Microbial Population Biology

Dear all,

This weekend, please read as many of your classmate’s blogs as you can, commenting upon at least two of them. I encourage you to make connections and add content (links, shared points, images, new ideas, etc).  As individuals, you’ve already done a nice job of considering where your favorite bacterial species/lineages/strains came from, but as a class, your contributions are transformative.

Next week we’ll explore experimental evolution as a method and some of this growing body of research. Then we’ll tackle one of the most influential papers using this approach and decode it in recitation.

VC

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Dear class,

Tomorrow (thursday) we’ll be working on a computer laboratory that tackles “the species question” head-on.  The lab is here.  I’ll bring paper copies, but feel free to download and complete on your computer.

Before we begin I’ll complete the last few slides of my lecture on the challenges of developing a theory of bacterial speciation.  And for this weekend, I ask that you consider:

Where do bacterial species come from?  And more to the point, how did your favorite bacterial species (or set of species) come to be?  Please venture out into the primary scientific literature and provide a working link to the paper.

VC

PS: A few of you have expressed an interest in “+1-ing” your classmate’s posts.  So I’ve activated this plugin. To activate on your blog, go to your Dashboard, find the “Configure the AddThis plugin to enable users to share your content around the web” and click “configuration options.” It’s fairly self-explanatory after that.

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Dear all,

1) Create and customize your blog. Be sure to take advantage of the help links if you are confused.

2) Edit your “Hello world” post, in which you:

a. Introduce yourself: your major, career goals, why you’re taking this course, and what you hope most to learn.

b. Comment on the assigned article. You might consider how it affects your sense of “everything is everywhere, the environment selects,” and you might define what a species-area curve (or a plot of beta-diversity) might look like for Prochlorococcus.  Most importantly, what about this article appealed to you, what is confusing, and what questions did it raise for you?

(for reference, the lectures are posted on the blog).

3) Remember that Chuck Traverse will be giving a guest lecture. I’ll upload the PPT as soon as I can for everyone’s reference.

PS:  Several of you noticed that some of the old blogs had been archived so you couldn’t see them (although I, as admin, could). I’ve now “unarchived” a few from 2010 for your reference, and will consider opening few others for your reference.  Their names are now changed with the suffix “-2010″ to denote prior students.

PPS: Sorry that some of you had your blogs marked as spam. This was a result of new settings of this site that were unfamiliar to me. I think I’ve prevented further occurrences, but if you encounter trouble, email me directly.

Cheers

VC

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Dear all,

I’ve added you all to the site and created a blog for you, following your requests in nearly all cases (I had to avoid some duplicates).

Please check your email and let me know if problems arise.

Comment here if general issues are apparent.

VC

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Welcome to Microbial Ecology and Evolution, GEN713/813, 2012. There is no meeting on Tuesday, 1/24. On Thursday, 1/26, we’ll meet at 11:10 am in SLS G16 and at 2pm in Rud G40.

Vaughn

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Hi guys,
As I complete evaluating your drafts, I am putting the paper copies in a box outside my door. Some are available now.

Please be sure to follow an accepted reference format such as the ASM format specified in the grant proposal assignment. In general, reread the assignment page and make sure your grant conforms.

Also, please give the budget a shot and suggest what agency might be willing to fund your work.

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A summary of your minimum assignments in the second half of the course:
1) A post on an original article on the evolution of sex (3/30)
2) A post summarizing one of the Myxococcus articles (4/6)
3) A post on an original article on the evolution of virulence (4/13)
4) A post on an article or podcast on our body’s microbial communities (4/20)
5) For this week: a comment on one of your classmates’s posts.

In addition, each group should post a report of their laboratory as soon as possible, for better or worse. Only one post per group is required.

A reminder that our second exam is on 4/27 and will cover all of the material since the first exam.

Your grant proposal DRAFT is due April 29th and your final proposal is due on May 6th in class.

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A reminder that you should summarize the article that you read on some aspect of the evolution of virulence (why are some parasites so virulent, and others so mild?) on your blog.

thx

MGMT

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Dear all,

Check out: http://microbewiki.kenyon.edu/index.php/MicrobeWiki

if you seek background on your potential microbial study subjects.

VC

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Hi all,

To remind you, I will be absent on 3/30 but expect each of you to come to class having read the Turner and Chao, “Prisoner’s dilemma in an RNA virus” paper.  It can be found here: turner chao virus PD

As promised I have put together an introductory set of slides providing some background on the system and the experiments. In these slides, I assign each of you to groups who should focus specifically on one of six sections of this short paper. By dissecting it in sections, and then reconvening at the end to share your conclusions, I hope you’ll understand and appreciate how even simple organisms can play evolutionary games.

The introductory slides and group assignments can be found here: 713 lecture 10, sex and cheating in RNA viruses

Though I couldn’t find a legal link to the introduction to Prisoner’s Dilemma from the movie A Beautiful Mind, feel free to search YouTube for lots of related spinoffs and homemade tutorials. There’s one from Dilbert that is humorous, if not particularly informative:

http://www.youtube.com/watch?v=ED9gaAb2BEw

PS: Posted an article on winemaking microbes (both good and bad) on my micropopbio blog, which now feeds to the right –>

UPDATE (noon on 3/30): Your blog assignment this week to find and discuss an article on the evolution of sex will be late, and receive less than full credit, if posted after today.

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