Re: [DIYbio] Re: Requesting your thoughts on a yogurt-based nutraceutical platform

Wouldn't error-prone PCR and re-transformation count as "mutagenesis",
without the hazard of genome wide mutation?

Broadly in agreement with you Nathan, that if you're going to do GMO,
just do GMO. Detractors *don't give a crap* how much effort you've put
in, they'll just shout "frankengrapeyoghurt" as loud as they can and
fund thugs to break into your lab and boil your fermenters.

When asked by the media, you tell the truth; "we're using grape genes".
You're going to have to adapt the genes to work in L.bulgaricus anyway;
codon usage, shine-dalgarno, bacterial promoters, potentially a
rho-independent terminator or two. By that time, why does it matter if
you've optimised the gene any further? It's already a
frankengrapeyoghurt by then. Hiding behind appeals to nature and
essentialism just make it seem like there's something wrong with technology.

However, where I disagree with Nathan is when you talk to slightly more
savvy but no less fearmongering regulators. Yes, they may want the genes
to appear as "natural" as suits their essentialist-aesthetic, and so
perhaps the less you change things the more warm they'll be to licensing
it. For one thing, changes to DNA are (AFAIK) never allergenic, but
changes to proteins might be..but they probably have procedures in place
to assess allergenicity potential.

So why not ask them and work so as to avoid the issue? If they just run
a pBLAST against known allergens, you can do that too and reject mutants
that get scores above a certain threshold. Do the regulatory screening
for them, in advance, and make their job easier while not having to tie
your hands back just to appease serfdom-romanticising hippies. :)

On 09/10/13 06:27, Nathan McCorkle wrote:
> I may have been a bit misleading in the last email, as I was ranting more
> about mutagenesis as it refers to 'shotgun genetic engineering' aka using
> chemo and radio mutagenesis. With Synthetic Biology *wink wink*, one could
> simply use a computer program to mutate nucleotide by nucleotide the
> protein's gene. After a while it might just happen to look like a
> heterologous gene, but assuredly it wouldn't be cross-species, simply
> evolved in-silico.
> On Oct 8, 2013 7:54 PM, "Nathan McCorkle" <nmz787@gmail.com> wrote:
>
>> On Mon, Oct 7, 2013 at 8:40 PM, Richard Yu <ryu@radiantgenomics.com>
>> wrote:
>>> Hi Patrick-
>>>
>>> Thanks so much for your support!
>>> Good points. I don't know how Lacto will differ from Ecoli in terms of
>>> expresion of active C4H, or what the flux will be like in Lacto. We're
>>> hoping to stick with the simple things- expression levels, perhaps
>> protein
>>> fusions might also do the trick (analogous to (Zhang, Y et al, JACS
>>> 128:13030-13031 (2006))). Fusing PAL to C4H, or C4h to 4CL? Get that
>>> substrate channeling thing going. The farther we get away from native
>>> proteins, though, the farther we get away from that food-grade criteria
>> for
>>> a food product. It's an interesting set of scientific and non-scientific
>>> constraints to match :). Will be fun to see how far we can bring standard
>>> metabolic engineering and strain improvement techniques into the fold,
>> too.
>>> (mutagenesis and selection, for example- not GMO!).
>>
>> Realistically though that logic doesn't make sense. Is it possible to
>> not play that card in the marketing department? It just allows
>> ignorant unscientific claims to claim traction via your teams hard
>> work and sweat. Please, whatever you do, don't ever allow people to
>> think GMO is any worse or better than mutational or selective
>> breeding.
>>
>> Microarray analyses reveal that plant mutagenesis may induce more
>> transcriptomic changes than transgene insertion
>> "Finally, we believe that safety assessment of improved plant
>> varieties should be carried out on a case-by-case basis and not simply
>> restricted to foods obtained through genetic engineering."
>> http://www.pnas.org/content/105/9/3640.full
>>
>

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