Microbial Population Biology

For tomorrow’s lecture, you might want to give this news article a quick read:

http://dx.doi.org/10.1371/journal.pbio.0050074

It speaks of the controversies surrounding microbial bioprospecting efforts, esp. those of Venter et al.

Another booklet that describes metagenomics and its goals and promises can be found here:

http://dels.nas.edu/dels/rpt_briefs/metagenomics_final.pdf

The complete version of the report from the National Academy of Sciences on metagenomics can be found here:

http://books.nap.edu/openbook.php?record_id=11902&page=12

And for your final blog posts, to be evaluated:

1) Please post your creative thoughts on either microbial bioprospecting or the evolution of flu virulence

2) When all is settled, please post your abstract of your grant proposal, which should clearly spell out your specific objectives.

Hi guys,

You may wish to check out my friend Mike’s blog on why influenza virus may either evolve towards increased virulence or decreased virulence.

http://scienceblogs.com/mikethemadbiologist/2009/04/nonoptimal_virulence_and_avian_1.php

Vc

The Airborne Metagenome in an Indoor Urban Environment

http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0001862

All, please take this opportunity to read this and comment upon the science, either here on this blog or there, on the article itself!  I’m sure the authors would appreciate your thoughts.

Gang,

A reminder that, by next Tuesday, you are to find an article on the evolution of virulence that addresses this question using “population thinking.”  This means not the mechanisms that underlie one strain’s methods of being virulent, but rather why various alternatives exist, or how they interplay with variation among hosts, etc.

I look forward to your diverse findings on your blogs.

VC

Hi guys, a reminder for you to comment on the article of Greg Velicer’s that you chose to read.  We’d all appreciate reading what you learned, what you think of the experiment, what more you’d like to know, any criticisms, etc.

Also, for today’s lecture on how one can find the underlying genetic mechanisms of selfishness and cooperation, here are some links on next-generation sequencing methods:

454 sequencing:
http://www.454.com/products-solutions/how-it-works/index.asp

Solexa sequencing:
http://www.illumina.com/pages.ilmn?ID=203

In realizing that the amount of data you have to analyze is substantial, and that the goals of the analysis are not totally clear, please:

1. Analyze your data and only the group to the right of you on the spreadsheet.  If you’re last, also do the first group.

2. The experimental design involved two genotype entrants of your choice. You streaked these out, and I picked two clones of each (these are experimental replicates).  I then inoculated three wells of each of these clones (these are technical replicates).  First, calculate the AUC for each of these twelve wells. Next, to find out which clone of yours is a superior performer, take the mean of each of the three technical replicates, then take the average of the two experimental replicates for each genotype.  This is your final AUC score, in units OD600/min.

3. Please post your results as well as your analysis of your spreadsheet neighbor on the right.  Peer review will help us all avoid errors.

Hope this makes some sense.

Dear all,

As promised I have created a Google Docs spreadsheet in which you should all post your motility data.  The link for this motility data is:

http://spreadsheets.google.com/ccc?key=ppblk1ndCOl3ovQ_PRem-Ow

The link for the growth curve data is here:

http://spreadsheets.google.com/ccc?key=ppblk1ndCOl3xZHQDX2Ijaw

and:

microbial-triathlon-2009 (XLS file)

Let me know (by commenting), if you have any questions or problems. I will add the growth curve data here soon and will also add more information about how to analyze these data shortly.

Instructions for the lab are here:

triathlon-lab-2009

Enjoy, VC

Dear all,

Hope you’re enjoying this foray into the world of cheating in viruses (and soon, bacteria).  To reiterate the assignment I sketched out in class today, please write on your blog (by next Tuesday) regarding this subject, answering the following questions:

1) How does Prisoner’s Dilemma (PD) operate in viruses? Do you think it’s broadly relevant?

2) How might PD operate in other, non-human biological systems?

3) How might organisms escape from the dilemma? What would they have to do, or what sort of environmental change favor such an escape?

For more information, please visit Steffen’s past post on this topic:

http://micropopbio.org/steffen/2007/11/05/important-background-information-about-game-theory-and-prisoners-dilemma/

and also:

http://en.wikipedia.org/wiki/Nash_equilibrium

http://en.wikipedia.org/wiki/Stag_hunt

http://en.wikipedia.org/wiki/Game_of_chicken

(the last game is analogous to the Snowdrift game, which I play after each large snowstorm with my neigbhors. Being a Midwesterner I am always a sucker…)

Hi guys,

I invite you all to visit and use the forum (see the linkon the top of the page) to post questions, concerns, or idaes, or to contribute knowledge for the benefit of your classmates.  I will weigh in on questions as I can for everyone’s benefit.

Thanks,

Vaughn

Hi guys,

Please check out this article by Olivia Judson.  It’s a fine example of experimental models being used to tackle big macroevolutionary problems:

http://judson.blogs.nytimes.com/2008/01/29/the-repeater/