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

By Uri Alon

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

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Additional info for An Introduction to Systems Biology: Design Principles of Biological Circuits

Sample text

Similarly, new edges can be added to the network by mutations that generate a binding site for transcription factor X in the promoter region of gene Y. Such sites can be generated, for example, by mutations or by events that duplicate or reposition pieces of a genome, or that insert into the genome pieces of DNA from other cells (Shapiro, 1999). Hence, edges in network motifs must be constantly selected in order to survive randomization forces. This suggests that if a network motif appears in a network much more often than in randomized networks, it must have been selected based on some advantage it gives to the organism.

The maximal unrepressed promoter activity is b, and K is the threshold for repression of a target gene (the concentration of X* needed for 50% maximal repression). indb 14 1/26/07 9:36:14 AM Tr ansc r i ption net w or k s : b asic conce pts < 15 Since a repressor allows strong transcription of a gene only when it is not bound to the promoter, this function can be derived by considering the probability that the promoter is unbound by X* (see Appendix A). 2c), that is, when X* = 0. Half-maximal repression is reached when the repressor activity is equal to K, the gene’s repression coefficient.

To understand why negative autoregulation is a network motif, we analyzed its dynamic behavior. The dynamic analysis can be phrased as an engineering story. Think of evolution as an engineer working to design a gene circuit that would reach a desired steady-state concentration Xst. One possible design, design A, is simple regulation with a production rate set to reach Xst. Design B is negative autoregulation, with a stronger initial production rate, which, as X builds up, is suppressed to result in the desired steady-state.

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