Maróy Ákos
accumulating all the stuff I do
Entries Tagged as 'bio.display'
DIY bio groups forming
As reported by an article titled “Am I a biohazard?” in The Scientist, DIY bio groups are forming all around, doing simple genetic modifications & similar at home labs. The whole aura has a sence of being outcast – like not being able to join the iGEM Synthetic Biology competition, which touts itself as being accessible, even hosting domains like OpenWetware – but in fact being closed and only accessible by academic institutions.
Go, kitchen labs, go!
bio.display on display at Green Revolution, Nieuwe Vide
bio.display is on display at the Green Revolution exhibition at the Nieuwe Vide gallery in Haarlem, the Netherlands between 13th May - 10th June 2009, among works by fellow bio-artists Jon Ardern, Art Orienté Objet, Bureau d’Etudes, Bureau of Inverse technology, Critical Art Ensemble, Emre Hüner, David kremers, and Alice Miceli.
and here we fail again
Unfortunately things have not worked out yesterday either. The printing is done, but fluorescence is very vague. Maybe the 20% arabinose solution used is still too dilute.
Therefore, nothing else remains for tomorrow, but to show documentation at the exhibition. This is always the last resort, and, frankly, it is quite shameful.
The opening is tomorrow afternoon at the Nieuwe Vide gallery in Haarlem, the Netherlands.
here we glow again
Maarten de Smit has pinpointed yesterday the problem we’ve faced so far: the concentration of arabinose used was wrong. The protocol page I wrote last year was ambiguous - is it a 5mg/ml arabinose concentration to be used, or is the final concentration of arabinose 5mg/ml in the liquid culture / LB agar? It turns out, it’s the latter, and we need to use a 20% arabinose solution to fix the problem.
So here we glow again.
Unfortunately, as I have only one day to prepare plates and print them, the installation will be a bit downscaled. From a Sinclair ZX Spectrum screenshot, I’ll go for Space Invaders imagery, which can be set up more flexibly, even on the site. Printing a bunch of aliens on separate plates makes it easy to assemble the final picture on location.
(working with) life ain’t easy
Nothing turned fluorescent for today either. Now the most probably cause is that the bacteria mutated somewhat, so that either it’s not procuding the fluorescent proteins at should, or the produced proteins are not fluorescent.
So we took the deep frozen (-70 °C) bacteria again, and are growing them out as a liquid culture to see. Some are grown with arabinose, so they should glow right away - to show that they are capable of doing so. As a control, I’m also growing some of the same bacteria that was used until now, from the same plate, with arabinose as a liquid culture, to see that indeed it just doesn’t turn fluorescent.
Unfortunately this means that the the original plan of a 256×192 pixel (16×12 plate, 2m x 1.4m) image cannot be realized until the exhibition opening. It might be that nothing can be realized until then. The best that can be done, if the newly grown bacteria works, is to make plates tomorrow, print them on Friday, and then see if they are OK on Saturday.
nothing works
I got in today into the lab with the hope that at least some of the plates I printed yesterday would in fact show fluorescent signs, that resemble the shape of intention. To my disappointment, about the 50+ plates I made, none have done so.
Looking at the possible causes for this, the most probable one is that the LB agar I used on Sunday to prepare the plates was too hot for the bacteria to survive in. It was uncomfortably hot for my hand to hold - which means likely above 45 °C - which is deadly temperature for the bacteria. My hope is that the plates I made yesterday were made with cooler LB agar (indeed, they were not so hot to hold), so the prints I’m making today will be visible.
If not so, with great embarresment I’ll have to go with some Plan B™.
Which would be sad, as I managed to print about 70 plates today, and made it up from row 11 to row 5 in the desired image - that’s 7 rows out of 12. If it worked, the prints would be ready by Thursday.
But then again, maybe not…
first set of rows printed today
Started to print the first batch of plates, that were prepared yesterday. Interestingly, a large number of them were quite bad - not even, but there was a ‘hole’ in the middle of the plates. Maybe this was due to mishandling them at a stage where they started to solidify. Also, as I put the lid on the plates right away after pouring the hot LB agar into them, there’s moisture on the lids, which flows back, creating a flowing layer of water on top of the agar. This is not good either.There were some problems with printing as well, initially. Neither the plates, nor the table is level (well, the agar in the plates is not level because the tables are not level). Thus the needle of the syringe in the 3D printer doesn’t always touch the agar surface. Sometimes it goes in quite deep, thus the drop is not touching the surface.
Looking at printing issues, I made a number of improvements in the process. Now, the printer, after reaching the target location, pushes out the drop before descending onto the agar surface. This way, the drop has some time to come out. This approach also has the advantage that if the syringe is pushed inside the agar - the arabinose actually stays on top, as it’s already at the top of the syringe. The other improvement I found is that one can manually adjust the height of the printing process in case it’s too high or too deep.
We’ll see tomorrow if the prints make sense.
Unfortunately the day didn’t start so smoothly - it was pretty much like a Monday morning after a national holiday - materials were delivered a bit late, I didn’t have internet access, etc. But now these things are solved mostly.
I have a total of 12 rows to print. The plan is to print 3 rows per day - which would make everything ready in 4 days. Of course, we’ll have to see about errors, mistakes…
preparations for an exhibition
I started preparations today for an exhibition at the Nieuwe Vide gallery in Haarlem. I’ll be creating a 256×192 pixel image - a screenshot from a ’80s Sinclair ZX Spectrum game, all made by fluorescent bacteria. The image is going to be 2m x 1.4m in size - kind of luxurious for a Spectrum screen 
But this takes a lot of effort in the lab. Currently I can work with 12×12cm plates, which can display an icon of 16×16 pixels. I need 16 of these in each row to get 256 pixels horizontally, and 12 rows to have the vertical 192 pixel resolution - all in all, 192 plates have to be made.
My plan is to create 50 plates per day, so that I even have a little room for failure - as 5 days x 50 plates = 250 plates. I started to scale up the quantities that have to be used - 6 liters of LB agar are used per day, in each liter:
- 250µl of carbenicillin (100µg/ml concentration -> 25µg in total)
- 55ml of overnight liquid culture
thus I need to create about 350-400ml of liquid culture as well every day.
Today’s results show that out of 1 liter of LB agar, I can pour about 13 plates. I made a total of 70 plates from 6 liters of LB agar.
A lot of preparations have already been done, thanks to Olga Crapels from the Arts & Genomics Center, and to Maarten de Smit, who has prepared the first batch of liquid culture, by growing out the bacteria permanently stored in deep freeze. Trudie Brouwer and her colleague, Arjan have established all the materials and supplies I need.
Meanwhile, Roland Vos from the Nieuwe Vide gallery is building the glass housing, that will act as a frame for the whole image. The original plan was to hang it from above, so people can just lie down below it comfortably on pillows, and enjoy the view - but, unfortunately this is not feasible at the moment, as it would take too long to get the hardened glass that is sure to hold up the weight of all the bacteria. Thus, the display will be set at 45 degrees - but, still, we’ll have pillows around.
Meanwhile, a new bug has been introduced in the Linux kernel, which prevents the ’supposed’ cdc-acm driver from working with the Fab@Home controller firmware. So I have to use the usbserial driver instead. Unfortunately Oliver Neukum could not reproduce the issue, so there’s little chance of him fixing it.
bio.display featured in Lukas Hajek’s diploma thesis
Lukas Hajek, from the Czech republic included bio.display in his diploma thesis, among other bio-art projects. You can download the thesis in the Czech language, in PDF format from his web site - or here.