Team:Edinburgh UG/Medal Criteria

Edinburgh iGEM 2018

Medal Criteria

Bronze Medal Criteria

#1 Registration and Giant Jamboree Attendance

We had a great iGEM season and see you all at the Giant Jamboree!

#2 Competition Deliverables

While reading our wiki, we hope you are excited to see our poster and presentation as well! We have also submitted a Judging form.

#3 Attributions

Our team is proud to state that we conceived the idea for Maxed OOT and subsequently designed and carried out all experiments ourselves. That said, there are many advisors who we would like to thank for helping to provide continuous advice and support, because, without them, we would not have been able to have achieved our goals. You can read more about people, teams and companies who helped us here.

#4 Characterization / Contribution

We successfully participated in InterLab study (see here). We performed and obtained successful results after performing both plate Reader and CFU and Flow Cytometry protocols.

Also, we characterised two parts from iGEM 2012 Paris Bettencourt. You can find out more about our improved parts here.

Previous parts we have improved Description Supporting information
BBa_K914009 P1003* Ser133->Amber Codon contain a kanamycin resistance gene with one two serine -> amber codon mutation
BBa_K914018 P1003** Kan resistant gene with 2 Amber Codon contain a kanamycin resistance gene with two serine -> amber codon mutations

Silver Medal Criteria

#1 Validated Part / Validated Contribution

Our validated parts:

Parts Validated Description Supporting information
BBa_K2725016 J23108 - SupD Serine amber suppressor tRNA gene under J23108 Anderson promoter
BBa_K2725004 FabV + Low expression cassette Triclosan resistance gene from Vibrio fischeri
BBa_K2725013 KanR 10* P1003 kanamycin resistance with 10 amber stop codons

#2 Collaboration

We have done Modelling Collaboration with team Vilnius-Lithuania. We have attended meetups and hosted one of our own (see here).

#3 Human Practices

(See gold medal criteria #1 Integrated Human Practices)

Gold Medal Criteria

#1 Integrated Human Practices

The Edinburgh UG project looks to solve a fundamental problem facing synthetic biology – the lack of a chassis for safe environmental release – by developing a novel chassis. We had to ensure our chassis had all the basic characteristics that a synthetic biologist would require. Therefore, we consulted with a number of active researchers in synthetic biology in order to gauge what they would require in an ideal chassis. These consultations became a basis of our project design as a whole, and often changed the direction of large parts of our work. We recorded these consultations and decisions on a timeline (see here) so that anyone may follow and understand the progression of our project.

#2 Improve a Previous Part or Project

We have improved upon the sequence of the previous part BBa_K914009 which contains a kanamycin resistance gene with one serine codon -> amber STOP codon mutation. We have increased the number of serine -> amber STOP codon mutations up to 5 in our part BBa_K2725012 and so it now confers decreased kanamycin resistance in the absence of a suppressor tRNA, i.e. we have reduced the leakiness of the gene. See here for more information.

Parts Description Supporting information
BBa_K914009 P1003* Ser133->Amber Codon We have improved the characterisation of this part
BBa_K2725012 P1003 Cassette with 5 amber STOP codons This is our new part which is an improvement on the previous part BBa_K914009

#3 Model Your Project

Rational design of biobrick parts and protocols is an iGEM principle that Team Edinburgh UG have embraced this year through mathematical modelling. The mechanistic modelling of our DNA degrading killswitch was used to check for the viability of our project and to decide which promoters and ribosome binding sites to use in the final build of our system. We created a model which would tell us how often our semantic containment system would theoretically fail and allow horizontal gene transfer. This allowed us to be more informed when approaching the human practices side of out project. We also trained an ordinal logistic regression classifier to be able to take growth curve data and identify which of our Semantic Containment parts was present within an organism. This provided a quick way to diagnose instances of Semantic Containment failure. For more information please read here.

#4 Demonstration of Your Work

All aspects of our project combine to provide a novel chassis for Synthetic Biology: Maxicells. These maxicells are easy to use and can be safely deployed into the environment through the use of our Triple Lock System (link)

• We have assessed various methods of maxicell production and have concluded that they are easy to make through UV exposure and homing endonuclease action.

• The Triple Lock System - Colicin E2 kill switch, semantic containment and triclosan resistant plasmid backbone was produced

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