Team:NTNU Trondheim/Logg

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Revision as of 18:17, 11 May 2012

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.

Hope you are all having a nice day and get to enjoy some sun!

--Oyas 09:45, 9 May 2012 (CDT)

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;-)

Thursday 26.04.12

Today, all the groups from last time started with giving an overview of possible project within their topic. Then we discussed for quite a long time, and in the end we decided we wanted to work with cancer. But we also decided to keep the biosynthesis of fatty acids as a side project. The electricity project turned out to be quite hard to complete in only two months, so we decided to drop it.

Our final project idea is then to make bacteria, for example E.coli cells, produce anti cancer drugs; preferably as many different molecules as possible. We have read about both enzymes and endpoints of metabolic pathways that are disadvantageous for cancer cells. Our engineered cells should also be able to respond to a signal molecule secreted in larger amounts from cancer cells than from normal cells, for example a signaling molecule that promotes angiogenesis. When the cells detect the signal molecule from the cancer cells, they should lyse, releasing the anti cancer molecule close to the tumour. Another approach to reach the tumour could be to take advantage of the fact that the environment inside tumours normally is oxygen deficient. And as E.coli cells naturally migrate towards areas low in oxygen, a possible solution is also to activate the lysis gene when the cells are in an are with little oxygen. Rahmi told us about a promoter that gets activated by low concentration of O₂. This could regulate the lysis genes.

For the main project, we have to make the cells lyse at a certain concentration of an outer stimuli. For our side project it could be interresting to do the oposite; making the cells lyse when they have produced a certain amount of fatty acids.

Friday 20.04.12

Today, we decided on the overall top three projects for the team. We added the points all the team members have given to the different projects, and the list then becomes as follows:

Project	Number of points
Cancer (search and destroy)	14 points
Biosynthesis of fatty acids	10 points
Bacteria as electrical switch	6 points
Water purification - hormones	3 points
Water purification - sucralose	1 point
Oil spill removing bacteria	1 point
Biomining	1 point

We decided to look deeper into the overall top three projects. We formed three groups of two and two, and decided to look at the following things for the next meeting:

Look at earlier projects on the topic
Come up with some specific project ideas
Look at the feasibility of the proposed projects
Look at which biobricks we would need for each of the proposed projects, and see if they are present in the registry, or if we would have to make them ourselves.

The groups:

Eirin and Jarle - Biosynthesis of fatty acids
Rolf and Ove - Bacteria as electrical switch
Nina and Gunvor - Cancer (search and destroy)

We also elected Ove as wiki chief:-)

Friday 13.04.12

Since we have quite a few project ideas to choose between now, we decided that for next meeting, all team members should pick their three favourite projects. We decided to give our favourite project three points, the project on second place two points, and our third favourite project one point. Before the next meeting we will add all the points together, and se which projects we should look at more in depth. At this meeting, we also discussed activities for Researchers Night. So far we have thought about making a construction kit to make the attendants on RN understand how we can combine different biobricks. We also discussed bringing pipettes, letting the attendants make alginate beads with different colours that they could bring home, and bringing a microscope and coloured cells (harmless, of course).

Friday 30.03.12

We kept discussing possible projects, and we now have several projects that would be interresting to work with. Here are the topics we have discussed so far:

Fatty acid synthesis in E.coli (EDA and DHA production)
Using cells in water purification
- Using bacteria to remove hormones from wastewater
- Using bacteria to remove sucralose from wastewater
Be able to control pili production in order to control electron transfer between cells
Biosensor detecting cancer cells, starting synthesis of chemoterapeutic drugs when cancer cells are detected
Biosensor detecting harmful bacteria
Making bacteria destroy oil spill
Digitalize a signal from an environmental stimulus
Biomining (using microorganisms to extract metals

Friday 16.03.12

We had a meeting, where we started discussing ideas for this year's iGEM project. We also decided to eat lunch together once a week, to get to know one another. For the outreach part of the project, Gunvor suggested that we could collaborate with Studentersamfundet to make a "lørdagsmøte" about synthetic biology.

Monday 27.02.12

We had our first meeting, and the team members met each other for the first time!

Friday 17.02.12

We recieved emails from Eivind letting us know that we are the ones that have been selected to represent NTNU in iGEM 2012. Everybody is happy!