Microbial Population Biology

The motility and growth curve data from your environmental isolates are in, and they can be found here:

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.