Team:Sheffield/Notebook

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!align="center"|[[Team:Sheffield|Home]]
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!align="center"|[[Team:Sheffield/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Sheffield Official Team Profile]
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!align="center"|[[Team:Sheffield/Project|Project]]
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!align="center"|[[Team:Sheffield/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Sheffield/Modeling|Modeling]]
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!align="center"|[[Team:Sheffield/Notebook|Notebook]]
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!align="center"|[[Team:Sheffield/Safety|Safety]]
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|'''Friday 28th May 2010''' - The whole team's very first brainstorm. Focusing on the water industry, we managed to develop some interesting ideas to research further, which include:
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1. Self healing pipes - a method for pipes to 'recover' from damage using bacterial biofilms.
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2. Water desalination - how we can use specialised bacteria to lower the salt content of sea water to make it drinkable.
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3. Lowering nitrate levels - using bacteria to lower nitrate levels in rivers, helping to promote healthy living conditions for fish
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4. Carbon, nitrogen and phosphorus ratios - alteration of these using bacteria to inhibit growth of pathogenic bacteria
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5. "Bactoshave!" - the bacterial shaving system... (patent pending)
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<a href= "https://2010.igem.org/Team:sheffield/preweek1">Pre-week</a> - Very early brainstorming about the project
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<a href= "https://2010.igem.org/Team:sheffield/week1">Week 1</a> - The biosensor project area is decided and plans are made for the upcoming weeks.
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<a href= "https://2010.igem.org/Team:sheffield/week2">Week 2</a> - Our biosensor idea is examined in terms of cell proteins and feasibility.
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<a href= "https://2010.igem.org/Team:sheffield/week3">Week 3</a> - Some progress is made on deciding what genes to order, we practice transformations in the lab and our genes are ordered.
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<a href= "https://2010.igem.org/Team:sheffield/week4">Week 4</a> - We give our presentation in Newcastle and and progress is made in terms of human practices/transformations.
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<a href= "https://2010.igem.org/Team:sheffield/week5">Week 5</a> - Plasmids are ordered and progress is made on the modelling work.
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<a href= "https://2010.igem.org/Team:sheffield/week6">Week 6</a> - Growing up our BarA knockout cells. We conduct most of our human practices interviews and socio-technical circuitry.
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<a href= "https://2010.igem.org/Team:sheffield/week7">Week 7</a> - The wiki template is finished and made live, primers are ordered and the human practices socio-technical circuits are brought up to date.
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<a href= "https://2010.igem.org/Team:sheffield/week8">Week 8</a> - The human practices collage and most interviews are finished. Work begins on the pgaA promoter.
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<a href= "https://2010.igem.org/Team:sheffield/week9">Week 9</a> - We begin characterising the pgaA and hapR promoters.
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<a href= "https://2010.igem.org/Team:sheffield/week10">Week 10</a> - Modelling success, and transformation of the promoters & genes.
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<a href= "https://2010.igem.org/Team:sheffield/AfterWeek10">After week 10</a> - Final summary of our work after the 10 weeks
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'''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
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Previous 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.
 
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The Wikis we noted were:
 
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2009:
 
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- Lethbridge, City College San Francisco and Missouri (bacterial fuel cells)
 
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- Columbia (sea water salt detection)
 
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- Wisconsin (increased resistance to salt)
 
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- Brussels (E.coli glue)
 
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- Newcastle (ion sequestering)
 
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2008:
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[[Image:Sheffield sponsors.png]]
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- Heidelberg (targetting biofilms in pipes)
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- Brown (electrical reporting system)
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- Lethbridge (Search and destroy harmful hydrocarbons)
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- Calgary (pathogen killing machine)
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- Illinois (cholera detection)
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- Newcastle (''B. subtillus'' as a biosensor)
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- Edinburgh (producing starch from cellulose and biomass)
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2007:
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- Columbia (biosensor)
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- Glasgow (fuel cell)
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- MIT (clearing mercury contamination)
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- Turkey (pH dependent metal ion transporter)
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- South Utah (cyanide biosensor)
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- Brown (Lead contamination)
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2006:
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- Edinburgh (sensing arsenic in drinking water)
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'''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.
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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 disposal methods.
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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).
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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.
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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.
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Final note - team lunch of pizza at Rise @ the Hallamshire is definitely something worth considering again.
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'''Tuesday 29th June''' - Today we got a guided tour of our labs for the very first time courtesy of Qaiser Sheikh. Exciting stuff!
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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 one 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.
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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).
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Finally we're looking into developing 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.
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Lunch today - sandwiches in the sun in Weston Park. Tom, Narmada and Caroline revealed their vegetarianism to the rest of the group *gasp*.
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'''Wednesday 30th June''' - 09:30 start to try tie up loose ends on initial ideas before the 14:00 meeting with team advisors.
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Okay, so the 09:30 start went slightly less to plan than 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.
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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 further research the ion channels that 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.
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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.
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Quotes of the day:
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"We could do that, but we should probably do something good instead." - Andy
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"I don't get the joke." - Tom
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"I think of other stuff in the shower too, but I probably shouldn't talk about it." - Nii.
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"Then we can get all bioinfornatics on its ass!" - Greg
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Trivia: Sheffield's team members are probably quite rare - 3 of the 4 veggies (Andy too) are lefties!
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'''Thursday 1st July''' - the team say "White rabbit" for good luck. The aim is 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.
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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.
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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.
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After the excitement of all that drawing a few of the team headed home. Tom and Steve paid Qaiser another visit to have a look 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 alignment 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.
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Productive day overall, but chances are tomorrow will be more poductive if our trend so far is anything to go by.
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'''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!
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~12:00 we were joined by Andy, who was clearly impressed by our logos... okay minor exaggeration, he just laughed a lot. Following this he reminded us of our initial 'drip-drop' idea modified with his own design. We'll get that created on photoshop pretty soon hopefully.
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After a lunch of bread cakes in the park, we started on our first 'human practices' lesson from Andy. We learned about 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.
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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!
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'''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.
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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.
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Word of the day: '''Igemdems'''
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'''Tuesday 6th July''' - The team's first proper lab day!
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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.
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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.
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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...
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'''Wednesday 7th July''' - 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.
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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!
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'''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 DH5-alpha strain, but we had a funny email from Kate to lighten our moods. It read:
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Hi all,
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Hope you had a good gay yesterday - I'm still ploughing away with this work
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which I have to hand in tomorrow, but will be there tomorrow fingers crossed!
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Hope it's all going good...
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Kate
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Note the spelling mistake. Yes, we are immature for laughing.
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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.
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We should probably record how far the planning has gone - so here goes:
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'''Plan'''
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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.
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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).
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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.
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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.
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'''Friday 9th July''' - The team meet with Professor Artymiuk to talk about the best point to create the fusion protein.
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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.
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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.
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Barbecue in the evening at Caz's - perfect opportunity for team banter and to take advantage of the Sheffield sunshine.
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==notebook==
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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.
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Latest revision as of 19:03, 27 October 2010

Template:Navigation


Pre-week - Very early brainstorming about the project
Week 1 - The biosensor project area is decided and plans are made for the upcoming weeks.
Week 2 - Our biosensor idea is examined in terms of cell proteins and feasibility.
Week 3 - Some progress is made on deciding what genes to order, we practice transformations in the lab and our genes are ordered.
Week 4 - We give our presentation in Newcastle and and progress is made in terms of human practices/transformations.
Week 5 - Plasmids are ordered and progress is made on the modelling work.
Week 6 - Growing up our BarA knockout cells. We conduct most of our human practices interviews and socio-technical circuitry.
Week 7 - The wiki template is finished and made live, primers are ordered and the human practices socio-technical circuits are brought up to date.
Week 8 - The human practices collage and most interviews are finished. Work begins on the pgaA promoter.
Week 9 - We begin characterising the pgaA and hapR promoters.
Week 10 - Modelling success, and transformation of the promoters & genes.
After week 10 - Final summary of our work after the 10 weeks


Sheffield sponsors.png

Retrieved from "http://2010.igem.org/Team:Sheffield/Notebook"