SynBERC:Parts
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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.
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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