Eating Glow in the dark yogurt

[Jonathan Cline]

Has anyone eaten a synthetic bio organism?
Is anyone eager to try?
How about eating biohacked yogurt?
I asked this a couple years ago and there were no takers yet.  Perhaps opinions have changed.



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[Anselm Levskaya]

> Has anyone eaten a synthetic bio organism?

Anyone living in the U.S. is guaranteed to have eaten plenty of
genetically engineered foods. Corn, soybeans, etc. If you're
referring to engineered microbial foodstuffs, (yeasts, yogurts,
cheeses) then I believe all of those on market are historical
cultures. However most hard cheeses are made with chymosin (rennet)
produced by a genetically engineered aspergillus niger species (there
are other GM chymosin bugs too).

A variety of people out here in SF are really interested in
manipulating brewer's yeast for novelty beer fermentations. I imagine
that it will happen within a decade or so.

I've eaten plenty of genetically engineered strains of yeast, though
I've never tried to ferment them or use them as leavening agents. I
can thus safely report that GFP tastes like the autumnal sun refracted
through droplets of morning dew.

> How about eating biohacked yogurt?

So long as it's competently made yogurt.

Many people are happy to eat engineered foodstuffs. Look at velveta.
So long as the organism isn't an actual pathogen or producing toxic
secondary metabolites / protein toxins there's no real issue with
adding novelty genes. The really difficult job is making interesting
changes that actually appeal to the culinary aesthetic. Cooks are
much more demanding about their ingredients than the FDA.

-anselm

[Katherine Gordon]

Hello 

If I eat Biolumenescent yogart will I then GLOW in the dark??

That would be very cool

Kate

www.needamassage.net

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[Daniel C.]

On Wed, Jun 13, 2012 at 10:53 PM, Katherine Gordon
<kthrn...@gmail.com> wrote:
> Hello
> If I eat Biolumenescent yogart will I then GLOW in the dark??

Here are some questions to consider.

1. What (in general terms) makes the yogurt glow in the dark?
2. What would it take to make you flow in the dark?
3. What happens to yogurt when you eat it?
4. What happens to the answer to #1 (what makes the yogurt glow in the
dark) after you eat it?

-Dan

[Cathal Garvey]

To answer the original question in a word, no.

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[David Murphy]

> If I eat Biolumenescent yogart will I then GLOW in the dark??

 

well.... if it glows because it's been made from the milk of an animal engineered to concentrate radioactive waste then yes.

 

[Cathal Garvey]

But only if:
A) You drink enough to reach similar concentrations in your own skin.
B) The radioactive agents are absorbed in the digestive tract in the
first place.
C) The form of radiation creates visible-spectrum ionisation that the
human eye can perceive.
D) You survive an extended dose of radiation to the digestive tract long
enough to attain concentrations listed in (A).

[Katherine Gordon]

Hello All DIYB,

Thank you all for your humorous answers

I am a sci fi script writer.....thanks again

very thoughtful yes...

Kate

[Simon Quellen Field]

If it is a humorous sci-fi project, you might have the protagonist scream in the

dark just before flushing.

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[osazuwa]

Is this yogurt made from bacteria transformed from GFP or bioluminescent gene?

>> diybio+unsubscribe@googlegroups.com.

[Cathal Garvey]

Either, I guess. The GFP is just a protein, with no specific
digestion-resistant domains or likely antigens. Not a problem as far as
I'm concerned, and there are youtube videos of people eating GFP-sushi
out there; they're not dead. It's almost certainly harmless.

Bioluminescence (that is, vibrio sp. bioluminescence) is something I
looked into from this safety angle; it turns out that the aldehyde used
to generate light is actually occasionally used as a food
additive/flavouring, but the relative quantities are nigh impossible to
quantify through duckduckgo-ing the question. In other words, the
aldehyde is safe in the levels added as a flavouring, but how much do
you get from a yoghurt full of glowing bacteria? More? Less?

I'd probably still risk it if it were legal to do so over here,
personally, but only because I know the risks. I'd never suggest to
someone that it's "probably safe" until I saw a study that demonstrated
as such, because reactions to odd things like rare aldehydes are hard to
predict.

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[Meow-Ludo]

Toxicity of GFP

On Thursday, June 28, 2012 11:12:46 PM UTC+10, phDIY wrote:

If by synthetic organism, you mean one that's been completely generated from a computer (like at Synthetic Genomics) no. 

If you just mean bioengineered: you've already likely eaten a strain of streptococcus thermophilus or lactobacillus acidophilus (bugs used to make yogurt) that have been actively or passively engineered to produce  that yogurt.

as a microbiologist myself, I dont know if I would eat a bio-luminescent yogurt.  There's no information on the allergenicity of the proteins used to make them glow.   the GFP proteins are from jellyfish, originally, but have been substantially modified from their original form. 

[David Murphy]

I believe I know what you may be refering to.

There were some announcements about Alexey Surov and a study feeding hamsters GM soy.
It did the rounds on all the anti GM sites like naturalnews and got heavily distorted.

http://veganskeptic.blogspot.co.uk/2011/10/alexey-surov-and-gm-soy-recurrent-tale.html

 

 

April 16, 2010 “Voice of Russia” (a Russian radio station site) on an article: “Russian scientists have confirmed that GM food is harmful”

 

 

On Thu, Jun 28, 2012 at 3:27 PM, Barra Darcy <bara...@gmail.com> wrote:

I don't think eating anything GM is a good idea (but that's just my opinion...don't let me spoil the fun). I did hear a program on the radio a while ago, they were interviewing some scientist who worked with testing GM crops on mice. He said he'd filed some unpublished report that said the crop fed to mice had actually 're-arranged' their insides:-/

but in the interests of science....

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[Jonathan Cline]

On Wednesday, June 13, 2012 12:11:30 AM UTC-7, Anselm Levskaya wrote:

> Has anyone eaten a synthetic bio organism?
Anyone living in the U.S. is guaranteed to have eaten plenty of
genetically engineered foods.  Corn, soybeans, etc.

Anyone run protocols to determine if grocery-store soybeans, for example, are genetically engineered?   

The following looks to be written as a high school level lab:

 * PCR-Based Detection of Genetically Modified Foods, Diana L. Brandner 

http://ucbiotech.org/resources/methods/GMO_detection.pdf

More refs:

http://www.google.com/search?q=filetype:pdf+Detection+of+genetically+modified+organisms+food

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[Chowe]

I wanted to revive this thread to see if anyone has found any new info or studies on the safety/toxicity of eating GFP or bioluminescent systems? 

[Bryan Jones]

While I haven't seen any studies investigating this, I would think that eating recombinant GFP is extremely unlikely to cause any negative effects. I would jump at the chance to eat GFP lactobacilus yogurt or GFP saccharomyces beer. 

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[Cathal (Phone)]

..neither of which are likely to work, sadly: GFP needs oxygen to fold. Other fluorophores are probably OK?

Look up "traffic light sushi" by the center for genomic gastronomy. They are glofish and are not dead yet. :)

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[Chowe]

It looks there are some fluorescent proteins developed recently in lactic acid bacteria that are functional under anoxic conditions. http://www.ncbi.nlm.nih.gov/pubmed/26129953 

Has anyone heard of any examples of humans consuming organisms that are expressing the bacterial lux operon? 

On Wednesday, June 13, 2012 at 12:38:15 AM UTC-6, Jonathan Cline wrote:

[Patrik D'haeseleer]

On Monday, May 30, 2016 at 9:45:10 PM UTC-7, Chowe wrote:

Has anyone heard of any examples of humans consuming organisms that are expressing the bacterial lux operon? 

I know that firefly luciferase and a range of fluorescent proteins have been expressed in animals before with no toxic effects. I highly doubt that they would be any more toxic when ingested rather than expressed in the animal's own cells.

Anyone know if the bacterial lux operon has been used as a bioluminescent marker in animals?

Patrik

[Raza]

Incidentally, I recently briefly looked into the safety and feasibility of fluorescent proteins as food dyes. Attached a safety evaluation I found for red fluorescent protein, which makes a case for GFP in the process for comparison. General conclusion was "theory points to it very likely being safe".

I still need an answer to my own follow-up question of whether it is feasible to keep these proteins stable in food, though, and under what kind of circumstances. Well, maybe not for GFP anymore, thanks a poster above!

[Patrik D'haeseleer]

Here's an interesting thought I've been toying with:

One of the classical yogurt making bacteria is Streptococcus thermophilus, a close relative of S. pyogenes, which is the source of the canonical Cas9 gene.

Turns out that S. thermophilus has a native Cas9 system. So in theory, all we need to do genome editing in S. thermophilus would be to provide it with an artificial CRISPR casette!

Completely bypasses any IP issues around Cas9 as well...  :-)

Patrik

[Sebastian S Cocioba]

Why doesn't someone just put a GFP plasmid with kanamycin selection into the yogurt. Might need a different ORI but it would be worth the effort to just do it and not speculate. If it does not fold or the chromophore does not oxidize then so be it but I think its worth attempting nonetheless. The low pH might be an issue so go for a more pH stable fluorescent protein like RFP. 

Sebastian S. Cocioba

CEO & Founder

New York Botanics, LLC

Blog: ATinyGreenCell.com

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[Brian Degger]

Gfp lollipops anyone ?
http://licknlight.com/lnl-en/

Have seen/tasted at labeasy/event by madlab/arts catalyst and collaborators.

And their safety info.
http://licknlight.com/lolipop/safety/
Looks to me gras (generally regarded as safe).

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[Koeng]

I PCRed one of the native CRISPRs out, believe it had AGAAW or something like that as the PAM. I didn't have enough funding or time to fully clone it, but I do plan on it soon. If I remember correctly, the crRNA is on the 3' of the Cas9 rather than the 5' like normal Cas9. Would be convenient if you need hard regulation of it's expression.  

https://www.amazon.com/gp/product/B001MV5PB0/ref=oh_aui_search_detailpage?ie=UTF8&psc=1

PCRed a 500bp fragment of that Cas9 off of this. It was a couple years ago though. There's like 2-3 CRISPRs in it I think, depending on what strain you have. 

I also think I have a broad range gram positive plasmid that expressed GFP from B subtilis. Would have to dig that up. Would most likely work in S thermo. I think the yogurt starter has one other strain though. 

-Koeng

[ukitel]

Depending on the particular chassis and device used, I would.
E.g. GFP expressed in a joghurt strain of B. subtilis, yes.

[Raphael Laurenceau]

Something to note on this topic: if GFP is expressed from a plasmid in the lactic acid bacteria, then antibiotic will be required in the yoghurt for the strain to maintain the plasmid and GFP expression to be efficient. In the absence of an antibiotic selection pressure, bacteria usually loose the added plasmid rapidly. I personally would not like to like to ingest antibiotics just for the fun of eating a glow in the dark yoghurt!

A solution is to integrate the GFP gene within the bacteria genome. Chromosomal edits are much more stable over generations. They are inserted along with an antibiotic resistance gene to select for the bacterial transformant, however they don’t require continuous antibiotic selection to be maintained. 

Another problem though: even if antibiotic are not added in the yoghurt, the antibiotic resistance gene will be present in the bacterial strain. Lactic acid bacteria are known to persist in the gut, and horizontal gene transfer is known to occur significantly within the gut microbiome. Since antibiotics used in molecular biology are the same as antibiotics used for treating bacterial infections, it’s unreasonable to voluntarily eat bacteria containing the resistance genes and taking the risk to spread them. 

The solution in that case is to perform ‘scarless’ genome editing, by removing the antibiotic resistance gene after selection. It is extra work but it is definitely feasible.

Concerning Streptococcus thermophilus: an even bigger advantage  than the fact it naturally has a crispr-cas system, in my opinion, is the fact that it is a naturally transformable bacteria. Natural transformation can be harnessed to make genetic engineering extremely easy. A Streptococcus thermophilus strain with an easy way to trigger natural transformation could make a really nice strain to play with for the DIYbio community.

Has anyone ever tried anything in that direction? 

2 papers showing the feasibility:

Fontaine et al. (2010). Development of a Versatile Procedure Based on Natural Transformation for Marker-Free Targeted Genetic Modification in Streptococcus thermophilus. Applied and Environmental Microbiology.

Haustenne et al. (2015). Modeling of the ComRS Signaling Pathway Reveals the Limiting Factors Controlling Competence in Streptococcus thermophilus. Frontiers in Microbiology. 

Cheers,

Raphael

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Postdoc researcher at MIT

Microbiology / Horizontal Gene Transfer / Cyanobacteria

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[Simon Quellen Field]

Since GFP is easily detected, how about selection by microfluidics?

Send a stream of them into a Y, and have the glowing ones go left and the dark ones go right?

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[Koeng]

I've tried growing S thermo. It is not as naturally transformable as sources say. It is also a lot more difficult to grow. I was part of an LA biohacker project working with it and B subtilis, and B subtilis was much easier to transform, grow, and get strains of. 

When people say "naturally transformable" that's usually an exaggeration of the truth. B subtilis is naturally transformable, but good luck getting a higher efficiency than you would with some E coli and simple CaCl heat-shock. 

Personally, I like S cerevisiae the most when it comes to genome engineering. It is easier than B subtilis to transform, integrates PCRed DNA better (B subtilis requires >125bp of homology, S cerevisiae only requires 40, which can be added with PCR). S cerevisiae can also be transformed with Cas9/sgRNA for genome engineering. However, don't expect too high of transformation efficiency with raw DNA and an sgRNA, usually we have to screen at least 8 colonies. Since it is a eukaryote, it is a lot more similar to humans for the people looking in that direction. It can also make bread and beer which is pretty cool. 

If you can get a DIY flow cytometer, I'd be one of the first people in line for it. Even used machines cost thousands of dollars, brand new flow cytometers go from the 10s to 100 of thousands of dollars.

-Koeng1

[Gordana Ostojic]

I think it's doable. I am currently making DIY capillary electrophoresis with impedance detection so I guess it would be quite similar (even less expensive because it wouldn't need high voltage power supply). The whole impedance detection parts cost less than 30$ (+ need some voltage supply, + arduino or similar board for voltage analog to digital conv), is very simple and quite sensitive.