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 Holiday
Nov. 18 Jen Forcina
Nov. 25 Nancy Gegbe
Dec. 2 Megan Striplin
Dec. 9 Alice Duncan

Thursdays

23-Oct open
30-Oct Kazu Okamoto
6-Nov Vaughn Cooper: “Adaptive radiation into a synergistic biofilm community”
13-Nov Neal Callahan
20-Nov Roy Richardson
4-Dec Alex Ensminger, Tufts University
“From broad host range to isogenic prison: genotypic plasticity in experimentally evolved strains of Legionella”
Dec 11 Krys Morris

Fridays

Oct. 24 Chongxu Zhang “”Investigation of PAB1 Protein”
Oct. 31 Feseha Abebe-Akele
Nov. 7 Wei Yao
Nov. 14 Dean Fitzgerald
Nov. 21 Sarah Comeau
Nov. 28 THANKSGIVING
Dec. 5 Laura Benton
Dec. 12 Deb Swinbourne

Spontaneous Deletion of a 209-Kilobase-Pair Fragment from the Escherichia coli Genome Occurs with Acquisition of Resistance to an Assortment of Infectious Phages

Yasunori Tanji,^* Kenji Hattori, Kohichi Suzuki, and Kazuhiko Miyanaga

Enjoy!

http://rationalwiki.com/wiki/Lenski_affair

Please comment here or there if some of this makes you smile

I encourage you all to read the following:

http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php

http://www.pnas.org/cgi/content/abstract/0803151105

See: http://www.sciencemag.org/cgi/content/abstract/315/5815/1126

The PDF can be found here:

http://micropopbio.org/cooper/2008/05/04/comparing-microbial-communities-to-understand-rules-for-their-assembly/

PS: I am reviewing each of your grant proposal drafts and will email my comments to you by Monday midday.

micr-713-2008-growth-curves.xls
713-swim-and-swarm-motility-spring-2008.xls

With this spreadsheet, you now have enough data to figure out who is the lucky winner of the grand prize for the second running of the Bacterial Tri(quad)athlon. The prize can be picked from the following site: http://www.giantmicrobes.com.

Your assignment is as follows:

1) Download the spreadsheets and examine the raw data for each isolate. Note that growth was conducted in two environments: SOC medium (rich) and M9 + 1% galactose. Also note that Steffen kindly plotted the data for you on two worksheets AND calculated the mean OD for each time point.

2) Now, FOR ALL lines and FOR ALL INDIVIDUAL WELLS, calculate the final “fitness” as the Area Under the Curve (AUC). By this I mean that you should calculate AUC for each replicate of your growth curve and then the mean and standard deviation of the three AUC values, not just a single AUC value derived from the mean of the three curves.

AUC can be estimated accurately as follows: sum of(_(i,j)(X_j - Xi)*((Y_j+Y_i)/2)), which means that for all time intervals (which are each 15 minutes), calculate the area of the region described by the change in time, X, and OD, Y, and then add each of these areas up. Since Y changes over time, you estimate its value as the mean of Y1 and Y2, i.e. (Y1+Y2)/2. I hope this is clear; if not, please comment here and/or email me.

3) Write a laboratory report reporting your findings based on the data from the entire class, including the relative rankings of each event and the overall winner. To remind you, the final rankings will be determined by which isolate performs the best on all 4 trials. So, a strain that is #1 on swim motility, #1 on swarm motility, #3 in SOC and #4 in minimal would have a final value of 1+1+3+4 = 9. Explain these findings and speculate why we see them, and how you might change your isolate picking the next time. I also encourage you to argue for another method of calculation, analysis, or scoring that might change the results, particularly in your favor.

Email me your lab reports directly by Tuesday May 6th.

I also presented results from my old paper with Paul Ewald:

http://micropopbio.org/cooper/files/2007/11/cooper-et-al-2002-proc-r-soc.pdf

You all presented very interesting papers as riffs on the theme of why virulence might evolve. Please post these articles on your blog and provide a very brief summary. It’s up to the rest of us to read one or more of these articles and comment on them.

For Thursday, I will introduce how we might do experiments to understand how communities are structured. Thus, we will come full circle to community ecology, now that we’ve spent several weeks understanding how microbial species might interact at a small scale. Two articles relevant to these questions are:

http://micropopbio.org/cooper/files/2007/11/gordon-zebrafish-mouse-transplant.pdf
http://micropopbio.org/cooper/files/2007/11/gordon-zebrafish-mouse-supp-methods.pdf

Also: http://collections.plos.org/plosbiology/gos-2007.php

Also see this recent meta-metagenomic study: www.nature.com/doifinder/10.1038/nature06810

Nice job on choosing papers.  Here is a summary of what I heard.  Please comment on this post to add to, correct, or question my brief overview.

All readings can be found at:

http://micropopbio.org/cooper/2008/04/17/student-chosen-readings-for-evolution-of-community-structure-in-space-or-time/

In chronological order of publication,

1) Dave, who chose Bull JJ Molineaux IJ, Rice WR. 1991. Selection of benevolence in a host-parasite system.  Evolution 45:875-82.

They evolved a plasmid pBR322-phage M13 chimera under high-fidelity (had to stick with E coli host) and low fidelity (were allowed to infect multiple partners) conditions.  Found that each became more fit in the selective environment, and that high-fidelity phagemids lost the ability to infect horizontally as a consequence of a reduced phage genome.

2)  Sam, who chose: Tamas Czaran, Rolf F. Hoekstra, and Ludo Pagie.  2002. Chemical warfare between microbes promotes biodiversity.  PNAS.

Simulated the same basic rock-paper-scissors dynamic of Kerr et al, but allowed as many as 14 different toxin/antitoxin/susceptible combinations to evolve. Studied  rates and influences of mutation and recombination in a spatial matrix.  Found that a frozen state of coexistence of “hyperimmunity” is likely but can be disrupted by either recombination or asynchronous temporal scales of dominance between players (eg toxin killing is faster than resource competition).    Very interesting discussion of their findings — see the paper.

3) Dan, who chose: R. Craig MacLean & Ivana Gudelj.  2006. Resource competition and social conflict in experimental populations of yeast.  Nature.

Used two strains of yeast that were 1) capable of respiration and fermentation or 2) capable only of respiration.  The latter was superior in head-to-head mixed competition under chemostat conditions in which glucose was not limiting.  The 2 stably coexisted in batch culture owing to the need to ferment in stationary phase and because the cheater (no fermentation) was sensitive to toxic metabolic intermediates produced by its own growth.   Also, from the article, “In agreement with our hypothesis, the itness of the cooperator at the level of the metapopulation is both positive frequency-dependent (F1,7 ¼ 55, P , 0.0001; Fig. 4) and negative density-dependent (F1,7 ¼ 41, P , 0.0001; Fig. 4), implying that a metapopulation of cooperators can resist invasion by a rare cheater provided that the number of cells that colonize each patch is below a critical threshold. Positive frequency-dependent selection for cooperation also implies that a rare cooperator cannot invade a
population of cheaters.”

4) Laura, who chose: Federico Prado. and Benjamin Kerr. 2007. THE EVOLUTION OF RESTRAINT IN BACTERIAL BIOFILMS UNDER NONTRANSITIVE COMPETITION. Evolution.

The authors modeled a system similar to the original Kerr paper involving colicin production, resistance, and sensitivity, and found that in structured communities containing these players, the players neither evolve maximum toxicity or resistance.  That is, the conditions favor an intermediate state of restraint.

5) Abe, who chose:  Brockhurst, MA. Population Bottlenecks Promote Cooperation in Bacterial Biofilms.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000634/trackback

Reasoning that kin selection is strongest in smaller populations where the probability of genetic relatedness among individuals is highest, the author tested effects of bottleneck size on the evolution and stability of cooperative traits in the Ps. fluorescens system of Rainey, Travisano, et al.  From the text: “In line with predictions, the frequency of evolved cheats within the populations increased with increasing bottleneck size. This result highlights the importance of ecologically mediated population bottlenecks in the maintenance of social traits in microbes.”

Sanjuro, I welcome your addition, and others, please feel free to comment!

1) Many of your blogs are becoming woefully out of date.  Please post 1) on Turner et al phi6, and specifically your likes/dislikes of these designs, and 2) on your digest of the Velicer et al. Myxo article that you chose to present on Thursday.   Please do so ASAP.

2) Please read the papers found at the following link.  I will outline the 1981 Chao and Levin PNAS paper tomorrow (Tues), and we will discuss the Kerr et al Nature 2002 paper on Thursday, AND you must find a paper related to the problem of evolution of cooperation, cheating, antagonism IN SPACE (or in structured populations) to present briefly on Thurs.

http://micropopbio.org/cooper/2008/04/14/cooperation-and-cheating-in-space-and-time/

Thanks!

I have posted the 2 papers that you are to read for this week, as well as some supplementary papers that may help you understand the Myxococcus xanthus experiments.

Vaughn will be lecturing on Tues. on this material to help get you started, but feel free to start reading.

Steffen