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 includes:
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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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<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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5. "Bactoshave!" - the bacterial shaving system... (patent pending)
 
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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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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.
 
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The Wikis we noted were:
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[[Image:Sheffield sponsors.png]]
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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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- 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 desposal 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 an 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 was 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 Quaiser 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 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.
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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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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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'''Tuesday 29th 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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==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

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