All entries for June 2006
June 26, 2006
Title: "Synchronization, singularities and circadian clocks: lessons from Art Winfree's pre–molecular approach to systems biology"
Part one: Synchronization:
Coupled ocillators in experiment:
- emerging coherence Chemical oscillators: Kiss Science 2002
- Repressilator coupled by quorum sensing, Garcia-Ojalvo PNAS 2004 and McMillen PNAS 2002
Part two: Phase singularities in circadian clocks:
Title: "Programming bacteria: wiring synthetic sensors and circuits to heterologous outputs"
Three systems in E.Coli:
- Competition 6 month time limit. iGEM Genetic Engineering Competition
- a national student competition
One: Light Sensor:
- Bacterial Photography. Change gene expression on light.
- on known photoreceptors in E.coli. just in other organisms.
- Phytochromes in Cyanobacteria, Arabidopsis.
- kinase that is activated on light induction
- compine e.coli osmotic shock sensor with cph1, ouput lacZ
Two: Bacterial Thermometer:
- Heat shock and Cold shock repsonse promoters
- Cold: Hypb, ansb, cspa_x promoter
- Heat: htpG
Synthetic Logic (AND gate):
- Examples of other gates in ecoli, yeast and mammal cells
…and it comes back to haunt you. Need to make an overview of the Heidelber conference. Let's look at the Collins talk first :
Title: "Integrating synthetic biology and systems biology"
Collins, J. J., 20 Oct 2005
- Building synthetic gene networks: Gene toggle and RNA swithces
- Applications in microbiology: (anti)toxins and cell death pathways
- Inferring genetic networks: using the network model to infer the mode of action of drugs
To one. Synthetic gene networks:
- Forward Engineering. Design switch, simple modeling,produce plasmids and see if it works. Gardner in Nature 2000. (Toggle switch in E.coli).
- moving from e. coli up to yeast and mammalian systems. coupling to natural systems.
- RNA based synthetic biology: Enginieered ribo–regulators. Issacs Nature Biotechnology 2004
To two. Applications in microbiology:
- biosensors and programmable cells
- wirkung von toxins. Afif 2001 CcdB
- gradielles anschalten von toxins, antibiotics. following along the cell death pathway. iron comes in at later stage. unpublished at the time.
To Three. Infering genetic networks:
- Reverse engineering gene networks
- overexpress genes of interest, obtain expression profiles, feed into NIR algorithm, reverse engineer regulatory network
- Yeung PNAS 2002 and Tegner PNAS 2003
- Example with E Coli SOS pathway: Gardner Science 2003
- 9 gene subnetwork. perturb gene expression. output by real time pcr. algorithm gives graphs, sign and strength of interaction.
- next step: use result to find key players with most influence over the other genes. recA, lexA which confirms previous biological results.
- Most exciting application: Infer the mode of action of compounds.
- drugs: know drug hits some target. but: what else does that drug hit? difficult
- now if you know the network and you know the output, you can infer what the input was.
- test approach with the sos pathway by upregulating recA, lexA, measure output, run NIR and infer that recA, lexA was upregulated. horay.
- up to higher organism. very costly to turn genes up or down. So you are only left with the output. hope is that by a lot of perturbations like drugs, mutations etc. might still infer network. Bernardo Nature Biotechnology 2005
- Mammalian Systems
- Network based drug development
- Multi–scale approaches