The Epiphany Room

It’s a quiet Wednesday morning. In the spirit of British summer, it is tipping it down outside, and soon I’m going to have to walk up to campus in that weather. At the moment, I’m working at home. One of the slightly unfortunate things about being the first iGEM team for the university is that I’m not sure people know we exist. Despite having been delightfully able to sail into research without having to tell funding bodies how important it is first, we sometimes aren’t given a room when Researchers-Of-Vital-Things need it instead. As such, someone More Important Than Us has booked room 108, and our second home of choice isn’t free until the afternoon. Maybe if we get to the Boston final they’ll donate a room to next years team. Maybe they’ll call it the Mary Beton Synthetic Biology Epiphany Room (Note to College of Life and Environmental Sciences – the room name really has a charming ring to it, doesn’t it?).

We had another work experience student with us yesterday. She’s called Sophie and she’s lovely. It’s absolutely brilliant practise for us to have loads of people to coherently explain our concept to, which is why I always leave it to Freddie.

Some unmentioned delay is preventing our last few genes from reaching us, so we haven’t been able to really get started on the core of the project yet. With only four weeks to go, I have not got a good feeling about this…

 

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.

Minions

Our genes have arrived! Yaaaaay!

Well…two. Of four. One of the missing genes couldn’t be synthesised without substituting a leucine for a proline, a change which Christine darkly predicts will doom the protein to inactivity. We’re all convinced she’s right, but we’ve ordered it partly as a backup plan, partly out of curiosity.

Embarrassingly, we overlooked the fact that our gene (WbbC, in case your interest is piqued) is present in Bl21 strains, so we could have just got it from there on the cheap in the first place. Fail. Highly convenient fail. Consequently, we will have two slightly different copies. Fingers crossed one actually works.

The work experience girls leave tomorrow. Sad face 😦 – but on the plus side, they make our lab skills look terrible, so although there are two people fewer to talk to in the lab (and they’re really lovely so it will be a shame to lose them) we will at least only have postdocs and professors around to make us look bad, not A level students too.

Ryan is leaving on holiday as well this weekend! For three weeks! How outrageous! He’s supposed to be my lab minion, how can I successfully construct an operon via two assembly methods without a minion?! On the plus side, we gain Andy back. Hoorah!

…I’ve just decided who my new minion will be.

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.

The Cunning of Dr Tom.

Three things I did today:

  • Had a PR meeting.
  • Bulked up some of the parts in the lab. Hopefully.
  • Emailed a man called Hugo.

 

The PR meeting was interesting. As a dewy-eyed undergraduate, wowed by the glossy prospectus, manicured website and towering buildings of mighty academia, you don’t see much of the work that goes into representing it all. I’ve seen some of it now. The PR people we met were savvy and asked lots of pertinent and useful questions. I feel it was another step on the road to getting our project regimentally organised, which Doctor Tom has, I feel, also sneakily been doing in his own mild-mannered way. He keeps subtly designating tasks and subverting our natural rebellion against structure. Cunning. I feel we can overcome this yet.

We got started in the lab! I was dejected to hear that another team submitted a biobrick the other day. Well, we’ve started now, so they’d better hope that head-start got them somewhere. It was only transforming some E. coli, but…Yay! I did science!

Hugo is an iGEM-er from Wageningen University in The Netherlands. We are hoping, rather, for a collaboration with them as their project is vaccine based. Hurrah! More doors and windows of opportunity! Let us leap out of them, and onto the veranda of wonder! (And hopefully not down the unexpected several-storey drop of failure.)

 

Mary B.