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Team:UCL/Diary/W1
From 2014.igem.org
Contents |
Week 1
Monday 21/07
Whatever you have done in a given week spit it out here. Make sure you are editing and adding every day or we will hunt you down.
Postgrads just use monday as your whole week, I know you don't all work full time and it's fine we love you anyway.
Edo
Went to Second symposium on the origin of life at UCL (http://www.ismb.lon.ac.uk/origin_of_life.html) Useful things happened there: Met Vitor Pinheiro and some people from his previous lab, had a chat with Alex Taylor. Interesting to see the opinions of “truly synthetic” biologist (life out chemicals) on iGEM (standardised parts of DNA) side of synthetic biology. Met Adam Rutherford, he wants to keep in touch with iGEM teams (wrote two chapters on iGEM in his book) and particularly with UCL as it is his Alma Mater. Invited him for our debate (reconfirmed later in the week for the 26th). He coming. (yeey) Best talk by Pierre-Alain Monnard “Prebiotic amphiphiles, early membranes and protocell functions” and Philip Holliger (Vitor’s best friend) “Towards RNA self-replication Aything else happened that day?
Lewis M
Did something I dont totally recall. Was definitely in school. Most likely the day I observed and did some grunt work with Tanel and Sohaila, doing transformations. Most likely worked on the new web home page template.
Sanjay
Lost my phone whilst cycling, managed to get it back like 3 hours later at Waterloo; and I've only been in London for a few hours.
Maurice
Joy
Ning
Pamela
Bez
Spent most of my time in the lab this week performing analytical restriction digests on transformed biobricks and transformed plasmids from Lisbon. We have had varying success shown in the lab book but will need to repeat some next week.I also saw how to perform minipreps and nanodrops.
Outside of the lab I have been sending out e-mails to biotech companies for sponsorship which will be followed up with calls next week. We have also been contacting various environmental, political and legislative organisations in order to have representatives for our debate in August.
Daniel
Sohaila
Participated in the team meetings about more effective lab planning for the next few weeks. We talked about the cloning strategy in detail and developed an idea of future lab plans. Going to take responsibility for allocating lab weeks to people and having an outline ready for each weeks lab agenda before beginning the lab work for the week. Participated in human practice meeting and discussion about obtaining speakers for the debate. Went with Edo to a few talks at the origin of life conference and later to the talk by Adam Rutherford. Spoke to him about our project, gave him a business card and invited him to be a speaker at the debate which he was quite receptive to.
Georgia
Yan-Kay
Tanel
Adam
Kevin
I have been finalising the preliminary version of a literature review on synthetic biology as a dual-use technology. In that regard I discussed how iGEM and UCL iGEM 2014 fit into its conceptual and theoretical framework through sustainable governance strategies that try to bridge concerns of security with discourses on ecological modernisation and innovation. I sent this literature review to my MSc dissertation supervisor. Kevkey 09:00, 26 July 2014 (CDT)
Dave
Lewis B
Rob
Miriam
Alberto
Tuesday 22/07
Edo
- - Found some really good images of azo dyes crystals that could do for the wiki and/or other aesthetic content (https://www.flickr.com/search/?q=azo%20dyes). Contacted Linden Gledhill (Author of the pictures) and got positive response on using his material as long as we with credit him and link to the commercial web site (Linden Gledhill Photography
- - Discussed with him about a potential collaboration: he has some really good footage of the crystalisation that could do for some of our video (on these lines https://www.youtube.com/watch?v=QWam1HlKGkI).
- - Ordered Azodyes (food colouring, non toxic E129) to try to do some pictures of the crystalisation myself with microscope at home/ one at ucl
http://www.lindengledhill.com/).
Lewis M
Was an interesting day as there was a mash of meetings, one of which was a rather important meeting with the Webcomms and human practice people. We decided on what graphics were needed for the new website design and how they would be taken and then implemented. Also we had a bit of a kerfuffle regarding the deadline of the final site. All in all it was a hectic day but a lot was organized.
Sanjay
Meetings in the morning, meetings in the afternoon, something in the evening; I don't think I even had time to eat lunch. We should get lunch sponsorship.
Maurice
Joy
Ning
Pamela
Bez
Daniel
Sohaila
Attended meeting with Darren in the morning. He stressed that we should get at least one BioBrick moving which I am taking into account for planning next steps in the lab. After the meeting I read up on the use of microbial fuel cells in degradation of azo-dyes for the meeting in the afternoon.
Went to Westminster with Bioprocessing team (Joy, Maurice, Sanjay) to talk to Godfrey about MFCs and see how this could fit in with our project. Asked a lot of questions as to feasibility and he was extremely forthcoming with help about contacts and papers related to our project. He showed us the MFC prototypes and even offered some materials if we should need them. Told us that university of Reading may have some ready-to-use MFCs which we could procure.
After the meeting we re-grouped at Costa to plan our next steps. Decided that we most probably will not pursue the MFC angle as it does not really include azoreductase and current generated is not much. But we will keep it in mind as a possible secondary idea to build on our regular bioprocess. I will be doing literature reviews and research as to how to set up our bioprocess.
Georgia
Yan-Kay
Tanel
Kevin
Today, I have been reading on methodology literature for the discourse analysis of the team. Condering that UCL iGEM 2014 is the empirical subject of my dissertation, I started reading more on the various ways in which a social scientist conducts a case study. In addition, I am looking into ethnography as a method especially considering that I am embedding myself as a researcher among a team of students and scientists-in-the-making. Considering that a lot of what they do happens online, I am also consulting some of the literature on ethnography that apply to social media. Kevkey 09:09, 26 July 2014 (CDT)
Wednesday 23/07
Edo
Went to the lab and set up a gel. Talk by Brenda Parker "Loop the loop: sustainable biorefining and bioremediation". Notes here https://docs.google.com/file/d/0B-tWFSYdf2ODV0pHUVMxbW5ndUk/edit.
Read more about big italian textile company that had issues with toxic dyes. http://en.wikipedia.org/wiki/Marzotto I have get in contact and visit after ETAD
Had a look into make a chemical distance map of azodyes from cofactors found in living organisms to implement metabolic firewall for the xenobiological approach to biosafety. Will probably get a nice image with Rob useful to explain what trying to do. Some help might come from xenobiology lab at ucl.
Lewis M
Had a burrito and wrote some script. Great day. Can't think of anything else.
Sanjay
Maurice
Joy
Ning
Pamela
Bez
Daniel
Sohaila
Attended meeting with Darren in the morning. He stressed that we should get at least one BioBrick moving which I am taking into account for planning next steps in the lab. After the meeting I read up on the use of microbial fuel cells in degradation of azo-dyes for the meeting in the afternoon.
Went to Westminster with Bioprocessing team (Joy, Maurice, Sanjay) to talk to Godfrey about MFCs and see how this could fit in with our project. Asked a lot of questions as to feasibility and he was extremely forthcoming with help about contacts and papers related to our project. He showed us the MFC prototypes and even offered some materials if we should need them. Told us that university of Reading may have some ready-to-use MFCs which we could procure.
After the meeting we re-grouped at Costa to plan our next steps. Decided that we most probably will not pursue the MFC angle as it does not really include azoreductase and current generated is not much. But we will keep it in mind as a possible secondary idea to build on our regular bioprocess. I will be doing literature reviews and research as to how to set up our bioprocess.
Georgia
Yan-Kay
Tanel
Kevin
Still reading further on the ethnographic method and case studies. However, today I found a book that deals with both methods but from the perspective of sustainability research. It even contains an elaborate example of a case study on biosecurity. In the afternoon I went to the Human Practice meeting with the team. We discussed our social media presence on Twitter and just started sending out some tweets with the idea that this tool can also be used to blog - microblog - our thoughts on the subject of synbio. I also asked Lewis about how I could edit my own space of the wiki. Subsequently, I went back to the Science Library to write some of my methodological ideas down and write a bit of the introduction for my methodology chapter. Kevkey 09:18, 26 July 2014 (CDT)
Thursday 24/07
Edo
Learned how to use snapgene and put together the Lisbon plasmids into a plasmid map (with fragment inserted into the plasmid the way they did it). Simulated gel of CotA (laccase) and it seems we got the right thing there.
Went to Institute of Making and printed out Azoreductase. I found a way to make it print, now we have the two monomers, I need to finish polishing them and then find a really cool printer and some money to get a really good one printed.
Also tried to print the bioreactor BUT met mike (biochemeng postdoc) and just using a jar is just so much better to have an easily deployable bioreactor, then we can print some of the specific pieces. @Joy
Lewis M
Debugged and got the homepage HTML, CSS, and JS reading for the introduction of graphics. Super psyched I got this done. Consolidated all of the designs for the new site. Began studying genetic algorithms, cause I felt like it. At this point I had a discussion with the other team members and we are going to make sure the other sites are perfect to give us some more buffer time to get the final site done and pretty. Also began talks with Edo about setting up a blog/diary.
Sanjay
Maurice
Joy
Ning
Pamela
Bez
Daniel
Sohaila
Georgia
Yan-Kay
Tanel
Kevin
Not really been doing much today. I stayed in the library most of the time, primarily editing another wiki but ending with -pedia, just because I felt like it.Kevkey 09:23, 26 July 2014 (CDT)
Friday 25/07
Edo
//ALL THIS STUFF WILL HAVE TO GO INTO THE LAB BOOK - just here temporarily to work out best way to make a lab book//
Ran a gel with lots and lots of wells:
What should come out (question marks are for double band of the undigested negative control)
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This is what came out:
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The 4 wells on the right are the PCR products and doesn't fit with what we expected, might have mislabeled the tubes. The rest looks quite right :) Doing it again on monday to double check the PCR results.
Lewis M
Friday was a crazy day. Spent most of my day in the morning sorting out non-igem stuff like bills, cleaning, disposing of dead bodies etc. the usual day-to-day stuff. Came in around lunch and discovered there was quite a bit of unexpected craziness. Sat down and with the other team liaisons and refined and redefined the mission statement as well as what we were expecting of our campaign. Also spent a fair amount of time creating deadlines. Had a diet coke and chocolate muffin... highlight of my day.
Sanjay
Maurice
Joy
Ning
Pamela
Bez
Daniel
Sohaila
Georgia
Yan-Kay
Tanel
Kevin
Have been reading some more on methodology. I have been also looking into different strategies to retrieve discursive data from the team and process it for analysis. Kevkey 09:56, 26 July 2014 (CDT)
Weekend
Edo
Woke up without cognition of being in this universe and cycled to science library. Set up this diary page on the wiki with Lewis to save us from iGEM oblivion. Put some azo dye music to entertain myself and Lewis since we are the only current occupiers of this library. https://www.youtube.com/watch?v=eERi_OQiiLM Wrote down what i did this week. Both impressed and depressed. Made up some things. Harrassed people on fb to do it. I am afraid that this will have to happen again.
Azo dyes arrived! Red, pretty and ready to be used for some side experiments :)
Lewis I
Got up at 8 and had some bacon. Got to school and went to the library. Started working and made this diary with Edo. He really cracks the whip.
Kevin
Back working in the library again. Trying to do some serious writing but potentially failing at it. Still waiting for my supervisor to give some comments on my literature review. Now I was thinking I could actually step up my dissertational game and do my discourse analysis with a little help of some Foucauldian theory and concepts. I mean, why not combine the notions security apparatuses and neoliberal governmentality with the ideological discourse of ecological modernisation?? Sounds like a plan...for now :s Kevkey 10:09, 26 July 2014 (CDT)
