Difference between revisions of "Stochastic Gene Expression in Single Gene Oscillator Variants"

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(Created page with "{{Paper |Title=Stochastic Gene Expression in Single Gene Oscillator Variants |Authors=Anandh Swaminathan, Marcella M. Gomez, David L. Shis,Matthew R. Bennett, and Richard M. M...")
 
 
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|Source=2016 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference
 
|Source=2016 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference
 
|Abstract=It is infeasible to understand all dynamics in cell, but we can aim to understand the impact of design choices under our control. Here we consider a single gene oscillator as a case study to understand the influence of DNA copy number and repressor choice on the resulting dynamics. We first switch the repressor in the oscillator from the originally published lacI to treRL, a chimeric repressor with a lacI DNA binding domain that is inducible by trehalose. This slightly modified system produces faster and more regular oscillations than the original lacI oscillator. We then compare the treRL oscillator at three different DNA copy numbers. The period and amplitude of oscillations increases as the copy number is decreased. We cannot explain the change in period with differ- ential equation models without changing delays or degradation rates. The correlation and phase coherence between daughter cells after cell division also tend to fall off faster for the lower copy oscillator variants. These results suggest that lower copy number variants of our single gene oscillator produce more synchronized oscillations.
 
|Abstract=It is infeasible to understand all dynamics in cell, but we can aim to understand the impact of design choices under our control. Here we consider a single gene oscillator as a case study to understand the influence of DNA copy number and repressor choice on the resulting dynamics. We first switch the repressor in the oscillator from the originally published lacI to treRL, a chimeric repressor with a lacI DNA binding domain that is inducible by trehalose. This slightly modified system produces faster and more regular oscillations than the original lacI oscillator. We then compare the treRL oscillator at three different DNA copy numbers. The period and amplitude of oscillations increases as the copy number is decreased. We cannot explain the change in period with differ- ential equation models without changing delays or degradation rates. The correlation and phase coherence between daughter cells after cell division also tend to fall off faster for the lower copy oscillator variants. These results suggest that lower copy number variants of our single gene oscillator produce more synchronized oscillations.
|URL=http://www.cds.caltech.edu/~murray/preprints/swa+16-seed.pdf
+
|URL=http://www.cds.caltech.edu/~murray/preprints/swa+16-seed_s.pdf
 
|Type=Conference paper
 
|Type=Conference paper
 
|ID=2016b
 
|ID=2016b

Latest revision as of 23:25, 28 May 2016

Title Stochastic Gene Expression in Single Gene Oscillator Variants
Authors Anandh Swaminathan, Marcella M. Gomez, David L. Shis,Matthew R. Bennett, and Richard M. Murray
Source 2016 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference
Abstract It is infeasible to understand all dynamics in cell, but we can aim to understand the impact of design choices under our control. Here we consider a single gene oscillator as a case study to understand the influence of DNA copy number and repressor choice on the resulting dynamics. We first switch the repressor in the oscillator from the originally published lacI to treRL, a chimeric repressor with a lacI DNA binding domain that is inducible by trehalose. This slightly modified system produces faster and more regular oscillations than the original lacI oscillator. We then compare the treRL oscillator at three different DNA copy numbers. The period and amplitude of oscillations increases as the copy number is decreased. We cannot explain the change in period with differ- ential equation models without changing delays or degradation rates. The correlation and phase coherence between daughter cells after cell division also tend to fall off faster for the lower copy oscillator variants. These results suggest that lower copy number variants of our single gene oscillator produce more synchronized oscillations.
Type Conference paper
URL http://www.cds.caltech.edu/~murray/preprints/swa+16-seed_s.pdf
Tag swa+16-seed
ID 2016b
Funding AFOSR BRI
Flags