lecture 4: statistical mechanics of gene regulation rob phillips california institute of technology...
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Lecture 4: Statistical Mechanics of Lecture 4: Statistical Mechanics of Gene RegulationGene Regulation
Rob PhillipsCalifornia Institute of Technology
(Beautiful work of David Goodsell)
The Single Molecule Census Continued: The Single Molecule Census Continued:
Gene Expression Gene Expression
(Beautiful work of David Goodsell)
RNAP+DNA+mRNA
Lac Repressor
CRP and DNA
Products of the Lac Operon
All Together Now: The Lac OperonAll Together Now: The Lac Operon
Our goal: mathematize the story told by all of these cartoons.In particular, compute the probability of RNAP binding as a function of concentration of all the other molecular actors.
Measure the Concentration of the Gene Measure the Concentration of the Gene
Product: Fluorescence Product: Fluorescence
(Elowitz and Leibler)
Repression in the Lac Operon: the Role of Repression in the Lac Operon: the Role of
Looping Looping
(Elowitz et al.)
Beta-Galactosidase ActivityBeta-Galactosidase Activity
Ian B. Dodd et al. Genes Dev. 2004; 18: 344-354
(Dove et al.)
(Lawrence et al.)
Measuring the mRNA Content of a Cell Measuring the mRNA Content of a Cell
(Yeast microarray data – Brown Group at Stanford)
Real-Time PCRReal-Time PCR
CYCLE NUMBER AMOUNT OF DNA0 11 22 43 84 165 326 647 1288 2569 512
10 1,02411 2,04812 4,09613 8,19214 16,38415 32,76816 65,53617 131,07218 262,14419 524,28820 1,048,57621 2,097,15222 4,194,30423 8,388,60824 16,777,21625 33,554,43226 67,108,86427 134,217,72828 268,435,45629 536,870,91230 1,073,741,82431 1,400,000,00032 1,500,000,00033 1,550,000,00034 1,580,000,000
www.biorad.com
2a. excitation flters
2b. emission filters
1. halogen tungsten lamp
4. sample plate
3. intensifier
5. ccd detector 350,000 pixels
Measuring Promoter Occupancy:ChIPMeasuring Promoter Occupancy:ChIP
http://www.vincibiochem.it/ChIP-IT.htm