house synthetic biology components as vehicles for application delivery in the field of environmental detoxification.

Dr Caitlin Cooper, Research Scientist, CSIRO Health & Biosecurity


My background is in genome engineering in agricultural species. My PhD focused on the impacts of feeding milk from genome-engineered goats and cows containing recombinant human antimicrobial proteins on intestinal infections in pigs. My first postdoc at the CSIRO Australian Animal Health Laboratory was aimed at decreasing the spread of pathogens from poultry products. I developed two lines of genetically engineered chickens that overexpressed native chicken antimicrobials. These antimicrobials reduced the growth of several pathogens in their meat and eggs. I also invented a novel way of delivering gene editing tools known as sperm transfection assisted gene editing, or STAGE. During my second post-doctoral fellowship I expanded my focus to include not only poultry but also genome engineering in aquatic species, specifically on cane toads to develop novel genetic tools for invasive species. Currently, I am a research scientist involved in multiple projects involving gene editing in agricultural and invasive species.


The cane toad (Rhinella marina) is one of the best-known and least-loved of Australia’s invasive pest animals. The goal of this research was to develop protocols for CRISPR/Cas9 genome editing in the cane toad to assess the potential for genetic biocontrol of an invasive vertebrate pest species. We have established a colony of wild-caught cane toads and developed successful protocols for sperm and oocyte production to enable timed fertilisation. Our first CRISPR/Cas9 target was the tyrosinase gene, which generates pigment in the skin, using microinjection of fertilised oocytes – three mosaic founders resulted. In subsequent experiments we adapted the STAGE (sperm transfection assisted gene editing) method for use in the cane toad. Using STAGE we were able to successfully knock out an important toxin production gene in the cane toad and generated over ten founder animals.

Currently, CSIRO is supporting a multi-business unit project to test a variety of genome engineering tools. These tools will be assessed based on ability to design and generate reagents, efficacy of the tools, and the freedom to operate in research and commercially with each tool. This project is looking across eight different model species ranging from yeast, to wheat, and zebrafish. The projected outcomes of this project will provide CSIRO and our partners a clearer understanding of the current future landscape of gene editing from both a technical and commercial point of view.