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Team:St Andrews/diary
From 2011.igem.org
Diary
Pre-Summer
Meeting 1
On our very first meeting, we had a brain storm about possible projects. The first ideas can be seen on the mind map below.
Meeting 2
On our second meeting we tried to refine the ideas and come up with more possible projects.
Meeting 3
After doing some further reading, we narrowed some of the topics down.
Meeting 4
At this meeting we discussed the possibility of our team participating at the St. Andrews annual outreach event during the NSEW (National Science and Engineering Week) between the 11th and 20th of March.
“National Science & Engineering Week shines the spotlight each March on how the sciences and engineering relate to our everyday lives and helps to inspire the next generation of scientists with fun and participative activities.” from British Science Association
The plan was to tell children about the functions of specific sections of DNA – promoters, ribosome binding sites etc., and create a simple game which could enhance their understanding of genetics. We decided on using mega-blocks of different shapes to represent a promoter, a ribosome binding site, a gene and a terminator and allow the children to put the pieces together in the correct order to make a “bio-brick”.
Meeting 5
For the NSEW event we decided to use a poster and instructional cards to aid in our ability to help children understand the functions of different segments of DNA. After a lot of deliberation, we came up with the following poster.
Meeting 6
At this meeting we discussed the idea of using apoptosis as a means of drug delivery and thus using the cell as a factory for drug creation. We realized, however, that the destruction of the cell's organelles and components upon apoptosis may lead to the destruction of the drug. We then discussed other means of transport of the drug such as a pump that could release the drug molecules when it encounters an environmental trigger such as pH.
We also discussed contacting members from last years’ St. Andrews iGEM team to familiarize us with various laboratory procedures that we would use over the summer.
For our next meeting we decided to do some research into whether the pump we required existed and what restrictions it would place on the drug's molecular structure.
Meeting 7
We discussed the possibility of modifying our project -"Drug Delivery to the Gut using bacteria" to make the bacteria produce another drug or a protein which could potentially treat or cure another disease.
We also considered exploring prokaryotic cell death signals as apoptosis is not very feasible in prokaryotic cells like bacteria.
Meeting 8
In our last meeting before summer we explored the possibility of making bacteria secrete other substances in the gut which could enhance immunity – or perhaps create a kill switch in the bacteria which could have various applications in drug delivery. At this point we explored the functions of anti-microbial peptides and how we could use them to create a kill switch.
We did some research on antimicrobial peptides and decided that our project would be to create a ‘kill switch’ where we would insert a gene (protogrin-1) coding for Anti-Microbial Peptides (AMP’s) into E. Coli. The idea was to then use different promoters to switch on the expression of these proteins in certain conditions
Summer
Week 1 - 11/07/11
Day 1:On our first day back the team and Dr. Anne Smith had a meeting where we discussed our project idea of creating a kill switch by using antimicrobial peptides. We proceeded to divided the different tasks amongst ourselves and came up with an action plan for the next few weeks. The purpose of this was twofold, to make our team more efficient and have some sort of way of measuring progress.
We made sure that we all knew the IGEM 2011 Judging Criteria and recorded all deadlines posted on the IGEM website on our team board.
The lab team familiarized themselves with the lab where we would be carrying out our experiments over the summer and we did some simple lab chores such as autoclaving various jars and bottles, preparing Luria broth for plating and storage and learnt about different lab procedures necessary for our experiments.
Max began work on the St Andrews team wiki, while Christina began creating a list of an assortment of labs and companies that we could contact for sponsorship.
Day 2:
Charlie began work on the Project Description while Sam and Max continued work on the team wiki.
Lamya and Christina collected the notes of previous IGEM meetings that took place during the semester and built mind maps to be put on the wiki.
To finalise the lab team prepared overnights of E. coli in Luria broth so that they could run a practice transformation and gel electrophoresis later in the week.
Day 3:
We completed the Project Summary form and Safety Proposal and put them on the team wiki, the team then concentrated in finishing with the pre-summer meeting material. After completing the sponsorship proposal Christina began emailing potential sponsors.
In the meantime the lab team made the E. coli from the overnights and carried out practice transformation experiments using a biobrick which provides resistance to ampicillin.
Day 4:
Charlie and Ogaga began researching various constitutive and positive promoters, in order to complete our basic biobrick sequence and order DNA.
We booked the flights and taxis for the trip to Norwich and created a St Andrews IGEM Gmail, Facebook, Flickr and Twitter accounts. The latter would be used to communicate with other IGEM teams throughout the project.
The lab team made more overnights of the transformed E. coli colonies for the experiments to be carried out on the following day.
Day 5:
The lab team ran a mini prep, a restriction digest and a gel electrophoresis. The results of the gel electrophoresis showed that no DNA was present in our gel so we discussed the possibility that we had let the DNA sit in the wells of the gel for too long causing it to sink through the gel. In order to corroborate this we decided to run another gel on Monday morning.
The team continued contacting sponsors, receiving some positive responses. For our human practices project the team brainstormed various ideas such as conducting surveys, etc.
Week 2 - 18/07/11
Day 1:The lab team re-did the gel electrophoresis which had previously shown no presence of DNA, with a smaller gap of time between preparing the gel and running the DNA on it. Our experiment was successful and the results confirmed our hypothesis.
Charlie and Ogaga further explored different promoters and regulators and completed the basic biobrick sequence for the project. With this done Anne ordered the necessary DNA.
Christina and Lamya continued emailing and calling sponsors while Max continued working on the team wiki.
Day 2:
The team explored conjugation and drug-delivery as potential applications of our project and we explored the IGEM registry for biobricks that could help us test the feasibility of our applications.
Later on we brainstormed ideas for our human practices project and discussed some potential questions that could be addressed.
Day 3:
As a part of our human practices project, the team decided to explore the possibility of conducting a meta analysis on the data provided by the human practices projects of previous IGEM teams in order to find some correlations between the projects of different university over the world.
Sam, Ogaga and Lamya collated the data for all the 2010 human practices projects and concluded that the projects were too divergent to show any significant trends that could be used to draw conclussions. Leading us to abandon the idea of using this idea as our human practices project.
Day 4:
We prepared and practiced the presentation we planned to give at the UK IGEM Meet-up in Norwich on Monday while Max continued working on the wiki. Charlie and Ogaga concentrated in designing some experiments and controls to test the potential applications of our project.
Day 5:
The team discussed further on potential ideas for the human practices component of our project and we agreed on a brilliant and inovative project. This project however required support from organisers from external events, so we drew a clear HP plan and contacted the relevant parties.
Week 3 - 25/07/11
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Week 4 - 1/08/11
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Week 5 - 8/08/11
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Week 6 - 15/07/11
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Week 7 - 22/08/11
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Week 8 - 29/08/11
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Week 9 - 05/09/11
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Week 10 - 12/09/11
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