iGEM 2016 — Team Edinburgh_OG

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# Team:Edinburgh OG/Notebook

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* TEAM

  [About Us](https://2016.igem.org/Team%3AEdinburgh_OG/Team)
  [Attributions](https://2016.igem.org/Team%3AEdinburgh_OG/Team#attributions)
  [Collaborations](https://2016.igem.org/Team%3AEdinburgh_OG/Collaborations)
* PROJECT

  [Description](https://2016.igem.org/Team%3AEdinburgh_OG/Description)
  [Design](https://2016.igem.org/Team%3AEdinburgh_OG/Description#design)
  [Method](https://2016.igem.org/Team%3AEdinburgh_OG/Experiments)
  [Proof of Concept](https://2016.igem.org/Team%3AEdinburgh_OG/Proof)

  [Results](https://2016.igem.org/Team%3AEdinburgh_OG/Results)
* EXPERIMENTS

  [Team Cyanobacteria](https://2016.igem.org/Team%3AEdinburgh_OG/Experiments/Cyanobacteria)
  [Team Rhodococcus](https://2016.igem.org/Team%3AEdinburgh_OG/Experiments/Rhodococcus)
  [Team Fungi](https://2016.igem.org/Team%3AEdinburgh_OG/Experiments/Fungi)
  [Notebook](https://2016.igem.org/Team%3AEdinburgh_OG/Notebook)
* [PARTS](https://2016.igem.org/Team%3AEdinburgh_OG/Parts)
* [SAFETY](https://2016.igem.org/Team%3AEdinburgh_OG/Safety)
* [INTERLAB](https://2016.igem.org/Team%3AEdinburgh_OG/Interlab)
* [HUMAN PRACTICES](https://2016.igem.org/Team%3AEdinburgh_OG/Human_Practices)

  [Silver](https://2016.igem.org/Team%3AEdinburgh_OG/HP/Silver)
  [Gold](https://2016.igem.org/Team%3AEdinburgh_OG/HP/Gold)
  [Integrated Practices](https://2016.igem.org/Team%3AEdinburgh_OG/Integrated_Practices)
* [AWARDS](https://2016.igem.org/Team%3AEdinburgh_OG/Awards)

## Notebook

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  #### January 1st - 31st

  #### Our Humble Beginnings

  Our group members each sign up to be the first Edinburgh Overgraduate iGEM team!
* ![]()

  #### 1st - 14th February

  #### Brainstorming Session

  The team meet together for the first time and brainstorm initial ideas for the project.
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  #### February 15th - 17th

  #### Innovative Learning Week

  During Innovative Learning Week the team head to the Firbush Outdoor Centre in the Scottish Highlands for some canoeing, team building and a quick dip in an ice cold loch! Oh and to pitch our ideas for project too, of course.
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  #### April 6th - 8th

  #### SynBioBeta

  Our team headed to SynBioBeta London, where we were lucky enough to meet Randy Rettberg! We also heard many inspiring talks on the future of the field, met with the Stockholm team and pitched our ideas to Twist Biosciences and Desktop Genetics.
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  #### May 1st - 8th

  #### Exams Done

  With our exams and assignments from semester 2 complete we set about outlining the details of the team's project and identifying a dissertation subject for each team member.

  The team met with Jane Calvert to discuss the stakeholders in the project, including industry, research teams, other iGEM team and the public. The consideration of safety issues surrounding the use of heterologous parts in uncharacterised hosts and potentially unseen hazardous consequences sprang from this meeting and was expanded on throughout our project.
* ![]()

  #### May 9th-20th

  #### First Weeks In The Lab

  Our first day in the lab, where we found our beloved starter kit. The following 2 weeks were focused on literature research, ordering of reagents and kits, lab preparation and finding sponsors for our project. The team also received an introduction to MoClo and training in Benchling, which we relied on heavily over the next few months.

   After receiving our safety forms the rhodococcus team started growing Rhodoccocus jostii on plates. The synechocystis team received the pPMQAK1 plasmid to be used for cloning in E. coli before transformation into Synechocystis.

   The team Fungi made initial cultures from a freeze dried sample and observed growth. Also the P444 plasmid arrived!

   Team MoClo received CIDAR MoClo plasmids from Laura Tuck.
* ![]()

  #### May 23rd - June 3rd

  #### Let The Experiments Begin

  After much deliberation, we finally decided to use the Bba\_ P10500 Phytobrick Universal Acceptor Vector as our destination vector for all (level 0) MoClo compatible DNA parts. The order for the synthesis of DNA gBlocks for our parts was placed through IDT.

   The MoClo team finished their primer design for mutagenesis and began cloning plasmids for template.

   The fungi team designed and ordered primers to clone parts from the P444 plasmid with the new PhytoBrick standard by PCR.
* ![]()

  #### June 6th - June 17th

  #### In The Swing of Things

  Our first MoClo assembly was finally performed using DNA parts found in the CIDAR MoClo kit. However, very few colonies were obtained and therefore our MoClo reaction mixture and conditions were adapted.

   Mutagenesis was conducted to remove illegal sites from the Rhodococcus vectors. Mut2 and Mut3 showed a good result.

   Our fungi team worked on their MoClo protocols in order to start assembling devices with our the designed PhytoBricks and achieved great efficiency at LV0. We also worked on optimisation of transformation protocol in P. roqueforti.

   Jane Calvert and Deborah Scott helped the group to delve deeper in to the social dimensions of the project and human practices, with discussion focused on new questions of patents, GMOs and ethics that powerful and enabling genetic technologies such as CRISPR/Cas have brought up.

   The first microorganisms for the CARE tool were chosen and its secondary metabolites retrieved.
* ![]()

  #### June 20th - July 1st

  #### Halfway There!

  All of our designed parts were shipped to the lab and were then cloned into the PhytoBrick Universal Acceptor Vector.

   The fungi team designed multiple gBlocks fragments for synthesis of the AMA1 sequence that was to be assembled using a Gibson strategy. Problems were encountered both with the transformation of P. roqueforti and the assembly of LV1 parts.

   The data mining for the CARE tool database began.
* ![]()

  #### July 7th - July 12th

  #### Hotting Up In The Lab

  We attended Synbiobeta Activate, a great and informative event that celebrated the official opening of the BBSRC-funded Edinburgh Genome Foundry - the first fully automated DNA assembly platform in the UK!

   Later in this week we also went to the Design Meets Synthetic Biology workshop at the Genome Foundry, where the limits of synthetic biology were discussed in reference to the the capability of the host organism or chassis.

   The MoClo team used Gibson assembly to successfully generate the level 1 MoClo vector for Rhodococcus.

   Meanwhile the fungi team faced troubles with initial attempts to assemble the AMA1 gBlock fragments. On a positive note, all other LV0 parts fungi parts were confirmed by sequencing.

   On a more positive note, Scotland experienced it’s one and only sunny day of the year!
* ![]()

  #### July 18th - July 30th

  #### Northern Meet-up

  This week we co-hosted the iGEM Scotland and Northern England meet-up! It was a great chance to meet with fellow iGEM-ers and share ideas, tips and some pizza, courtesy of The Industrial Biotechnology Innovation Centre.

   LTeam MoClo demonstrated combinatorial assembly using parts library to show that our vectors are functional. Successful transformation of Rhodococcus was also demonstrated.

   During the last days in the lab the fungi team were busy adjusting several protocols to achieve a successful transformation of P. roqueforti and MoClo assembly of LV1 and LV2 devices.
* ![]()

  #### August 1st - August 18th

  #### The Dissertation

  Laboratory work was stopped during this timeframe in order to give us enough time to work on our individual Master’s dissertations. We celebrated the end of our dissertation lab work with some doughnuts and a goodbye and thank-you to Heather Barker for supporting our project.
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  #### August 18th - August 27th

  #### Back To Work

  After handing in our dissertations (what a relief to be done!) we’re straight back to work on the characterisation of our parts in our new home in Chris French’s lab.

   We also said goodbye to the team members who had to return home or start new jobs. The remaining members worked hard on characterising the Sac-6 promoter.
* ![]()

  #### August 29th - September 9th

  #### Collaborations

  During this time we focused on expanding our collaborations with the University of Newcastle and Dundee High School iGEM teams. We also spread news of our CARE tool and engaged 20+ teams in our chassis safety assessment.
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  #### September 12th - October 7th

  #### Home Straight

  Finishing touches for the project and preparations for Boston!
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  #### October 10th - October 19th

  #### Wiki Freeze

  Full-throttle to finalise the Wiki!
* #### Be Part Of Our Story!

### Thank you to our sponsors for their support

[![](https://static.igem.org/mediawiki/2016/7/79/T--Edinburgh_OG--Matin_Sponsor_UoE.png)](http://www.ed.ac.uk)
[![](https://static.igem.org/mediawiki/2016/f/f7/T--Edinburgh_OG--Matin_Sponsor_UoE_Bios.png)](http://www.ed.ac.uk/biology)
[![](https://www.idtdna.com/img/idtlogos/IDT-Logo-2014-sm.png)](http://www.idtdna.com)
[![](http://www.bbsrc.ac.uk/bbsrc/assets/Image/logo.png)](http://www.bbsrc.ac.uk)
[![](https://www.sebiology.org/App_Data/Sitefinity/WebsiteTemplates/SEB/App_Themes/SEB/build/images/logo.png)](http://www.sebiology.org)
[![](https://static.igem.org/mediawiki/2015/7/74/CamJIC-Sponsors-WT.png)](http://www.wellcome.ac.uk)
[![](http://www.gsk.com/assets/img/gsk-logo.png)](http://www.gsk.com/)
[![](http://www.ibioic.com/files/media/IBioIC_Logo.jpg)](https://www.ibioic.com/)
[![](https://static.igem.org/mediawiki/2016/2/28/T--Edinburgh_OG--Matin_Sponsor_Deskgen.png)](https://www.deskgen.com/)
[![](https://static.igem.org/mediawiki/2016/a/a8/T--Edinburgh_OG--Matin_Sponsor_Twist.png)](https://www.twistbioscience.com/)

#### **ABOUT US**

We are the University of Edinburgh Overgraduate iGEM Team, competing in the new application track in iGEM 2016.

[read more](//2016.igem.org/Team%3AEdinburgh_OG/Team)

#### **LOCATION**

School of Biological Sciences
The University of Edinburgh
King's Buildings
Edinburgh EH9 3JF,
United Kingdom

#### **FOLLOW US ON**

#### **CONTACT US**

Email: [edigemmsc@ed.ac.uk](edigemmsc%40ed.ac.uk)

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