SynBERC:Parts: Difference between revisions

Latest revision as of 04:52, 15 March 2007

This is a draft list of research topics that the SynBERC Parts Thrust is considering for support.
Please contribute & edit with impunity.
We need to get the set of topics correct and then organize ourselves (and anybody else who wants) around getting the work done. Sign up for the parts mailing list!

Goals

1. Parts collection, registry

2. Parts characterization

3. Parts engineering

a. New function
b. Tune strength, timing
c. Orthogonal, composable function
d. Develop general methods for part redesign

Part Families

Transcriptional

repressors, DNA binding proteins
terminators
promoters

Translational

RBS
Riboregulators
mRNA procesing

Degradation

degrons

Secretion

Targeting sequences

Sensing/actuating

protein binding
small molecule ligand binding
light sensing
switches

Assembly

Protein-protein interactions (orthogonal set)

Phosphorylation logic control

Kinases
Phosphatases
Docking motifs
phosphorecognition

Biosynthetic enzymes

Transporters

Cell adhesion

Chassis parts

Vectors
YAC components
Transposon components

Projected Parts Application to Testbeds

Tumor Killing Bacteria[1]

Gene expression devices
- Transcriptional parts
- Translational parts (riboregulators)
Post-Translational device
- Degradation
- Phosphorylation logic
Sensing/actuating/signaling devices
- Sensing/actuating parts
- Assembly – assembly based logic
- Riboregulators
- Phosphorylation logic
- Cell adhesion, targeting
Chassis parts

Microbial drug factory

Gene expression devices
- Transcriptional parts
- Translational parts (riboregulators)
Post-Translational device
- Degradation
- Phosphorylation logic
Biosynthetic devices
- Engineered metabolic enzymes (malic acid to malic semi-aldehyde)
Sensing/actuating/signaling devices
- Sensing/actuating parts
- Assembly – assembly based logic
- Riboregulators
- Phosphorylation logic
- Transporters
Chassis parts

@@ Line 3: / Line 3: @@
 '''This is a draft list of research topics that the SynBERC Parts Thrust is considering for support.'''  <br>
 <font color="red">'''Please contribute & edit with impunity.'''</font><br>
 We need to get the set of topics correct and then organize ourselves (and anybody else who wants) around getting the work done.
+'''Sign up for the [[List:Synberc-parts|parts mailing list]]!'''
-==I.  Goals==
+==Goals==
 ===1. Parts collection, registry===
@@ Line 14: / Line 15: @@
 *c. Orthogonal, composable function
 *d. Develop general methods for part redesign
+==Part Families==
+===Transcriptional===
+*repressors, DNA binding proteins
+*terminators
+*promoters
+===Translational===
+*RBS
+*Riboregulators
+*mRNA procesing
+===Degradation===
+*degrons
+===Secretion===
+*Targeting sequences
+===Sensing/actuating===
+*protein binding
+*small molecule ligand binding
+*light sensing
+*switches
+===Assembly===
+*Protein-protein interactions (orthogonal set)
+===Phosphorylation logic control===
+*Kinases
+*Phosphatases
+*Docking motifs
+*phosphorecognition
+===Biosynthetic enzymes===
+===Transporters===
+===Cell adhesion===
+===Chassis parts===
+*Vectors
+*YAC components
+*Transposon components
+==Projected Parts Application to Testbeds==
+===Tumor Killing Bacteria[http://openwetware.org/wiki/SynBERC:TKB]===
+* Gene expression devices
+**Transcriptional parts
+**Translational parts (riboregulators)
+* Post-Translational device
+**Degradation
+**Phosphorylation logic
+*Sensing/actuating/signaling devices
+**Sensing/actuating parts
+**Assembly – assembly based logic
+**Riboregulators
+** Phosphorylation logic
+**Cell adhesion, targeting
+* Chassis parts
+===Microbial drug factory===
+*Gene expression devices
+**Transcriptional parts
+**Translational parts (riboregulators)
+* Post-Translational device
+**Degradation
+**Phosphorylation logic
+*Biosynthetic devices
+**Engineered metabolic enzymes (malic acid to malic semi-aldehyde)
+* Sensing/actuating/signaling devices
+**Sensing/actuating parts
+**Assembly – assembly based logic
+**Riboregulators
+**Phosphorylation logic
+**Transporters
+* Chassis parts