Ideas for What to Test for in an Introductory PCR/Gel Workshop

[xox]

Hey everyone!

I am considering ideas for an introductoy PCR/Gel workshop - what could we test for?  I remember being part of such a class/workshop a bit back - we sampled our saliva and tested for some gene that some people have, I can't remember which (though it might have been the "bitter taste gene" listed below).

I like using saliva and the simple premise of testing for the presence of x gene, as it simplifies the DNA extraction and the overall concept so we can focus on the tools and concepts of PCR and Gel-running.  

Possible topics?

I thought at first of the so-called human mendelian traits, like the classic ones you learn in high school to talk about basic genetics (tongue-rolling, widow's peak, etc) though it seems many of these are generally bogus and/or don't have worthwhile gene to home in on anyway.  The two I did come up with were:

1. ABO Blood Type - I guess we could take a pinprick blood sample and proceed with that?

2. TAS2R38 - a "bitter taste receptor" that some have

What are everyone thoughts?  What are some good subjects for an introductory pcr/gel session, and what human genes are of interest to test?  Any comments from people with ideas, who've been part of such introductory classes or have any related things to say are welcome.  Shouts out from the biohackers in Vancouver

erik

[DIYBIO Groningen]

Hi Erik,

we did a similar workshop few months ago during a mini maker faire. We extracted human DNA from saliva and we amplified some high variable region of human chromosomes to make DNA fingerprinting, it is easy, fast and worked well. All we used was a really slow centrifuge (1000 RPM are enough), an OpenPCR, a water boiler and gel electrophoresis apparatus.

Check our post about it and if you are interested I can give you all the needed information.

http://www.diybiogroningen.org/diy-bio-groningen-at-the-mini-maker-faire-2013/

Cheers,

Alessio - DIYbio Groningen

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[Jonathan Cline]

Neanderthal test - easy to do yet?


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[Cathal Garvey]

Kind of westphalian, given that mostly only Europeans will have decent
odds of bearing Neanderthal DNA.

There are a few other species lineages that wound up mixed into Homo
Sapiens in other areas; a friend told me lately that one of the
lesser-understood species along the West-Asia route got integrated over
there, and that there's a border somewhere in between where you can even
detect all three species in some populations.

Goodness knows what other "dark matter" is out there if you study enough
populations; there are how many known Homo-group species described now
that "went extinct" but probably interbred? Most of whom we have scant
fossil evidence for? Someday, that'd make a great workshop idea; not
"find out if you're part neanderthal" but "find out what other hominids
are hiding in your DNA". But even then, it's exclusive, because some
populations are pretty much pure Homo Sapiens; Africa, for example,
where the species emerged originally. Africa has the best general
genetic diversity, but little evidence so far of hybridisation with
other hominids.

So, interesting, but if untargeted then a bit exclusive?

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[Nathan McCorkle]

No one would be excluded from performing the test though... how is it
exclusionary in your opinion? By that logic we should stop testing for
allergies, or the bitter taste gene, stop 'sciencing' at all because
it organizes things into categories which may not overlap.

[Rikke Rasmussen]

Yes, but for an introductory workshop, it's nice to use something with a decent chance of yielding positive results.

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[Cathal Garvey]

This. But also, that the nature of the test is that people of
exclusively African descent, for example, will already know the outcome
with high certainty. It's unlikely to reveal anything participants with
enough knowledge wouldn't already suspect.

[Jonathan Cline]

Although you implied testing saliva, another idea is testing
common foods for bad things.   The below comes to mind;
I bet many will be surprised to know there is very likely to
be cockroach DNA in their kitchen turmeric. 

Quote
Ref: "FDA Draft Risk Profile: Pathogens and Filth in Spices" 2013

Types of Pathogens and Filth Adulteration Found in Spices

Microbial pathogens that have been found in spices include
Salmonella , Bacillus spp.  (including Bacillus cereus ),
Clostridium perfringens , Cronobacter spp., Shigella , and
Staphylococcus aureus . Filth adulterants found in spices
include insects (live and dead whole insects and insect
parts), excrement (animal, bird, and insect), hair (human,
rodent, bat, cow, sheep, dog, cat and others), and other
materials (decomposed parts, bird barbs, bird barbules, bird
feathers, stones, twigs, staples, wood slivers, plastic,
synthetic fibers, and rubber bands). 
 
Foodborne Illness Outbreaks from Microbial Contaminants in Spices

During the period 1973-2010, fourteen reported illness
outbreaks were attributed to consumption of
pathogen-contaminated spice. Countries reporting outbreaks
includeNew Zealand, Norway, Serbia, United Kingdom, and the
United States1946 reported human illnesses, 128
hospitalizations and two deaths.

End Quote

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On Friday, February 7, 2014 7:58:33 AM UTC-8, xox wrote:

[Jonathan Cline]

Cathal, I believe you overestimate the bio knowledge of the public or those coming into an introductory session of an open bio lab or even amongst biologists themselves (which itself is a broad field).  Basically speaking, the overwhelming majority of people off the street still believe, as a analogy, that the earth is flat.

On Sunday, February 9, 2014 2:18:13 AM UTC-8, Cathal Garvey wrote:

This. But also, that the nature of the test is that people of
exclusively African descent, for example, will already know the outcome
with high certainty. It's unlikely to reveal anything participants with
enough knowledge wouldn't already suspect.
 

[Cathal Garvey]

Sure, but anyone who's familiar enough with the word "Neanderthal" to
get excited about it, is fairly likely to have read onwards down the
wikipedia article to the part where it says "European". :)

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[CodonAUG]

Make sure to have some positive controls. Such as gender testing.

On Friday, February 7, 2014 7:58:33 AM UTC-8, xox wrote:

[Kermit Henson]

You can look for muscle structure (actn3), drug metabolism (any CYP450), lactose intolerance (mcm6), etc
The workshop is technical (how works pcr) or divulgative (why is this cool)?
May interest in help