Revision as of 16:29, 6 July 2012

Notebook: Week 4

Aims For This Week

Our aim this week is to transform the ¬¬curli, ribosome binding site and GFP biobrick for Module 1 – Binding to Plastics. The Modelling Crew are aiming to finish their ocean model, and begin modelling their 1st receptor model – for the Curli biobrick. The Human Practice team would also like to begin contacting other teams via the iGEM headquarters, to recruit for our radio show, and plan an exhibition at the Dana centre.

Monday

Meeting – Construction/Characterisation Bouran, Leonard, James and Aurelija had a meeting with our main supervisor Darren Nesbeth to discuss our progress on construction/characterisation and to set realistic aims for the week. Several aspects of construction were discussed. The main focus was on the detection module which was based on the human oestrogen receptor (ER). From the data collected on ER folding and activity in prokaryotic cells, it became clear to us that it is extremely difficult to make ER function in prokaryotic cells. Consequently, we decided to look for alternatives for our detection system. However, as we already have ER on our kit we decided to evaluate its functionality soon to see if our assumptions about it were correct.

Modelling. Joanne, Aurelija and Erin started working on our first model for degradation module. First we looked for the right software. Initially we were considering both COPASI 4.8 as well as Matlab . We finally decided to use Matlab as it will give greater flexibility to our model. The aim for the degradation model is to represent degradation of polyethylene in two different environments: ocean as well as lab.

Human Practice Today Yeping, Martina and Carina planned our activities for UCL Open Day that will take place on Wednesday (4th of July). This is a great opportunity for us to highlight the problem of microplastics to society. We decided on the several interactive activities that we will be offering to the prospective UCL students during the open day. These will include a demonstration of motion video that has been created by our team members and which represents the idea behind our project; also we decided to prepare several questions about microplastics pollution to enhance the awareness amongst the perspective students. The interactive activity 'make your piece of art using plastic waste' was chosen as well; for this we will need to collect some plastic waste before Wednesday.

Tuesday

Wet lab-agar preparationToday our lab work was concerned with agar plate preparation which allow us to start transformations tomorrow. Three team member prepared the following agar plates: LB, LB+Ampicillin & LB+Chloramphenicol. This will allow us to begin biobrick transformation.

Modelling. We managed to deduce the equation for our degradation model that is based on specific activity of our enzyme of interest which is laccase. Tomorrow we will be able to write a code for this specific reaction on matlab. The equation deduced today is only initial, as we progress we might additional 'noise' representations to it.

Achievement - Open day! Today Carina created an amazing poster that will be used during the open day tomorrow as our project representation! It shows all the land that will be available for all of us to inhabit once the plastic island is created.

Wednesday

Wet Lab - Transformation of Competent Cells. Todays lab team, Rhiannon, Bouran and Leonard, transformed cells with the Curli Cluster, Ribosome Binding Site, and GFP Biobrick. These three biobricks are involved in the binding module

Modelling. Erin invested time today learning how to use MATLAB GUI to make a user interface for our degradation module.Outcome: Erin produced a skeleton code which we can fit the equations into. This is signficant progress because this code can also be user to model our other modules

Human Practice - Outreach at UCL open day

@@ Line 24: / Line 24: @@
 <div class="notebook-training">  ''' Wet lab-agar preparation'''Today our lab work was concerned with agar plate preparation which allow us to start transformations tomorrow. Three team member prepared the following agar plates: LB, LB+Ampicillin & LB+Chloramphenicol. This will allow us to begin biobrick transformation. </div>
-<div class="notebook-modelling">Modelling. We managed to deduce the equation for our degradation model that is based on specific activity of our enzyme of interest which is laccase. Tomorrow we will be able to write a code for this specific reaction on matlab. The equation deduced today is only initial, as we progress we might additional 'noise' representations to it. </div>
+<div class="notebook-modelling">'''Modelling'''. We managed to deduce the equation for our degradation model that is based on specific activity of our enzyme of interest which is laccase. Tomorrow we will be able to write a code for this specific reaction on matlab. The equation deduced today is only initial, as we progress we might additional 'noise' representations to it. </div>
 <div class="notebook-achievement">  '''Achievement - Open day!''' Today Carina created an amazing poster that will be used during the open day tomorrow as our project representation! It shows all the land that will be available for all of us to inhabit once the plastic island is created. </div>
+== Wednesday ==
+<div class="notebook-training"> '''Wet Lab - Transformation of Competent Cells'''. Todays lab team, Rhiannon, Bouran and Leonard, transformed cells with the Curli Cluster, Ribosome Binding Site, and GFP Biobrick. These three biobricks are involved in the binding module</div>
+<div class="notebook-modelling">'''Modelling'''. Erin invested time today learning how to use MATLAB GUI to make a user interface for our degradation module.Outcome: Erin produced a skeleton code which we can fit the equations into. This is signficant progress because this code can also be user to model our other modules </div>
+<div class="notebook-human"> '''Human Practice - Outreach at UCL open day'''
+</div>

Team:University College London/Notebook/Week4

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