By Vaughn on Jan 28, 2008 in Assignments, biogeography, molecular typing, phylogeny | 0 Comments
Is everything everywhere? How much does the environment select? Are there barriers to dispersal for microbes? We’re still working on these questions, so to help us focus we will dig into our first reading(s) (one mandatory, one optional). They are:
1. http://www.ncbi.nlm.nih.gov/pubmed/12881573?dopt=Abstract
and
2. (optional) http://www.ncbi.nlm.nih.gov/pubmed/16093568?dopt=Abstract
Both are posted in full under the Assignments page.
For this week, please read [...]
By Vaughn on Jan 23, 2008 in Class notes, General, biogeography, molecular typing | 0 Comments
Hi gang,
I’ve prepared an overview of several recent studies that attempt to answer this question about microbial communities. The slides are posted on the assignments blog, at
http://micropopbio.org/cooper/2008/01/24/micropopbio-lecture-1/
For your reference, the articles that I refer to in this lecture can be found at:
http://aem.asm.org/cgi/content/abstract/66/12/5448
http://www.pnas.org/cgi/content/abstract/104/8/2761
http://www.nature.com/nature/journal/v432/n7018/abs/nature03073.html
By Vaughn on Sep 13, 2007 in Class notes, molecular typing, phylogeny | 0 Comments
Today we covered:
The Cho and Tiedje paper, “Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil”, AEM. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11097926
This article relied heavily on two methods: BOX-PCR, a molecular typing method, and UPGMA, a method of estimating similarity and indirectly, phylogenetic distance. Good descriptions for each of these can be found at:
BOX-PCR (in the context [...]
