Yesterday was rubbish. Having worked out our operons, we started the task of sorting out which DNA to order for de novo synthesis. Freddie downloaded Gene Designer and spent the entire day Not Quite Destroying His Laptop. Alex found the sequences of genes and sent them to Freddie, and I designed primers for Gibson assembly. Then I designed them again. Then I found out I’d have to design them again. Then someone pointed out (probably Tom, and I can’t believe I didn’t think of this days ago) that we didn’t need primers for Gibson assembly if we were getting the DNA synthesised for us. Now we still have to design overlap sequences of the correct length – I don’t feel like we got anywhere at all yesterday.
We kept feeling we were getting somewhere yesterday and then not quite managing it. We even skipped a lunch break, believing we were on a roll, and we weren’t, so we had a quick YouTube break later. At that point Christine walked in and found us laughing our heads off at really immature videos that really weren’t funny AT ALL (we didn’t find them funny, Christine. We were laughing because we disapproved). All that effort and everyone thinks we’re slackers. Sulk.
On the plus side, Ryan clearly isn’t a slacker because apparently he’s been staying up until ungodly hours of the night working on the wiki and it’s paying off. Good work, wiki team – it looks really neat. Hopefully it will be online by tomorrow. Then I can play with it. Press buttons ’til my heart’s content, and imagine I actually contributed towards that. Heh.
Yesterday we found the forum coffee shop is, unsurprisingly, the location most conducive for inspired thought. I’m all up for moving there permanently. We could get them to sponsor our iGEM team and set up our lab on the table in the corner.
While there, we discussed our gene assembly and cloning strategy. A few days ago we discussed this with Nic too. Avoid restriction enzymes, he said. Gibson assembly is brilliant, but don’t use it for the entire thing.
Thanks for the advice, Nic. The good news is we don’t want to use restriction enzymes. The bad news is we’re using Gibson assembly for the entire thing. You stick all your DNA in one vessel and ignore it for an hour. What could be more appealing? Provided it Actually Works (and it looks more likely to than biobricking or anything else we’ve looked at) then we don’t have to mess around trying to get a complete plasmid for two weeks.
We also got an overview of what everyone was working on yesterday. We’ve splintered off into separate tasks, so it’s quite nice to understand what the group is up to again. Liam, in his mysterious absences, turns out to have modelled gene expression, and while I was busy being obnoxiously unimpressed with his plasmid design (it was practically the same as ours) he meekly pointed out that we’ve been looking for the wrong sort of promoters, which was a bit of a bolt from the blue. If he hadn’t pointed that out, our project would be screwed. Liam, we owe you one.
Ryan vanished to the physics tower yesterday and worked on the wiki most of the day, as far as I can tell. I am reliably assured that the physics tower is widely known as The Eye of Sambles after one of the eminent professors there. In my mind, however, it has become ‘One-Love’s Wizard Tower’.
We are having a sedate morning in our Byrne House bolthole. Ryan, Andy, Alex C, James and Alice are hard at work on wiki stuff and filling out applications for young-bright-things conferences. Alex B. has trimmed down our list of 128 appropriate glymabobs (glycosyltransferases) to 20, partly through scientific reasoning and partly by picking the names that we liked most. The progress of this is hampered slightly by Becca’s sudden fascination with Alex B’s duckdowny hair. She strokes it regularly. She’s currently rubbing her face against it. Alex continues making brave progress in spite of such opposition.
Liam hasn’t actually surfaced yet – we don’t really know what he’s doing. Maybe he’s perched on a library shelf somewhere.
The room is punctuated regularly by Becca’s guinea-pig laugh. She wants to change it to something more sophisticated. Wouldn’t be half so funny.
Our aim is – To design a system to synthesise bespoke polysaccharides from E. coli.
It’s nifty elaboration on our logo tagline ‘engineering the fourth polymer of life’. It completely fails to assist when yet another person asks ‘what’s the use of polysaccharides?’ (my short answer is always vaccines. It impresses people). Sounds cool, though. And why participate in a Synthetic Biology competition if you don’t want to sound cool?
Speaking of logos, we have one! Sort of. We have two, which are brilliant, and Ryan and Alex C. are currently having a logo-off at the other side of the room. Who can get the most impeccable placement of the letter e? Who has the best colour scheme? It’s getting hairy. Ryan-the-fencer will get his foil out soon while Alex will resort purely to his bare and livid fists. The window is open, my escape is planned. If Liam has not yet planned his emergency route, I won’t have time to help him. So long, sucker.