Comments on: Molecular Biology of Soil: DNA Isolation Part I http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/ Tue, 13 Dec 2011 00:32:47 +0000 http://wordpress.org/?v=2.9.1 hourly 1 By: Suzanne Kennedy http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-11382 Suzanne Kennedy Wed, 26 Oct 2011 15:20:04 +0000 http://www.mobio.com/blog/?p=596#comment-11382 Hi Liliana, OK- I will email you directly. Best, Suzanne Hi Liliana,
OK- I will email you directly.
Best,
Suzanne

]]> By: Liliana http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-11377 Liliana Tue, 25 Oct 2011 15:16:47 +0000 http://www.mobio.com/blog/?p=596#comment-11377 Dear Suzanne, Can you please suggest some method to extract DNA from nitrocellulose membrane? currently we cut the membrane with scissors and put the fragments in the vial, but I'm not sure about the efficiency. Thanks and best regards, Liliana Dear Suzanne,
Can you please suggest some method to extract DNA from nitrocellulose membrane?
currently we cut the membrane with scissors and put the fragments in the vial, but I’m not sure about the efficiency.

Thanks and best regards,
Liliana

]]> By: Deepak Sharma http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-10971 Deepak Sharma Thu, 08 Sep 2011 17:11:14 +0000 http://www.mobio.com/blog/?p=596#comment-10971 Dear Suzanne, I tried the MoBio PowerSoil DNA kit to isolate the microbial DNA from the excreta solid waste of tomato longhorn worm. The sample looks more green in color possibly because of they feed on tomato leaves. I was not able to get any DNA as i am using 0.25 gm of sample. Do you think, there would be any kind of modification needed and is the kit made to handle that sort of starting material. I would appreciate for any advice. Thanks and best regards, Deepak Dear Suzanne,
I tried the MoBio PowerSoil DNA kit to isolate the microbial DNA from the excreta solid waste of tomato longhorn worm. The sample looks more green in color possibly because of they feed on tomato leaves. I was not able to get any DNA as i am using 0.25 gm of sample. Do you think, there would be any kind of modification needed and is the kit made to handle that sort of starting material.
I would appreciate for any advice.
Thanks and best regards,
Deepak

]]> By: Suzanne Kennedy http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-10502 Suzanne Kennedy Tue, 31 May 2011 19:56:10 +0000 http://www.mobio.com/blog/?p=596#comment-10502 Hi Agnieszka, I would recommend you try the PowerSoil Kit instead. I will contact you for more info. Best, Suzanne Hi Agnieszka,
I would recommend you try the PowerSoil Kit instead. I will contact you for more info.
Best,
Suzanne

]]> By: Agnieszka http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-10403 Agnieszka Sat, 21 May 2011 10:38:06 +0000 http://www.mobio.com/blog/?p=596#comment-10403 Dear Suzanne , I use ultraclean DNA isolation kit to isolate DNA from samples coming from wastewater plants e.i. sewage sludges. I have a huge problem with A260/280 ratio, which is often below 1.5 but never below 1.2. Yields are about 20 ng per ul so I am wondering if that kit is fine for such samples. Should I use some kit for purification? I wash column twice with S4 solution. I would be very grateful for any advice. Best regards, Agnieszka Dear Suzanne ,

I use ultraclean DNA isolation kit to isolate DNA from samples coming from wastewater plants e.i. sewage sludges. I have a huge problem with A260/280 ratio, which is often below 1.5 but never below 1.2. Yields are about 20 ng per ul so I am wondering if that kit is fine for such samples. Should I use some kit for purification? I wash column twice with S4 solution.

I would be very grateful for any advice.

Best regards,
Agnieszka

]]> By: Suzanne Kennedy http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-10315 Suzanne Kennedy Mon, 09 May 2011 16:22:54 +0000 http://www.mobio.com/blog/?p=596#comment-10315 Hi Ross, The PowerSoil method will isolate total DNA, however, most of the DNA from dead organisms will probably have a lot of degradation and be small in size. The PowerSoil binding solution preferentially binds the high molecular weight species. If the DNA is free in the soil, it can be recovered but it will not be intact. It is likely that most of the DNA recovered from soil comes from live organisms. Hi Ross,
The PowerSoil method will isolate total DNA, however, most of the DNA from dead organisms will probably have a lot of degradation and be small in size. The PowerSoil binding solution preferentially binds the high molecular weight species.
If the DNA is free in the soil, it can be recovered but it will not be intact.
It is likely that most of the DNA recovered from soil comes from live organisms.

]]> By: Ross http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-10275 Ross Wed, 04 May 2011 04:38:52 +0000 http://www.mobio.com/blog/?p=596#comment-10275 I presume that the Power Soil kit extracts all DNA from the soil, including both live and dead organisms. Do you know how long DNA from a dead organism might persist in a temperate soil. I presume that the Power Soil kit extracts all DNA from the soil, including both live and dead organisms. Do you know how long DNA from a dead organism might persist in a temperate soil.

]]> By: Suzanne Kennedy http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-9283 Suzanne Kennedy Mon, 14 Mar 2011 22:17:35 +0000 http://www.mobio.com/blog/?p=596#comment-9283 Hi Derek, Yes- we have done a lot of work with clay soils. I'll email you directly. Best, Suzanne Hi Derek,
Yes- we have done a lot of work with clay soils. I’ll email you directly.
Best,
Suzanne

]]> By: Derek M http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-9279 Derek M Mon, 14 Mar 2011 20:45:00 +0000 http://www.mobio.com/blog/?p=596#comment-9279 can you possibly help me with isolation of DNA from clays and the types of molecular methods for determination of microbial community in those environments? can you possibly help me with isolation of DNA from clays and the types of molecular methods for determination of microbial community in those environments?

]]> By: Suzanne Kennedy http://www.mobio.com/blog/2010/01/17/molecular-biology-of-soil-dna-isolation-part-i/comment-page-1/#comment-8109 Suzanne Kennedy Tue, 01 Feb 2011 14:40:51 +0000 http://www.mobio.com/blog/?p=596#comment-8109 Hi Reader, Thanks for posting! Are you talking about the 260/280 ratio of 260/230 ratio? What was the DNA yield? There are several reasons that a ratio can be lower than expected. What we have observed is that when the DNA yield is low (for the Nanodrop, below 10ng/ul) the ratios will be off. That's just because if there isn't enough DNA in the sample to get a good 260 peak, then you can't have a correct ratio. Basically, you are getting a semi-flat line across the wavelengths. So it doesn't always mean the DNA is not pure. Sometimes it just means that you can't accurately get a ratio. So we would need to know more about your samples and the yield to tell you if this is too low. For a 260/230 ratio, sometimes the problem may be remaining humics acids. If this is the case (does the sample have any brown tint?), then I would recommend you switch to the PowerSoil Kit or PowerLyzer PowerSoil Kit. The inhibitor remival technology in that kit is much stronger. However, in general, as long as the ratio is over 1.2, it should be fine for a PCR reaction. Best, Suzanne Hi Reader,
Thanks for posting! Are you talking about the 260/280 ratio of 260/230 ratio? What was the DNA yield? There are several reasons that a ratio can be lower than expected. What we have observed is that when the DNA yield is low (for the Nanodrop, below 10ng/ul) the ratios will be off. That’s just because if there isn’t enough DNA in the sample to get a good 260 peak, then you can’t have a correct ratio. Basically, you are getting a semi-flat line across the wavelengths.
So it doesn’t always mean the DNA is not pure. Sometimes it just means that you can’t accurately get a ratio.

So we would need to know more about your samples and the yield to tell you if this is too low.
For a 260/230 ratio, sometimes the problem may be remaining humics acids. If this is the case (does the sample have any brown tint?), then I would recommend you switch to the PowerSoil Kit or PowerLyzer PowerSoil Kit. The inhibitor remival technology in that kit is much stronger.
However, in general, as long as the ratio is over 1.2, it should be fine for a PCR reaction.

Best,
Suzanne

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