Here the data for the students to analyze:


Online Tool for calculating mutation rate using the Ma-Sandri-Sarkar ML Estimator method

FALCOUR

Possible Extension: Luria-Delbrück fluctuation test in spatially-structured populations

(if you're interested talk come and talk to me: Oskar Hallatschek, ohallats@berkeley.edu - office #2114, or Diana Fusco)

The classical fluctuation test by Luria and Delbrück measures the distribution of resistant mutants that arise in microbial populations grown in liquid culture under constant shaking. Many bacterial infections involve biofilms, and it is not clear whether the distribution of pre-existing resistant mutations in such spatially-structured populations is similar to the Luria-Delbrück distribution.

Therefore, it would interesting to explore the impact of spatial structure on the distribution of resistant mutations. To this end, I suggest to carry out a simple variant of last week’s Luria-Delbrück experiment to study emergence of resistance in colonies rather than liquid cultures:
  • Inoculate 45 colonies on, say 10, agar dishes (same medium as last week) from a small amount of initial cells – use same inoculum size as last week for the 96-well plates.
  • Incubate for a couple of days to get colonies of >1cm in diameter (this requires that the inoculations are spatially well-separated so that the colonies have space to grow)
  • Remove each colony from the agar dish, dissolve in medium and thoroughly mix.
  • Plate the resulting 45 populations on antibiotics to count single colonies, in just the same way as you did last week.

Just as a teaser, here is a simulation result for mutant clones emerging in growing colonies (by PhD student Alex Anderson, Berkeley):

Colony.png

Sectoring arises in many contexts – we’ve studied it’s population genetics, see e.g.
[1] O. H. and D. R. Nelson "Life at the front of an expanding population", Evolution 64:193–206, 2010.
[2] O. H., P. Hersen, S. Ramanathan and D. R. Nelson "Genetic drift at expanding frontiers promotes gene segregation"
PNAS, 104(50):19926-19930, 2007.