Revision as of 17:21, 14 August 2012

Notebook: Week 9

Aims of the Week

The aims of the week include continuing with attempts at ligation in the lab, and the transformation of any remaining BioBricks. On the wiki, we hope to get a more detailed account of our research on the site, and continue with our new Lab book. As far as modelling is concerned, we need to create a more advanced version of the degradation model, and to create a basic model for cell toxicity and salt tolerance. With regard Human Practice, our speed debate is this week, so we want to hear the different opinions from the public regarding the release/use of synthetic organisms to combat pollution, and also explore into the ethical, social and legal issues concerned with this.

Monday 6th August

Achievement. We were successful with our Beacon Bursary application! The panel were impressed by our project and are helping us fund the workshops in our collaboration with London Hackspace.

Modelling - Ocean Model. Erin began the ocean model, which is intended to inform us about the movement of plastic particles in the ocean.

Wet Lab. The main aim of wet lab team for today was to PCR the following plasmid backbones: PSB1A3, PSB1C3, PSB1K3. The PCR was done with Taq polymerase. The outcome was that the gel showed no bands. It was concluded that phusion kit will be used next time. The second aim was to inoculate samples from Friday’s transformation (we transformed four biobricks). There were three innoculations made per biobrick, which yielded twelve falcon tubes. In addition we wanted to repeat the inoculation of the ligation product (J23119+ B0034)because last week the nano drop for this ligation yielded very low concentrations after the miniprep. Overall we had 15 tubes in a shaker overnight.

Tuesday 7th August

Human Practice -Speed Debate: We hosted an evening of speed debating to deliberate the question “Should synthetic organisms be released in the ocean to combat plastic pollution?”. The evening was a success! Attendees ranged from all different backgrounds including Bloomberg, London Futurists group, London Hackspace and the Guardian. Check out the Speed Debating wiki page.

Meeting - Supervisor. The whole team met with Darren, our supervisor to discuss our problems in the wet lab.

Wet Lab. Today we minipreped yesterday’s inoculated samples of the following biobricks: J23100, J23106, B0030, 1750016 as well as the ligation product (J23119+ B0034). The outcome of inoculation was that only 6 out of 15 falcons had growth in them (three samples of J23106 and three samples of the ligation product) so the miniprep was done only for these six samples/falcon tubes. The result of miniprep was very low concentrations were found and the shape of the graph did not indicate the presence of DNA. This led to the conclusion that the transformations were not successful. Also PCR for the same plasmid backbones as yesterday (PSB1A3, PSB1C3, PSB1K3) plus an additional one (PSB1T3) was repeated (from yesterday) with phusion kit this time. As a result of this, the bands for the plasmid backbones were found to be in the right region (around 2000 bp) for three out of four samples (PSB1A3, PSB1C3, PSB1K3). There was no band for the fourth plasmid backbone.

Wednesday 8th August

Meeting - wiki. Philipp and Bethan met to discuss a contact web to visually acknowledge all of the people that have contributed to our project.

Modelling - Ocean Model. The model is essentially complete but needs further refinement.

Wet Lab. The aim for today was to colony pcr irrE and laccase genes. Irre gene came from Deinococcus Radiodurans that was provided by Prof John Ward, one of our advisers. The laccase was taken from the E. coli.

Thursday 9th August

Achievement - Good Article. The team were really pleased to find that the Good had written an article about our project.

Wet Lab. Today we were keen to test the success for irrE as well as laccase PCR from yesterday. Unfortunately, there were no bands in the 2000bp regions only in the regions of 100bp. We suspected that it was not DNA but RNA. As we had a few unsuccessful transformations previously we decided to test the effectiveness of our antibiotics. All antibiotics (ampicillin, chloramphenicol, tetracyclin, kanamycin)that we had were plated out together with LB agar. We are hoping to see no growth tomorrow to conclude that antibiotics had nothing to do with our unsuccessful transformations.

Saturday 11th and Sunday 12th August

Bournemouth Beach 'Fact-Finding Mission' Given the nature of our project, it was absolutely essential that we spent a weekend ~~topping up our tans~~ data-collecting on sunny Bournemouth beach. Our first task was to measure the temperature of the water, for which we used the well-established method of going in up to our ankles and standing around squealing. Having established that some of us were less keen than others to get our hair wet in the name of science, we moved on to something drier. Over the two days we took sand-samples from two different beaches - both the crowded sands of Bournemouth Beach (a tourist hotspot), and the quieter Sandbanks (popular with dog-walkers and for a spot of yachting). Our samples were sent back to the lab to be analysed for quantity of microplastics, and we've since beent in contact with a local environmental analysis company to see if they can give us any tips on how best to do this.

Reflections

This week has been an encouraging change to the previous weeks in the lab. We received further training in the lab, in an attempt to eliminate some of the problems we have been experiencing, and to enable us to work more efficiently. We also had our speed debate on Tuesday which was a great success, with an interesting turn-out of people.

Speed Debate.

Taq Polymerase.

@@ Line 32: / Line 32: @@
 <div class="notebook-wetlab"> '''Wet Lab.''' Today we were keen to test the success for irrE as well as laccase PCR from yesterday. Unfortunately, there were no bands in the 2000bp regions only in the regions of 100bp. We suspected that it was not DNA but RNA. As we had a few unsuccessful transformations previously we decided to test the effectiveness of our antibiotics. All antibiotics (ampicillin, chloramphenicol, tetracyclin, kanamycin)that we had were plated out together with LB agar. We are hoping to see no growth tomorrow to conclude that antibiotics had nothing to do with our unsuccessful transformations.</div>
+== Saturday 11th and Sunday 12th August ==
+''' Bournemouth Beach 'Fact-Finding Mission' ''' Given the nature of our project, it was absolutely essential that we spent a weekend <strike>topping up our tans</strike> data-collecting on sunny Bournemouth beach. Our first task was to measure the temperature of the water, for which we used the well-established method of going in up to our ankles and standing around squealing. Having established that some of us were less keen than others to get our hair wet in the name of science, we moved on to something drier.  Over the two days we took sand-samples from two different beaches - both the crowded sands of Bournemouth Beach (a tourist hotspot), and the quieter Sandbanks  (popular with dog-walkers and for a spot of yachting).  Our samples were sent back to the lab to be analysed for quantity of microplastics, and we've since beent in contact with a local environmental analysis company to see if they can give us any tips on how best to do this.

Team:University College London/Notebook/Week9

From 2012.igem.org