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Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

Abstract

Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called 'spacers' into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population. (paper)
Authors:
Han, Pu; Niestemski, Liang Ren; Deem, Michael W; [1]  Barrick, Jeffrey E, E-mail: mwdeem@rice.edu [2] 
  1. Department of Physics and Astronomy, Rice University, Houston, TX 77005 (United States)
  2. Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712 (United States)
Publication Date:
Apr 15, 2013
Product Type:
Journal Article
Resource Relation:
Journal Name: Physical Biology (Online); Journal Volume: 10; Journal Issue: 2; Other Information: Country of input: International Atomic Energy Agency (IAEA)
Subject:
60 APPLIED LIFE SCIENCES; BACTERIA; BACTERIOPHAGES; DNA; MUTATIONS; PLASMIDS; RECOMBINATION; STOCHASTIC PROCESSES
OSTI ID:
22172106
Country of Origin:
United Kingdom
Language:
English
Other Identifying Numbers:
Journal ID: ISSN 1478-3975; TRN: GB13I9255126554
Availability:
Available from http://dx.doi.org/10.1088/1478-3975/10/2/025004
Submitting Site:
INIS
Size:
[12 page(s)]
Announcement Date:
Dec 13, 2013

Citation Formats

Han, Pu, Niestemski, Liang Ren, Deem, Michael W, and Barrick, Jeffrey E, E-mail: mwdeem@rice.edu. Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. United Kingdom: N. p., 2013. Web. doi:10.1088/1478-3975/10/2/025004.
Han, Pu, Niestemski, Liang Ren, Deem, Michael W, & Barrick, Jeffrey E, E-mail: mwdeem@rice.edu. Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. United Kingdom. doi:10.1088/1478-3975/10/2/025004.
Han, Pu, Niestemski, Liang Ren, Deem, Michael W, and Barrick, Jeffrey E, E-mail: mwdeem@rice.edu. 2013. "Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system." United Kingdom. doi:10.1088/1478-3975/10/2/025004. https://www.osti.gov/servlets/purl/10.1088/1478-3975/10/2/025004.
@misc{etde_22172106,
title = {Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system}
author = {Han, Pu, Niestemski, Liang Ren, Deem, Michael W, and Barrick, Jeffrey E, E-mail: mwdeem@rice.edu}
abstractNote = {Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called 'spacers' into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population. (paper)}
doi = {10.1088/1478-3975/10/2/025004}
journal = {Physical Biology (Online)}
issue = {2}
volume = {10}
journal type = {AC}
place = {United Kingdom}
year = {2013}
month = {Apr}
}