Notebook: Week 1

Aims For This Week

In the upcoming week we will be learning the skills to implement the many ideas we have generated over the last few months. This includes a tight schedule of exciting talks by advisors from various fields, to inform us about various topics relating to our project, and lab-training in the UCL’s Advanced Centre for Biochemical Engineering (ACBE). We hope that by the end of the week we will gain the skills to begin our lab-work, and will have some guidance from our advisors as to how best to proceed. In particular, we look forward to meeting Paola Gomez-Pereira – a specialist in marine microbiology from the National Oceanographic Centre at Southampton University.

Monday

General Meeting – What is left to design? The team met early to discuss issues remaining in our project. Our particular focus was to find a means to prevent plasmids from our bacteria entering the marine ecosystem (Containment Module). Bacterial conjugation – the key means of exchanging DNA – is our primary target, but minor forms must also be included.
The team met later for a talk from Elena Pallari - a participant in the UCL iGEM team of 2010. She advised us about managing an iGEM team efficiently, and offered to hold weekly meetings to support us as we progress. Following this, we underwent a reminder of the safety protocols for the ACBE labs, and a brief talk on the basics of synthetic biology.

General Meeting – Reviewing Biobrick Construction. The team met with our supervisor Darren Nesbeth for further discussion of biobrick construction and, importantly, to narrow down the selection of names for our project. A vote identified three popular names – Plastic Republic, Syntopia and Biotopia. A poll was set up on our facebook to see which was most popular with our facebook followers.

Tuesday

We met early for a talk on the basics of synthetic biology, and for an introduction to Gibson Assembly, given by Ben Mackrow. Ben has a lot of personal experience of using this technique, and gave us a lot of useful advice about the benefits and limitations of such technique.

Press Team Meeting – What Should a Press Kit Contain? The team met to discuss how we can convey our project to the Press – in particular whether it would be best to place the focus on the problem of microplastics, or the concept of an island as a solution for this problem. For the press release, and for our other forms of media, we have decided to focus on the island. Though an ‘island’ it is an illusory endpoint to our project – it is highly visible, and will foo idea that synthetic biology can be used to improve the state of the planet.

Construction Crew Meeting – Conjugation. The Construction Crew continued their search for a way to prevent conjugation. They discussed ‘geneageddon’ - a theoretical biobrick enabling bacteria to secrete nucleases, which will digest any plasmids released during cell lysis. Also, they considered using the Imperial iGEM 2011 toxin/antitoxin system to prevent gene transfer by conjugation. Our GMO would carry a toxin gene on its plasmids and an antitoxin gene on its chromosomal DNA. Upon conjugation, only the toxin gene would be delivered to the wild-type recipient, and so any conjugation between GMO and wild-type would be lethal for the wild-type. Spread of genetically modified DNA would therefore be prevented. In particular, we aim to combine these genes on a single plasmid, and therefore improve the Imperial biobrick.

In the afternoon, there was Wet Lab Training. We were trained to use various equipment around the lab, and how to make important solutions for our experiments. In particular, we were trained to carry out a restriction enzyme digest, and how to inoculate bacteria.

Wednesday

Today we had a very informative presentation by Paola Gomez-Pereira regarding her research into marine microbiology.

Modellers meeting - Using models to inform experimental design. This afternoon there was a meeting between computer Modellers, Advisors, and the Construction Crew to discuss specific variables required for modelling our experiments.

This afternoon we met for further wet lab training, particularly for the process of miniprep for transformed cells, and ‘nanodropping’.

Wiki meeting – implementing the wiki. Prior to this meeting, the Wiki Team had discussed ways in which to make the wiki coherent, and had developed a number of new ideas and designed a number of layouts. This evening, we began writing the content of the wiki, and the process of creating the site.

Human Practice - This afternoon we undertook filming of the first episode of our documentary, with Jazz Croft interview each team member about their experience of iGEM so far.

Thursday

This morning we had a talk from Erick Ramos - a member of the ACBE lab that helped on a previous iGEM project, and gave us advice about iGEM and an update on his current research on biobricks. We also discussed with Kate Oliver - Commmications, Marketing and Events Organiser - the practicality of our human practice ideas.

Friday

This morning we had a talk from Yanika Borg - a member of the ACBE lab who explained the key concepts of computer modelling, how we can represent our modelling, and how she has used it in her own research. This was followed by a talk by Alex Templar who described his work on ultrafast PCR.

The team also recieved the great news that our proposal for the Rathenau Debate has been accepted.

Construction - The Construction Crew worked hard all afternoon to produce a final document of all the biobrick circuits.

Reflections

We survived training week! This week we've had a lot of informative and insightful training lectures and workshops and we are now ready to go. We have talked to some great advisors who will help guide our project, and we are particularly excited about using roseobacterium - a marine bacterium Paola (our fantastic advisors on all-things-ocean from Southampton) suggested as a chassis.
End of week: Construction plans finalised, wiki started - Week 2 can come.

Friday evening update: The Rathenau Institute accepted our debate proposal for the "Meeting of Young Minds". Yay!

Team:University College London/Notebook/Week1

From 2012.igem.org

Contents