Posted by Josiah Zayner, Ph.D. on 5th Dec 2016
One of our main goals at The ODIN is to make biological engineering and genetic design accessible and available to everyone. We believe that as a technology, biological engineering will revolutionize how everyone lives life for the better.
We understood that in order for biological engineering to enter the home there needed to be an application. We needed to give people the ability to create something tangible and not just experiment with Science. For the past year we have worked on developing a kit that allows people to engineer yeast and not just lab yeast like our first yeast engineering kit, because despite our best attempts lab yeast was not good at doing the thing yeast should be good at i.e. making CO2 and alcohol from sugar. With our new kit we wanted to market it to home-brewers and others, so people could use it to make yeast and alcohol never seen or tasted before. Yeast are engineered and then eventually cultured by the user and it is up to the user to make sure that they take proper precautions in preparation so that the materials are food grade.
There are three main things to be worried about with new foods 1) Allergenicity, 2) Toxicity 3) Digestibility.
The yeast kit we currently provide and future yeast kits we plan to provide create new proteins that are not normally in yeast. That means that there is a chance that these proteins could be allergenic. This is an interesting problem because we can't just feed it to humans to test it(though I and many others have consumed the yeast to no ill effects). So what Scientists normally do in a case like this is compare the new protein's amino acid sequence(protein's are chains of amino acids) to the amino acid sequences of all known protein allergens. If any of these sequences are similar there is a possibility of "cross reactivity" meaning that our new proteins could also be an allergen. From Generally Regarded As Safe(GRAS) notices filed at the FDA, most people use the University of Nebraska allergen database (http://www.allergenonline.org/) to compare their protein to known allergens. We ran the same test and there are no matches between any of our proteins and known allergens even using the most stringent matching criteria(8 amino acids). Many proteins currently in use in our food chain are determined to be GRAS by the FDA with much less stringent matching.
Are the proteins used toxic? To determine this researchers in GRAS notices use a similar technique that is used above, they compare the sequences of their proteins to a database of proteins and attempt to determine if the protein matches any known toxins or venoms. This time we used the Uniprot database (http://www.uniprot.org/blast/) as others have done. We could not find any reasonable matches that were either known toxins or known venoms.
I don't quite understand the digestibility part yet and assume it is in regards to protein accumulation. As in, if the proteins are not digested they could accumulate and be hazardous. Most GRAS notices I have read either don't mention digestibility or just say something to the extent that "of course their protein would be digested". Pepsin is the main enzyme in our guts that digest proteins. Going to get a bit Sciencey here so stay with me. Pepsin cleaves preferentially at hydrophobic amino acids and more so at aromatic "hydrophobes", phenalalynine, tyrosine and tryptophan. All of our new proteins had in excess of 20 different cleavage sites. Meaning our new proteins should be easily digested.
Argument Against Regulation
Currently, almost all yeast used to create beer has not had its genome sequenced. This means that despite the yeast being considered safe by the FDA we have no idea the exact proteins that are inside these yeast. The changes someone would make using our kit are known and can be screened for safety as seen above but "natural yeast" that have been in use are considered safe only because they have been in use and no one appears to have been harmed or died from them. Do any of them contain proteins that could be harmful? Unknown. Is it possible for a "natural yeast(Saccharomyces cerevisiae) to evolve the same fluorescent protein we are using? Yes, it is possible. In fact, yeast, especially in brewing evolve much faster than yeast in their natural environment because of selection pressures and quick generational turnovers because of optimum living conditions. During brewing, it would be trivial for yeast to accumulate mutations and difficult to test every new protein. This is good for incumbent industry but bad for technological innovation. I would assume at least based on reading GRAS notices(obviously I have not read them all), that very few if any of these yeast which have been evolved to have different characteristics and different proteins have been evaluated by the FDA.
When you drink kombucha, the kombucha contains unknown organisms. Yes, that's correct, it contains a combination of yeast and bacteria that is unknown and different for every kombucha. None of the organism's genome, much less the proteins are known.
A San Francisco sour dough is made with a starter that was inoculated from the air. Yeast and bacteria(bacteria are usually what give it the sour flavour) are present in the bread and the species are unknown. Again, genomes unknown, proteins unknown.
Many beers, including Lambics and Sours are sometimes left open to the air to be inoculated by yeast and bacteria. The yeast and bacterial species are usually unknown, the genomes unknown, the proteins unknown.
Maybe the question the FDA and consumers should be asking is not whether a known protein used to change a yeast genetically is safe(we have showed above that they are) but whether there are unknown proteins in the yeast we currently consume that are harmful. It would cost less than $1k to sequence the genome of a brewing yeast.
There has never been a case of a protein added genetically to a food product that then later caused harm to people.
This past Sunday we traveled into San Francisco for a Middle School Maker Faire. In our setup we hosted one of our classic kits put together for The ILIAD Project. It allows you to test biological matter from your environment for antibacterial qualities. Brad walked each student through the process of mashing plants into a [...]
This past Tuesday we went to the San Jose Tech Museum for an event. We brought in a tasting station, and the concept was to connect with the participant on a physical level. How cool is it to taste science? So we set up 8 different amino acids with particular taste characteristics we thought would [...]
Monday Feb. 1st at 6PM PST, 8PM CST, 9PM EST The ODIN presents our first live video broadcast Josiah Zayner will be hanging out with Oregon BioHacker Jake Palumbo and they will be chatting about all things Science and Career possibilities for Biohackers, is graduate school a good idea? Feel free to join us for an audience [...]
This is a guest blogpost by Mississippi BioHacker David IsheeWhat is a living thing but the expression of code being computed by reality? We're the manifestation of information moving through matter over time. Why not take control of that, why let chance determine what's written there? What about the life around us, why leave that code to chance? What [...]
For the past few months we have been developing DIY CRISPR kits for bacteria and yeast so anyone can learn about modern Synthetic Biology techniques by doing!Check out our campaign to get your kit first!http://igg.me/at/CRISPR
The ODIN is starting to ship restriction enzymes and ligase! Enzymes are pretty heat stable. T4 DNA ligase is another matter, it requires ATP, ATP hydrolyzes. I need a few people to test out some T4 DNA ligase and reaction buffer that has been shipped. Shipping of Taq and other Master Mixes has worked and [...]
I heard something said by a collaborator, Vidhi Mehta, which moved me. "Will the next Nobel Prize be given to a citizen scientist?"I sat back and I imagined. What if this week a phone call was made to a Biohacker that I know, instead of the usual academic Scientist? Wouldn't that be something?Thinking about my life [...]
We just added two PCR machines to our inventory. The great thing is that these machines are much cheaper than OpenPCR and other custom DIY PCR Machines. All machines are tested thoroughly and ready to go and include a 30 day guarantee. Check them out:http://www.the-odin.com/ptc-100-60-sample-pcr-mach...http://www.the-odin.com/minicycler-16-sample-pcr-m...