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thescientist
Registered: 03/09/02
Posts: 807
Loc: Dade County
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Molecular phylogenetics, specifically CO I mtDNA
#14380743 - 05/01/11 01:03 AM (12 years, 8 months ago) |
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Are there any lab monkeys or gel junkies around here?
Anyone working with CO I mtDNA, ITS or B-tubulin?
no, I didn't use the search function, however I thought this post might be worthy in turning a few heads toward a shared interest.
Cheers
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thescientist
Registered: 03/09/02
Posts: 807
Loc: Dade County
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: thescientist]
#14384352 - 05/01/11 07:08 PM (12 years, 8 months ago) |
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Does anyone have any idea what I'm talking about?
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Feelers
Anti-Myth-Rhythm-Rock-Shocker



Registered: 06/18/02
Posts: 1,806
Loc: Land of Oz
Last seen: 5 years, 8 months
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: thescientist]
#14395101 - 05/03/11 04:03 PM (12 years, 8 months ago) |
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There's a few people here who have this experience. I've been slowly building up a lab to get some genetics stuff done. While I did genetics at university building up a specific method with all the reagents/steps necessary I'd be needing some help with.
Perhaps you might be able to offer assistance?
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thescientist
Registered: 03/09/02
Posts: 807
Loc: Dade County
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: Feelers]
#14395877 - 05/03/11 06:29 PM (12 years, 8 months ago) |
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Well, one would need access to PCR and sequencing. The primers are available for the regions I mentioned above.
This is not a home lab type of scenario, unless you have a few hundred grand to drop on it.
cheers
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Alan Rockefeller
Mycologist


Registered: 03/10/07
Posts: 48,276
Last seen: 8 hours, 45 minutes
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: thescientist]
#14396375 - 05/03/11 07:45 PM (12 years, 8 months ago) |
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I do sanger sequencing using ITS primers.
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Feelers
Anti-Myth-Rhythm-Rock-Shocker



Registered: 06/18/02
Posts: 1,806
Loc: Land of Oz
Last seen: 5 years, 8 months
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: Alan Rockefeller]
#14397415 - 05/03/11 10:46 PM (12 years, 8 months ago) |
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I have my own PCR machine, but sequencing is a little more expensive, but you can still get it done through a lab. 
Fastfred is one of the key people on here, he hasn't been seen for a few months unfortunately. Have a look at some of his posts, he's pretty clued up. My long term goal is to make a bioluminescent cubensis, but for now a more practical option is a protoplast fusion between cubensis and a potent wood lover. If we could work together on a practical step by step game plan that would be awesome.
Bioluminescent Cubensis Mr Gene
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thescientist
Registered: 03/09/02
Posts: 807
Loc: Dade County
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: Alan Rockefeller]
#14397874 - 05/04/11 12:56 AM (12 years, 8 months ago) |
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Is this at home or in a lab?
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thescientist
Registered: 03/09/02
Posts: 807
Loc: Dade County
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: Feelers]
#14397898 - 05/04/11 01:03 AM (12 years, 8 months ago) |
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Hey Feelers that is great. Very interesting and exotic project ideas you have.
Does anyone know what kind of data is available through genbank etc?
Perhaps I should take a poke in the literature.
I work on a different group of organisms, however there is plenty of overlap with the fungi.
Great to see some advanced mycology in this forum.
Thanks for the links
TS
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Feelers
Anti-Myth-Rhythm-Rock-Shocker



Registered: 06/18/02
Posts: 1,806
Loc: Land of Oz
Last seen: 5 years, 8 months
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: thescientist]
#14397945 - 05/04/11 01:18 AM (12 years, 8 months ago) |
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I have a PCR at home and I'm looking to do this in my basement. After the economic crisis there's been a load of old equipment offloaded to ebay. My PCR machine was $30.
I picked up a really valuable protein fractionator - but I can't really think of what to do with it. It can separate different proteins into 20 different vials, and can purify a protein by 1000x in one cycle. Got it for $60 but the RRP price is $5500 US, there's a lot of bargains going down!!!
That patent is pretty new, it's a pretty big discovery. In terms of creating a DNA sequence that I could buy and use, I need a lot of help. Primers, introns etc, it takes a lot of forward planning. Gene insertion methods as well, I could build a home made gene gun for about $200, use agrobacterium, and there's also a method that uses liquid nitrogen; I managed to get a cryogenic freezer for $130!
The possibilities are out there!
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Feelers
Anti-Myth-Rhythm-Rock-Shocker



Registered: 06/18/02
Posts: 1,806
Loc: Land of Oz
Last seen: 5 years, 8 months
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: Feelers]
#14397981 - 05/04/11 01:31 AM (12 years, 8 months ago) |
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When I learnt to use genbank it was for a proposed university project that was too expensive. It's basically a hodgepodge of all the sequencing people have done, for loads of organisms. For building family trees and finding relatedness it's where people turn to.
From memory the most common unit for mushrooms with either the large/small ribosomal subunit, but that's hazy. Somewhere someone made a giant family tree of all mushrooms, and it caused quite a stir because things that were thought to be closely related were waaay off.
The shake up is still occurring, there's been a lot of big revisions.
EDIT - I made a thread with this in it at sometime in the past, check out the PDF download at the bottom, called 117 Clades of Eugarics... http://www.shroomery.org/forums/showflat.php/Number/6177297#6177297
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Alan Rockefeller
Mycologist


Registered: 03/10/07
Posts: 48,276
Last seen: 8 hours, 45 minutes
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: Feelers]
#14397983 - 05/04/11 01:33 AM (12 years, 8 months ago) |
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At that rate you will be able to sequence dna for under $500.
We have some bio hackers around here that build their own PCR machines and are working on ways that people can sequence things in their garage.
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thescientist
Registered: 03/09/02
Posts: 807
Loc: Dade County
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Re: Molecular phylogenetics, specifically CO I mtDNA [Re: Feelers]
#14406815 - 05/05/11 06:54 PM (12 years, 8 months ago) |
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Very cool. I had no idea people were offloading this kind of equipment. I wonder where it's all coming from??
Check out the boldsystems.org site. try the taxonomy browser. very cool project. industrialized, which creates some issues with centralization of data etc. however, much is happening here.
great part is, is that you can send them a sample and the sequences are uploaded online. with the right primers you could create the same data at home, however there are great gains in economy of scale, division of labour etc
of course one does lose some degree of self sufficiency if that is important to you.
great stuff guys
cheers
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