By Uri Alon
Provides layout rules that govern the constitution and behaviour of organic networks equivalent to gene circuits, highlighting uncomplicated, habitual circuit parts that make up the community. This ebook offers a quantitative conception for which circuits are present in a given setting and a mathematical framework for knowing organic circuits.
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Extra info for An Introduction to Systems Biology: Design Principles of Biological Circuits
1986). A Genetic Switch. Cell Press and Scientific Publications. Ptashne, M. and Gann, A. (2002). Genes and Signals. Cold Spring Harbor Laboratory Press. Overview of Transcription Networks Alon, U. (2003). Biological networks: the tinkerer as an engineer. Science, 301: 1866–1867. Levine, M. H. (2005). Gene regulatory networks for development. Proc. Natl. Acad. Sci. A. 102: 4936–4942. , and Collado-Vides, J. (1998). From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.
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 protein is degraded/diluted at rate α. b. Note that mRNA is often degraded at a much faster rate than the protein product αm >> α. Can this be used to form a quasi-steady-state assumption that mRNA levels are at steady state with respect to slower processes? What is the eἀective protein production rate b in terms of bm, αm, and p? What would be the response time if the mRNA lifetime were much longer than the protein lifetime? Solution: a. 4) b. In the typical case that mRNA degradation is faster than the degradation/dilution of the protein product, we can assume that Ym reaches steady state quickly in comparison to the protein levels.
An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon