redirecting evolution - · pdf fileredirecting evolution. ... rich bonneau, nyu; ... lee hood,...
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Nitin S. Baliga Professor
Institute for Systems Biology, Seattle
“Ask not what you can do for evolution,ask what evolution can do for you”
Redirecting Evolution
Acquisition of complexity: Conditionally activated control inside genes
Koide, Reiss, et al. (2009) MSB
DNA
RNA
Protein
Metabolites
Phenotype
Genotype
ENVIRONMENT
Genetic information processing is dynamic
Systems Approach:Perturb, Observe and Model
Environmental Perturbations
Phenotypes
Genes/Proteins
Parts of a system
Consequences of small changes resonate
throughout the network
Baliga NS, Science (2008)
Tagkopolous et al., Science (2008)
Constrained Evolution
Barrett et al. PNAS (2005); Baliga NS, Science (2008) ; Tagkopolous et al., Science (2008)
II. Few dominant states
I. Interlocked architecture
System wide data:looking at the same phenomenon through different lenses
• Concentrations of molecules
– Transcription starts, stops
– mRNA levels
– Protein levels
• Interactions among
molecules
– functional
relationships/associations
(phylogenetic pattern)
– genome organization
(operons, chromosomal
proximity)
• Enzyme reactions
• Modifications of molecules
Reiss et al, BMC Bioinformatics (2006), Bonneau et al., Genome Biology (2006)
Reverse engineering biological circuits
Tracking individual cells
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Time (min)
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Flu
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Copper (via tracer)
Single cell yvgX (via GFP)
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Time (min)
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Tracking individual cells
Copper (via tracer)
Multiple single cells yvgX (via GFP)
Rich Bonneau, NYU; Marc Facciotti, UC Davis; Paul Shannon, ISB; Vesteinn Thorsson, ISB
Tie Koide, U of Sao Paulo; Amy Schmid, Duke U; Kenia Whitehead Lee Hood, Bill Longabaugh, Jocelyne DiRuggiero, Carl Johnson
John Tainer and MAGGIE investigators
Funding from NSF, NIH, DoE, DoD, Battelle, Luxembourg and NASA
Acknowledgements
http://baliga.systemsbiology.net
6 TBPs
7 TFBs
Acquisition of complexity:I. Gene Family Expansion
Turkarslan et al. in preparation; Facciotti et al., (2007) PNAS