Where Now?

I thought I’d fit in a quick blog entry while I waited for my lab supervisors to turn up. Getting used to a lab very different from the one we were based in over our iGEM-ey summer is a weird experience: I’m not sure I understand the concepts of fitting lab work around lectures and not working nine til five with as much squeezed in as possible. I enjoy it, but I don’t think it will ever give me what iGEM did.

Amsterdam was fantastic. We didn’t get to the Boston finals but we know we did very well, and I think we all feel quite proud of the group as a whole and very grateful to Tom for deftly and patiently shepherding us there without getting directly involved in our choices and work output. I sometimes wondered how he stopped himself wrestling the agar plates from our hands and carrying on himself.

An undergraduate degree is all well and good, but for someone like myself who still doesn’t know what to do with themselves when it’s over, I just don’t really have anything to aim for beyond a number. Last Christmas holiday, while I was supposed to be revising, I sort of lost it and ended up reading Sherlock Holmes novels instead. I attempt not to sound trite: I probably would have been stuck if Nic Harmer hadn’t advertised iGEM to us and I hadn’t been in a peculiarly impulsive and confident mood the day I decided to apply. To put my new-found (quite minimal) web skillz to use-

<overemotional>Where would I be without iGEM?!?</overemotional>

I’m currently investigating methods of avoiding the post-iGEM feeling of deflation, and I think the answer is another project which means something to me (it’s going to have to be my third year project). I frankly do not understand why, after the past two weeks of late nights in bed and a workload which took me by surprise, I can’t manage to be happy that iGEM is over. Then again, the team spent several months living in each others’ pockets (I feel like I’m related to Freddie having spent so much time in the lab with him) and mutual enthusiasm for a goal spurs you on.

I might put some Amsterdam photos up if the mood strikes me. Life feels very odd right now.

 

Mary B.

Amsterdam

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.

Mary B.

Hectic

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.

 

 

Mary B.

Homeopathic PCR

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.

Mary B.

Postmodern Ironic

If you want to know what four o’clock in the morning on Friday the seventeenth of August, two thousand and twelve was like, here is my summary:

Wet. Cold. Very dark. For some reason everything was preposterously funny, even when the minibus didn’t turn up until half five. Unusual entertainments were provided on the journey, largely in the form of Becca putting her makeup on which fascinated the guys.

We arrived at the Google Campus in a timely fashion, despite the late minibus. If you haven’t been there yourself or seen photos, I would describe it for you as distressed industrial with quirky ironic features and several throwbacks to an era of stark, aesthetic postmodernism (n.b. my quick online attempt to become an expert on understanding interior design was not successful, but feel free to use these randomly connected words if you also wish to pretend you’re a well-informed person.)

Our presentation was frankly beautiful. Frankly. Honestly. Movingly beautiful. I thought. But really, we have selected three excellent speakers and we didn’t use a boring PowerPoint (no offence, Microsoft. Want to sponsor us…?) And Tom whipped the whole thing into shape. Narrative beauty. Visual delights. Wonder. Excitement. Hooraaaaaaay! It could not get more amazing, until I realise that I get to see the whole thing once more in Amsterdam. Pass me a handkerchief, and catch me if I should faint from joy!

Today I am in a room with Ryan and Freddie. They push the elastic limits of my admittedly small and moderate quantity of the abstract and sublimely ridiculous, with their abject nonsense. Freddie is currently whistling overexcitably. In a minute we will probably have another rendition of the Wombles theme tune, sung for all of the Biosciences building to hear. Bizarre.

Mary B.

Competition

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.

Mary B

Homework

Tom suggested we spend time contemplating potential uses of polysaccharides, in a future where, having proved you could make any polysaccharide, people do. Here is my list:

-The principle component of unicorn horns, imbued with particular dazzlement.

-To make the flowing hair of the unicorn more shiny and wondrous.

-To harden the hoof of the unicorn like a diamond, that it may gallop forth and spread its beauty and joy across the earth!

-To elucidate the value of the Common Agricultural Policy for me.

-Anything that can help make a more lustrous unicorn.

All the other bioscientist iGEMers spend a lot of time imagining their future PhDs and asking me if I’m going to do one. My answer is Most Probably Not, unless it gives me the chance to make a unicorn.

Since unicorns don’t currently exist (to my immense chagrin) I don’t know what I can suggest which is of current use. Polysaccharides already do everything, so where am I expected to start? They cure cancer, give eternal (facial) youth, stop pathogenic diseases, ulcers, diarrhoea, are used as building materials, increase immunity, I’m pretty certain they can be used to increase food security, water purity, love and harmony between all peoples of the earth etcetera etcetera. There’s even a lady making jackets out of polysaccharides (she’s called Suzanne Lee, Google her. As a dressmaker myself, I think this is marvellous). She desperately wishes you could make that bacterial-spun cellulose a dab more hydrophobic. What a shame you can’t. YET.

Here is my suggestion, Tom: slightly more hydrophobic cellulose. Or a hydrophobic polysaccharide to put on cellulose. Or, actually, to rephrase that:

-What they currently do, but better, and not limited by bioavailability.

I totally believe, in spite of not coming up with a suggestion more brilliant than unicorns (although unicorns are brilliant) I have just given the smart-Alec answer which ensures my homework is done. Excellent.

Mary B.

Tantrum

AAAAAAAAAAAAAAAAAH!!!!!

Today has thrown up a few issues.

One of our genes, SacB, kills E. coli by cementing it into its own little coffin of levansucrose, unless it’s extracellular, so Becca is now looking for signal peptides.

Another of our genes, WbbC, has a low GC region. So they can’t synthesise it. They might be able to mutate it, leading to a replaced residue and frame shift which turns half the gene into nonsense.

It’s a disaaaasterrrr! I’m going to sit on the floor and throw a tantrum while Freddie, Alex and Tom sort this out. Partly because the alternative solutions have been largely turned down by IDT and we might have to change the gene for something else. Hello Gibson primer designing, it’s been such a long time since we met, but I have a feeling I will see you soon, like an unwelcome distant relative turning up unannounced on my doorstep. I do not want you, and will only put you in the spare room if I feel there is no alternative.

Mary B.

The Pecking Order

News! We have three new iGEM team members. In a manner of speaking. Two A level students here for a week of work experience, and another who is staying for a few weeks longer. Suddenly we are not the lowest in the lab pecking order. Cackle.

In other news, the Gibson assembly primers have arrived, but the synthesised genes have not. Sigh.