Science Hack Day - Useful OS project ideas for the entire DIY Bio community? Anything on your wish list?
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Ryan Bethencourt
Sep 25, 2013, 3:46:31 AM9/25/13
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Dear All,
As some of you may know the Science Hack day at the San Francisco Academy of Sciences is fast approaching this weekend and we were wondering if you had any ideas or suggestions on projects that the entire DIY Bio community might find useful?
A big group of us are looking to do a project that could benefit the entire DIY Bio community, would be fully open source and in which we could realistically build a prototype within a weekend to share with the broader DIY Bio community. Anything on your wish list? :)
All the best,
William Heath
Sep 25, 2013, 5:34:14 PM9/25/13
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My wish is a 3d cell growth embryological simulator that accurately shows protein cascade diffusion that drives cell growth, direction, and diffusion. It should be possible to use hedge hog genes etc... to create a beginning in building 3d structures with a single fertilized cell etc...
Another idea I had was a diybio kind of virtual lab that was completely web based where pipettes etc... could be virtually simulated to do igem type experiments.
I think my biggest request is a way to accurately redo every igem experiment virtually.
-Tim
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Nathan McCorkle
Sep 25, 2013, 6:31:23 PM9/25/13
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vacuum formed gel boxes... made with commonly available plastics from
a supplier like TAP or even grocery store picnic plates. The goal is
to make them cheap enough to give to school children, etc...
-Nathan
a supplier like TAP or even grocery store picnic plates. The goal is
to make them cheap enough to give to school children, etc...
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-Nathan
Patrik D'haeseleer
Sep 26, 2013, 4:07:37 AM9/26/13
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Hi Ryan,
One of he projects that has been on my backburner for a while is to develop a chromogenic agar medium from edible ingredients - so we can teach some "biosafety level 0" microbiology demos. The end goal would be to be able to distinguish between colonies of safe microbes such as baker's yeast, lactobacillus from yoghurt, and maybe some kombucha isolates, based on color changes on an agar plate.
Promising chromogenic ingredients include plant pigments that change color with pH such as turmeric and cabbage juice (yeast and kumbucha strains will create a lower pH, so you'll get a colored halo around each colony on the plate). But pretty much any brightly colored foods are worth trying: tomato juice, spinach, saffron, you name it. Make an agar plate with each of them, streak with yeast, lactobacillus and kombucha, and check for differentially colored colonies the next day...
I'm signed up to do a 15 minute lightning talk on DIYbio at Science Hack Day at 11:05, and this is one of the three project ideas I'll be talking about (the other two being Heart in a Jar and steam distillation of essential oils). I've actually been meaning to make a little international DIYbio competition out of this: offer a cash prize for whomever in the DIYbio community comes up with the best, fully documented recipe using all food-safe ingredients that can distinguish between at least two or more food-safe microbes...
By the way, here's an example of a commercial chromogenic agar plate, used to distinguish E. coli from other coliform bacteria in contaminated water. E. coli colonies will be purple/blue and coliform colonies will be pink/red:
Patrik
One of he projects that has been on my backburner for a while is to develop a chromogenic agar medium from edible ingredients - so we can teach some "biosafety level 0" microbiology demos. The end goal would be to be able to distinguish between colonies of safe microbes such as baker's yeast, lactobacillus from yoghurt, and maybe some kombucha isolates, based on color changes on an agar plate.
Promising chromogenic ingredients include plant pigments that change color with pH such as turmeric and cabbage juice (yeast and kumbucha strains will create a lower pH, so you'll get a colored halo around each colony on the plate). But pretty much any brightly colored foods are worth trying: tomato juice, spinach, saffron, you name it. Make an agar plate with each of them, streak with yeast, lactobacillus and kombucha, and check for differentially colored colonies the next day...
I'm signed up to do a 15 minute lightning talk on DIYbio at Science Hack Day at 11:05, and this is one of the three project ideas I'll be talking about (the other two being Heart in a Jar and steam distillation of essential oils). I've actually been meaning to make a little international DIYbio competition out of this: offer a cash prize for whomever in the DIYbio community comes up with the best, fully documented recipe using all food-safe ingredients that can distinguish between at least two or more food-safe microbes...
By the way, here's an example of a commercial chromogenic agar plate, used to distinguish E. coli from other coliform bacteria in contaminated water. E. coli colonies will be purple/blue and coliform colonies will be pink/red:
Patrik
Cathal Garvey (Phone)
Sep 26, 2013, 4:41:52 AM9/26/13
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It's not chromogenic per se, but when I was isolating G.xylinus from kombucha I used agar with suspended Calcium carbonate: it dissolves as acid is produced. Best poured when very visuous to prevent settling.
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Patrik D'haeseleer
Sep 26, 2013, 4:58:37 AM9/26/13
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Yep - that one is definitely on my list of things to try as well. It would be great to have a dye with affinity for cellulose, to definitively identify G. xylinus based on its production of bacterial cellulose. I bet you'll get nice red colonies with Congo red. Not exactly non-toxic though...
Patrik
Patrik
Cathal Garvey (Phone)
Sep 26, 2013, 5:23:41 AM9/26/13
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Odd thing I found was that, on a petri dish, cellulose grew in 'grains' or 'tumours' near but not on bacterial colonies. PreCellulose monomers like to assemble on existing fibers so you get a crystallisation effect rather than a direct association with the producing cells.
Also, cellulose was produced well into stationary, around 5 days or more. Definitely calls for humid incubator to prevent dryout, but also makes for poor differentiation: other species have ample time to overgrow and confuse matters.
Acid is the best first-pass selection system, followed by observation of axenic (single species) plates for cellulose grains.
Also, cellulose was produced well into stationary, around 5 days or more. Definitely calls for humid incubator to prevent dryout, but also makes for poor differentiation: other species have ample time to overgrow and confuse matters.
Acid is the best first-pass selection system, followed by observation of axenic (single species) plates for cellulose grains.
Biotech Ryan
Sep 28, 2013, 5:38:43 PM9/28/13
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This are awesome ideas, thanks everyone! We pivoted to something a little easier a Wikibook for Citizen Science... more to come soon :)
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