Tuur Van Balen hacks Lactobacillus

Designer Tuur Van Balen gives an interesting presentation where he hacks the yogurt producing bacteria, LactoBacillus, using DNA pulled from the Parts Registry.

If you’re interested in hacking yogurt yourself, I’d recommend starting with Cathals “Beginners Guide to Yogurt Hacking“.

Note: Tuur Van Balen has done some pretty crazy science/design experiments, I highly recommend checking out his past works.

How to make glow-in-the-dark or Flourescent Yoghurt

Photoshop Mockup.

Glow in the dark yoghurt is something that has been floating around the DIYbio community for a while now, though to my knowledge no one has actually made a batch. Hopefully that will change now that Cathal Garvey of IndieBiotech has released a “Beginners” guide to hacking yoghurt. As you can see from the excerpt below beginner here is code for you are going to learn alot.

For our project then, we want DNA that resembles the following:

A diagram showing the format of the desired DNAColourised and labelled sections of the DNA, presented with the unnamed section of target DNA. This assumes the simplest scenario where no “cleanup” mechanisms are included to remove the resistance gene.

The promoter (Prom) should be a constantly “on” promoter, termed “constitutive”. The terminator (Term) is a region of DNA that prevents the gene from transcribing beyond its normal context, which could cause unintended interruptions of cellular functions; unhappy bacteria could result, and the gene could end up unstable. The antibiotic should be chosen to avoid medically significant antibiotics such as ampicillin; this is a civic responsibility matter, as otherwise your yoghurt could end up assisting dangerous pathogens in becoming resistant to medicines. Ideally your antibiotics would be self-excising once they become unnecessary, leaving a yoghurt containing only harmless fluorescent proteins and nothing else.

Open Source, Inkjet based oligonucleotide synthesizer and microarrayer

At last weeks SB5.0 conference, Siyuan Chen, an engineer from Agilent Technologies, remarked during his talk that one “shouldn’t try to get DNA synthesis to work with a home computer because it wouldn’t work”. This is a gauntlet thrown if ever I did see one. And I promptly accepted said gauntlet over twitter. Yet it would seem that someone has actually beat me to the punch. In 2004, Christoper Lausted et al. out of The Institute for Systems Biology published a wonderful paper titled “POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer” complete with all the necessary schematics and assembly instructions(pdf linked). The design is quite impressive and extremely low cost using mostly off the shelf components. I have a feeling it was a bit ahead of its time and that with the advent of DIYbio could find new life as an active Open Source project.

The POSaM platform. (a) Overview. The complete inkjet printing system is enclosed in an air-tight acrylic cover, 61 × 91 × 122 cm. (b) View from above showing the array holder. One slide is shown secured by the vacuum check with room for 26 additional slides. (c) Front view showing the print/wash head. Five PTFE wash lines deliver acetonitrile, oxidizer and deprotecting acid in bulk. Six vials supply tetrazole and phosphoramidites to the inkjet print head. (d) Lower-front view of the inkjet print head showing droplets passing through the QC laser beam. The presence of a droplet produces forward-scattered light, visible as bright red flashes (arrowed).

 

Original Paper: http://genomebiology.com/2004/5/8/R58

Biobytes 2.0 streamlines plasmid construction

A group of students from the University of Alberta have developed an innovative way of putting together BioBricks.  Before if you wanted to add Biobricks together it would require a series of cuts and ligations which could end up taking days to complete.  People often likes to compare Biobricks to legos but the metaphor didnt seem to fit with such long construction times.   With Team Albertas new protocol and toolkit ,which they are calling Genomikon, decreasing construction time to minutes comparing bibricks to legos makes a whole lot more sense. And if that wasn’t a good enough, Genomikon also eliminates the need to keep a sterile environment or use expensive equipment. Making it not only perfect for high school bio labs but citizen scientists as well. Especially with an estimated sale price at $179.

All pictures and Excerpts courtesy of Team Alberta
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