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DNA extraction from Vermiculite


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#1 Ensyeh

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Posted 15 May 2014 - 05:48 AM

Hello scientists,
Does some one have an idea about the DNA extraction from Vermiculite medium?( a mineral clay material), so far I couldn't get it using MO BIO kit and also phenol-chloroform procedure (that has worked for my soil samples).
Thanks in advance 


#2 Ensyeh

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Posted 15 May 2014 - 07:16 AM

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#3 hobglobin

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Posted 15 May 2014 - 08:17 AM

Well as you said it's a mineral (and not organic), so why do you expect DNA there? If it was used as a substrate already i.e. there is "contamination" with soil and/or it's life forms then you might find DNA...


One must presume that long and short arguments contribute to the same end. - Epicurus
...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.

#4 bob1

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Posted 15 May 2014 - 01:40 PM

Clays in general are extremely strong cation exchange compounds - so cations are probably being sequestered from the buffers and hence stopping the DNA being salted out on the addition of alcohol.  I don't have any ways of stopping this - but you could try searching for clay DNA extraction.



#5 hobglobin

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Posted 16 May 2014 - 10:48 AM

if there's really DNA it might be bound itself to the vermiculite too quite strongly...check e.g. this:

http://www.ncbi.nlm....les/PMC2747842/


One must presume that long and short arguments contribute to the same end. - Epicurus
...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.

#6 El Crazy Xabi

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Posted 18 May 2014 - 05:43 PM

Do you have DNA or cells in the vermiculite? If you have cells, better try a cell detachment and concentration protocol before doing the DNA extraction.



#7 Ensyeh

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Posted 19 May 2014 - 09:46 AM

Thanks you all,
I had inoculate several actinabacteria species in the vermiculite medium( because it is  the  most like to the soil), I couldnt get any thing on the gel but fortunately and surprisingly the qPCR worked and I could get reasonable data. But it is still a question how to get a good yield with this medium? as I searched there hasnt been an experiment about the bacterial DNA extraction from this medium in the past( however it is like to the soil mineraly but extraction seems to be different so I dont think  hobglobin's paper would be useful). The El Crazy Xabi's offer would be good if I could find a protocol for that or find a way for avoiding of cation compounds effects as bob1 said. I need a good yield for the next time and will try your offers. Thanks again.


#8 Ensyeh

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Posted 19 May 2014 - 09:47 AM

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#9 El Crazy Xabi

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Posted 19 May 2014 - 04:04 PM

There are several methods for cell detachment and the efficiency may depend on the species to detach. Probably the most reliable method to quantify would be FISH or CARD-FISH on the attached cells and counting them under CLSM but it is tedious, time consuming, needs specific equipment, chemicals and probes, and some experience with the CLSM.

Try with the protocol in Kallmeyer, J. et al., 2008. New cell extraction procedure applied to deep subsurface sediments. Limnology and Oceanography: Methods, 6, pp.236–245. I used a modified version for some samples from acidic environments that were resistant to other methods including few soil kits, and it was the only way I could get DNA good enough.






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