Team:Sheffield/Notebook

1. Self healing pipes - a method for pipes to 'recover' from damage using bacterial biofilms.

2. Water desalination - how we can use specialised bacteria to lower the salt content of sea water to make it drinkable.

3. Lowering nitrate levels - using bacteria to lower nitrate levels in rivers, helping to promote healthy living conditions for fish

4. Carbon, nitrogen and phosphorus ratios - alteration of these using bacteria to inhibit growth of pathogenic bacteria

5. "Bactoshave!" - the bacterial shaving system... (patent pending)

Wednesday 23rd June - A small meeting between Thomas Leach, Narmada Herath and Steven Garrett comparing 2006, 2007, 2008 and 2009 IGEM projects from other universities. Particular interest was taken in microbial fuel cells, as these may be adapted for desalination. We're hoping to look further into exploiting this to desalinate samples of water possibly in cartridge form

The projects using search and destroy bacteria and self healing pipes were also considered in some detail. These will be discussed further during the next meeting.

The Wikis we noted were: 2009: - Lethbridge, City College San Francisco and Missouri (bacterial fuel cells) - Columbia (sea water salt detection) - Wisconsin (increased resistance to salt) - Brussels (E.coli glue) - Newcastle (ion sequestering)

2008: - Heidelberg (targetting biofilms in pipes) - Brown (electrical reporting system) - Lethbridge (Search and destroy harmful hydrocarbons) - Calgary (pathogen killing machine) - Illinois (cholera detection) - Newcastle (B. subtillus as a biosensor) - Edinburgh (producing starch from cellulose and biomass)

2007: - Columbia (biosensor) - Glasgow (fuel cell) - MIT (clearing mercury contamination) - Turkey (pH dependent metal ion transporter) - South Utah (cyanide biosensor) - Brown (Lead contamination)

2006: - Edinburgh (sensing arsenic in drinking water)

Monday 28th June - 10 week IGEM placements officially begin. Our next meeting is planned aiming to narrow down the project to something realistic and attainable during the 10 weeks.

The session was attended by all the undergrads and Andy. A twitter account was set up - already Steve is addicted. Catherine received lots of our quizzing emails. We emailed Xia Huang, regarding the paper Cao, X., et al. "A New Method for Water Desalination Using Microbial Desalination Cells." Environmental science & technology 43.18 (2009):7148-7152. We emailed Environmentalbiotech.com to find out more information about their grease eradication system and also Sheffield Forgemasters about their waste desposal methods.

A few ideas about order and layout of the wiki were talked about during the meeting, with some designs being drawn up for a logo. We've decided to go with 'Drip & Drop'... or 'Drop & Drip' the water droplets as team mascots (still a BIG ongoing debate between a few members).

For desalination we decided an in-situ method would be most realistic. We would probably require well characterised halo-tolerant bacteria that can form a biofilm on an electrode. The system in theory would have a middle chamber where salt water is placed. Two flanking chambers would contain opposite electrodes sepatated from the middle chamber by selectively permeable membranes to either anions or cations.

A broad area we looked at on this day was the destruction/removal of pollutants/pathogens from water supply. Our potential targets included iron, lead, nitrates, pharmaceuticals, fats, oils, grease, sewage, various pathogens e.g. cholera and toxins.

Final note - team lunch of pizza at Rise @ the Hallamshire is definitely something worth considering again.

Tuesday 29th June - Today we got a guided tour of our labs for the very first time courtesy of Qaiser Sheikh. Exciting stuff!

We looked at the proteins TonB and ExbB for potential use in our desalination cell. The fuel cell desalination idea was adapted to just a desalination cell consisting of 3 chambers without electrodes, with chambers following the same order as before, but this time with a chloride sequestering bacteria in once chamber and a sodium sequestering bacteria in the other. This still needs some research to work out how realistic this idea is. We liked Newcastle's project from 2009 and considered how Bac-Man might be able to aid our project this year in this area.

Removing nitrate in sewage treatment plants may also hold potential. We would be looking at ways to lower the amount of nitrate released by the plants using novel bacteria with a consortium of enzymes to 'mop up' the excess. The process could also be energy productive, opposed to energy consuming (where aeration is concerned).

Finally we're looking into completing the work done by the Sheffield 2008 team. This was a project aiming to detect the presence of cholera, however due to complications the team could not complete their project.

Lunch today - sandwiches in the sun in Weston Park. Tom, Narmada and Caroline revealed their vegetarianism to the rest of the group *gasp*.

Wednesday 30th June - 09:30 start to try tie up loose ends on initial ideas before the 14:00 meeting with team advisors.

Okay, so the 09:30 start went slightly less to plan as we'd hoped, ranging from a few members arriving bright and breezy to those not so bright and breezy ones (Matt "12pm" ford). That aside the morning consisted of drawing up ideas for parts needed for desalination (e.g. ion channels or the 'bacman system' created by Newcastle University). Further work on Sheffield iGEM 2008 was made. We're now in the hope of modifying the system with an easier reporter (e.g. those used by Cambridge 2009's E.chromi). This could potentially give rise to a universal pathogen detector E.coli, with various colour outputs depending on the pathogen present. There is potential to engineer this system in B.subtillus as a proof of principle project to produce a dry, portable biosensor for pathogens.

Following lunch at Interval, we met up with advisors fearing a grilling. Overall however, our hard work appears to have paid off, with all ideas appearing realistic within the 10 weeks (except using fuel cells for desalination, which Greg is having a further look into for us). We're now going to research further the ion channels which might make desalination possible. Improving Sheffield 2008's project was very popular at the meeting - many ideas have now been born from this, so full steam ahead at looking for biobricks tomorrow.

Post-grilling we took some nice photos to go up on here and visited the molecular biology and biotechnology labs with Qaiser. We finished off the day with a round of drinks at the University Arms where we talked about the 1000000 keyrings Steve's ordering, Nii's gloves and performing our Jamboree presentation through the medium of dance.

Quotes of the day:

"Mmm yeah... but try thinking of a good idea instead Krish" - Andy

"I don't get the joke" - Tom

"I think of other stuff in the shower too, but I probably shouldn't talk about it" - Nii.

"We'll just have to go all bioinfornatics on its ass!" - Greg

Trivia: Sheffield's team members are probably quite rare - 3 of the 4 veggies (Andy too) are lefties!

Thursday 1st July - the team say "White rabbit" for good luck. The aim's to look at the catalogue of parts, decide what we need and a create suitable logo. We should check out getting Visas for the Jamboree too. Potential for some Wiki work today - ours is looking a bit scruffy at the moment.

Following the trend so far of 'every other day is a slow going day' we kept the theme going. The morning started with sending out a few emails and a bet for who would be the first to reply. Catherine won the race and Caroline lost a bet. A look was taken at the biobricks from the registry and the important ones were noted down.

Following a working lunch, we held a logo design competition with a 10 minute time limit. Of the designs, we managed to produce a 'killer-coli' (complete with blood of the Cholera it had just dismembered... lovely), a 'Dr. E.coli' (stethoscope included), good vs evil microbes under a microscope and numerous others. As all designs seemed quite well matched in skill and imagination, we decided to postpone deciding on a winner for another day and let Andy have the final verdict.

After the excitement of all that drawing a few of the team headed home. Tom and Steve paid Qaiser another visit to have alook at some of the 2008 samples in cryogenic storage and to talk about some more possible ideas to expand the project. Ideas included thinking about different ways our biosensor could be used and apparatus that would make this successful. We also talked about the hybridized protein we're hoping to create - sequence allignment suggests this should be okay, but there's only one way to find out for sure, by testing! Next stage is to identify the region that needs to be annealed from the cholera receptor protein.

Productive day overall, but chances are tomorrow will be more poductive if our trend so far is anything to go by.

Friday 2nd July - normal 10:00 Am start. As predicted, the team were more awake and attentive, it was "Fantastic Friday" after all. The day started with some explanations of the main stages of our project on the white board. A few parts were ordered in the morning, now looking forward to receiving our first biobricks!

~12:00 we were joined by Andy, who was clearly impressed by our logos... okay minor exaggeration, he just laughed a lot. Following this though he reminded us of our initial 'drip-drop' idea with his own design. We'll get that created on photoshop pretty soon hopefully.

After a a lunch of bread cakes in the park, we started on our first 'human practices' lesson from Andy. We learned how science is essentially exists from human deduction, inductive observations and how science is now thought to be falsification based. Over the next few weeks we're hoping to learn and show on our wiki how we understand our own identities, roles, status , diciplinary identities, project roles and differences between each other within the realms of synthetic biology. Are we students? Are we synthetic biologists? Is iGEM a competition or a collaboration? Is Catherine our peer or our boss? These questions we hope to answer in the form of interviews as the project goes along.

A lot to take in this week, but it's been a fun one. Plenty of 'in-jokes' going on to keep us lauging for the next 9 weeks. Next stop: the lab!

Monday 5th July - 10:00 am start again. 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 cithy view cafe where we began filming. Nii provided some interesting information about his family history also, which would be nice to look through agaiin on video (not all true apparently). The afternoon was spent designing a layout for the wiki with Andy inventing new lyrics to Rhianna's 'rude boy' - a version probably best left until after the watershed. Our ideas for the wiki have now taken a comic book theme - images now 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

Tuesday 6th July - 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

'Waifer' forms

Thursday 8th July - 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 DH1 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.

notebook

You should make use of the calendar feature on the wiki and start a lab notebook. This may be looked at by the judges to see how your work progressed throughout the summer. It is a very useful organizational tool as well.