UCL iGEM

Continuing our series on interesting synthetic biology applications: For the first time, an episode of a Netflix series has been stored in synthetic DNA. Scientists at ETH Zurich encoded the episode from binary code into a sequence of DNA bases. This code was used to create strands of synthetic DNA that can be stored for thousands of years.

https://www.businesswire.com/news/home/20200820005290/en/Twist-Bioscience-Synthetic-DNA-Stores-New-Netflix

Join us at the global meetup where we’ll be hosting a discussion on equality, diversity and inclusion in STEM and iGEM. We hope to see you there!

We’ve started designing our wiki page. We began by finding an editor for writing and running html and css files collaboratively. Initially, we planned to use the jsfiddle playground but it didn't support creating multiple files. Eventually, we decided to use Atom which satisfied all our requirements: create, preview and share multiple files easily within the team.

If you're interested in using Atom, you can download it from github: https://github.com/atom/atom/releases

Has your team started with your wiki? If you have, which software are you using? Also, if you have any questions or advice on coding the wiki, please let us know!

We are researching specific areas of the world that simultaneously suffer from plastic pollution and freshwater scarcity.

If any iGEM team knows any academics or companies that are working in these two areas please let us know!

We’ve decided to start a biweekly series where we share an interesting synthetic biology application we’ve read about. This week it’s growing fish meat without the fish.
With commercial space travel becoming more of a reality, the challenge of transporting food to space will need to be tackled.
Finless food is a company that uses biology to grow seafood meat cells in the lab. “This offers a more sustainable and humane alternative to today’s livestock agricultural system”. Last year, they sent fish muscle cells to the International Space Station where a team of astronauts were able to culture fish cells in space.

Fishcakes In Space? How One Biotech Startup Is Fermenting Far-Out Food - SynBioBeta Cellular agriculture companies can use fermentation to grow meat, chicken, and fish from cell cultures in a lab-like setting, offering consumers—and astronauts—a sustainable source of nutritious foods without the animals.

We are now announcing the challenge! We encourage teams to have team members personally takeover their Instagram and Facebook accounts on every Monday of the week and show their individual experiences with iGEM in this extraordinary year.

We would like to see your workplace, your daily routine and your personal interests! Feel free to add anything else you find relevant to iGEM or the wider field of Synthetic Biology and want to share with the rest of the iGEM community!

Despite wet lab restrictions, we would like to investigate our S. onediensis MR-1 strain’s behaviour upon the anode of our Microbial Desalination Cell (MDC). To this aim, we are employing Cellular Automata (CA) modelling. Here is a great CA resource for beginners:
https://towardsdatascience.com/algorithmic-beauty-an-introduction-to-cellular-automata-f53179b3cf8f

We are using ‘Conway’s Game of Life’ code to model biofilm growth and the influence on desalination efficiency.

https://media.giphy.com/media/d7SnByEMkrdeoVQ2lT/giphy.gif

If any other teams are also using CA modelling, please get in touch!

growth

Algorithmic Beauty: An Introduction to Cellular Automata An overview of simple algorithms that generate complex, life-like results.

Our team is now starting to digitally develop and explore DNA constructs and BioBricks via Benchling for our project this year! It was useful to again reiterate the importance and benefit of standardisation in Synthetic Biology with this following summary by Tom Knight - one of the original founders of IGEM:

https://dspace.mit.edu/handle/1721.1/21168

Idempotent Vector Design for Standard Assembly of Biobricks

Our team is starting to look into the intersection between philosophy and synthetic biology. This paper has been an interesting read on the topic, and has made us reflect on how we view synthetic biology.

https://journals.sagepub.com/doi/full/10.1177/0971721813498501 #

In order to identify the enzyme within our PET degradation pathway (see below) that would maximise the final product yield when over-expressed, we are using Flux Balance Analysis (FBA). This in turn will inform our SynBio choices that will aim to degrade PET more effectively.

In FBA, the mathematical representations of the metabolic reactions are then solved using linear programming. The COBRA Toolbox is a freely available Matlab toolbox for performing these calculations: https://nature.com/articles/nprot.2007.99

Greetings!

We have now started to develop the synthetic biology aspect of our project for iGEM 2020. We have found that Benchling is a good platform for developing protocols, constructs and BioBricks! We are also extending our thanks to Benchling for helping iGEM teams this year and hosting a great webinar series on how to effectively implement their platform for the competition!



Here is the video that got us started:

iGEM Webinar Series – Webinar 1: Introduction to the Benchling Platform (2020) In the first webinar of our iGEM 2020 series, we introduce you to Benchling’s core applications – Notebook, an electronic lab notebook, and Molecular Biology...

Recently, our team created our own Youtube channel to share casts of our educational webinars. We have hosted two sessions of Zooming in on Biology via zoom with high school students and teachers to introduce our team members’ and supervisors’ majors. Link to our videos can be found here:

UCL iGEM 2020