Thursday, 16 February 2012

Facebook, Sponsored Events, and the Project - a Quick Update

Thought we'd provide a quick update on events, as things have been moving at a fast pace over the last few days. In the beginning, we assumed that after the application for our stipend we would pretty much have nothing more to do (except of course the mountain of work that is our second semester modules) between now and summer than research and perfect our actual project. Currently, however, the project plan can be summarised as follows: find the genes encoding the proteins responsible for the polystyrene degradation, clone them out and stick them into an expression vector which we can induce to make a high concentration of the aforementioned proteins.

Of course, we know full well that there is a lot more to it than that, and that we have much more research to do and many kinks to iron out before summer. Indeed, there will potentially be many unforseeable obstacles that we will simply have to tackle as we encounter them, but that's another story. For now, however, there is our project (we do have a few more details, both in previous posts and our own notes/minds, and they will be collected into a seperate page on the blog shortly - watch this space).

So why is our project idea not yet as perfect as we would like? Well, it's not through lack of effort. The problem is that the direction of much of our effort happens to be elsewhere - namely, fundraising. The stipend we receive, if we receive it, will cover us for living expenses over summer. However, there are other considerations; resources, flights and accomodation for the jamboree(s), attendance at the jamboree(s) and - most pressing of all - $2000 (just under £1500) for registration by the end of March. We have had meetings (both amongst ourselves and with our supervisors), hijacked other meetings, produced leaflets (which Dr. Badge kindly agreed to hand out at a lecture on Dolly the sheep earlier this evening), waved collection tins at people, and organised various fundraising events, including a sponsored walk of potentially 25 miles (and, potentially, in costume - if it raises enough I will be wearing a bright red full body lycra "Morphsuit" and a Stetson) (there's a donation button on the right hand side of the page) and an online quiz (again, watch this space).

The biggest problem, in my opinion, is the fact that we cannot yet set up our nice professional Wiki page; reason being, the page is provided by iGEM after we register. The reason this is problematic is because we would like to write to a number of businesses to offer them the opportunity to sponsor us, but we don't want to do that without the Wiki, which of course we will need the $2000 to obtain.

So in summary, any donation you are willing to make will be gratefully received. Also, sharing the blog with others is a great way to help us get the message out there, and our official Facebook page, set up just today, is a good way keep up to date with events and raise our online profile. More information about the walk can be found at the top of the page, and there is also a link to the Facebook page on the left.

Anthony Cox - Vice Project Leader.

Tuesday, 14 February 2012

The project

The project
- Background

After countless ideas, decision, research and discussions about the pros and con's of various ideas, we whittled the list down to a few Key ideas, involving detection of prions (a form of infectious misfolded protein), production of bio fuel such as hydrogen gas from waste products, and polystyrene degradation. After talking to our supervisor, Dr Badge, who also brought a few of his own ideas to the table, we decided to go with designing a bacteria to degrade polystyrene. However until that point, we were unaware of any known bacteria that used polystyrene as its sole carbon source. This set us on the laborious task of trying to find mechanisms of degrading the individual parts of the molecule. Breaking it down in to pieces that the normal bacterial mechanics could use, for instance the fatty acid degradation pathway. As well as methods to take in the molecule and deal with the benzene ring. This process resulted in a bundle of pieces of paper and lots of worn out pens next to text books, but leaving us with a hypothetical pathway with lots of "well hopefully that could do that, it looks like it should" statements thrown in. Nevertheless, Wikipedia isn't always correct. After a somewhat lucky Google Search we found a article from the African Journal of Microbiology Research, whereby it listed 4 very slow growth strains of Bacteria which had been isolated and sequenced, giving us a much better start and project idea.
This lucky search along with a few other papers we then looked at, changed around the project and made it into a much more feasible idea. However your probably thinking now, "well there is a bacteria that can do it, why do you need to do anything with it?" This bacteria has out competed its competitors as it can utilize the carbon source being polystyrene while the others have not. Making it a evolutionary winner as such even with such a slow growth rate. Consequently as it is so slow, it would never be a feasible method for removing or utilizing polystyrene for any industrial purposes as it would take far far too long. Which is why we came up with our revised project.
More to follow Shortly.

Christopher Morton - Project Leader

Thursday, 9 February 2012

Where it all began

First news about this opportunity was on the 2nd of January from a fellow undergraduate at the university, Anthony Cox, and from here there was a avalanche of ideas, questions, what if's and could we's. This all started from one little Facebook message with a link to the International Genetic Engineered Machine competition (iGEM for short), which now with all fingers crossed will be the sole aim for Summer 2012 to be completing this mission. The mountain which we needed to climb was that of a very quickly approaching deadline on the 20th of Jan for wellcome trust stipend funding, with at the same all of the parties involved having at least 2 if not 3 exams during that final week. Upon first hearing of the summer placement idea i was skeptical of it getting off the ground, however it leaped up and decided it would start to gallop through the efforts of the first 5 confirmed members of the team, being Anthony Cox, Nathan Hanna, Luke Thompson, William Harrison and Myself.
Our first challenge was to find the much needed 2 supervisors in order to have a hope of starting a team. This was achieved by a very lucky email to Anthony's Personal Tutor at the University Dr. Badge, who coincidentally had previously been wanting to enter a team and was extremely enthusiastic already , almost by fate we secured our first. Nevertheless we needed a second, so more emails we're sent to contacts in the university, eventually hearing back from Dr Badge that we had secured another supervisor from the genetics department.
          Nevertheless we still had other fish to fry, the largest of those being trying to come up with feasible ideas for a project. After exploring the countless avenues of fuel production, animal feed-stock production, bio-degradation, improving the readability of bio-sensors, 3rd world bio-sensors and bio-sensors to detect prions (A form of protein in a misfolded form making it infectious), we came up with a list of many different ideas each researched to a basic level. At the same time as we were doing this, we were also sending emails to fellow friends at the university on the biological sciences course's, as well as other disciplines and managed to recruit other fellow undergraduates to fill the remaining 5 places on the team. Which on its own was quite a feat with many solely concentrating on revising for the 1st semester of 2nd year exams, which i can assure you, needed revising for. However through combined efforts of the first 5 confirmed, we somehow managed to pull it all off and presented our ideas to our supervisor directly after the first exam, he also having ideas of his own. From this meeting the now main idea was finalized and we proceeded to fill out the form for the Wellcome trust stipend.

Christopher Morton - Project Leader.