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Invisiblec10h12n2o
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FYI: DNA-Based Taxonomic ID Available to Customs and LE * 6
    #23486807 - 07/28/16 06:14 PM (7 years, 8 months ago)

hello my friends. I was doing some reading on academic databases (a lovely source for cutting edge mycology info/studies), and found something that people should probably be aware of.
Quote:

Title:
DNA-based taxonomic identification of basidiospores in hallucinogenic mushrooms cultivated in “grow-kits” seized by the police: LC-UV quali-quantitative determination of psilocybin and psilocin. (Viniero et al, June 2016)




Basically, a group has established a process to ID the tissue and basidiospores of hallucinogenic mushroom species relatively easily using DNA, from spores or spawn media, without having to fruit them.

This is a really big deal, because up until now, it has been virtually impossible for even a professional mycologist to definitively distinguish one species from another, just from the spores or myc. This has probably had a large influence on the way laws are written in many countries (ie  spores are legal but live cultures are not)

in fact, my pug dog knows a goat who got caught with 5 totally colonized cubensis monotubs in a state where cannabis possession has mandatory minimums, a bunch of spore syringes, agar cultures, etc. LE had no idea how it worked and started digging around in the colonized substrate looking for the mushrooms 
:loldongs:

fortunately, everything turned green before anything visibly illegal like fruit bodies got the goat cooked. apparently, lawyers have often been able to get people out of trouble sometimes by demanding that the state prove that the fungus was actually an illegal species (which was nearly impossible to do)

spores  are even harder, and i imagine that the difficulty in proving the species of a spore syringe in court (without first having to commit the "crime" of fruiting them), probably plays a large role in the legal status of spores vs cultures

In light of this new DNA-based method and the fact that it is being made available to LE and customs, it would be wrong to assume that a culture or spore sample could not be identified without fruits.

It is important for shroomerites that it is about to become much easier for those who have an interest in proving that a sample is indeed illegal to do so. Do not rely on anyone's inability to ID, as the days of DNA taxonomic ID are here. Know the laws of your country, and stay safe!


--------------------

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"Convictions are more dangerous enemies of truth than lies"
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Invisiblefalsereality


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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: c10h12n2o] * 1
    #23486853 - 07/28/16 06:23 PM (7 years, 8 months ago)

Rule 1) Don't get caught.

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Invisiblec10h12n2o
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: falsereality]
    #23486927 - 07/28/16 06:38 PM (7 years, 8 months ago)

lol yeah that helps

crazy thing is, billy goat didnt get caught himself, his neighbors had a warrant for selling weed and the cops raided the wrong place!! apparently it took them forever to believe that the monotubs werent weed


but the point of the DNA ID stuff is a lot deeper than that. I suspect many more states will soon ban all active species spores in addition to cultures, since it is more enforceable now


--------------------

C10's Agar Guide + Tips and Tricks | c10's Flow Hood Build Guide


"Partial knowledge is more triumphant than complete knowledge; it takes things to be simpler than they are, and so makes its theory more popular and convincing."

"Convictions are more dangerous enemies of truth than lies"
― Friedrich Nietzsche

Edited by c10h12n2o (07/28/16 06:39 PM)

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InvisibleSanguin3
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE *DELETED* [Re: c10h12n2o]
    #23487085 - 07/28/16 07:21 PM (7 years, 8 months ago)

Post deleted by Sanguin3

Reason for deletion: .

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Offlinespirit_shadow
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Sanguin3] * 1
    #23487183 - 07/28/16 07:55 PM (7 years, 8 months ago)

Dna testing now? You......are NOT the boomer! JERRY! JERRY!


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Invisiblec10h12n2o
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: spirit_shadow]
    #23487476 - 07/28/16 09:35 PM (7 years, 8 months ago)

yeah that was my first thought when i saw this, immediately started building my library. i figured it was important to let others know for the same reason

Quote:

spirit_shadow said:
Dna testing now? You......are NOT the boomer! JERRY! JERRY!




lol except tax payers cover the bill instead of the illustrious mr springer


--------------------

C10's Agar Guide + Tips and Tricks | c10's Flow Hood Build Guide


"Partial knowledge is more triumphant than complete knowledge; it takes things to be simpler than they are, and so makes its theory more popular and convincing."

"Convictions are more dangerous enemies of truth than lies"
― Friedrich Nietzsche

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OfflineX2QE
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: c10h12n2o]
    #23742186 - 10/16/16 11:23 AM (7 years, 5 months ago)

Thanks for sharing this info. I would have not seen it otherwise.

I need to stock up.

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OfflineAlan RockefellerM
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: c10h12n2o]
    #24718404 - 10/17/17 11:11 PM (6 years, 5 months ago)

Quote:

c10h12n2o said:
Quote:

Title:
DNA-based taxonomic identification of basidiospores in hallucinogenic mushrooms cultivated in “grow-kits” seized by the police: LC-UV quali-quantitative determination of psilocybin and psilocin. (Viniero et al, June 2016)




Basically, a group has established a process to ID the tissue and basidiospores of hallucinogenic mushroom species relatively easily using DNA, from spores or spawn media, without having to fruit them.




I read this paper carefully, and there is nothing new in it.  They don't identify the spores at all - they are only testing the mycelium and fruits.    People have been doing the DNA part for over 20 years and the chemical tests for over 60 years. 

The paper was not written by people with English as their first language and they are not mycologists, so it is easy to misread and think that they identified the spores.    However actually what they did is inoculate the substrate (or maybe it already came that way), then incubated 20 days, and tested 100 mg of the colonized substrate or fruits.


Quote:

This is a really big deal, because up until now, it has been virtually impossible for even a professional mycologist to definitively distinguish one species from another, just from the spores or myc.




Since colonized substrate has plenty of psilocybin, it has been easy for law enforcement to identify the mycelium as an illegal species by GC-UV analysis since the 1960's. 

The paper says nothing about identifying spores.  Grinding and trying PCR on spores is something I have been meaning to try.  I don't really expect it to work, and even if it does, it probably takes a lot of spores to get enough DNA to PCR.  Spores are typically not identified since they are rarely per-se illegal, and in the three states where spores are illegal the spore laws do not appear to be enforced.


Quote:


in fact, my pug dog knows a goat who got caught with 5 totally colonized cubensis monotubs in a state where cannabis possession has mandatory minimums, a bunch of spore syringes, agar cultures, etc. LE had no idea how it worked and started digging around in the colonized substrate looking for the mushrooms




He is lucky they didn't take any mycelium for testing, as it is common for people to get busted for having cubensis mycelium even when there are no fruits.


The only thing done in this paper that is not standard law enforcement procedure is that they sequenced the mycelium to determine the species.  The reason law enforcement does not do this is that under the law the psilocin is illegal and the species does not matter.  They are not going to start doing this because they don't care what species they find, and it is pretty much always cubensis anyway.

Here is a link to the paper:  http://sci-hub.bz/10.1016/j.jpba.2016.03.043#

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InvisibleAdden
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Alan Rockefeller]
    #24718568 - 10/18/17 02:35 AM (6 years, 5 months ago)

Can't you just KaOH mycelium?

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OfflineAlan RockefellerM
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Adden]
    #24718599 - 10/18/17 03:15 AM (6 years, 5 months ago)

Quote:

Adden said:
Can't you just KaOH mycelium?




To extract the DNA and sequence it?

Yes, I do that all the time.  I scrape up some mycelium from a petri dish and get good sequences back. 

A lot of the time when people say they have a "non-fruiting strain", what they actually have is some other fungus with a long name you never heard of, which is super common in soil but never makes any sort of fruiting body.  There are thousands of species like that, they look great on agar or grain, but just never make any mushrooms.

Sometimes people send me agar cultures to sequence to check to see if what they are growing is what they think they have.  Half the time it is, half the time it isn't.

Would be cool to be able to do it right from the print though without having to germinate it.

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Offlinechibiabos
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Alan Rockefeller]
    #24718603 - 10/18/17 03:22 AM (6 years, 5 months ago)

Quote:

Alan Rockefeller said:
Quote:

c10h12n2o said:
Quote:

Title:
DNA-based taxonomic identification of basidiospores in hallucinogenic mushrooms cultivated in “grow-kits” seized by the police: LC-UV quali-quantitative determination of psilocybin and psilocin. (Viniero et al, June 2016)




Basically, a group has established a process to ID the tissue and basidiospores of hallucinogenic mushroom species relatively easily using DNA, from spores or spawn media, without having to fruit them.




I read this paper carefully, and there is nothing new in it.  They don't identify the spores at all - they are only testing the mycelium and fruits.    People have been doing the DNA part for over 20 years and the chemical tests for over 60 years.



Name one other paper where somebody used sequence alignments to identify hallucinogenic mushrooms...At the very least I call bullshit on the idea that people have been doing it for over twenty years.  Granted that I only checked the NCBI database, but the earliest sequence I could find using "psilocybe" was published in the database in 2000.  And that was a partial sequence for a gene coding for rRNA.  Either way, I'm not sure what your point is.

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Offlinechibiabos
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Alan Rockefeller]
    #24718607 - 10/18/17 03:26 AM (6 years, 5 months ago)

Quote:

Alan Rockefeller said:
Quote:

Adden said:
Can't you just KaOH mycelium?




To extract the DNA and sequence it?

Yes, I do that all the time.  I scrape up some mycelium from a petri dish and get good sequences back. 

A lot of the time when people say they have a "non-fruiting strain", what they actually have is some other fungus with a long name you never heard of, which is super common in soil but never makes any sort of fruiting body.  There are thousands of species like that, they look great on agar or grain, but just never make any mushrooms.

Sometimes people send me agar cultures to sequence to check to see if what they are growing is what they think they have.  Half the time it is, half the time it isn't.

Would be cool to be able to do it right from the print though without having to germinate it.



Just out of curiosity, what protocol are you following to determine sequences?

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OfflineAlan RockefellerM
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: chibiabos] * 2
    #24718771 - 10/18/17 06:52 AM (6 years, 5 months ago)

Quote:

chibiabos said:
Name one other paper where somebody used sequence alignments to identify hallucinogenic mushrooms...




http://www.czechmycology.org/_cmo/CM64207.pdf


Quote:

At the very least I call bullshit on the idea that people have been doing it for over twenty years.


 

Here is one from 16 years ago, and it wasn't the first:  Redhead, Scott A.; Vilgalys, Rytas; Moncalvo, Jean-Marc; Johnson, Jacqui; Hopple Jr., John S (February 2001). "Coprinus Pers. and the disposition of Coprinus species sensu lato". Taxon. 50 (1): 203–41. JSTOR 1224525. doi:10.2307/1224525.

People have been sequencing for much longer than 20 years, but in the 1970's they had to read each base on an electrophoresis gel, so it was really expensive to get the data.



Quote:

Granted that I only checked the NCBI database, but the earliest sequence I could find using "psilocybe" was published in the database in 2000.  And that was a partial sequence for a gene coding for rRNA.  Either way, I'm not sure what your point is.




My point is that the following claim in the OP is not true:  "This is a really big deal, because up until now, it has been virtually impossible for even a professional mycologist to definitively distinguish one species from another, just from the spores or myc."

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Offlinechibiabos
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Alan Rockefeller]
    #24719406 - 10/18/17 12:50 PM (6 years, 5 months ago)

Quote:

Alan Rockefeller said:
Quote:

chibiabos said:
Name one other paper where somebody used sequence alignments to identify hallucinogenic mushrooms...




http://www.czechmycology.org/_cmo/CM64207.pdf


Quote:

At the very least I call bullshit on the idea that people have been doing it for over twenty years.


 

Here is one from 16 years ago, and it wasn't the first:  Redhead, Scott A.; Vilgalys, Rytas; Moncalvo, Jean-Marc; Johnson, Jacqui; Hopple Jr., John S (February 2001). "Coprinus Pers. and the disposition of Coprinus species sensu lato". Taxon. 50 (1): 203–41. JSTOR 1224525. doi:10.2307/1224525.



The first paper is totally different from what OP shared.  They'd already identified their specimens as being some novel species and then computed a phylogeny. 

And I can't find any text for the second paper that isn't behind a paywall.  Either way, neither of those support your claim that people have been doing this for more than twenty years.  Neither of those were published twenty years ago.

I'm also still curious about what your protocol is for sequencing.

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InvisibleStonehenge
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: chibiabos]
    #24719998 - 10/18/17 04:37 PM (6 years, 5 months ago)

Cops will not use this unless and until it gets to the point they can put spores in and instantly analyze them. Sort of like a roadside breathalyzer test. Customs are not going to do it nor post office if they find them because even if they prove its an illegal species there is no evidence the receiver knew about it or possessed it

When customs finds spores or seeds they just toss, same as when they find a few pills. They may send a letter asking you to come in and claim it, I call that the "how stupid are you?" letter


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OfflineAlan RockefellerM
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: chibiabos] * 2
    #24721020 - 10/19/17 01:58 AM (6 years, 5 months ago)

Quote:

chibiabos said:
I'm also still curious about what your protocol is for sequencing.





Here is a webpage I wrote on how I sequence mushrooms:  https://wiki.counterculturelabs.org/DNA_sequencing

I will be teaching a class on DNA sequencing and mushroom identification on Oct 28 and live streaming it.

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Offlinechibiabos
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Alan Rockefeller]
    #24721073 - 10/19/17 03:26 AM (6 years, 5 months ago)

No shit?  A friend of mine has been trying to get me to get involved with that group.  :lol:

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OfflineAlan RockefellerM
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: chibiabos]
    #24721622 - 10/19/17 10:51 AM (6 years, 5 months ago)

Yes, Oct 28 @ 10:30am until some time in the afternoon.  I will teach a class on sequencing mushrooms, and also using PCR to detect GMO foods.  (its almost the same process)  While the PCR machine is running, Mario and I will teach mushroom identification.  Three hours later the PCR will finish and we will do electrophoresis to see which mushroom sequencing reactions worked, and which food samples have GMO's. 

You can have your friend ping me closer to the date of the class, or just keep an eye on this event:  https://www.meetup.com/Counter-Culture-Labs/events/fspbbnywnblc

I'll update that link when I know for sure about the class.  It is going to cost $10, but no one has to pay.

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Offlinechibiabos
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: Alan Rockefeller]
    #24722535 - 10/19/17 04:38 PM (6 years, 5 months ago)

Shouldn't you be running your gel before sequencing anything from your PCR steps?  Seems like you'd probably want to know that you're studying a sequence instead of several of them before you get to the actual sequencing step.  Otherwise it seems like sort of a waste of whatever consumables go into your actual sequencing step.

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OfflineAlan RockefellerM
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Re: FYI: DNA-Based Taxonomic ID Available to Customs and LE [Re: chibiabos]
    #24723258 - 10/19/17 09:03 PM (6 years, 5 months ago)

Quote:

chibiabos said:
Shouldn't you be running your gel before sequencing anything from your PCR steps?




Yes, I should have said to see which PCR reactions worked.  If the gel shows a good band, then I drop off the PCR product at Genewiz.  There is a black box in Berkeley, if I get it in there by 8pm I get the results in my email the next morning, and they charge me $7 per reaction.

The gel is saving me $7 per failed PCR reaction.  Well funded places skip that step, but I have to work for my money...

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