CHE.496/2008/Responses/a14

Biological networks

• Discussion leader: Eyad Lababidi (Discussion guide)

Kevin Hershey's Response

• Biological Networks
  • The review by Arkin and Alm discusses the development of systems using gene interactions in biological systems. It discusses how this is possible through high-throughput genetic sequencing techniques. It then goes on to discuss biological networks, and the modules and motifs which compose it. Alm and Arkin define modules as discrete units of function separable from the whole and motifs are the arrangement of specific molecular functions to do something useful. These networks can then be engineered, using synthetic biology practices, but multiple networks tends to complicate things with interference.
• Programming and Engineering Biological Networks
  • This article is very similar to the Chin article for 4/2/2008. In this article, Chin begins by discussing a mammalian toggle switch. Then, he moves onto yet another explanation of Ron Weiss’s ‘bullseye’ configuration. He then finishes by discussing post-translational control and orthogonal ribosomes, as he did in the article Modular Approaches to Expanding the Functions of Living Matter.
• KPHershey 12:26, 2 April 2008 (EDT)

Kevin Hershey's Response

• Biological Networks
  • The focus of this paper is on a more general view of biological networks than Chin’s paper. An important point made in the paper is that biological networks are similar to other complex networks – in which we can use our understanding of complex networks such as hierarchal networks (i.e. the internet) to lend increased understanding of the modus operandi of biological networks – especially metabolic pathways. As before in other papers related to biological networks, modules are brought up; but motifs are described in far more depth with applications mentioned. The paper ends by adding that computer modeling of biological networks is an important step to be made in elucidating and predicting their behavior.
• Programming and Engineering Biological Networks
  • The purpose of this article is to describe different biological networks that have already been developed. Notably the toggle switch in mammalian cells, among others such as pattern-forming circuits (the bulls-eye) and synthetic riboregulator. One of the interesting points brought up in the paper is the use of post-transcriptional control of gene expression utilizing synthetic RNA’s. There is the way of using natural transcription factors (we have read about this in the previous paper for systems biology. Furthermore, Smolke’s antisense agents are another interesting tool for gene expression, too.
• Patrick Gildea 17:44, 2 April 2008 (EDT):