Team:University College London/Notebook/week15

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= Notebook: Week 15 =
= Notebook: Week 15 =
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== Aims of the Week ==
== Aims of the Week ==
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This week Erin and Joanne are focused on the modelling section of wiki while Leonard and James are finish the characterisation experiments and uploading the data. Rhiannon is developing explanatory videos for the wiki research pages.
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== Monday 17th September ==
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== Monday 16th September ==
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<div class="notebook-paris"> '''Paris visit''' - Philipp and Bethan are in Paris to meet the iGEM Paris Bettencourt team and speak with Thomas Landrain, the founder of la Paillasse, the Parisian Hackspace. </div>
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<div class="notebook-meeting"> '''Paris visit''' Philipp and Bethan are in Paris to meet the iGEM Paris Bettencourt team and speak with Thomas Landrain, the founder of la Paillasse, the Parisian Hackspace. </div>
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<div class="notebook-hackspace"> '''Hackspace''' - Yeping finished planning the workshops for the collaboration with the London Hackspace. We're really looking forward to the workshops starting on Wednesday! </div>
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<div class="notebook-meeting"> '''Hackspace''' Yeping finished planning the workshops for the collaboration with the London Hackspace. We're really looking forward to the workshops starting on Wednesday! </div>
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<div class="notebook-achievement"> '''Wet lab: Laccase''' - Aurelija succesfully ligated the laccase gene. </div>
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== Tuesday 17th September ==
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<div class="notebook-wetlab"> '''Characterisation: IrrE''' - Leonard and James produced the first set of growth curves demonstrating the salt tolerance of our plasmid transformed with the IrrE gene: https://2012.igem.org/Team:University_College_London/Module_5/Results </div>
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<div class="notebook-meeting"> '''Darmstadt Collaboration''' Bouran swapped address with Henrik from Darmstadt today, we'll be sending them Laccase for characetrisation, while they are sending us a cutinase enzyme for expression in our Roseobacter.</div>
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== Tuesday 18th September ==
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<div class="notebook-meeting"> '''Purdue Collaboration''' James was in touch with Chris from Purdue again to discuss swapping protocols for curli characteristion. </div>
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<div class="notebook-bielefeld"> '''Bielefeld exchange''' - We received the protocols from Bielefeld for their plasmid and Philipp sent Bielefeld our laccase! </div>
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<div class="notebook-meeting"> '''Lab clean-up''' Safety always first. We had a huge clean-up of the lab, including scrubbing the microwave spotless! We're now ready for our last month in the lab. </div>
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== Wednesday 19th September ==
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<div class="notebook-rathenau"> '''Meeting of the Young Minds''' - Erin, Joanne and Leonard skyped with Virgil to discuss what kind of participants we expect to take part of our panel for the Meeting of the Young Minds debate.</div>
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== Wednesday 18th September ==
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<div class="notebook-diybio"> '''Hackspace Exhibition Preparation''' - Philipp, Bethan and Howard went to the Hackspace to help design a box for the exhibition of a gel with the Public BioBrick from our collaboration. </div>
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<div class="notebook-meeting"> '''Practice Presentation''' Philipp and Bethan met with Roland Jackson to discuss our DIYbio collaboration. </div>
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<div class="notebook-meeting"> '''Hackspace Day 1''' We went en masse to the London Hackspace this evening for the first workshop. Carina, Yeping, Philipp, Martina and Bethan were all present. Howard met us there. We bought a glycerol stock of W3110 ''E. Coli'' and empty petri dishes to show the biohackers how we make minimal agar plates for day 1 protocol of making competent cells. Quite a few people turned up and they were very keen to have a go!</div>
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<div class="notebook-meeting"> ''iGEM connection''' Bethan is organising with iGEM Paris-Bettencourt a trip to Paris to discuss how our two project approach biosafety, and also discuss aspects of our DIYbio collaboration with members of the CRI's Education X.0 project. Paris iGEM also invited us to participate in their debate on the 16th! </div>
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== Thursday 19th September ==
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<div class="notebook-wetlab"> '''Characterisation: Laccase''' - James finalised the graph for the syringaldazine assay of laccase activity: https://2012.igem.org/Team:University_College_London/Module_3/Results</div>
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<div class="notebook-meeting"> '''Hackspace Day 2''' Together with the hackers, Bethan helped to build a shaker to agitate our cells overnight. This involved using a number of equipment only available at the Hackspace, including hand saw, glue gun and motor. The biohackers were very keen to give us an electronics tutorial as we build our circuit for the shaker. A variable resistor was included in the circuit design so we can control the speed of the shaker.</div>
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<div class="">We also performed PCR of the cholorophenicol plasmid backbone required for our ligations. At hackspace, they have a very cool 'ancient' thermocycler. It has no heated lid so mineral oil has to be added to samples to prevent evaporation. The biohackers showed us how to program the machine. There are so many steps compared to the one used in our lab!</div>
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== Thursday 20th September ==
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<div class="notebook-sponsor"> '''Beacon Bursary Kick-off Meeting''' - Philipp and Bethan represented our team at the funding meeting to discuss how we are planning and evaluating our use the Beacon Bursary, a public engagement grant we were awarded to run the workshops and exhibition for our collaboration with the biohackers from the London Hackspace. </div>
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 +
<div class="notebook-wiki"> '''Wiki Characterisation Data''' - James finished the plots of IrrE characeterisation to upload onto our wiki and the Registry. These graphs show how salt tolerant our cell is in comparison to our control. </div>
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<div class=""> </div>
== Friday 20th September ==
== Friday 20th September ==
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<div class="notebook-meeting"> '''Hackspace Day 3''' Our shaker from yesterday was still alive today and the liquid cultures in falcon tubes are all cloudy showing growth! Together with the biohackers we ran a 1% gel of the PCR product from yesterday using their DIY gel tray. Their tray didn't have a cover, you can also see how the wires are connected!  Using a hand held UV filter and UV light, we visualized our gel. The PCR has worked! Gel shows the expected band at 2070bp. PCR clean-up is to be done at the UCL workshops since the centrifuge at Hackspace is only estimated to be able to do 5000rpm </div>
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<div class="notebook-achievement">'''Achievement: Ligation''' - Aurelija's ligation of the Wnu nuclease + linker worked! </div>
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<div class="notebook-meeting"> '''Press''' C-lab published an <html><a href="http://c-lab.co.uk/blogs/visiting-london-hackspace-with-ucl-igem.html" title="C-Lab" target="_blank">exciting write-up</a></html> of our 1st day at the Hackspace </div>
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<div class="notebook-news"> '''Press: C-lab''' - C-lab published an <html><a href="http://c-lab.co.uk/blogs/visiting-london-hackspace-with-ucl-igem.html" title="C-Lab" target="_blank">exciting write-up</a></html> of our 1st day at the Hackspace </div>
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<div class="notebook-hackspace"> '''Hackspace Collaboration: Evaluation''' - Philipp interviewed Aurelija, the last interview with an UCL iGEM team member for the UCL-Hackspace evaluation. </div>
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== Saturday 21st September ==
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<div class="notebook-wetlab">'''Wetlab: Nuclease Sampling''' - Aurelija was in the lab bright and early this morning to begin Nuclease sampling. </div>
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<div class="notebook-modelling"> '''Modelling: meeting''' - Erin & Aurelija met to talk over the density model and calculations for curli synthesis predictions.
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Latest revision as of 21:31, 26 September 2012

Contents

Notebook: Week 15

Preparations | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 14 | Week 15 | Week 16

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Aims of the Week

This week Erin and Joanne are focused on the modelling section of wiki while Leonard and James are finish the characterisation experiments and uploading the data. Rhiannon is developing explanatory videos for the wiki research pages.

Monday 17th September

Paris visit - Philipp and Bethan are in Paris to meet the iGEM Paris Bettencourt team and speak with Thomas Landrain, the founder of la Paillasse, the Parisian Hackspace.
Hackspace - Yeping finished planning the workshops for the collaboration with the London Hackspace. We're really looking forward to the workshops starting on Wednesday!
Wet lab: Laccase - Aurelija succesfully ligated the laccase gene.
Characterisation: IrrE - Leonard and James produced the first set of growth curves demonstrating the salt tolerance of our plasmid transformed with the IrrE gene: https://2012.igem.org/Team:University_College_London/Module_5/Results

Tuesday 18th September

Bielefeld exchange - We received the protocols from Bielefeld for their plasmid and Philipp sent Bielefeld our laccase!

Wednesday 19th September

Meeting of the Young Minds - Erin, Joanne and Leonard skyped with Virgil to discuss what kind of participants we expect to take part of our panel for the Meeting of the Young Minds debate.
Hackspace Exhibition Preparation - Philipp, Bethan and Howard went to the Hackspace to help design a box for the exhibition of a gel with the Public BioBrick from our collaboration.
Characterisation: Laccase - James finalised the graph for the syringaldazine assay of laccase activity: https://2012.igem.org/Team:University_College_London/Module_3/Results

Thursday 20th September

Beacon Bursary Kick-off Meeting - Philipp and Bethan represented our team at the funding meeting to discuss how we are planning and evaluating our use the Beacon Bursary, a public engagement grant we were awarded to run the workshops and exhibition for our collaboration with the biohackers from the London Hackspace.
Wiki Characterisation Data - James finished the plots of IrrE characeterisation to upload onto our wiki and the Registry. These graphs show how salt tolerant our cell is in comparison to our control.

Friday 20th September

Achievement: Ligation - Aurelija's ligation of the Wnu nuclease + linker worked!
Press: C-lab - C-lab published an exciting write-up of our 1st day at the Hackspace
Hackspace Collaboration: Evaluation - Philipp interviewed Aurelija, the last interview with an UCL iGEM team member for the UCL-Hackspace evaluation.

Saturday 21st September

Wetlab: Nuclease Sampling - Aurelija was in the lab bright and early this morning to begin Nuclease sampling.
Modelling: meeting - Erin & Aurelija met to talk over the density model and calculations for curli synthesis predictions.
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