* ''Constructed a control growth curve of our bacteria with an without chloramphenecol.''
+
* ''Constructed a control growth curve of our bacteria with and without chloramphenicol.''
* ''Analytical digests of plasmids''
* ''Analytical digests of plasmids''
<br>
<br>
Line 208:
Line 208:
* ''A gel has been run for the previous days digest''
* ''A gel has been run for the previous days digest''
* ''We have transformed a plasmid that will produce GFP for some preliminary fluorescence measurements''
* ''We have transformed a plasmid that will produce GFP for some preliminary fluorescence measurements''
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* '' the team has been working on a summer school workshop for 6th formers in the middle of august''
+
* ''The team has been working on a summer school workshop for 6th-formers in the middle of August''
-
* '' Still waiting on our assembly primers''
+
* ''Still waiting on our assembly primers''
-
* '' Also it's Yorkshire day!!''
+
* ''Also it's Yorkshire day! Up the Yorkists! Down the Lacastrians!''
+
* ''[[Team:Leeds/Team#Paul Turner|Paul]] butchered some wiki code and html to get [http://commons.wikimedia.org/wiki/Commons:Video#Uploading_a_video video embeds] working, with the videos [https://2013.igem.org/Requirements/Wiki hosted on the iGEM servers!] He has then passed the code on to [[Team:Manchester|Machester]] and [[Team:Newcastle|Newcastle]] to use for their modelling tutorial videos.''
Here's our lab log, you can read about what we've been doing in the lab. (We're working hard, promise)
June 2013
Week 1
24th June
We’ve moved into our office, deep in the basement of the research labs in the Miall building.
Our time has been taken up getting acquainted with our office ( and our coffee machine!) and roughing out the fine details of our protocol.
We’ve pulled together a combination of the teams' various projects to create our final idea, we’re now looking at making a detector platform for physically binding substrates to activate a reporter. (Scintillating no?)
Our team has been busy thinking of inventive assay design to characterise our biobricks; frantically trying to code our wiki and taking our team photos (important work)
25th June
Jeni, one of our first year biochemists has been working on her primer design, getting everything ready to start in the labs next week. We’ve been compiling our part list and getting our order ready; a buffer and bacteria shopping spree.
26th June
We’re trying to plan out our outreach programs, so watch this space. We’re going to be doing instructional videos on RFC-10 and Golden Brick assembly; as well as some more basic introduction to Synthetic Biology for younger students, alongside running some SynBio workshops for summer students that’ll be here at Leeds.
27th June
Today we've been working on our presentation; getting it ready for the YSB conference by running it past some of our lecturers; scary stuff
We've also been getting comfortable in the lab space, making up stacks of LB broth and preparing for some serious bacterial colonisation
28th June
It's been a busy week here at Leeds iGEM HQ. We've got a Biochemist and a Physicist (a rather handsome pair) frantically working on coding the wiki and creating images for the presentations and posters, it's gonna be beautiful (we hope)
We've had a team of biochemists (all 3 of them) hard at work designing primers and getting ready to steamroll into the lab next week.
July 2013
Week 2
1st July
With our primers in the post, we've been mass producing growth media and agar plates. We've resuspended and transformed a selection of the biobricks we plan on using, including YFP, GFP, INP, and some terminators.
The wiki team have been locked in the basement and they're not allowed out till it looks beautiful.
2nd July
Today we've been writing out scripts for our tutorial videos, they'll be a series aimed at younger students with an introduction to Synthetic Biology, and a series aimed at Synthetic Biologists on things like Goldengate and Gibson assembly.
Then we locked our token nanotechnologist into a lab with a couple of thousand pounds worth of microfluidics chips and we're hoping for the best (and a minimal number of perforations)
3rd July
Been a busy day; plasmid preps, glycerol stocks and further transformations of quorum sensing biobricks (pLux and LuxR), promoters and cyan fluorescent proteins.
We then had a skype conference with Cyrille Pauthenier, the advisor for the Evry iGEM team.
Went into great detail on Goldengate and Goldenbrick assembly methods and their pros and cons.
We ended our day doing soundtests for our educational videos; watch for the remix.
4th July
Another day of plasmid preps and innoculations in the lab of our newly transformed BioBricks.
Meanwhile in the office we have been working on our poster for the Young Synthetic Biologist confrence in London next week.
5th July
Today we have done further plasmid preps getting ready for our assembly!
In the office we've been working on our poster and presentation for the upcoming Young Synthetic Biologist confrence in London
There has also been organisation of trips into schools making a presentation for 6th form students on Synthetic Biology
Finally we have been double checking primers and DNA sequences for Gibson assembly
Week 3
8th July
Our first BioBrick assembly has been done!(A green Flourescent protein). It will be tested to see if it has worked tomorrow
Presented our ideas so far to two more academic staff.
We have been doing the finishing touches to our poster for the Young Synthetic Biologist confrence in London this weekend
Jonah has been working very hard on our first Youtube tutorial video
9th July
Rewrote parts of the presentation
Created a new survey on Synthetic Biology to send out to the public
Started editing the video
Reviewed the wiki design
10th July
Sent the poster for YSB-London to the printers
Recorded the next audio track for a new video
Corrected typos on the wiki, our presentation and the poster
Uploaded our first [http://www.youtube.com/watch?v=Hz7pPXJvhVE Youtube Video]
Sent out fresh surveys via Artynet
11th July
Collected our poster for YSB 1.0
Practiced presentation for YSB 1.0
Transformed components for Device 2
Met with Rose Bavage and Louise Crabtree to discuss outreach events
12th July
Caught a very early train down to London for YSB 1.0
Met the other UK iGEM teams at YSB 1.0
Prepped to present tomorrow at YSB 1.0
Collected soil sample tubes from Norwich for Hadrian's Wall
Discussed collaboration with nearly every team at YSB 1.0
Week 4
15th July
Had a great time at YSB 1.0
Jumped back into script writing for Tutorial Videos
Ordered primers for Si4 binding domain
16th July
Edited and uploaded our 2nd [http://www.youtube.com/watch?v=GJC6kxtji9E Youtube] video
Transformed an INP/YFP fusion
Innoculated prior transformations to grow overnight
Created a workshop plan for Friday, with visiting 6th form students
17th July
Meeting with our new sponsors, BioLine
Added repeating background image of DNA to wiki
18th July
Finalised protocols for the labs
Had a meeting with Paul Beale and Fiona Meldrum from the Chemistry department about our project
Plasmid preps and more innoculations!
Met with some school teachers to discuss a workshop we will be doing with year 13's in September
19th July
Done some PCR (Translation from Yorkshire to English: Did some PCR)
Recorded more audio for our Youtube videos
Had our weekly Friday meeting
Presentation and Ethics Workshop with STEM subject 6th Formers - went very well, lots of good feedback!
Week 5
22nd July
Fixed broken wiki-code and js for galleries
Ran PCR to amplify INP, GFP and D2-Term
D2-Term didn't work, re-programmed PCR to run overnight at different gradient, hopefully optimised for the primer melt-temperature
Drafted simplified model for characterising Cpx Pathway
25th July
Recorded more Audio tracks for videos
Edited together more videos, uploaded onto [http://www.youtube.com/watch?v=pBzLZIVTkes Youtube]
Ran more PCR - it is being rather finicky!
26th July
Uploaded revised versions of two [http://www.youtube.com/watch?v=KwpLMyV3YTA videos] for [http://www.youtube.com/watch?v=T3vFTUXfxvk Youtube]
Meeting with Sarah and Mike, got advice on gels and updated them on our progress - to quote Mike, "I'm really impressed!"
Paul revised more of the simplified Cpx Pathway model, hopefully have basic version coded in BNGL by Monday
Plotted out workshop ideas for Summer School Students
More vids and audio recorded!
Week 6
29th July
Hard-coded alpha-version 0.3 of Cpx Pathway model
Ran yet more gels
Had a project update meeting with S.D.Evans
30th July
Paul has been continuing to develop our model for the Cpx pathway.
In the labs more gels have been run to make sure our PCR products are what they should be.
Characterisation protocols are being finalised
31st July
Constructed a control growth curve of our bacteria with and without chloramphenicol.
Analytical digests of plasmids
August 2013
Week 6
1st August
A gel has been run for the previous days digest
We have transformed a plasmid that will produce GFP for some preliminary fluorescence measurements
The team has been working on a summer school workshop for 6th-formers in the middle of August
Still waiting on our assembly primers
Also it's Yorkshire day! Up the Yorkists! Down the Lacastrians!
Paul butchered some wiki code and html to get [http://commons.wikimedia.org/wiki/Commons:Video#Uploading_a_video video embeds] working, with the videos hosted on the iGEM servers! He has then passed the code on to Machester and Newcastle to use for their modelling tutorial videos.
2nd August
x
Week 7
5th August
Paul starts hiking along Hadrian's Wall for charity!
6th August
Day 2 of hiking for Paul, raising money for the Crohn's and Ulcerative Collitis Unit in the Leeds Teaching Hospitals Trust.
7th August
Day 3 of hiking for Paul. He should be very tired by now.
"
