Team:UCL/Contribution
Overview
Our team is contributing to the iGEM community in three main aspects:
Part 1: Plastic Degradation Constructs
Our synthetic biology group aimed at expressing PETase and MHETase in E. coli for PET degradation. While previous attempts have been made by iGEM teams including a fusion protein design proposed by 2019 Yale team, there has not been a fusion protein of PETase and MHETase documented in the registry. Through continuous communications with the Yale team, Prof. John Ward at UCL, and Prof. John McGeehan at University of Portsmouth, we designed 2 PETase MHETase fusion constructs containing a LamB secretion tag, a 3-repeat G4S (Gly-Gly-Gly-Gly-Ser) flexible linker, and a His purification tag.
For more information, please visit our Parts page
Part 2: Summary of Previous Plastic Degradation Parts
Since day one of our project, PETZAP, our team has dived into the research of existing constructs carrying plastic degradation functionalities. Although it was initially challenging to grasp all the great efforts from past iGEM teams, our exploration of the Registry provided us fruitful insights and inspirations. As iGEMers, we are very grateful for having rich information from existing documentations to base our project on and are thrilled to share a summary of plastic degradation Biobricks here for any future teams passionate about developing a project in this field. In the following table, our team has summarized characterizations of constructs relevant to PET degradation, TPA transportation, and TPA degradation. Hopefully, this summary could facilitate future plastic degradation research.
Part 3: Advice for Future Teams
Our team has organized resources that played fundamental roles in our work, including Synthetic Biology research, Modeling, Human Practices, Education, as well as deliverables. We would love to share information of tutorials, papers, and software we found helpful with future teams and walk them through our process of troubleshooting. This section has been divided into subsections unfolding our iGEM journey in 2020.
Advice from Science Communication Group
General Advice
"Nothing in science has any value to society if it is not communicated." - Anne Roe
Try to use simple language to communicate brilliant ideas.
Resources
Graphics Design:
- Canva: an online platform available for free (or pro version for a fee), very helpful to produce attractive posters and presentation slides for various educational activities. Gives you access to wide range of templates and graphics.
- PowerPoint: very famous tool to make great presentation slides but can also produce great graphics. Although not as detailed and sophisticated as Adobe Illustrator or Affinity Designer, PowerPoint is a decent, free, backup option to satisfy your creativity.
Presentation polls:
- Ahaslides: An interesting alternative to in-built poll tools. This platform enables you to create interactive presentation slides which include multiple choice and open-ended questions, as well as live word clouds. It requires an external link for your audience to join in but enables them to give their opinion, useful in the context of large webinars. The results can then be downloaded anonymously for future use and analysis. There is a free version which limits the number of participants you can have but can be upgraded for a small fee.
Advice from Synthetic Biology Group
General Advice
Our Synthetic Biology group was formed by members all coming from different degree programs including Molecular Biology, Biochemistry, Bioprocessing, and Biochemical Engineering. The collaboration perfectly combined the skills from each of us which not only improved our work efficiency, but also provided us the invaluable opportunity to learn from each other. We would highly encourage future synthetic biology teams take into account the academic background and technical skills of each member and distribute tasks in the way that all strengths are integrated, and all members are gaining new skills from the group.
Resources
Constructs Design:
- Benchling
- Snapgene
Structural Biology:
Tutorials:
Graphics:
Advice from Flux Balance Analysis (FBA) Group
General Advice
Our group commenced with very little experience in FBA in the beginning of the iGEM season, however, finished up modeling three organisms. There were lots of learning, debugging, improving in this process and we are more than willing to share with future teams the key steps taken and helpful resources used.
Key steps:
Resources
Key papers:
- Basics of FBA: What is FBA?
- E. coli: Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
- P. putida: High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
- B. subtilis: Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data
Key COBRA tutorials:
Advice from CA Modeling Group
Resources
Python:
- Learn Python the hard way - By Zed A. Shaw -
3Blue1Brow on Linear algebra and Calculus:
- Differential equations, studying the unsolvable | DE1
- The Essence of Calculus, Chapter 1
- Vectors, what even are they? | Essence of linear algebra, chapter 1
Online training for the bioscience community:
Advice on Wiki Development
General Advice
Just like many other teams, our Wiki group explored a variety of resources throughout the iGEM season. Here we would love to share tutorials, software, websites that we found helpful as well as our tips. Please visit our Github account linked in the footer to access templates we developed for future teams!
Resources
Tutorial:
Cheat Sheets:
- HTML cheat sheet
- HTML key concepts overview
- CSS cheat sheet
- CSS key concepts overview
- Encyclopedia for UCL iGEM 2020 Wiki
Prototyping:
Collaborative web development environment:
Templates:
Colors:
- Digital Color Meter on Mac
- RGB to HEX converter