Microbial Population Biology

This is an odd but temporarily convenient place to put this schedule. The MCBS seminar schedule for the remainder of Fall 2008 is as follows:
Tuesdays
Oct. 28 Erin Allgood “The effect of diet and polybrominated diphenyl ether exposure on whole body and adipocyte metabolism in male Wistar rats”
Nov. 4 Cliff Rosen
Nov. 11 Veteran’s Day [...]

Dear all,
I understand that Steffen led today’s lecture given my flu-induced absence.  As I’m sure you didn’t want to share a small room with my contagion I figured you didn’t mind.  I apologize for my absence in any case.
To clarify our plans for Thursday, I will present a lecture that integrates some of the material [...]

Dear MicroPopBio students,
In the spirit of keeping this class current, I’ve assigned one of the latest papers on “The Species Question” by the leading expert on this question, Fred Cohan.
Please read this article for tomorrow, and by the end of this week, write a blog post that outlines a set of criteria you would recommend [...]

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 [...]

This is a long time coming, but it took Jess Jarett’s email (below) to motivate me to post this:
Hi Vaughn,
Do you know of free software or a website where I can make trees for my proposal? I know what I want them to look like but it will take me ages to make them freehand. [...]

 My most recent blog on the Lee et. al. article has got me thinking about many aspects of ecology. Sometimes the most interesting ideas come from inspiration found in strange places. I think virulence can easily span to pathogens infecting other hosts than humans, and plants deserve some attention as well once in awhile.
 Although perhaps less strictly related to [...]

Dear class,
Here are the slides for Lecture 4 on phylogenetic methods and for Lecture 5 on experimental evolution.
713-lecture-4-phylogeny.ppt
713-lecture-5-experimental-evolution.ppt
Cheers,
Vaughn

Hi all,
For this week we’ll review phylogenetic methods, as described in the Holder and Lewis review, learn more generally about experimental evolution methods, as reviewed by me, and then spend the rest of the time focusing on the question:
What are the effects of chance and history on adaptation and evolution, in general?
I point you to [...]

Hi guys, go to:
http://micropopbio.org/cooper/2007/09/25/phylogenetics-background-reading/
to find the link to the review on phylogenetic methods. Included in this review are descriptions of parsimony, distance, maximum likeklihood, Bayesian analysis, and assessing the quality, or confidence of any given tree model.

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 [...]