An Introduction to Systems Biology: Design Principles of by Uri Alon

By Uri Alon

Provides layout ideas that govern the constitution and behaviour of organic networks akin to gene circuits, highlighting easy, routine circuit components that make up the community. This booklet presents a quantitative conception for which circuits are present in a given setting and a mathematical framework for figuring out organic circuits.

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The experiment used green fluorescent protein fused to the TetR repressor as a reporter and automated fluorescence measurements on growing E. coli cells. Protein concentration was normalized to its steady-state level. Shown also are the analytical solutions for a simply autoregulated gene and for a negatively autoregulated gene with a Hill input function with n = 1 in the limit of strong autorepression (thin lines). 1 Positive Autoregulation Slows R esponses and Can L ead to Bi‑Stability Some transcription factors show positive autoregulation, in which they activate their own transcription.

What are the dynamics of X and Y? What are the response 1/26/07 9:36:30 AM 4 0 < C hapte r 3 times of X and Y? Assume logic input functions, with repression thresholds K xx, K xy for the action of X on its own promoter and on the Y promoter, and Kyy for the action of Y on its own promoter. b. At time t = 0, production of X stops after a long period of production, and X concentration decays from its initial steady-state level. What are the dynamics of X and Y? What are the response times of X and Y?

Most nodes in the network stand for genes that encode proteins that are not transcription factors. These proteins carry out the various functions of the cell. The inputs to the network are signals that carry information from the environment and change the activity of specific transcription factors. The active transcription factors bind specific DNA sites in the promoters of their target genes to control the rate of transcription. This is quantitatively described by input functions: the rate of production of gene product Y is a function of the concentration of active transcription factor X*.

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