Team:NTNU Trondheim/Notebook/May

From 2012.igem.org

NTNU IS B.A.C.K.
Bacterial Anti-Cancer-Kamikaze

Notebook May


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Friday 25.05.12


We started continuing our dicussion on which toxins we should make our cells produce. If we manage to make the cells lyse only in the presence of the signaling molecule we chose to go with, it shouldn't mather what the cells produce, but if the system turns out to be leaky, it will be a problem if the toxins we prodce is too toxic. That way we would also kill healthy cells. Also, another problem with too toxic molecules is that we will need a special lab to work with them. So we decided to go for the happy mean. We also discussed the posiibility of making the intracellular concentration of toxins a checkpoint for lysis, so that even if a signal molecule is present, or the cells is experiencing an oxygen deficient environment, they would still not lyse until the concentration of anti cancer molecules is high enough.

We now have three different modules involved in our project; a production part, a detection part and a lysis part. We decided to split in three groups and investigate these modules in depth;

  • Production - Nina and Ove
Nina and Ove will investigate further what kind of molecules we could make our cells produce, and since we got the names of some people working with toxins on the meeting with prof. Otterlei, we decided to contact them to hear if they can help us. We will also be contacting Jay Bradner.
  • Detection - Eirin and Gunvor
Eirin and Gunvor will look at possible signaling molecules we could use for detection of cancer cells. So far, we have decided to investigate HGF, the growth factor prof. Otterlei suggested, and VEGF.
  • Lysis - Jarle and Rolf
Jarle and Rolf will look at different ways to make a cell lyse, and they will also investigate the suicide switch used by the Tokyo team.

We also decided that we need a PR chief. Rolf volunteered!

Wednesday 23.05.12


We had our first meeting with our new advisor, Marit Otterlei, and we discussed which signal molecule we could use to detect the cancer cells in addition to using the O2 promoter to detect oxygen deficient areas. Prof. Otterlei suggested that we could use the Hepatocyte Growth Factor (abbreviated HGF), which is a growth factor regulating cell growth, cell motility and morphogenesis, that has the ability to bind to a tyrosine kinase. Prof. Otterlei also told us that many toxins can be produced by cells, so we decided to look more at making the cells produce toxins in addition to the ones we've already talked about.

Friday 18.05.12


We began this weeks meeting with going through the to-do-list from last meeting.

  • Eirin:
Has concacted Christopher Anderson by email to ask how his system works, but apparently he was unnwilling to give away too many details, as his work is not yet published.
But we also came to the decision that specially because his work is still not published, we can't really be sure what his system looks like, and it is not our fault if it turns out that our systems actually work the same way, therefore, we shouldn't care too much that he is working on a similar project. But still; Rahmi and Eirin will try to get some more details out of him.
  • Rolf and Jarle:
Have been looking at possible sponsors. So far; we know that we will get a discount at VWR, so if we need something they sell, we should order it from them. Also, we have gotten a semi-positive response from Sigma-Aldrich.
Before next meeting, Rolf will talk to more companies.
  • Gunvor:
Has since the last iGEM-meeting had a meeting with Gaute Brede, who is a postdoc working in the cell biology group at institute of cancer research and molecular medicine. I tried to ask him about signal molecules we could use, and his idea was to use ATP or adenosine, as cancer cells secrete more ATP than a normal cell. This is a signal molecule that attracts the attention of the immune system, so to avoid an imune reaction, the cancer cells also secrete enzymes called ectonucleotidases, which job is to degrade ATP to adenosine, which does not attract the immune system. Also healthy cells secrete ATP, but in smaller amounts than cancer cells. And healthy cells does not secrete CD39 and CD73, which is the ectonucleotidases responsible for degradation of ATP. So in summary; since cancer cells has these ectonucleotidases, they have lower levels of ATP in their surroundings compared to healthy cells, and higher levels of adenosine in their surroundings compared to healthy cells. Also, it seems like most types of cancer cells secrete CD39 and CD873.

We discussed the possibility of using adenosine as a signal molecule, but Rhami was sceptical, as he thinks adenosine and ATP are taken up by the cells through passive transport. So that means we might have to look for another signal molecule. Since we have few ideas ourself, we decided to have a meeting early next week instead, and try to get our new advisor Marit Ottelei to attend the meeting, since she might have some ideas.

In the time leading up to the next meeting, Rolf will continue looking for sponsors, and the ones who has time should start looking at different ways to lyse a cell.

Friday 11.05.12


We had our weekly meeting. We started by going through what we have done since last week:

  • Eirin:
Since last week, Eirin have been reading Christopher Andersons article. It seems like several parts of his project is similar to what we are planing now. But we still don't know if the cells Anderson used lysed by a stimulus given by the cancer cells. We have to find out if he did this or not, so before the next meeting, Eirin vil send an email to ask him.
  • Ove:
Ove will be looking more at making a calender function, so we can see a calendar on top of the page and be able to click different dates. Gunvor suggested that he could take a look at the code the NTNU team used to generate a calendar last year.
  • Nina:
Nina has found several new potential anti cancer drugs that can be syntheszed by cells, but she will be looking for more potential drugs in the time leading up to next meeting.
  • Gunvor:
Has asked around at Institute of Physics for cancer cells we could use in some of the experiments we are planning. She talked to the engineer responsible for the cell lab, and she said that they would like to provide us with cancer cells, but it would be an advantage if we could get some bottles of cancer cells from someone who is already using them. The problem is, she is going to leave for summer vacation in the middle of june, and if she's not here, we have to start our own cell line, which means that one of us will have to spend some hours a day in the cell lab attending to the cancer cells for about two weeks, which is the time it takes from the cells have been thawed to they are ready to be used in experiments.
Since this solution doesn't seem optimal, Gunvor instead talked to a postdoc at her research group who has collaborations to researchers in the hospital. She has planned a meeting with one of her collaborators next wednesday, and Gunvor will follow her there to talk to them.
She have also sent Marit Otterlei (professor at Institute of cancer research and molecular medicine) an email, and contacted Terje Espevik, who works with confocal microscopy at the hospital, about how we can characterize the O2-promoter using fluorescence microscopy.

We also decided that we should start looking for sponsors. We will submit an application for funds to Programme of Bioinformatics (PBI), and Rolf and Jarle is going to contact VWR, Sigma-Aldrich, and Fisher Scientific.

Eivind reminded us that it is important to come up with an idea for what our genetic construct will actually look like as soon as possible, so we can start the modelling. We decided that we will decide on an idea for a genetic circuit on next meeting, which will be on friday 18.05, at 13:30.

Have a nice weekend:-)

Wednesday 09.05.12


I have been playing around with a wiki design scheme today which can be found here. I hope we can discuss the wiki design a little bit this friday. Also I have been trying to make a calendar solution, but I haven't found any easier or more user-friendly way to implent this than to simply use the default wiki setup. So, at least for now, I think we should just keep using this site the way it is and add updates the way Gunvor did below (and I am doing now) ;) When you have added a new post to a day, you can click the button "Your signature with timestamp" in the editing menu to add your username along with the current time and date.

Thursday 03.05.12


We had a meeting, and we discussed several things we would like to look more into before we start planning what our genetic circuit will actually look like.

Here is a list of what we decided to do, and who will do it:

  • Check Christopher Anderson's article to see how similar his project was to ours - Eirin
  • Make a calendar on our wiki page - Ove
  • Look deeper into what kind of anti cancer drugs we could make our cells synthetize - Nina
  • Check if we have access to cancer cells, and find out more about molecules that are secreted form cancer cells in larger amounts than by normal cells - Gunvor
  • Find out more about the O2-sensitive promoter - Rahmi
  • Rolf was also going to do something, but I have forgotten what he was going to do...

- We also decided to have our next meeting at 13:30 next friday, and we decided to eat lunch together on wednesdays

- Rahmi came with a suggestion for characterization of the O2-sensitive promoter:

We could make the promoter control the expression of a fluorescent protein, then transform the system to cells, grow the cells on a soft medium they could migrate into, let them grow for a while, and then investigate the medium for coloured cells.
Suggestion from Gunvor: We could use TIRF (Total Internal Reflection Fluorescence) microscope, which allows us to investigate the fluorescence in a certain layer of the medium.

Wednesday 02.05.12


Gunvor and Rahmi held an introductory lecture to cloning techniques. Gunvor held a crash course in molecular biology, the biobrick concept, and the most common molecular biology techniques, while Rahmi covered more advanced cloning techniques like SLIC and Gibson. If anyone wants more information on for example SLIC and Gibson, google j5 assembly;-)



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