I’ve just been given a complimentary cocktail by the waiter of the top floor hotel bar. It’s apple-ish, and reminds me of Christmas. If I drank, life would be amazing right now. I’m pretty sure I can see half of Amsterdam from the window; very sparkly.
It would be nice to say that we are all flawless ambassadors for the university, but though we’re trying so hard (we really are) somehow some of us look like less-than seasoned travellers. After haphazardly making our way across the city on the metro system, we managed to find our hotel (it’s fairly hard to miss, i.e. tall and ugly) somebody accidentally got us two extra twin hotel rooms. Fools. After ten hours in the foyer it was sorted out.
The hotel is great when you have the right number of rooms. The room plays seductive music as you enter for the first time and the TV addresses you by name. Stellar. We’re less fans of the public transport system, which has thrown up a few hurdles. Our beloved supervisor, Tom, rocked up a day after everyone else (he’s a busy man) and got stuck in the metro barriers. Did we rescue him? Yes we did.
The trains run like clockwork, from the engines to the doors, and even more enjoyable than rescuing Tom was watching as the whole team piled off the train apart from Becca, whom Raf attempted in vain to rescue. I wish I had photographed her expression as she left us staring on the station, but I did not.
I could tell other stories of our social inadequacy, about failing to get food from a restaurant or about butchering the Dutch language in public places, but to be frank it’s been a crazy day and I’m knackered. Time for bed: we’ve got some sort of presentation tomorrow morning apparently. Wonder if that’s important.
It’s been over a month since I last put a post up, but I swore that if I didn’t have time I would make sure I blogged something after the wiki-freeze. Actually it’s a bit misleading to imply I haven’t had any time, I took two weeks off on the advice of a Doctor, two Professors and My Mum (you don’t ignore advice like that). Boy am I glad I did – iGEM life has been mental when I’ve not been taking time off it. I’d be misleading you again if I didn’t mention that I loved it anyway.
The last two weeks I spent in the lab (I call them Jill and Melinda) were chaotic. In a whirlwind of determined fourth attempts, unexpected successes and camaraderie, we all became slightly peculiar. There was a day when it was imperative that we spoke like farmers, and another day when we giddily carried out nearly 100 minipreps. Alex C. began to prod me conspiratorially at regular intervals. I gained a slight touch of paranoia that our faithful little E. coli which we boiled up for proteins would return from the dead on a destructive path of vengeance. Freddie and I once lost it completely and giggled wildly at Ryan because he was sitting on a chair. Ryan then made it his artistic pursuit to sit on the chair in a fashion befitting a physicist (he put his hands on his stomach and looked thoughtful). We all got disproportionately excited about running an SDS-PAGE. It all seemed reasonable at the time.
The preparation for the wiki-freeze was a similar experience, but since it was mostly carried out on computers from different locations, the hysteria was expressed more through YouTube videos and memes, which Ryan does as a matter of course anyway (it occurs to me that Ryan does a lot of things as a matter of course). I hope Ryan spends most of today in bed – he got very little sleep while putting the wiki together. Tom probably shouldn’t get out of bed either, I think the left-til-last-minute stress may have been too much for him.
What do I do with myself now? I’m expected to settle into uni life again? What is this?! I can’t cope with the inconsistency: a day should consist of going to the lab and seeing how long you can stay and how much you can achieve before you automatically get locked into a separate corridor from your house keys. On the plus side, we go to Amsterdam in a weeks time so it isn’t over yet, and what’s more I have a third year project in which, I am told, I will be taught cloning and PCR…heh heh heh.
Anyone who has purified genomic DNA and tried to PCR a gene out of it will probably be familiar with the notion of diluting it a lot to get your gene out. Being undergrads, we were not. Having spent several intense days fruitlessly increasing the concentration of DNA to frantically try and get The Gene (a gene which we needed…four weeks ago) we went on the long pilgrimage to the interweb forums of sage advice.
Naturally, because it’s so obvious, if you want more product (or any, in our case) you reduce the amount of DNA. It didn’t work. We swallowed our pride and got help from Christine. (She always dresses so well, and seems to like purple. Kudos.) She told us you sometimes need about one part per million to get anything out. Homeopathic molecular biology! Crazy. Armed with this knowledge, we strode back into the lab and began the fight. The PCR machine broke.
We’re taking this all in our stride. This is meant to be the ‘Nothing’s done. Nothing works. It keeps going horrifically wrong. OhmygoshIamsuchafailureeveryonewillhatemebecauseIcan’tbiobrick’ stage. It’s cool. We deal with it. Because otherwise, we would go deranged and Freddie would start living on the doorstep of the innovation centre cafe like a peculiar moneyed tramp while Ryan…continued to be Ryan. In any case, Freddie and I had great success with our first construct. Did I mention? It was, like, sixty bases long? Or forty. Maybe more like two. And we still got them to stick together anyway. We’re amazing, we just need PCR machines to stop conspiring against us. The tossers.
Tom yesterday told us to reserve our competitiveness for the other teams at the Amsterdam jamboree. In spite of this, I believe he is quietly stirring us with a proverbial pipette tip.
Alex and Liam have embarked on the task of cloning a gene out of the BL21 strain, while Freddie and I seem to have digested two fragments of 130 bp and 12 bp. Using a mere ten minute digestion time and 3A assembly, we managed (possibly) to get a complete working plasmid out of it. The jury is out as to which is more impressive. Team Alex has yet to finish, Team Freddie needs sequencing to prove if they managed it.
Tom, meanwhile, is watching from afar and occasionally suggesting why one might look more impressive than the other. If he comes back to us with an opinion poll from all the molecular biologists in the lab, I will not be surprised.
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.
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.
Having watched the slow, helpless death of our creative minds after agreeing to give our lives over to science, we’ve called in the experts to help reignite the artistic synaptic pathways!
It’s not what you know, it’s who you know, so of course having George’s wife Marian on call as our professional artist and design consultant is an amazing treat. A couple of fun-filled hours later and BANG we have an amazing new, concentrated project title and several logo ideas to choose from…… and not a word of marketing speak was spoken, thank God! Many thanks Marian!
In the typical style of our team, we had a little chat about how polymers have been created and used for umpteen years. Then we decided everyone else was going about it completely the wrong way, and we had to … Continue reading →