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From 2010.igem.org

Monday 5th July - Dems dems dey are!

At 10:30 we're meeting with Qaiser in the lab to plan some more about the project.

Meeting with Qaiser went well. We made a list of everything that was needed to buy for the lab work. Lunch in City View Cafe where we began filming. Nii provided some interesting information about his family history, which would be nice to look through again on video (not all his statements were true apparently). The afternoon was spent designing a a layout for the wiki with Andy inventing new lyrics to Rhianna's 'rude boy' song - a version probably best left until after the watershed. Our ideas for the wiki have now taken a comic book theme - image development in progress. The layout should be soon to follow once the images are produced. An important part of the afternoon was spent planning the project and what exactly needs to be done within specific time frames.

Word of the day: Igemdems

Tuedsay 6th July – Lab rats

The team's first proper lab day! We began with the boring part of washing apparatus, then by making liquid broth and agar cultures for the E.coli to be grown. As we waited for the equipment to finish autoclaving, we ventured to the IC to continue some more work and plans for the Wiki - note that more photos are now available on the 'team' page - mainly ridiculous ones from Facebook. In Steve's absence (from having to run in Glasgow), we chose an image on his behalf, which he's still yet to notice.

At 2pm we went back down to meet Qaiser to add Rosetta and DH1 alpha strains of E.coli to liquid media and agar plates (some with ampicillin). Basic microbiology technique was demonstrated to those who haven't had much experience of the lab. We also put Kate in control of the video camera while we were doing this - our collection now includes a video of Tom labeling ~50 plates... perhaps more work needed to be done on the lab videos.

After labelling, spreading and leaving to culture, we visited Catherine with Qaiser to discuss our progress and plans. Catherine seemed pleased, although following some of our questions, we left her pondering about what her superpower could be. Will she reveal this in our next meeting? Stay tuned to find out...

Wednesday 7th July - Maths, Jamboree and art.

10:00 AM we began the day by mixing up some samples with glycerol and putting them in the freezer. We were then given plenty of calculations to do by Qaiser, which took a while to warm up to, but we eventually got over our maths allergies & worked out the solutions. We also worked out which compounds we were missing from the buffer solutions, so these were added to Qaiser's list of things to buy.

In the afternoon, we decided to return to the IC to organise for the Jamboree and work on some more wiki. Visa 'waifer forms' were located and some of the details about going to Boston were done. 2 of the artwork buttons for our homepage were completed, 8 more to go!

Thursday 8th July - Planning

Meeting with Qaiser in the morning about the meeting in the afternoon. Unfortunately we couldn't do any more labs, as we're missing the DH5-alpha strain, but we had a funny email from Kate to lighten our moods. It read:

Hi all,

Hope you had a good gay yesterday - I'm still ploughing away with this work which I have to hand in tomorrow, but will be there tomorrow fingers crossed!

Hope it's all going good...

Kate

Note the spelling mistake. Yes, we are immature for laughing.

We worked through lunch ordering parts and plasmids. As we have not yet found the CqsA plasmid that 2008 used, we ordered another sample from the Bonnie Bassler institute, in the hope they'll once again be kind enough to supply us again. At 2pm we met with one of our microbial systems experts, Professor Jeff Green to talk about our idea and whether everything makes sense. He confirmed everything seems in order, but also liked our idea of trying the system two ways.

We should probably record how far the planning has gone - so here goes: Plan BarA is a sensory histidine kinase that sits in the E.coli cell membrane. CqsS is a cholera sensory histidine kinase, which detecs cholera autoinducers (quorum sensing molecules secreted extracellularly). We want to swap the outside sensory domain of the BarA protein with the outside domain with CqsS, then put the recombined BarA gene (with CqsS extracellular domain) into a high copy plasmid.

Meanwhile, we want to put a visible reporter, one of Cambridge's vibrantly coloured E. chromi protiens into the operon affected by the BarA internal kinase mechanism. This will be made in a BarA knockout strain (which we've ordered and hope to receive soon).

The alternative, which we will also give a go, is transforming the whole cholera CqsS system into E.coli, again with a visible reporter downstream.

When we arrived back from the meeting, productivity took a gradual decline and instead we finished the day discussing music and listening to Rhianna on youtube.

Friday 9th July - Andy's Philosophy

The team meet with Professor Artymiuk to talk about the best point to create the fusion protein. We met Qaiser in the morning to sum up our (very successful) Wednesday afternoon. 11:30 we went to our meeting with Prof Artymiuk, who agreed to help us with looking at the chimeric proteins.

Afternoon time we were taught another round of human practices by Andy. Today the main focus was on identity. This began with a brief history of how the philosophy of identity and language has changed over time, including insights from Plato (citizens and the noble lie); Descartes (demons and 'I think'), Nietzsche (leaves, saying yes!, creating our identities as we make them, the superman); Saussure (how perception itself can be based on language and the connectedness of meaning); and Feminisms. This was important for helping us understand how identity is made up as we go along - the meaning of something cannot be solidly defined, and is always within other related meanings that already exist. We'll have to have a think about how we can use this to help us approach our human practices questions about iGEM identity.

Barbecue in the evening at Caz's - perfect opportunity for team banter and to take advantage of the Sheffield sunshine.