Archive for January, 2008

Notes: Taxa-Area curves: Is everything everywhere? »

By steffen on Jan 29, 2008 in General | 0 Comments

S = AZ

S = species number
A = area
Z = between 0.1 and 0.4 (rate of turnover of species across space)

“A taxa-area relationship for bacteria” Bohannan et al. Nature

S = cAz

c = spatial scale constant

Salt marshes of Rhode Island: 945 16s (95% z approaches 0, 97%, 99% z>0.04)

88 operational taxonomic units = O.T.U.’s

523 Beta-proteobacteria… and [...]

Notes: How do you distinguish bacteria from one another? »

By steffen on Jan 29, 2008 in General | 0 Comments

1. 16s ribosomal RNA (encoded by DNA)- rrn (5s, 16s, 23s) HGT of this gene rare.

a. Copy number of this operon varies
b. Identity of this operon varies >They do homogenize
c. Highly conserved in general = slow evolving
1-2% divergence over ~1500 bp / 50 million years (Calculated from E.coli and [...]

First assigned reading of Spring ‘08: explaining extremophile biogeography »

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 [...]

Glossary Updated »

By steffen on Jan 24, 2008 in General | 0 Comments

The glossary is now updated. Please let me know of any other terms, theories, concepts, or individuals that you think I should add, now or at anytime during the semester.
Thanks,
Steffen

First class of ‘08: is everything everywhere? »

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

Class notes, discussion of “Why sex?” »

By Vaughn on Jan 10, 2008 in General | 0 Comments

Discussion: why sex?
· Eukaryotes - need 2 individuals to make 1
o The two-fold cost of sex
· How and why do sexual organisms overcome the two- fold cost of sex?
· Why use prokaryotic microbes to study [...]