Re: [DIYbio] DNA extraction and DNA Barconding

@Jhon

My hypothesis is if you can compare whole genomes, it is possible to find a set of regions that not match and that are stable enough to be considered to as a parameter to compare the different genomes. In this set is possible design primers to amplify parts of these regions and in almost an arbitrary size - I'm supposing that these regions have many different sizes, what makes this design flexible.

Whit this, just gel bands would be sufficient to say if the sample is from a species or another (just like you said, but in a different context), and the sequencing, what is needed in the case of barcodings, will not be necessary.

@Avery

I'm not referring to the Toradol by itself, but what comes with it, like this.

I didn't know that this drug need prescription. Thanks for the info.

Lets see if the prescription is needed here in Brazil too... I'll take a look.

@Sebastian

Sure, it is not so expensive. But I want use reagents that could be found in the day-to-day world of the audience. I want to bring the experiment for their context.

In short terms: I want the extraction to be the most "DIY" it can be. Just for the "show".

@Dakota

Thanks a lot for sharing your experience. Nice link, I was taking a look on this site; but I found yours better explicative.

It seems that one of the pursuits of barcoding the DNA is find a unique DNA sequence present in all (or almost all) life beings and that could be comparable - and to be comparable, it must have the balance between mutation rates and conservation, as you said.
My point is, if "barcoding is no substitute for taxonomy", so why do we need to keep trying to use the "universal" DNA piece if the uselfulness of what we call today "DNA barcode" only would be for identification of species?
If taxonomic correlations cannot rely upon DNA barcode, and taking in account the crescent viability of whole genomes sequencing, why not use little smart-chosen pieces of the thousands of non-matching sequences between genomes to identify species!? It could be possible design a set of bands of any size to confirm any species if whole genome sequencing was a trivial thing that ani DIYer could do. And in accord to the Carlson Curves, it might be so in the future.
So, my question is a little deeper: will we keep thinking on DNA barcodes as we think today if whole genome sequencing get popular!?
And, by the way, my idea is to use the known sequenced genomes to be able to identify the presence of DNA material of a suspected species "only by gel".

@Jeswin
Yeah, I'm looking for genomic DNA. I was making a comparison with the DIY extraction protocol described by Cathal on his blog.
And yes, this is exactly what I'm planning to do. Still need to do the bioinformatics. I will share here my results. Hope to find an interesting way to do this.
My intuition keeps me saying that someone already did that. But I found nothing so far. I'll appreciate if you could point anything for me take a look.

I'm even more excited about this with your replies. Thanks a lot. This is going to be very fun. :)

2015-01-15 20:58 GMT-02:00 Jeswin <phillyj101@gmail.com>:

On Thu, Jan 15, 2015 at 11:34 AM, Otto Heringer <ottowheringer@gmail.com> wrote:

> I'll look for genomic DNA instead of only plasmids (I'm using this
> protocol), but the problem of where to find some reagents persists. The only
> one that is hard to obtain is indeed Tris.
>
Plasmid extraction is only for bacteria. It's more difficult to do,
because we want to keep the genomic DNA from contaminating the plasmid
DNA. If you got the right reagents, its not difficult. Since you are
looking to determine beef, then you're looking for genomic DNA.

>
> And about barcoding, I see that there is a still open debate about the use
> of barcodings because of the supposition that it might "replace" taxonomy.
> Some say it is only useful for "biodetection" of some species and that
> taxonomy need more complex work.
>
You can barcode using PCR/electrophoresis if you got the correct
primer designed. Is there a sequence found in cows that is different
from one in goats, chicken, etc? With that specific sequence, you will
have an expected PCR product size. Maybe you should find more than one
highly species specific sequence. Then you can have a "fingerprint".

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