Team:Edinburgh OG/Integrated Practices

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Use of non-model organisms and GMOs


Inspired by the need to diversify available chassis, the Edinburgh OG 2016 iGEM team has worked to develop some of the foundational tools and protocols required the for genetic perturbation of a number of non-model strains. By working with such a diverse collection of species, each possessing a range of interesting biochemical features of relevance to environmental, health and commercial interests, we hope to contribute to expanding the range of work that the iGEM Registry supports.

Since every project has the potential to have a social and environmental impact, we own the responsibility to inform about the consequences of using these non-model organisms and GMOs, specifically regarding biosafety and biosecurity. Therefore, those issues were briefly discussed and some examples of previous iGEM projects were included to illustrate those points.

Current risk assessment practice

The team also reviewed the different framework regulations that detail current risk assessment practice and methods in the UK and US, along with some limitations because of SynBio’s fast paced developments. Because of those limitations, we came up with the idea of a program that would complement the current practice to strengthen biosafety and biosecurity in SynBio.

CARE tool

Said tool, denominated “CARE” (for Chassis Assessment & Risk Evaluation) will assess the toxicity of curated secondary metabolites (using the antiSMASH software) from non-model organisms as a precautionary step before any laboratory work is performed.

Outreach

We contacted 25 iGEM teams in order to determine which were their microorganisms of choice. Those microorganisms, along with our three non-model organisms, the non-model strains from 2014 and 2015 and other industrially relevant chassis, made up a total of 30 microorganisms which were used to test the functionality of the CARE tool. Although the majority of the iGEM teams still work with model organisms such as E. coli and S. cerevisiae, it is still significant that each year more teams engage with non-model chassis and we believe that the development of this tool would be of great elucidate and facilitate the use of said chassis.

Limitations

Besides needing to finish the front-ends of the CARE program, this intended online tool only accepts microorganisms that have the accession number of their complete genome, so not every non-model organism can be assessed. In order to make the results more accurate, a risk matrix for each result could be included in the database along with information of recombinases, virulent factors and CRISPR-Cas9 systems.