Science

http://www.researchgate.net/publication/224812866_Development_of_versatile_shuttle_vectors_for_Deinococcus_grandis

I googled for "D. Plasmid", often they characzterize minimal plasmids by cutting them and seeing what replicates in the species.
Worst case you can always try carbon whisker or electroporation

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Very excited to see personal spectroscopy take off. Would be fantastic for nutritional characterisation and accountability in food processing.

On Fri, Aug 28, 2015 at 12:26 AM, Cory Tobin <cory.tobin@gmail.com> wrote:
> Ultimately, though, I think it will be more useful (but more
> difficult) to judge plants on the functionality of their mutations
> rather than how those mutations arrived. IMO, good traits are good
> traits regardless of whether it came from a lab or cross-breeding or
> HGT. Same for bad traits.
>
> -cory

Thinking about it now, I think this is really a MUCH harder test,
which is why no one wants to talk about it. They all want to assume
change is bad, because there's no way to really validate except
through randomized real-world trials... which takes time, is plagued
by incomplete and bad/incorrect/biased reporting... etc.

If you think about it from a system validation standpoint, what would
you do? For every type of human proteome, for every type of GMO in
production, allow two human clones to live a full life with and
without consuming/being-exposed-to GMOs and evaluate their health and
genetics and epigenetics at many stages throughout life and at death
(comment: or maybe the exposure should be devoted to another clone or
two).

Ok, great, we wrote our test, that should clear things up. Oh, but
actually, we should expand on just iterating through each GMO and
include all non-GMO as well. (and I bet there are a lot more types of
non-GMO food to test)

So applying the best test with the best heuristics really depends on
what you want to capture. Worrying about whether something is good or
bad for you is certainly more interesting than is something is GMO or
not.... especially when there are so many /simple chemicals/ that can
be deadly/horrible contaminants.

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On Thu, Aug 27, 2015 at 11:47 PM, Cathal (Phone)
<cathalgarvey@cathalgarvey.me> wrote:
> I think the question was "For any given gene how would you detect
> modification of that gene". More of an informatics exercise than a molecular
> one: I imagine hidden markov modelling of the surrounding genome would help
> identify areas that are "too simple" because of our present difficulty and
> disinclination towards matching deep genomic patterns.
>

Yeah I was thinking along these lines... the answer to the question
"is this stuff (contaminated with) GMO" seems lie in some sort of
statistics or mathematical analysis.

That said, Cory's answer is perfect for a question like "aside from
statistical analysis, what is a good way to start checking for common
agro-industry-standard GMO". Rightfully as he pointed out, this is a
very crude test, as sequence construction can change at any point when
industry developments alternatives.

At that point, if you're really concerned about presence of GMO, you
might have much much bigger problems. If you want to /just/ detect Bt
corn, you can search for CaMV promoters, if that comes up empty you
can search for Bt protein sequence fragments, if that doesn't turn up
results maybe you want to check a Western Blot or ELISA for
functional/binding domains of Bt protein, if that doesn't turn up
results well who knows... maybe the engineers altered the structure
vastly and that turns up nothing. Or maybe this is really a GMO-free
sample.

So at that point the logic and procedure becomes quite circular in
terms of GMO, detection, form, function, role, etc...

If you screen only for common standards, you may find all standard
GMOs, but you will not catch non-standard (or newer standards that you
are not updated to, because they are trade-secrets, etc...). The only
reasonable thing to do at that point seems to be statistical analysis,
unless you have a BIG engineering budget and some serious reason to
get into blotting and enzyme function assays.

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> I think the question was "For any given gene how would you detect
> modification of that gene". More of an informatics exercise than a molecular
> one: I imagine hidden markov modelling of the surrounding genome would help
> identify areas that are "too simple" because of our present difficulty and
> disinclination towards matching deep genomic patterns.
>
> That's assuming you don't just glance at it and say "that's awfully
> prokaryotic for a plant!". :)


Oooh, I see. Yeah, I misinterpreted that question.

The good thing is that today, at least, all of the traits on the
market are large transgene insertions that look very different from
the plants' innate sequences. Prokaryotic and viral sequences spliced
to eukaryotic sequences surrounded by restriction sites. Plus, the
variety of sequences used in practice is quite limited: a handful of
promoters, herbicide tolerance genes and pest resistance genes. So
the number of things to look for is quite small.

In theory, though, someone could make single nucleotide changes that
would be completely indistinguishable from naturally occurring or
random X-ray or EMS induced mutations. In that case, like Cathal
says, there's not much you could do except build a statistical model
of what "natural" sequences look like and compare your observed
mutations against the model.

Ultimately, though, I think it will be more useful (but more
difficult) to judge plants on the functionality of their mutations
rather than how those mutations arrived. IMO, good traits are good
traits regardless of whether it came from a lab or cross-breeding or
HGT. Same for bad traits.

-cory

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I think the question was "For any given gene how would you detect modification of that gene". More of an informatics exercise than a molecular one: I imagine hidden markov modelling of the surrounding genome would help identify areas that are "too simple" because of our present difficulty and disinclination towards matching deep genomic patterns.

That's assuming you don't just glance at it and say "that's awfully prokaryotic for a plant!". :)

> I'm rather curious as to how one would go about testing for whether or not
> random genes were manually tweaked (and not naturally mutated/introduced
> through bacterial/viral horizontal gene transfer) in the first place.

Any transgenic sequences can be detected by PCR or, even better
RT-PCR. You would purify DNA from the plant, design primers for the
specific sequences you are looking for, do the PCR and then run it out
on an agarose gel.

Most approved traits will have the CaMV 35S promoter sequence so you
can use primers for that promoter. Although, it's not guaranteed to
be in every transgenic line. If you have a have a particular trait
you are looking for, use this website to find it. It will have links
to detection information that includes details of the transgenic
sequences and suggested primer sequences.
http://www.isaaa.org/gmapprovaldatabase/

For example, if you're looking to detect Hercules RW maize
(Glufosinate tolerance and root worm resistance), the search function
will bring you to this page:
http://www.isaaa.org/gmapprovaldatabase/event/default.asp?EventID=112
which details this particular trait. Click on "Documents and Links",
then on "GMO Detection Method Database". That will take you to a page
with sequences, primers, recommended detection methods, etc. The
recommended detection methods tend to be primers and Taqman RT-PCR
probes.

-cory

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Asking for people to stop unnecessarily hiking the work undertaken by
farmers who feed me isn't bias, it's common sense. For people who are
willing to pay a premium for oversight and traceability, there are
already plenty of options. Calling for labels is calling for the rest of
us to pay that premium without our choice or consent.

I'm the EU. I already deal with prohibitionism thanks to scaremongering,
and I am forbidden from choosing what to eat based on my own
environmental conscience. You can be sure that if I had the choice, I'd
choose GE foods, but thanks to very well-paid lobbyists I can't.

I call 'live and let live' collaboration, what do you think?

On 26/08/15 20:26, Jonathan Cline wrote:
> Cathal, It's nice that you ignore 95% of the content of a post and then
> slip in your bias. Stop arguing and collaborate for a change.
>
> ## Jonathan Cline
> ##jcline@ieee.org
> ## Mobile: +1-805-617-0223
> ########################
>
> On 8/26/15 11:27 AM, Cathal (Phone) wrote:
>> (trolling argument) Keep your mitts off the rest of our food, kthx.
>
>
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## Jonathan Cline  ## jcline@ieee.org  ## Mobile: +1-805-617-0223  ########################    

(trolling argument)  Keep your mitts off the rest of our food, kthx.