Notebook

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.