General Terms
In vitro (within the glass) experimentation using a controlled environment (ex. Test tube/petri dish) In vivo (within the living) experimentation using a whole, living organism (e.g. animal ex vivo (out of the living) testing, clinical trials) experimentation/measurements done in or on tissue in an artificial environment outside the in silico performed on computer or viaorganism with the minimum alteration of computer simulation natural conditions
Ex vitro
Tabor 2009
System Mask filters light detected by bacteria bacteria/ lawn detects edges + gives visual output
Concept of Detection System Bacteria in dark produce signal (green circle) Signal diffuses Only bacteria in light respond to signal; Response = expression of visible reporter gene
Y = 0 when theres light. cell-cell communication NOT light box X AND (NOT Y) IF NOT light produce signal; IF signal AND NOT (NOT light) produce pigment;
inverter
light, no signal, no pigment light, signal, pigment No light, no signal, no pigment no light, signal, no pigment
resp. reg.
light sensitive protein cph8 = [Cph1]+[EnvZ] Cph1 = photoreceptor domain of Synechocystis EnvZ = kinase domain of E.coli Inhibited with red light Requires phycocyanobilin (PCB) Covalently associated chromophore Produced from heme by genes ho1 and
Sensor
Phytochrome
Membrane bound extracellular sensor/photoreceptor Intracellular (response) regulator
Usu do not have DNA-binding domains Do not directly regulate gene expression
Photoreceptor Expression
PCB not produced in E.Coli Introduction of PCB synthesis genes Converts haem into PCB
Transduction Mechanism
Red light represses EnvZ auto-phosphorylation
Output
OmpR-P activates promoter linked to reporter gene lacZ reporter produce black compound
System Revisited
Light Canon