Team:Nottingham/Notebook

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Project Notebook

Take a look at what we've been up to

In order to work effectively and efficiently, our team were separated into different subgroups:

eugenia-profile saachi-photo

Subgroup 1: DBHB
Hi! We’re Eugenia and Saachi and we’ve been working with our supervisors Andrew Dempster and Alex Rawson on DBHB production. Our subgroup is responsible for mapping out the synthetic DBHB production pathways in C. sporogenes as well as additional research on intermittent fasting and the ketogenic diet.

You can view the subgroup lab book in detail here!

kieran-profile alistair-profile

Subgroup 2: Routes of Administration
Hi! we're Alistair and Kieran and as part of this subgroup, we were tasked with investigating the most suitable delivery method for NeuroTone. With supervisor Raquel Rodrigues guiding us, we tried to determine how we would deliver C. sporogenes to the gut microbiome. Taking advantage of its ability to form spores, many factors had to be considered including manufacturing, digestion time, germination and sporulation receptors, formulation and patient preferences.

You can view the subgroup lab book in detail here!

james-profile luke.w-profile

Subgroup 3: Control
Hi! We’re Luke W. and James, we’ve been working with our supervisor Patrick Ingle on the control mechanism for the biotherapeutic. A biological control prevents a genetically modified organism from causing harm to the environment or other organisms. They are an essential part of any GMO project that interacts with humans and control strategies need to be well thought out with multiple experiments showing their validity.

You can view the subgroup lab book in detail here!

aly-profile luke-profile

Subgroup 4: Modelling
Hi! We're Luke B. and Aly and we've been tasked the mathematical modelling for the dynamic and structural models of our C. sporogenes biotherapeutic. Dynamic modelling handled the administration of NeuroTone, along with its interactions with the gut. Aiming to determine what time a dosage should be given, how much a dosage should be, and whether DBHB should be produced immediately, whilst the culture was still small. With the project being entirely dry lab based, a lot of emphasis was placed on the modelling group to influence the decision about which pathway to pick. The structural model aims to answer this question by analysis which pathway is most productive, and is most likely to produce DBHB. The structural modelling took full advantage of the database the SBRC had to offer, adding metabolic formulas to ensure the reactions were balanced and feasibly possible.

You can view the subgroup log book here!

for more details about the modelling can be found on the modelling page.

Project Progress

  1. We had our first virtual team meeting! Students and supervisors introduced themselves and discussed potential roles that would be best suited for them on the iGEM team. We also all prepared a project idea ready to be presented in the following whole team meeting.
  1. Whole team presented their project proposals.
  2. Final project was decided: We plan to produce a biotherapeutic by genetically engineering a Clostridium strain of bacteria to increase the levels of DBHB (3-hydroxybutanoate) reaching the brain in order to reduce the onset of neurodegeneration.
  3. Underwent iGEM safety regulation workshop with the supervisors.
  1. Further preliminary reading of natural ketone production in the body, DBHB interaction with the brain, ketoacidosis. Collated all our research to identify all aspects of our project and delegated roles and modelling objectives. Brainstormed ideas for outreach and integrated human practice opportunities.
  2. Collated all our research to identify all aspects of our project.
  3. Delegated roles and modelling objectives.
  4. Brainstormed ideas for outreach and integrated human practice opportunities.
  1. Discussed carrying out a survey to find out more about the public’s perception of using GM in medicine.
  2. Decided to carry out a literature review to ensure our survey would be necessary and covering new information.
  1. Discussed the different Clostridium strains we could use.
  2. Discussed what factors would be important in selection our strain (virulence genes, genes advantageous for ketone production, preferred environment, etc.)
  3. Researched the identified potential strains, breaking down the pros and cons for each one.
  4. Researched the human microbiome project (a well known large source of microbe genomes) to see if there was any data we could access about the potential strains.
  5. Researched Ketoacidosis.
  6. Decided to start the Minecraft project to encourage community engagement in science.
  1. Shortlisted our three final strain choices.
  2. Prepared presentations for each of the strain choices.
  3. Considered poly-3-hydroxybutyrate and (R)-3-hydroxybutanoate as potential decisions for the ketone pathway to insert into our biotherapeutic.
  4. Looked up the genes involved in the acetyl-CoA and butyryl-CoA pathways.
  5. Discussed preliminary logo design options and colour schemes.
  6. Brainstormed fundraising ideas for the team.
  1. We decided on C. butyricum as our preferred strain.
  2. Presented the three potential Ketone production pathways (fatty acid metabolism, polymer pathway and butyrate pathway).
  3. Split the mathematical modeling into two groups – dynamic and structural modelling.
  4. Team logo finalised.
  5. Discussed product logo ideas.
  1. We had genome presentations for the different strains of Clostridium butyricum (DKU01, KNUL09).
  2. We determined the locations of the genes for the butyrate pathway in the genomes.
  3. Had a presentation on acetone – risks of overdose and the process of production.
  4. Researched the virulence and pathogenicity of chosen C. butyricum pathways.
  5. Had a presentation on ethanol production, highlighting the connection between the butyrate pathway and ethanol production.
  6. Discussed outreach ideas – Minecraft server and the QR code trail.
  7. Had an ethics tutorial from our human practices supervisor specifically focused on running a survey and data handling.
  1. Meeting with the 2019 Nottingham iGEM team in which we discussed approached to organising and improving our project.
  2. Finalised primary and secondary roles for subgroups.
  3. Reached out to several companies for sponsorship.
  4. Organised a meeting with Geocashing HQ to discuss collaboration over a QR code trail on campus.
  5. Changed our species of clostridium to C. sporogenes as it was a better sporulator and already produced a neuroprotectant naturally.
  6. Analysed various C. sporogenes strains for virulence and toxin genes to find the best candidate for our biotherapeutic.
  1. Subgroups formed (see individual subgroup notebooks for timelines of subgroup work).
  2. Discussed hosting a European team meet up.
  3. Had a presentation on the ethanol production from the new DBHB production pathway the team was working on.
  1. Had a discussion of the European meet up with Nemira (European iGEM Ambassador) - decided to change it to a commonwealth meet up to try and involve a more diverse range of teams.
  2. Worked on branding and social media posts for a commonwealth meet up.
  1. Filmed intro videos for the team introduction
  2. Discussed whether to use posters, QR codes or the Adventure Lab (from Geocashing) for our trail.
  3. Discussed whether posters or videos would be best for the trail project for science education.
  4. Discussed the poster presentation and the graphics and content we want to cover.
  5. Discussed starting a podcast for outreach.
  1. Shot the videos for Nemira’s UK video for the global meetup.
  2. Discussed entering the Tough Mudder challenge to raise money and awareness for a neurodegenerative disease charity.
  3. Meeting with Subin Saji (experienced podcaster and friend of the team) about how to run and edit a successful podcast.
  1. Made the podcast logo.
  2. Started recording vlogs.
  3. Finished the MolecularCloud livestream presentation.
  4. Finalised the platforms we would upload the podcast on.
  5. Each team member wrote a personal paragraph for the meet the team wiki page.
  1. Recorded first podcast (with our Nottingham student team).
  2. Contacted the Paris team - had a meeting to discuss opportunities for collaboration.
  3. Made a general poster with the basic guidelines to recording a podcast to send out to teams. Check out the poster here!
  4. Made a podcast guide on how to start up your first podcast!
  5. Minecraft promotional video produced.
  6. Finalised product name – NeuroTone.
  1. Discussed our approach to the Science Education and Modelling Special awards.
  2. Discussed ways to encourage science communication by setting up Reddit forums and accepting questions about Synthetic Biology from social media to be answered on out podcast recordings.
  3. Meeting with Kings College London iGEM team to discuss potentially fulfilling partnership criteria together.
    4. Recorded a podcast episode with the Paris-Bettencourt Team.
  1. Posted an advert for the Minecraft video on our social media. Here's the Minecraft video on our youtube channel!
  2. Finalised the project promotion video.
  3. Finalised the logo and our team hoodie designs.
  4. Recorded a podcast with Kings College London team.
  1. Recorded the strain choice video clips.
  2. Recorded a podcast with Warwick University team.
  1. Strain choice video finalised.
  2. Decided to post an ad for the podcast series on our social media.
  3. Recorded a podcast with Denmark team.