Thursday, May 31, 2007

Gel Dust Cleaner by Arnaud Amzallag


By way of my friend Mickey Danon, a Ph.D. student at Hebrew University of Jerusalem, I was put into contact with Arnaud Amzallag, a Ph.D. student at the Ecole Polytechnique Fédérale de Lausanne (EPFL) in Switzerland. He has developed a piece of software to help clean up gel images from spots and stains. Arnaud has also given me permission to make this software available to anyone who is interested. You will find both a link to download the software and to get directions on using it. Enjoy!

Arnaud describes the software as follows: "The idea of the program is that a DNA band will occupy the full width of the area you select, but a stain will not (very likely at least). The program can then discriminate between stains and DNA bands, and remove the stains."

To download the text of the software click here. To download the instructions, click here.

Tuesday, May 29, 2007

New Article


I'm pleased to report that the final manuscript from my thesis has just been published online in the new "International Society for Microbial Ecology (ISME) Journal". This manuscript is the culmination of my doctoral research and describes how the rhizosphere effect can affect different microbial taxa differently.

In the manuscript I also show how nested-PCR/DGGE can be employed to recover longer sequence information than the DGGE primers allow. For example, I developed specific primers for the genus Chryseobacterium and members of the family Oxalobacteraceae that amplified a fragment of the 16S rRNA gene of approximately 1000 bp in length. I performed cloning reactions on this initial PCR product, and then screened clones using the 341-907 primers (Muyzer et al. 1993; 1998). When I found a clone that had a band migrating to a position in the DGGE profile of an environmental sample, I sequenced that clone. The final sequence therefore contained roughly 1000 bp of sequence information, even though the primers 341-907 only amplify a region of 500-550 bp.

Currently, the manuscript is only available online in advance online publication. Enjoy!

Green, S.J., Michel Jr., F.C., Hadar, Y. and D. Minz. [2007]. Contrasting patterns of seed and root colonization by bacteria from the genus Chryseobacterium and from the family Oxalobacteraceae. ISME Journal. doi:10.1038/ismej.2007.33.