Microbial Population Biology

Dear all,

Judging from the oral presentations yesterday and the drafts, this will be a fabulous collection of grant proposals. Some final details for our collective benefit:

1. A hard copy is required for the final version, due in class.
2. The budget. This is supposed to be an interesting but not stressful exercise. Please make a good-faith estimate of your likely budget, spelling out how many years of person-labor at a particular rate, your bulk supplies, key services, and any special equipment that your fantasy home institution isn’t likely to have.  Then add 50%, and provide that number.  I am hoping to judge budgets much as “Price is Right” with a special prize (TBA) to the victor, but this is a very minor component of your proposal.  It just shows that you’ve thought about how one actually might do the work you propose. You should also state what agency might be likely to support your work.
3. References. Please use an accepted, consistent format such as the ASM example that I describe in the assignment and do not reference nonscientific, popular sources unless absolutely necessary.
4. Design/Outcomes. For most of you, a visual model of your design and a figure of your expected outcomes can go a long way to explaining exactly what you plan to do and justify your predictions.  Strongly consider including such figures.

Hi guys,

I’ve returned many of your drafts with comments, but to those of you still waiting, my apologies. I’ll return them tomorrow (Monday) asap.

Most of you are in good shape at this stage.

VC

Dear all,

As we enter the home stretch, I’ll remind you that:

1. Exam 2 is this Tuesday the 24th. Same format, slightly shorter, hence a few more points per question. Lectures 10-15 are the primary focus as well as all of the associated readings.

2. Grant proposal draft is due no later than 11:59pm on Thursday the 26th. This is not for credit but for your benefit; there is a very high r-squared for the correlation between writing a genuine draft and the final grade.  You may turn in a paper copy, which I will review and leave in a box outside Rudman 212 asap but by Monday evening, or you may email a copy of the draft with subject line MICROPOPBIO DRAFT and a file that begins with your name in the document title.  I will mark it up using Word Track Changes and Comments.

3. Blog: if you haven’t already, post on the evolution of virulence below. I encourage you to read your classmates’ articles.  There will be one more post for the final week, tba.

Good luck!

VC

Dear class,

For this week, please find an article from the literature that addresses this question in some way, uses “population thinking” and specifically addresses how/why virulence evolves.  We outlined a few “case studies” in today’s class in general terms, but the literature holds much, much more. If you can’t find a satisfactory explanation for your favorite bug, come up with a question?  Report what you find as efficiently as you can, and be sure to add links to your sources.

Great job defining your grant proposal topics; please keep the ball rolling!

VC

Dear class,

Now that you’ve posted on evolution in structured environments (last week) and evolution of prisoner’s dilemma (this week), and you’ve learned and read a lot about social interactions among Myxobacteria, it’s time to continue the conversation…with each other.  Your primary blog assignment for this week is to read as many of your classmate’s recent posts as possible, and COMMENT upon them.  Should you wish to post your reflections of what “Myxo mixing” means to you on your own blog, I’m sure many of us would appreciate it. But that is optional.

You also need to meet with your lab group to summarize your experimental findings, making sure that you count all the remaining plates and explain what they mean.  I have added page to the blog (“Laboratories” where your group can post its results and analysis.  Please send a .docx and a .PDF version to me and I’ll post it directly.  I might reply asking for updates as well.

And don’t forget that pending grant proposal!

PS: For those of you interested in the bird flu publication controversy:
http://www.biotechniques.com/news/Bird-Flu-Virus-Papers-Approved-for-Print/biotechniques-329080.html

Dear new game theorists,

As I described in today’s class, please blog on one of the following:

-Whether prisoner’s dilemma is ultimately a stable strategy in these viruses, perhaps referencing the second “Escape from PD” paper in the syllabus

-How PD might apply in another system, perhaps related to host-parasite interactions

-What game theory means to the material covered in this class or your research, in general.

As I mentioned, there’s a ton of great stuff on this topic out there on the web, so have fun looking and including in your post! This will be due next Thu as usual.

IN ADDITION, I spoke about how the engineering of a transmissible H5N1 influenza virus has attracted much attention and public debate, for good reason. For the week of 4/9, please give the following links a read and follow the news stories to the original article. This course material is timely!

http://nyti.ms/Hmg3iX

http://nyti.ms/t4ROmQ

FINALLY, for next week, complete the regularly scheduled readings on Myxobacteria and cooperation. Great stuff.

Stay tuned to your group pages for laboratory updates.

Dear all,

UPDATE from 3/27: in addition to this assignment, please be prepared to critically discuss the Turner/Chao prisoner’s dilemma paper in class on 3/29. How exactly did they quantify the payoff matrix?

I am looking forward to your critical interpretation of the Rainey and Travisano paper on adaptive radiation in P. fluorescens grown in unshaken tubes. In particular, please explain how communities become stable with more than three players and propose at least one modification to the design that might broaden or enhance its implications for complex communities in general.

If this is unclear, please comment here and I’ll try to follow up.

Thanks

VC

Hi all,

Thanks to a few of you, I fixed the link to the Ochman paper in the syllabus.

Regarding exam structure, you can expect about 15 questions, most multi-part or requiring a few sentences or a figure.  See the exam page for a bit more info, and I’ll try to edit that further asap.

VC

Dear all,

As a reminder, please nominate your best of your last several blog posts (or comments) for formal evaluation. Feel free to edit or append if you see fit. I read all of your work, but appreciate focusing on your best efforts for a grade.

For this next week, in light of dissecting the Travisano et al “Chance, History, and Adaptation” paper, please write on:

1. What macroevolutionary phenomenon would you like to test with microbes?
and/0r
2. Do you believe that microevolutionary models can shed light on macro-scale processes? Why/why not?

Thanks much to RobH who took nice photos of our chalkboard models in today’s recitation. It is posted here: chalkboard summaries of Travisano et al

PS: Some of you might be interested in a new article about our experimental evolution research with high school students. See: http://unhmagazine.unh.edu/w12/cooper.html

Dear all,

In response to your valuable feedback today, I’ve upgraded a key feature of the site today: the syllabus. Instead of the old, messy, not-quite-up-to-date table, I’ve changed it to a public Google Doc Spreadsheet, which you can also click directly to and download for your own. All links through Spring Break should be current and live.

I have also fixed dead links to prior slidesets, realizing that for some reason .pptx files don’t work.  Slides are now posted for this and next week.

I hope you find this helpful.  I’ll also provide printouts of the syllabus for those who want one.

As for more background reading and/or textbook-style reading, I’ll try to compile a few more reviews that are textbook-worthy, were I to edit one.

Next week, please nominate your ‘best-of’ post for evaluation, and feel free to edit and/or add to that content. It might even be an exchange with one of your peers, on your site or hers/his.