Corpora WordPress site created
So, I’ve set up this site so as to document the Corpora project, especially ongoing development and preparations for future exhibitions, such as at the Venice Architecture Biennale Hungarian Pavilion later this year.
Maróy Ákos
accumulating all the stuff I do
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the future doesn’t glow as bright
The sad news is, that the pGLO bacteria, which was extremely bright after performing the original transformation, doesn’t really glow now at all. The bacteria with the TorA-GFPmut3* GFP in itdoes glow, but not really bright. And it seems it has a tendency to glow when lit with lower wavelength UV light - which is dangerous to the bacteria itself an to humans as well.
Anyway, we put the TorA-GFPmut3* GFP version into deep freeze storage (-70 °C), under the code MS 903, so that it is readily available whenever needed.
light-switched bio-pixel on the way
Jos Arents just got back to me with the good news that he has found a pH sensitive fluorescent protein that has a kanamycin marker instead of ampicillin, and this he can combine this DNA with the one containing a light-dependent proton pump, so as to create bacteria that would change the level of fluorescence as a reaction to some light.
Thus the basic setup would be the following:
function1: light -> pH value change in the cell function2: change in pH value -> change in level of fluorescence
The original GFP in question comes from “ratiometric pHluorin”, and was used already in Bacillus Subtilis - let’s hope it works again in E. Coli as well. Jos will try to transform it into their already existing UT5600/b-caro/proteorhodopsin E. Coli strain, which already contains the light-dependent proton pump.
been at the Waag FabLab
I’ve visited the Waag FabLab, which is located at de Zwijger, which houses a range of interesting organizations. I met there with Rob van Kranenburg, and also Jean-Michel Molenaar, who is very handy with rapid protoyping. The FabLab itself is a spacious workshop room, with some nifty tools like:
- a laser cutter
- a large and a small CNC machine, the latter having a presision of 0.2 mm
- a sticker cutting machine, that can also be used to cut circuit boards
- and lots of enthusiasm
They are also constantly in touch with the Norwegian FabLab project and other places I don’t even know, via a video-conferencing link, so I had the opportunity to ask questions to the Norwegian guys right away. Got lots of interesting input and links on the hurdles of possibly creating a 2D plotter dispensing liquids myself, based on 3D printer designs. After all, they are dispensing also material through a syringe at specific locations.
Very nice place - sure to return there 
meeting at the UvA
I had a meeting today with Prof. Klaas Hellingwerf and Jos Arents at he University of Amsterdam Swammerdam Institute of Life Sciences. They work with differently colored fluorescent proteins and bacteria as well, so they actually have all the expertise I could ever need to this project when it comes to biotechnology. We’ve discussed possible issues with the pH-dependent fluorescence change, and also new exciting approaches on how to make this fluorescence change happen.
bacteria grown – let’s activate the DNA
The bacteria we put out in plates all grew out today - which was kind of expected. We grew them on plates without arabinose, so the DNA that was put into them would not be expressed. This is to make sure the bacteria are in their best form (the alien DNA may interfere with it somewhat), so can we can used these specimens for long term deep-freeze storage.
But to verify that these really are the ones we need, today we’ve put them on plates with arabinose as well. We’ll see if they glow tomorrow (or, actually Friday.)
iwiwE (exporter) klub az iwiw-en :)
Simon Benjamin februarban tarott eloadast az iwiwE nevu iwiw export eszkozrol - es lam, letre is hozott mostmar egy a temahoz tartozo klubbot az iwiw-en belul. Ha szeretned, hogy el tudd menteni a wiw-en orzott adataidat - csatlakozz te is!
looking for a 2D plotter
If the experiment verifications go right, and we can really change the level of fluorescence in bacteria by dropping acid on it, then the issue of dropping liquids on specific locations on a 2D area still needs to be solved. While this is a more traditional challenge, it’s not as easy as it seems.
But it’s a good thing that lots of DIY 3D printer movements are around by now, some of them are quite open, with blueprints, sourc code, etc. Finally, the physical world is opening up on the concept of sharing the source.
I’ve look at the some already, and they seem promising. After all, these are 3D plotters basically, and I only need to reduce their complexity to 2D - and there I go. Promising leads are:
- RepRap - a 3D printer that can partially build itself, and is on displayed at the London Science Museum
- Fab@Home - a much hyped 3D printer originating from around the Cornell University. The Waag FabLab here in Amsterdam has one of these
- CandyFab - a 3D printer that uses sugar as its medium, and is made of two used 1D plotter constructs
- ScribblerBot - a 2D plotter that is made as a physical extension for the Scribbler project
starting out with the real stuff
Along with the TorA-GFPmut3* E. Coli strain, we’ll also maintain the bacteria that came as a result from the BIO-RAD kit I experimented with earlier. Additionally, we also put in non-fluorescent bacteria that is resistant to ampicillin, as a control. Well, more can never be a problem, can it
So today we’ve basically put some of the bacteria on plates, which were made of LB and ampicillin. Tomorrow we’ll see what grows out, and which one will glow eventually.
