I want to GCMS Ponderosa Pine bark smell

[Nathan McCorkle]

I'm thinking sucking the air from between the bark with a syringe
should be good for sample collection, though not all cracks smell good
(like vanilla cream soda to me) and after smelling them you're
removing sample. Maybe I'd try a few syringes of
direct-suck-from-bark-crack and a few of exhaled lung air after I
detected the sweet smell.

Anywhere I could mail-order a GCMS test in the U.S.A.?

--
-Nathan

[Dakota Hamill]

I have access to a working GCMS. I'd say for samples a piece of pine bark or a swab of sap would be better than a syringe filled with air.  Most likely terpenes and esters would be present, but it'd be neat to see.  If you're interested I could get in touch with my professor and setup a day to run the samples, probably even video tape part of it and post it.

[Nathan McCorkle]

Cool, yeah I'm definitely interested. If you let me know the
parameters of the run, I can try to figure out a materials cost
(unless you already know that) and factor in prep time to
pay/reimburse and at least just get that number!

I'd rather not rip off any bark, but I guess it might be OK in the
name of science. It would answer my current question of whether
emanating from the bark (collect bark, let samples air for 0, 1, 10,
60 minutes), or seeping around it (any maybe soaking into the bark as
it seeps around).

It's a 4 hour drive to the spot in the Ponderosa forest where I camped
a night ago, I won't be able to make it out there for another 2 or 3
weekends. That'll give me time to order collection supplies though.

Let me know what you find out.
:D

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--
-Nathan

[leaking pen]

I've been told by a chem prof a decade ago that he's done similar, and among other things found vanilin.  these links might be of use as well. http://www.sdaos.org/wp-content/uploads/pdfs/Vol.%2029%201950/50p91a.pdf

http://www.nature.com/news/2009/090527/full/459498a.html

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[leaking pen]

ohh, and, the chemical is stronger in yellowbellies.  If you can, the Kaibabs up north of the Grand Canyon, you'll find older, mostly yellow trees. The smell after a rain and fresh sunshine, my god....

[Dakota Hamill]

I'll check on the GCMS and get back to ya.

[Jeswin]

Can't you get some sap from the pine cone? That's what give it the smell, right?

On Tue, May 21, 2013 at 9:59 PM, Dakota Hamill <dko...@gmail.com> wrote:
> I'll check on the GCMS and get back to ya.
>

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[Nathan McCorkle]

On Wed, May 22, 2013 at 6:55 AM, Jeswin <phill...@gmail.com> wrote:
> Can't you get some sap from the pine cone? That's what give it the smell, right?

Maybe, but the the air between the bark is what I've noticed smelling
most like vanilla.

The Ponderosa Pine wikipedia page says that the Jeffrey Pine smells
more strongly, so I guess I've got to track down a stand of them to
take a whiff!

Also, the Jeffrey Pine wikipedia page says it's tolerant of serpentine
soils, which is NPK deficient (the pine tree you see growing out of
rocks)... so maybe these would be good trees to play with in general.
Either as a selection tool, or to find microbial/fungal nitrogen
fixers.

[leaking pen]

Nope, the smell is not in the sap or the cone, its very much in the bark.  When the trees get a certain age, a lot of that black bark starts falling off, and the yellow underbark underneath (what is in the cracks) becomes the main bark. When that happens, the smell gets VERY strong. (I love ponderosas I used to camp in the Kaibab forest all the time as a kid. )

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[Patrik D'haeseleer]

Yeah, it's mainly vanillin. Vanillin is actually a common degradation product of the phenolic compounds in lignin. If anything, I'm surprised there aren't more woody plants that smell like it.

Next time you happen to visit a winery that has freshly toasted oak barrels, have a sniff: vanilla! That's where those vanilla overtones in some aged wines (or brandy, or tequila) come from.

Actually, there are a number of other aroma compounds that are offshoots of the lignin biosynthesis or modification pathways. Wikipedia has a surprisingly good page on aroma compounds that could be pursued for DIYbiosynthesis:

http://en.wikipedia.org/wiki/Aroma_compounds#Aromatic

Patrik

[Dakota Hamill]

Went to use the GCMS this weekend to give it a test run.  Seems like something is wrong with it and professor is trying to fix it.  I managed to grab a sample of pure vanillin from the orgo lab and was going to do that, as well as crushed up mint just as an interesting test.  If it gets up and running soon I'll keep ya posted.   Out of nowhere, the computer randomly shuts off...but it is a machine that has been on 24/7 for 5+ years so, I imagine some electrical parts might be starting to get tired?

[Nathan McCorkle]

Thermal shutdown safety mechanism? If you can see it's dusty inside,
I'd disconnect the computer, take it to a loading bay, open it up and
go nuts with a can of duster. Might need to remove the CPU fan to
clean the heatsink well.

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-Nathan

[Dakota Hamill]

Yeah that's actually not a bad idea, its pretty dusty in that old analytical lab and I imagine its never been cleaned.

[Muralidharan E.M.]

Headspace Gas chromatography is probably  a more appropriate method for analysis of the very volatile compounds that contribute to the "smell".

Murali

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[Nathan McCorkle]

Which is basically what I first proposed.

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-Nathan