Tuesday, January 17, 2006

First DGGE Update of 2006


Dear All -

Here are a few papers and thoughts of interest. I haven't made any specific modifications to the Guide itself, so if you download it, you won't find any changes. I've gotten another email from Dr. Josh Neufeld from the Department of Biological Sciences at the University of Warwick. He's suggested that members of the DGGE community check out his newest publication, listed below. In this publication the authors compare microarray and DGGE analyses for characterization of soil samples, and surprisingly, find good agreement between the two methodologies.

Neufeld, Josh D., Mohn, William W. and de Lorenzo, Victor (2006) Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environmental Microbiology 8, 126-140.

For a while, I had suspected that DGGE might be a technology on its way out, but recently I have had a feeling that we may continue to rely on it for some time to come. As long as we continue to incorporate significant sequence data, as well as gel analysis techniques, I believe that DGGE will be a solid tool for molecular biologists.

Other topics of interest:

An "In Press" publication showing DGGE analysis of dsrB gene. For those of you unaware, the traditional primers for the terminal reduction step of sulfate reduction ampliy a 1.9 kb region spanning both dsrA and dsrB. This amplificon is much too large to be separated effectively on DGGE. However, the authors, Joke Geets et al., amplify a 350 bp fragment of dsrB that appears to separate well by DGGE. This will most likely be a very useful addition to the suite of molecular tools for analysis of sulfate-reducing bacteria.

Geets, J. et al. In press. dsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria. J. Microbiological Methods.

Maurizio Castaldini (CRA - ISSDS, Italy) refers us to "Gel Handler", manufactured by Diversified Biotech (http://www.divbio.com/index.html -- look for Gel Products), for assisting in the manipulation of DGGE gels.

From Kees Roest, a suggestion to look at:
Florian Huber and Peter Peduzzi. 2004. Online Tool for Analysis of Denaturing Gradient Gel Electrophoresis Profiles. AEM. 70:4390-2. Also, check this link if interested: http://www.univie.ac.at/IECB/limno/equibands/EquiBands.html .

Also, slightly off topic, but relevant to statistical methods for comparing microbial communities, I highly recommend taking a look at these publications:

Lozupone, C. and R. Knight. 2005. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities. AEM: 71: 8228-35.

And an application of UniFrac:

Ley, R.E. et al. 2005. Obesity alters gut microbial ecology. PNAS. 102:11070-11075.

So, just a reminder. If you have an article that you'd like to highlight and it is relevant to any aspect of DGGE analysis, please email me and I will be happy to post it.