Team:UCL/Notebook

From 2013.igem.org

(Difference between revisions)
Line 122: Line 122:
3. Alex Bates - What will the killing mechanism be? A broad overview of cancer treatments is required, specifically detailing how a bacterium can administer the treatment.
3. Alex Bates - What will the killing mechanism be? A broad overview of cancer treatments is required, specifically detailing how a bacterium can administer the treatment.
</p>
</p>
 +
</p>
 +
Considerations:
 +
</p>
 +
a. The bacteria may secrete a toxin etc – how will we ensure that it doesn’t simply diffuse through the gut?
 +
b. If it is a toxin, what sort of biosynthetic pathway is required?
 +
c. Does the bacteria trigger apoptosis in the cancer cells (ie. an intracellular killing mechanism)? How can this be done from an extracellular bacterium? Perhaps beta-arrestin?
 +
d. Are there any treatments which we can take advantage of specifically because we are using bacteria?
 +
e. For example, a protein which creates holes in the cancer cells? Does using a bacterium open up the possibility of using a different cure that currently isn’t in use because we cannot target it to cancer cells – could the use of bacteria allow this?
 +
</p>
 +
4. Weiling Yuan - Targeting – do we use antibodies? What previous projects have used bacteria expressing antibodies? Are there any other ways of doing this? Perhaps the latching and initiation mechanisms can be incorporated into one protein?
 +
</p>
 +
5. StJohn Townsend - Initiation – mechanoreceptor activated upon latching? What other ways are there of doing this?
 +
</p>
 +
6. Tom Johnson - Past iGEM projects which we could incorporate into our own: Cancer projects, Gut projects, Protein engineering, Antibodies expressed in bacteria etc.
 +
</p>
 +
7th June -The team discusses findings from the initial research - further agreement that the 'Anti Cancer' project seemed to be the best idea, preparation of 'project sheets' to be sent to Dr. Darren Nesbeth for review and subsequent meetings.
 +
</p>
 +
11th June -looked a bit at the possible chassis species: salmonella, clostridium, helicobacter, E. coli. according to the tissue type/cancer type we shall decide which works with which. We start with E. coli in the lab.
 +
</p>
 +
We considered a pro-drug approach - bacterially directed enzyme pro-drug therapy which suggests that we may establish a transformed bacterial population with an enzyme capable to activate an ingested prodrug. This pro-drug would be connected to an antibody (possibly part of the tail) and would also have linking consensus sequence targeted by the enzyme produced locally by our bacteria.
 +
</p>
 +
From this above point Alex distinguished 2 scenarios built on the circuit sketch that he and Laia posted a while ago. These would be:
 +
</p>
 +
1) Kill unit produces tailed protein pro-drug (possibly tailed perforin) and signaling molecule, A. When A reaches a threshold amount, perforin and a protease to remove the confounding tail is produced, bacteria lyses and activated pro-drug acts on surrounding cells.
 +
</p>
 +
2) No protease is produced, because the tail can be cleaved off by matrix metalloproteases.
 +
</p>
 +
Goals for the end of this week:
 +
</p>
 +
- Alex, Andy and Weiling continue investigating possible candidates to fill in the parts for the scenarios
 +
</p>
 +
-Tom, KC and Ruxi make sure we have everything set up to start the work in the lab: protocol, parts etc.
 +
</p>
 +
12th June - Ruxi and Tom went through a general cloning protocol but then realised that the best way to prepare for the lab is to get familiarised with the iGEM distribution kits. We discovered that we are given almost everything we need in order to get it right.
 +
</p>
</p>

Revision as of 10:53, 5 September 2013

Notebook

January

First meeting was held after the team had been assembled. Introductions to each other and team building exercises take place to familiarise to help everyone get to know each other. Discussions take place with previous iGEM team members from UCL so the new team gain some context and guidance concerning how to approach an iGEM project.

Each member of the new team was told to present for 5 minutes on a 2012 based team, commenting on their strengths and weaknesses. Further discussions about the general area 'track' that the team would be interested in. Given that many team members have a medical sciences background, medical based ideas were favoured among the majority of the team.

February

First meeting was held after the team has been assembled. Introduction to each other and team building exercises take place to familiarise the team members with each other. Discussions take place with previous iGEM team members from UCL so the new team have some context and guidance concerning how to approach any iGEM project.

• Weight control yoghurt

• Anti-cancer yoghurt

• Zebrafish water cleaning system for Third World

• Athletic Drug testing

• Clean Urban Air

• Neural network with glowing bacteria and fibre optics

Visited a DIY SynBio group at The Arts Catalyst for feedback on our project ideas and to display posters we can created for them, in order to get feedback from the members of the public who came to the venuw for synbio workshops. Some of the members there were previous iGEM candidates from several countries, with many liking the anti cancer yoghurt idea. In general, the publlic found medical projects more appealing, partly becuase they tried to solve tangible problems that cannot be mitigated soley by 'electrical' or 'mechnaical' technologies. The 'neural networks' idea gathers interest with scientists at Cancer Reserach UK and members of the public alike becuase bringing apllying synethtic biology to study neuroscience seems both innovative and relatively original. The zebrafish idea gathers interest becuase of the novel chassis. The other ideas do not do so well due to commonly being seen in iGEM, and being common promises of synthetic biology in general.

March

Final meetings before exams, both internally and at the Arts Catalyst. In the mean time we had taken on board our feedback, and took the best ideas from each of the most popular project to come up with a new idea that combined takling a medical condition, with neuroscience, with using a novel chassis in an Alzheimer's disease project. The idea pool has now been narrowed down to:

• Anti-cancer yoghurt

• Zebrafish

• Alzheimer's disease

• Neural Network

Members of the group also held a probiotic yoghurt workshop for the anti-cancer project, where members of the public made yoghurt. The audience were informed about the project and opinions were gathered. Again, the fact that the porject was medical was well received, though some ethical concerns were raised so that we knew we would have to make bioethics a big part of our project from the start.

April & May

Exam period - iGEM work to commence full time after the slog through exams.

June

5th June - Group discussion concerning the project idea to be carried forward - favouring the 'Anti cancer project'. Roles were then assigned to team members present for intial research roles for the week: Cancer research roles:

1. Ruxi Comisel - Proteins upregulated in cancer of the intestines. Specifically in the outer epithelial cell (enterocytes) – in microvilli. Also, what actually is... gut cancer? A general overview would be useful…

2. Khaicheng Kiew - Our chassis (bearing in mind that we will also build it in E. coli as a backup). We need to think what would make a good chassis in our case (ie. naturally found in the gut in an obvious one), and how well does the chassis fit.

3. Alex Bates - What will the killing mechanism be? A broad overview of cancer treatments is required, specifically detailing how a bacterium can administer the treatment.

Considerations:

a. The bacteria may secrete a toxin etc – how will we ensure that it doesn’t simply diffuse through the gut? b. If it is a toxin, what sort of biosynthetic pathway is required? c. Does the bacteria trigger apoptosis in the cancer cells (ie. an intracellular killing mechanism)? How can this be done from an extracellular bacterium? Perhaps beta-arrestin? d. Are there any treatments which we can take advantage of specifically because we are using bacteria? e. For example, a protein which creates holes in the cancer cells? Does using a bacterium open up the possibility of using a different cure that currently isn’t in use because we cannot target it to cancer cells – could the use of bacteria allow this?

4. Weiling Yuan - Targeting – do we use antibodies? What previous projects have used bacteria expressing antibodies? Are there any other ways of doing this? Perhaps the latching and initiation mechanisms can be incorporated into one protein?

5. StJohn Townsend - Initiation – mechanoreceptor activated upon latching? What other ways are there of doing this?

6. Tom Johnson - Past iGEM projects which we could incorporate into our own: Cancer projects, Gut projects, Protein engineering, Antibodies expressed in bacteria etc.

7th June -The team discusses findings from the initial research - further agreement that the 'Anti Cancer' project seemed to be the best idea, preparation of 'project sheets' to be sent to Dr. Darren Nesbeth for review and subsequent meetings.

11th June -looked a bit at the possible chassis species: salmonella, clostridium, helicobacter, E. coli. according to the tissue type/cancer type we shall decide which works with which. We start with E. coli in the lab.

We considered a pro-drug approach - bacterially directed enzyme pro-drug therapy which suggests that we may establish a transformed bacterial population with an enzyme capable to activate an ingested prodrug. This pro-drug would be connected to an antibody (possibly part of the tail) and would also have linking consensus sequence targeted by the enzyme produced locally by our bacteria.

From this above point Alex distinguished 2 scenarios built on the circuit sketch that he and Laia posted a while ago. These would be:

1) Kill unit produces tailed protein pro-drug (possibly tailed perforin) and signaling molecule, A. When A reaches a threshold amount, perforin and a protease to remove the confounding tail is produced, bacteria lyses and activated pro-drug acts on surrounding cells.

2) No protease is produced, because the tail can be cleaved off by matrix metalloproteases.

Goals for the end of this week:

- Alex, Andy and Weiling continue investigating possible candidates to fill in the parts for the scenarios

-Tom, KC and Ruxi make sure we have everything set up to start the work in the lab: protocol, parts etc.

12th June - Ruxi and Tom went through a general cloning protocol but then realised that the best way to prepare for the lab is to get familiarised with the iGEM distribution kits. We discovered that we are given almost everything we need in order to get it right.

Retrieved from "http://2013.igem.org/Team:UCL/Notebook"