Bi

Adaptation of bacteria with CRISPR and adaptation on a rugged fitness landscape

Date
Feb 3, 2020
Time
2:00 PM - 3:00 PM
Speaker
Marija Vucelja
Affiliation
University of Virginia, USA
Language
en
Main Topic
Biologie
Host
Carl Modes
Description
I will tell you two stories of adaptation of populations aided and enriched by statistical physics approaches.

The first story is about the adaptation of bacteria with CRISPR. CRISPR-Cas is a famous biology buzz word, due to its applications to gene editing. However, CRISPR-Cas is also a prokaryote immune system. It works as a “library” of previous infections. This library contains snippets of exogenous genetic material. With a new infection, the library is consulted, and if a match is found, the attempt will be made to neutralize the intruding genome. Bacteria use CRISPR-Cas as an immune system against phages and plasmids. Such immunity is hereditary and dynamic — it can be gained and lost during the lifetime of the single bacteria. Also, the process of acquiring snippets when exposed to the same phage is stochastic, and the same strain bacteria in a population contain different CRISPR loci content and thus variable immunity to the phage. We use dynamical systems approaches to predict the shape of this diverse distribution of CRISPR loci content within a bacterial population as a function of two crucial parameters — the rate of acquisition and the immunity to the phage.

The second story is about adaptation on a rugged fitness landscape. A crude measure of adaption to a new environment called fitness. Often one defines fitness as the expected growth rate. The higher the fitness, the more thriving is a population. What happens over long times for a population with a finite genome — when all beneficial, fitness mutations, are exhausted? Contrary to expectations, the experiments show that fitness does not reach a plateau. Here we introduce a spin-glass microscopic model, where a genome can be represented as a spin configuration, and individual spins are genes. The fitness plays the role of minus the Hamiltonian of the system. We use numerical approaches and estimates to study hopping between metastable states on a rugged fitness landscape. We show that with gene interactions (interacting spins), double beneficial mutations (flipping of pairs of spins) can lead to a slow, logarithmic increase of fitness in a wide class of cases.

Last modified: Feb 4, 2020, 12:06:26 AM

Location

Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG Galleria)Pfotenhauerstraße10801307Dresden
Phone
+49 351 210-0
Fax
+49 351 210-2000
E-Mail
MPI-CBG
Homepage
http://www.mpi-cbg.de

Organizer

Max Planck Institute of Molecular Cell Biology and GeneticsPfotenhauerstraße10801307Dresden
Phone
+49 351 210-0
Fax
+49 351 210-2000
E-Mail
MPI-CBG
Homepage
http://www.mpi-cbg.de
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