Team:Calgary/Results



OVERVIEW

The following page describes the summarized results of our work in each of our subprojects. Please visit the corresponding links to the subproject specific pages to get more details on the background information and our methods.


ENGINEERING SUCCESS

Cellulase Integration

Go to Cellulase page

Our cellulase integration system makes Oviita sustainable and accessible to VAD communities. This year our goals were to design our cellulase parts and make sure they were suited for function in Y. lipolytica and do preliminary testing with commercial cellulose and cellulase to prove the functionality of our idea before we moved forward with genetic engineering.

Overall, this year we were able to:

✔  Select, model, and optimize our cellulase proteins for function in Y. lipolytica
✔ Contribute 20 parts to the iGEM registry
✔ Extensively plan all of our experiments for the next year
✔ Determine minimum amount of glucose concentration required to maintain Y. lipolytica
✔ Determine approximately how much cellulase enzyme is required to reach that minimum glucose concentration
✔ Verify that Y. lipolytica can grow on crude (and pure) cellulose when cellulases are present

Biocontainment

Go to Biocontainment page

We developed a sustainable and affordable biosafety system where two yeast strains will be co-cultured together in a syntrophic community. These strains will each be auxotrophic for a molecule the other strain has been modified to overproduce. This ensures that the two strains are co-dependent, reducing the chances of environmental escape. The organism can only proliferate if both strains are present in sufficient quantities to support each other’s growth. Ultimately, this novel method of co-dependent auxotrophy provides an easily implementable biocontainment strategy to prevent the escape of genetically engineered organisms.

This season specifically, we developed a proof of concept for our co-culturing system using a pair of already engineered S. cerevisiae strains. We are happy to say that by the end of this season, we accomplished quite a bit:

✔ We successfully characterised a proof of concept for our biocontainment system using a pair of already engineered S. cerevisiae strains:

  • Characterised the strains in terms of auxotrophy and amino acid overproduction
  • Created a viable co-culture demonstrating the ability of the strains to survive using the amino acid released by each of the complementary strains
  • Demonstrated the inability of the yeast to survive in environmental conditions outside of the expected growth vessel conditions

✔ We designed and submitted a total of eight parts to the parts registry that allow for the engineering of Y. lipolytica to create complementary overproducing, auxotrophic strains.


Thymol Production

Go to Thymol page

We developed a system where our supplemental yeast can produce thymol, an anthelmintic compound, which can serve as a temporary measure in between rounds of mass-deworming. This will allow the perforated intestines of parasite-infected children to heal and maximize vitamin A and micronutrient absorption.

This year in particular, we were able to do the following:

✔ Identified promoter and gene sequences for thymol production in Y. lipolytica


✔ Collected our reagents and C. elegans for testing


✔ Extensively planned all of our experiments and made troubleshooting plans



HUMAN PRACTICES

Creating a human-centred project

Go to Human Practices page

By following our HP pipeline, we were able to inform our design with help from experts in the community from start to finish, at every step in the project. We were careful to consult those with experience in every aspect of our project, from anthropologists, to NGOs, to medical doctors, to local health workers living in our target communities, and everything in between. By accessing a broad spectrum of viewpoints and experiences, we were able to consider the complex issue of Vitamin A deficiency holistiaclly, and create Oviita to address it from every angle we could. That direction by the community became the foundations of not only the Vitamin A production itself, but cellulases to ensure long-term financial sustainability, thymol production to address parasitic inhibition of vitamin absorption, Randall Cell to improve VAD diagnosis and public health data, and our plans for future implementation.


PROPOSED IMPLEMENTATION

Bioreactor

Go to Bioreactor page

With the help our our HP contacts, we have been able to make extensive plans for where, how, and by whom our project can best be implemented in order to maximize consumer acceptance of Oviita. This has meant minimizing cost and inconvenience, and maximizing accessibility and integration. By designing the FAB bioreactor with a flexible but effective design, it can now be adapted by communities to utilize the varying resources they have available. We have been able to recieve feedback from community members in VAD regions that these plans seem accessible and feasible within their local areas, and would be readily adopted. We also considered the taste of our product and ability to be incorporated into local diets. We were able to determine common regional dishes, with some aditional help from HP team members with family in affected regions of South Asia, and plan how Oviita could be incorporated into meals. To further increase economic viability, we developed plans and partnerships for the development of locally-led microenterprises forr the production and sale of yeast. Finally, we ensured using literature review that we could be confident of the safety of our product for future use.



PARTS

Characterize

Go to Parts Characterization page

We added new literature-review characterization to BBa_K2117000 from the iGEM registry and also made plans to experimentally characterize this part when we have further lab access. Furthermore, we have contributed the first engineered cellulases for Y. lipolytica to the iGEM registry (BBa_K3629013 and BBa_K3629016) and discussed our in-silico characterization and future experimental plans.


MODELLING, SOFTWARE, AND MEASUREMENT

Bellatrix

Go to Bellatrix page

The ultimate underdog story, though Bellatrix was never an underdog. It started as a quest to break free from the PDB standard into a format that provided more relational information. This crusade ultimately ballooned out of our expectations and finished with a beautiful piece of software, a manuscript, and has inspired many to reread the Harry Potter series.

Protein Modelling

Go to Modelling page

Jacques Vaché once said, "Nature is only another chimera.". This hits a little too close to home for our modelling team. Over the summer, we worked to improve, and then subsequently prove these improvements were not structurally detrimental to our two modified cellulases. The improvements took the form of literature review on what optimal chimeric protein could be made from the available components. This resulted in our two cellulases, dubbed Penny and SEGI-8 to be generated and verified in silico.

GausHaus

Go to GausHaus page

GausHaus was not like the other software sitting by the beach enjoying sparkling cider; it put in the work. GausHaus spent the summer confusing and terrorizing our statistician with sprinkles of success amongst an ocean of setbacks. Once it clicked though, we were off to the races with GausHaus coming through whenever called upon. This resulted in it being instrumental to our protein modelling, allowing the quantification of SEGI-8s dynamics along all three axes. It then also served as a software contribution to the iGEM community. And just when we thought it was done, it hit us. GausHaus' quantification of protein dynamics is an ideal measurement for teams during this renaissance of computational biology brought on by COVID-19. All in all we fought, we loved, and we demolished some molecular dynamics. What more could you ask for?

THE LITTLE GUYS - PERIPHERY SOFTWARE

Go to Software page

Not everyone can be a quarterback. This was apparent for our team this summer as we focused on our top two software: Bellatrix and GausHaus. Despite our focus, we found small software projects developing in the periphery. These projects include Sticks, iGAM 2.0, and our Hardware necessitated software. The Hardware Software was incredibly important to our bioreactor and Randles Cell Testing Device. iGAM 2.0 became a meaningful collaboration/development path with the KCL iGEM team. And Sticks homoured our gristled statistician with its cute GIFs. Overall Oviita benefited from these projects just as much as the ones we planned for.