Notebook: Week 6
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
Aims of the Week
Our main aim this week is to create a line of competent cells, by reinvigorating our previous cell line. This protocol began last week, and will be finished by Tuesday. At this point we can test the competency of the new line, and hopefully recommence our transformations. Also, with regards the wiki, we are hoping to make significant progress on its content. in particular we would like the get more of our information onto the Research page, and also set up a safety page, a protocols page, and a Lab Book. Also, Carina is working on some inforgraphics for our homepage, which will make the principles and aims of our projects much simpler. For the Rathenau debate, Erin hopes to make it half way through the first draft of the more detailed proposal Rathenau have asked for. Finally, for modelling, the aim is to develop the Matlab model for degradation, and we are waiting to hear back from Professor Rowley who will assist us with the degradation equation. In the meantime they will be working on buoyancy and the ocean model
Monday
Wet Lab - James and Aurelija continued the reinvigoration of the W3110 cell line today, after culturing it on agar over the weekend. Single colonies picked from minimal agar plates and used to seed 5ml cultures overnight in preparation for day 3 of protocol. We hope this will produce a more competent cell line, capable of more efficient transformation.
Modelling - Joanne, Aurelija and Erin continued their search for software for the ocean model representation, this included researching Ferret and Panoply, and lookinng into past iGEM modelling presentations. They are particularly impressed by Columbia 2011. Outcome: We have established the necessity to use Panoply software.
Design - Carina has been working on the caricatures of the team for a 'meeting the team' image for the homepage.
Tuesday
Meeting - Wiki - Rhiannon met with Aurelija and Yeping to discuss the details for the Research page. The Research page is still a work in progress, and while we work on some diagrams to make our project more comprehensive, we want to ensure the text explains our project as clear as possible. Outcome: We have a draft overview for every module that explains each module in context of the others, and how the system works individually. We also hope to include a more detailed explanation of the decision making process.
Meeting - Degradation Module. Rhiannon and Yeping met to discuss the search for the laccase gene for the degradation module. Unfortunately, attempts to get hold of the C208 strain of Rhodococcus ruber has failed, which was our preferred choice of laccase gene. We researched other laccase genes which may have plastic degradation properties, as well as alternative enzymes. Outcome: It was very difficult to find a gene for which the sequence was available. We did find the sequence for one, but we are unsure of its plastic degradation properties.
Wet Lab - James and Aurelija completed their reinvigoration of the W3110 cell line, and Rhiannon transformed a sample of this cell line with a reference plasmid, to determine how successful the reinvigoration was. The transformed cells were placed in overnight culture.
Design - Carina has been working on the design for the homepage of the wiki. She is designing a series of images to explain our project 'in a nutshell', to enable visitors reading the more detailed area of the wiki to understand the context and scientific principles behind our project.
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