Team:Imperial College London/Notebook/week1



This is our diary page which records the daily activities of the team. Click on the links below to see a summary of events and activities happening each week.

Week 1: 4th July to 10th July

Monday, 4th July

We had a briefing today chaired by James. Key action points of the day were to organize our CIDs, organize who was in charge of each team aspect and discuss the problems that we thought could be solved by Synthetic Biology. Once these problems had been discussed, we each chose one project that another team member came up with to research. We also were introduced to Professor Freemont and Professor Kitney who gave us an insightful talk about what awaits us. A trip to the Royal Society of Science exhibition ended up turning into a lunch in China town (the exhibition actually starts tomorrow) and we talked to Nicola Morgan who is interested in investigating the use of bacteria in making patterns on clothing. (Text by Chris)

Tuesday, 5th July

Today we started with a briefing from Frank where the main action points of the day were discussed. These included creating a cleaner and more standardized wiki code as to ease future editing as well as determining which projects that we had each researched the previous day could be a viable project. We also agreed to only use HTML code when writing in the wiki.

"Wiki Rules" were established by Frank:

1) You do not talk about wiki editing

2) You do not talk about wiki editing

3) All files are to be uploaded with the name : ICL_Exact_Description_of_File_with_a_number

4) Keep the formatting the same on every page

5) DO NOT change content that someone else has uploaded without talking to them first

6) Please always upload in HTML, not Wiki Formatting

7) Try and make your content look like the other content on the page

We established roles for everyone in the team that they will need to fulfil during the project: Rebekka - Stocks supplies protocols Nick - Human Practices Ming - Collaboration Yuanwei - Wiki Frank - Software/hardware Chris - Parts characterisation Nikki - Cloning Si - Modelling Nina - Photo/Media/Film

We spent around an hour or two clearing up and getting to know the HTML language. At around 11, three students from the RCA came to talk about their projects. Coby presented his ideas of growing furniture as well as trying to recreate his grandfather's psyche in a mouse. Pei-Ying presented her projects; using smallpox vaccines as a form of prevention against future terrorist attacks, nano diets where all the basic dietary requirements (vitamins, monosaccharides, amino acids, etc) are measured to the exact amount needed and a strange device that would store the voice of another human being if you were to touch them. CJ introduced us to several artists like Orlan and their ideas:

Koby: • Transferring life/soul into a project • Growing furniture parts

Pei-Ying: • Vaccine Beauty - smallpox can cause scarring - scar art - get newest virus to be infected by so that you are immune to the latest version • Minimal Nano-Diet Guide - transparent food • Use Genetic code as a way to protect data by encoding their voices

CJ: • SOBAgate - What happens if you modified people to react differently in response to feelings of greed, lust or anger - lust - all the blood goes to genitals and they pass out - anger - voice becomes squeaky - greed - gut bacteria release aspirin like chemicals so eating cake results in rashes, bleeding and bruises

Older artists Oron Catts - all about half-living/half-dead tissue • sets up a lab in a gallery • Pig wings - growing wings from pigskin • Half-living worry doll - people write worries into a computer and this altered the nutrients available to the doll • Victimless meat - grew little steaks • Victimless leather - grew a tiny leather jacket - got shut down due to contamination/fear

Orlan - Saint Orlan - did plastic surgery as performance - was interested in how her beauty affected other people • apparently gives amazing talks • harlequin suit inspired by Catts - grown triangles of skin from diff. races and animals and made them into a technicolour coat

Newer artists: David Benque - singing flowers • designed a range of plants that would make sounds • so diff. plants at diff. times of year would be musical • ie modified bacteria makes gas so flower would inflate and then the air would escape and make a sound - a fart sound • saying that synthetic biology doesn't have to be scary

Tuur van balen • Pigeon d'or - modify pigeons so that they shit soap • designed objects that people would have in that reality • leech - adapt how melancholy you felt using certain yeasts that affect your mood - leech assesses how melancholy you are and processes the blood and introduces endorphins • then blend leech and eat it

After this presentation we discussed our ideas with the students of the RCA over a lunch at Eastside. We continued brainstorming and decided that this idea might be possible though the use of vesicles, however, it is no longer a priority project.

Ideas Discussion Snake Antivenom - get lots of bacteria with a hypermutagenic region in a plasmid that makes a protein on the cell surface and then select for the proteins and therefore for the genes by testing the binding affinity of the cell surface markers and therefore the bacteria - This can then be used to select for the protein/proteins that have the greatest binding affinity to the venom proteins and so an optimum mixture of antivenom proteins can be made Melatonin - Not good as its just expressing something Chris' Vampires - More research needed - ask an expert on clots Si Chen's Leaves - Bit of a chemistry project - cellulases are tricky to work with Yuanwei - Waste is too vague, but a nice idea - possibly put on back burner Rebekka - dismiss food waste one as it is too vague • bacteria that can detect and fight staph aureus would be useful - may need more research - so it was put on the back burner

We have decided to split the team into 3 teams. Nicola, Nikki and Rebekka will be working on the prodigiosin pigment. Si, Nina and Yuanwei will be working on trying to improve on a bacterial hard drive that has already been tried in past iGEM projects. Frank, Ming and Chris will be working on the anti-venom idea. We will also try to use a little time to come up with more problems we could try to solve tomorrow. (Entry by Frank and Chris, edited by Rebekka)

Wednesday, 6th July

Action points for the day: -bios on the wiki -sci-fi meeting -characterisation talk -come up with more ideas -do more research on anti-venom and prodigiosin

We started the day off by brainstorming several idea and selecting the ones we thought were viable enough to be presented to the professors on Friday.

Brainstorming: Venom and BAS ideas to be presented on Friday! -desertification (overdone already) -thermophiles (make them express melanin so they can be heated up by the sun, saving energy) -cell-cell signal transduction (can be used as inhibition or activation) -desalination (commercial membranes are probably more efficient) -data storage in bacteria (use DNA to encode information has already been done but it might be useful to come up with a new way of retrieving the information. Storing data in RNA might be more efficient) -ocean metals (retrieving valuable materials from sea water, main problem: materials are only present at really low concentration and might be hard to retrieve) -cross-linking of hair to something useful -dictostylium -using melanin for heat production from sound in bacteria. The heat could then be converted into an output, producing sound sensitive bacteria. Is melanin really able to detect sound?? -modifying silk worms? -radiotrophic fungi (fungi that use gamma radiation to produce ATP - the pathway could be used in E. coli to absorb radioactivity but the exact pathway does not seem to be known (Wikipedia)) -serum bile acid as a biomarker of liver problems in pregnancy

After the brain-storming session we had a talk from Chris about characterisation giving me a glimpse into what I would be expecting in the weeks after the project has been pinned down on a single idea.

Characterization presentation by Chris: in vivo presentation -Timer vs. switch. need to know characteristics of parts. -How to characterise: Look at individual parts. What goes in, what goes out. What function is carried out. -What specifically do you want to characterise? Terminator, core-promoter, RBS, reporter, coding region. -Terminator requires several different characterizations. -Place promoter, coding region into an expression circuit with a reporter. -Standards are only existant for promoters. How strong promoters are. -Canton paper 2008: Base characteristics that you need to know about an inducible promoter. -How responsive (transfer function of response), dynamic? (output) All relative to J23101. -Synthesis rate, number of cells and divide your promoter output with standard which gives you a value relative to J23101. RPU (relative promoter unit) -RBS calculator gives you a value to how strong it is. Need to debug yourself. -Hard to characterise until we know what we want to do. -Plate readers look at OD, fluorescene, luminescence. -Individual cells analyzed for GFP and RFP. Chris works on methods to make it more high-throughput (automates to make faster). Won't consider optimizing something unless it worked twice on the assays. Fluorescence doesn't give use pinpoint accuracy. Can't be measured really well, only bulk events and not specific events. Enzymatic activity more done in vitro. You're working with factories that work depending on what they're in. Can find Chris though James at any time. Make sure positive and negative control will work. We currently have two running ideas; the anti-venom and a bile acid sensor. We have split off into two teams and each is working hard in order to build a system that the professors might agree to this Friday at 3:30pm. The deadline is approaching and we still require 2 more possible projects to present to the professors.

(Text by Rebekka and Chris)

Thursday, 7th July

Talk from LSE Things to consider in human practices: Safety, Security, IP-intellectual property, ethical, biohacking, global fairness For Anti-venom project Safety : handling toxin in the lab, storage and transportation of toxins Security : produce specificity problem, antivenom target for particular person Patent : only the process obtaining product(antibody) but not the product itself, patent cost a lot of money LEGO exercise: - different ways to describe the construction process - engineering language and user-friendly language

Contacts of people from RCA and LSE

RCA - Pei-Ying Lin : - Koby : - CJ :

LSE - Alex Hamilton : - Claire MArris : - Stephan Guttinges :

(Text by Ming, Nina, Si, Yuanwei and Nick)

Friday, 8th July

We, Imperial igem team 2011, hope you get well soon, James. :) Dear guys, these are the animes that I could draw. Sorry for low resolution since I just moved the house and I still couldn't find my drawing pad so I just hand draw it first. I am sure I will find my drawing pad soon.

Anyway way. Please vote for the drawing style you like 1. (already) handsome James 2. Cute James 3. Manga James 4. Hardcore James 5. Or if you have any other suggestions about the drawing style please tell me


Christopher Schoene

Action points:

Finish the powerpoint presentations.

Get new ideas.

Separate notebook and brainstorming on the wiki.

Today we continued brainstorming for ideas and we completed the powerpoint presentations for the Anti-venom and the serum bile acid sensor ideas. During the brainstorming session we found out that Brown is also researching the use of urease to make sand bricks for their mars expedition themed project so we scrapped the idea. However, we still looked into other ways of stopping desertification. We also came up with the idea of using different strains of bacteria that would become more or less buoyant depending on the amount of different heavy metals in the water. We also discussed maybe focusing on looking into engineering B. subtilis to produce spores that are more adept at crystallizing water crystals to continue a bioprecipitation project from a team back in 2009.

We also were introduced to some of the PhD. students from the department and got some delicious chocolate cake in the process. This was followed by us presenting our ideas to the aforementioned PhD students as well as Professor Freemont, Professor Kitney, Dr. Ellis and some other guests. Our two main ideas were shot down for being either too boring or too risky. Then we discussed the other ideas that we had and discussion ensued. The main point that I got out of this is that we tried to focus on two ideas too early and that we should not confine ourselves so early.