Latest revision as of 18:54, 26 September 2012

Notebook: Week 5

Aims for the Week

The Construction Crew are being ambitious this week, and will attempt to transform and purify eight biobricks. These are not from a particular module, but include many of the Promoters we want to use and the Ribosome Binding Site biobrick which failed to work last week. The Modellers wish to model the buoyancy biobricks because they have the most information for this, and using the Groningen 2009 modelling, they have a good idea of how to apply it to our project. They also plan on modelling the laccase gene for the degradation module, which we hope to obtain to transform into our bacteria. The laccase gene is from a strain of bacteria found to degrade polyethylene. Erin is taking a break from modelling to work on the proposal for the Rathenau debate, and hopes to get it in essay format by the end of the week. The Sponsorship team aim to complete their list of potential sponsors to email and create a detailed account of our budget. The key aim for Human Practices is to get a security license for our DIYbio event - without which we may have to downsize the scope of our event, and to confirm guests for our radio show. Our competition Poster is also making progress, and Carina and Aurelija will be meeting this week to ensure its completion. Finally, Rhiannon is aiming to finalise the application for the Transnatural Conference, which is due this week.

Monday 9th July

Wet Lab. - Using our batch of competent cells, we transformed the seven biobricks today, using the standard protocol. This included mainly promoters required across all of our modules

Poster - Carina arranged to meet Aurelija and Rhiannon this afternoon to discuss the design of the poster. So far we have a background with an artistic representation of the principles of our project, the design of the heading, and a provisional layout of the content.

Modelling. - Erin, Joanne and Aurelija continued to work on the degradation equation and GUI, with the particular aim of finding a interactive visual way in which to present the data.

Human Practice - Yeping emailed Jane Calvert from Edinburgh University to get some feedback on the DIYbio event. There is still uncertainty as to whether we will get the permission to proceed with this event, which is unfortunate as it would be a great means of extended Synthetic Biology into the community. Jane Calvert replied that it was a great idea and would certainly add value to the project, which has encouraged us to persist.

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

Tuesday 10th July

Wet Lab - Checking the agar plates have grown after yesterday's transformation. We discovered that only 2 out of the 8 transformations were succesfful combined with the low colony numbers from the previous transformations, we were forced to conclude that our cells have low competence. We are in the process of making new competent cells, and purifing the 2 biobricks that did successfully transform Yeping and Martina also ran a gel and undertook nanodropping to determine the DNA concentration of the Curli and GFP biobricks transformed last week.

Meeting - Wiki - Rhiannon, Carina and Philipp met to discuss the design and branding of our wiki. We worked mainly on how to represent our project on the homepage. We decided that the homepage should be entry level, and not too focused on the science behind the project. As a result we decided to go for a series of 'infographic' diagrams - each of which answer a different key questions about our project. The default picture will be of our Plastic Republic - the endpoint of our project - and a series of click-through infographics will explain the background of the project and the mechanisms of construction.

Modelling - Aurelija and Joanne continued working on the degradation model and GUI, and Aurelija explored Cell Designer and KAPPA to see how they might be employed in our project. Outcome: Their MATLAB code works but there are problems with their rate equation, so they are going to continue working on that.

Meeting - UCL media. - Martina arranged to meet with UCL media about writing an article about out work. Outcome: They have confirmed they will write and article, which hopefully will result in more people getting involved in our project

Wednesday 11th July

Training - Leika Light Microscope. - We're hoping to produce as many of our results as possible as visual data - to make our data more accessible to people with less experience of science. Steffan trained us how to control the microscope, how to connect it to a computer, and how to capture images of our cells.

Wetlab. - After the issues with cell competency, Rhiannon transformed a cell line by heat shock with a reference plasmid to do a formal test of its competency. Yeping also ran a repeat of the gel for the curli and GFP biobrick, after the bands from yesterdays gel were not clear.

Meeting - Human Practice. - Rhiannon, Philipp and Bethan met to discuss the Speed Debating event we plan on running for Human Practice. We have so far decided on six groups of people we would like to invite to run workshops on the debate topic, including representatives from environmental group and synthetic biology. After the workshops we would like to run a form of speed debate, whereby individuals pair up and have five minute debates before being rotated around the room. We hope that by running the workshop, we will enable anyone to form an opinion about the topic and carry out a debate.

Human Practice. - In order to determine whether we can go ahead with the DIYbio event, Yeping has been contacting health and safety personnel around UCL for advice about taking our science off UCL campus. Also, Philipp posted a debate on the TED website, in order to get opinions for the debate we are planning for our Speed Debating event.

Thursday 12th July

Wetlab - Reinvigorating Cells. - James and Aurelija began reinvigorating our cell line - with the aim of improving their competency. There has been increasing evidence over the last two weeks that there is a declining efficiency of transformation - with a reduction in success from 2/3 to 2/8. Outcome: Cells were ready for beginning the competency protocol on Friday

Training - Gibson Assembly - Bouran, Aurelija, Martina and Yeping attended training in Gibson Assembly protocol, to develop a strategy of how to use it in our project.

Achievement - DVICE article. - We found this afternoon that DVICE has published an article on our project on their website.

Modelling - Joanne and Aurelija met with Professor Rowley, who told them what was wrong with their degradation equation and offered to help modify and revamp it. He has also offered to help us use Excel as alternative to matlab modelling.

Human Practice. - Yeping and Philipp met the departmental GMO officer to talk about university regulations regarding the DIYbio event. It was felt necessary to before preceding to have a health and safety discussion with people from the DIYbio community at London Hackspace so they are able to set up their own health and safety framework.

Friday 13th July

Wetlab - Cell Competency. Given we have had mixed results with the competency of our cells, we decided to test their competency by transforming them with a reference plasmid of known concentration. A positive and negative control were also set up. Outcome: Cells are imcompetent - there was no colony formation. After reinvigorating their cell lines, James and Aurelija commenced the protocol to begin a new reinvigorated cell line. Outcome: Colonies appearing on minimal agar plates allowing continuation onto day two of the protocol - after weekend culture at 30 degrees.

Human Practice. - Yeping wrote up a lab schedule for DIYbio, and discussed the health and safety concerns with our supervisor, Prof. Eli Keshavarz-Moore. The team also confirmed speakers for the iGEM radio show, including Virgil Rerimassie from the Rathenau Institute.

Modelling. - Joanne and Aurelija discussed with Tom about the ocean model, and we're thinking of using alternatives to MatLab to create a more visual model.

Reflections

We are currently concerned about the problems we have experience with cell competency, and have taken steps this week to reinvigorate our previous cell line, as well as creating a new more competent cell line. Once we have a competent cell line, we feel confident that the lab work will progress rapidly. We have also been tackling concerns with Human Practice this week, notably the issues regarding the safety of our DIYbio project. While these aspects of the project have been difficult, we are encouraged by all the packages from in-kind sponsorship we have received this week.

Success of the Week We had two articles published about our project this week - Smithsonian and DVICE

Fail of the Week The competency of our cells is extremely low, and we will need to create a new competent cell line

@@ Line 5: / Line 5: @@
 {{:Team:University_College_London/templates/notebookmenu}}
+== Aims for the Week ==
+The '''Construction Crew''' are being ambitious this week, and will attempt to transform and purify eight biobricks. These are not from a particular module, but include many of the '''Promoters''' we want to use and the '''Ribosome Binding Site''' biobrick which failed to work last week. The '''Modellers''' wish to model the buoyancy biobricks because they have the most information for this, and using the Groningen 2009 modelling, they have a good idea of how to apply it to our project. They also plan on modelling the laccase gene for the degradation module, which we hope to obtain to transform into our bacteria. The laccase gene is from a strain of bacteria found to degrade polyethylene. Erin is taking a break from modelling to work on the proposal for the Rathenau debate, and hopes to get it in essay format by the end of the week. The '''Sponsorship''' team aim to complete their list of potential sponsors to email and create a detailed account of our budget. The key aim for '''Human Practices''' is to get a security license for our DIYbio event - without which we may have to downsize the scope of our event, and to confirm guests for our radio show. Our competition Poster is also making progress, and Carina and Aurelija will be meeting this week to ensure its completion. Finally, Rhiannon is aiming to finalise the application for the Transnatural Conference, which is due this week.
+== Monday 9th July ==
+<div class="notebook-wetlab"> '''Wet Lab.''' - Using our batch of competent cells, we transformed the seven biobricks today, using the standard protocol. This included mainly promoters required across all of our modules </div>
+<div class="notebook-sponsor"> '''Sponsorship.''' - Bethan was in contact with Promega, Mendeley and Lonza today and confirmed shipment of our in-kind products. These are eagerly awaited by the lab. </div>
+<div class="notebook-poster"> '''Poster''' - Carina arranged to meet Aurelija and Rhiannon this afternoon to discuss the design of the poster. So far we have a background with an artistic representation of the principles of our project, the design of the heading, and a provisional layout of the content. </div>
+<div class="notebook-modelling">''' Modelling.''' - Erin, Joanne and Aurelija continued to work on the degradation equation and GUI, with the particular aim of finding a interactive visual way in which to present the data.</div>
+<div class="notebook-human"> '''Human Practice''' - Yeping emailed Jane Calvert from Edinburgh University to get some feedback on the DIYbio event. There is still uncertainty as to whether we will get the permission to proceed with this event, which is unfortunate as it would be a great means of extended Synthetic Biology into the community. Jane Calvert replied that it was a great idea and would certainly add value to the project, which has encouraged us to persist. </div>
+<div class="notebook-news"> '''Achievement  - Smithsonian Article.''' - The team were really pleased to find that the Smithsonian had written an article about our project. </div>
+== Tuesday 10th July ==
+<div class="notebook-wetlab"> '''Wet Lab''' - Checking the agar plates have grown after yesterday's transformation. We discovered that only 2 out of the 8 transformations were succesfful combined with the low colony numbers from the previous transformations, we were forced to conclude that our cells have low competence. We are in the process of making new competent cells, and purifing the 2 biobricks that did successfully transform
+Yeping and Martina also ran a gel and undertook nanodropping to determine the DNA concentration of the Curli and GFP biobricks transformed last week.  </div>
+<div class="notebook-wiki"> '''Meeting - Wiki''' - Rhiannon, Carina and Philipp met to discuss the design and branding of our wiki. We worked mainly on how to represent our project on the homepage. We decided that the homepage should be entry level, and not too focused on the science behind the project. As a result we decided to go for a series of 'infographic' diagrams - each of which answer a different key questions about our project. The default picture will be of our Plastic Republic - the endpoint of our project - and a series of click-through infographics will explain the background of the project and the mechanisms of construction. </div>
+<div class="notebook-modelling"> '''Modelling''' - Aurelija and Joanne continued working on the degradation model and GUI, and Aurelija explored Cell Designer and KAPPA to see how they  might be employed in our project. '''Outcome''': Their MATLAB code works but there are problems with their rate equation, so they are going to continue working on that. </div>
+<div class="notebook-sponsor"> '''Sponsorship.''' - The Lonza and Promega packages arrived so the lab crew can proceed with miniprep. We also received eppendorf tubes, gloves, restriction enzymes, DNA ladders.</div>
+<div class="notebook-news"> '''Meeting - UCL media.''' - Martina arranged to meet with UCL media about writing an article about out work. Outcome: They have confirmed they will write and article, which hopefully will result in more people getting involved in our project </div>
+== Wednesday 11th July ==
+<div class="notebook-training"> '''Training - Leika Light Microscope.''' - We're hoping to produce as many of our results as possible as visual data - to make our data more accessible to people with less experience of science. Steffan trained us how to control the microscope, how to connect it to a computer, and how to capture images of our cells. </div>
+<div class="notebook-wetlab"> '''Wetlab.''' - After the issues with cell competency, Rhiannon transformed a cell line by heat shock with a reference plasmid to do a formal test of its competency. Yeping also ran a repeat of the gel for the curli and GFP biobrick, after the bands from yesterdays gel were not clear. </div>
+<div class="notebook-meeting"> '''Meeting - Human Practice.''' - Rhiannon, Philipp and Bethan met to discuss the Speed Debating event we plan on running for Human Practice. We have so far decided on six groups of people we would like to invite to run workshops on the debate topic, including representatives from environmental group and synthetic biology. After the workshops we would like to run a form of speed debate, whereby individuals pair up and have five minute debates before being rotated around the room. We hope that by running the workshop, we will enable anyone to form an opinion about the topic and carry out a debate.</div>
+<div class="notebook-human"> '''Human Practice.''' - In order to determine whether we can go ahead with the DIYbio event, Yeping has been contacting health and safety personnel around UCL for advice about taking our science off UCL campus. Also, Philipp posted a debate on the TED website, in order to get opinions for the debate we are planning for our Speed D''eb''ating event.</div>
+<div class="notebook-sponsor"> '''Sponsorship.''' - Bethan emailed a thank you to Promega for their in-kind sponsorship, including some photos of our lab work. </div>
+== Thursday 12th July ==
+<div class="notebook-wetlab"> '''Wetlab - Reinvigorating Cells.''' - James and Aurelija began reinvigorating our cell line - with the aim of improving their competency. There has been increasing evidence over the last two weeks that there is a declining efficiency  of transformation - with a reduction in success from 2/3 to 2/8. '''Outcome:''' Cells were ready for beginning the competency protocol on Friday </div>
+<div class="notebook-training"> '''Training - Gibson Assembly''' - Bouran, Aurelija, Martina and Yeping attended training in Gibson Assembly protocol, to develop a strategy of how to use it in our project. </div>
+<div class="notebook-news"> '''Achievement - DVICE article.''' - We found this afternoon that DVICE has published an article on our project on their website.  </div>
+<div class="notebook-modelling"> '''Modelling''' - Joanne and Aurelija met with Professor Rowley, who told them what was wrong with their degradation equation and offered to help modify and revamp it. He has also offered to help us use Excel as alternative to matlab modelling.</div>
+<div class="notebook-elsi"> '''Human Practice.''' - Yeping and Philipp met the departmental GMO officer to talk about university regulations regarding the DIYbio event. It was felt necessary to before preceding to have a health and safety discussion with people from the DIYbio community at London Hackspace so they are able to set up their own health and safety framework.</div>
+== Friday 13th July ==
+<div class="notebook-wetlab"> '''Wetlab - Cell Competency.''' Given we have had mixed results with the competency of our cells, we decided to test their competency by transforming them with a reference plasmid of known concentration. A positive and negative control were also set up. Outcome: Cells are imcompetent - there was no colony formation. After reinvigorating their cell lines, James and Aurelija commenced the protocol to begin a new reinvigorated cell line. Outcome: Colonies appearing on minimal agar plates allowing continuation onto day two of the protocol - after weekend culture at 30 degrees. </div>
+<div class="notebook-hackspace"> '''Human Practice.''' - Yeping wrote up a lab schedule for DIYbio, and discussed the health and safety concerns with our supervisor, Prof. Eli Keshavarz-Moore. The team also confirmed speakers for the iGEM radio show, including Virgil Rerimassie from the Rathenau Institute.  </div>
+<div class="notebook-sponsor"> '''Sponsorship.''' - Bethan has been in contact with promega about our project so they can publicise it on their facebook. </div>
+<div class="notebook-modelling"> '''Modelling.''' - Joanne and  Aurelija discussed with Tom about the ocean model, and we're thinking of using alternatives to MatLab to create a more visual model.  </div>
+== Reflections ==
+We are currently concerned about the problems we have experience with cell competency, and have taken steps this week to reinvigorate our previous cell line, as well as creating a new more competent cell line. Once we have a competent cell line, we feel confident that the lab work will progress rapidly. We have also been tackling concerns with Human Practice this week, notably the issues regarding the safety of our DIYbio project. While these aspects of the project have been difficult, we are encouraged by all the packages from in-kind sponsorship we have received this week.
+<div class="notebook-success">'''Success of the Week''' We had two articles published about our project this week - <html><a href="http://blogs.smithsonianmag.com/smartnews/2012/07/synthetic-bacteria-could-turn-ocean-garbage-into-one-big-island/" title="Article" target="_blank">Smithsonian</a> and  <a href="http://dvice.com/archives/2012/07/students-synthe.php" title="Article" target="_blank">DVICE</a></html> </div>
+<div class="notebook-fail"> '''Fail of the Week''' The competency of our cells is extremely low, and we will need to create a new competent cell line</div>
 {{:Team:University_College_London/templates/foot}}

Team:University College London/Notebook/Week5

From 2012.igem.org