CHE.496/2009/Responses/a13

Biological Networks

 * Discussion leader: Patrick

Patrick's Response

 * Biological Networks
 * A recurring point made in the paper is that biological networks are similar to other complex networks. We can extend our understanding of other complex networks such as hierarchal networks and the tools used to study those networks. Such as graph theory, in which they use to describe metabolic networks with genes as nodes and pathways as edges. Other networks the paper mentions that could be studied further in depth using these techniques is the protein-protein interaction network, transcriptional regulatory network, and metabolic networks. The paper goes through the techniques being applied to elucidate these biological networks such as ChIP for protein-DNA networks. Furthermore, the authors describe a manner of compartmentalizing biological networks by defining modules as discrete units of function separable from the whole and there are different approaches to building modules as described by the paper. In addition, motifs are defined as a set or genes or gene products with specific molecular function arranged together to perform “useful” behavior. Motifs are not modules in that they are not discrete functions separable from the whole. One could think of motifs as something similar to genetic circuits and modules as something similar to the operon structure of the bacterial gene regulatory network. Studying biological networks that interact with other networks greatly complicates analysis, but in the Network Benchmarking Article mentioned in the previous assignment. It is possible to isolate a synthetic biological network and control the inputs as to understand how the network functions. It may come to the point that in order to study very complex networks, pieces of the network may have to be built synthetically and studied and then the pieces are brought together to complete the network. Since each component of the network has been studied, understanding the entire network has been simplified, especially if you can control how intermediate products move through the network as demonstrated by Cantone.
 * Programming and Engineering Biological Networks
 * The article goes through notable biological networks that have already been developed. For example: the toggle-switch in mammalian cells, pattern-forming circuits, and the synthetic riboregulator. Furthermore, an interesting topic to discuss in the discussion is the use of post-transcriptional control of gene expression utilizing synthetic RNA’s (we can include material from Dan’s paper in this from Project 1?). Christina Smolke’s antisense agents are another interesting tool for gene expression, where a targeted protein has its translation inhibited by the binding of oligo-nucleotides to the target mRNA.
 * Patrick Gildea 05:06, 6 April 2009 (EDT):

Thaddeus Webb's response
Biological Networks Thaddeus Webb 09:46, 6 April 2009 (EDT)
 * Several molecular interaction networks are being elucidated including
 * protein-protein interactions
 * Transcriptional regulatory network
 * Small molecule metabolism
 * High Throughput data analysis is giving picture of genetic parts.
 * There is a significant gap between sequencing data and reality
 * High throughput techniques
 * Two hybrid, the domains of a transcriptional activator are cut in half and fused to random proteins. When proteins interact activator works and activates reporter.
 * MS based, purify complex using affinity chromatography and identify with MS
 * Results from techniques did not overlap as much as expected.
 * Huge number of false positives up to 50%.
 * Only considering interactions predicted by both techniques reduced false positive but decreased coverage.
 * Proteome chips, fix labeled protein to chip. Pass extract over it and see what binds.
 * ChIP used to find protein DNA interaction
 * Biological networks share features of general complex networks. Both modular and scale free properties.
 * Although biological and engineered systems appear similar in topology node function is distinct.
 * A simple model of domain creation predicted domain classes created at constant rate and class members made by duplication matched E. Coli and Yeast data.
 * Network topology and genome sequence data can be combined to examine the evolutionary impact of network structure on proteins.
 * Proteins that interact evolve at same rate through co-evolution.
 * Genes sharing regulatory motifs are co-regulatory.
 * Interactions between different networks can complicate study.
 * Engineering de novo is a good test of our knowledge.

Programming and engineering biological networks
Epigenetic toggle switches
 * respond to transient stimuli to elicit changes
 * created from two repressor proteins that negatively regulate each other’s expression
 * can toggle between two stable expression states

To create a toggle switch in eukaryotes:
 * use two antibiotic-inducible transcription control systems (PIP ON, E ON)
 * SEAP used to measure the output for the switch
 * Erythromycin and Pristinamycin I are the transient stimuli

Goal:
 * Bacterial toggle switches can track the fate of individual cells and their daughters in multicellular organisms in response to diverse stimuli

Post-transcriptional control of gene expression using synthetic RNAs
 * control gene expression either at the transcriptional or translational level
 * append a nucleotide sequence to the 5’ end of the natural transcript
 * sequence forms a hairpin with the sequence containing the natural RBS and repress gene expression
 * produce a second RNA in trans that binds to the cis repressor sequence for translation

Orthogonal ribosomes
 * synthesizes cellular proteins encoded in mRNA
 * testing the possibility of creating multiple orthogonal ribosomes that function independently of the natural ribosome in cells

Biological Networks
1)Yeast two-hybrid technology: a bait protein is fused to DNA binding domain to attract a prey protein fused to a transcriptional activation domain, resulting in expression of a reporter gene 2)MS-based assays: bait proteins are tagged and potential complexes are purified from cellular lysate using chromatography. Individual components are isolated by SDS PAGE and identified by MS.
 * Studies on protein-protein interaction:
 * Experimental techniques lead to the collection of interactions between various biomolecules. However, these interactions have few quantitative labels, high error rate and little cellular context.

Different philosophies on how to use network information to develop our understanding of biological systems: 1)Complementary approach-taking existing hypotheses and using the extensive network data to either support/reject them 2)Reformulation of old qstions from a network perspective- the relationship between the evolution of genes and the networks they constitute
 * Biology from a network perspective

De novo design- designing genetic circuits from existing genetic parts
 * Engineering networks

Rohini Manaktala 15:36, 6 April 2009 (EDT)