SynBERC:Parts

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'''This is a draft list of research topics that the SynBERC Parts Thrust is considering for support.'''  <br>
'''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>
<font color="red">'''Please contribute & edit with impunity.'''</font><br>
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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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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]]!'''
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'''I.  Goals'''
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==Goals==
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1. Parts collection, registry
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===1. Parts collection, registry===
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2. Parts characterization
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===2. Parts characterization===
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3. Parts engineering
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===3. Parts engineering===
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a. New function
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*a. New function
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b. Tune strength, timing
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*b. Tune strength, timing
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c. Orthogonal, composable function
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*c. Orthogonal, composable function
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d. Develop general methods for part redesign
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*d. Develop general methods for part redesign
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==Part Families==
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===Transcriptional===
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*repressors, DNA binding proteins
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*terminators
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*promoters
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===Translational===
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*RBS
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*Riboregulators
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*mRNA procesing
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===Degradation===
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*degrons
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===Secretion===
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*Targeting sequences
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===Sensing/actuating===
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*protein binding
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*small molecule ligand binding
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*light sensing
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*switches
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===Assembly===
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*Protein-protein interactions (orthogonal set)
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===Phosphorylation logic control===
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*Kinases
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*Phosphatases
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*Docking motifs
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*phosphorecognition
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===Biosynthetic enzymes===
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===Transporters===
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===Cell adhesion===
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===Chassis parts===
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*Vectors
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*YAC components
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*Transposon components
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==Projected Parts Application to Testbeds==
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===Tumor Killing Bacteria[http://openwetware.org/wiki/SynBERC:TKB]===
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* Gene expression devices
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**Transcriptional parts
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**Translational parts (riboregulators)
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* Post-Translational device
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**Degradation
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**Phosphorylation logic
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*Sensing/actuating/signaling devices
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**Sensing/actuating parts
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**Assembly – assembly based logic
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**Riboregulators
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** Phosphorylation logic
 +
**Cell adhesion, targeting
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* Chassis parts
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===Microbial drug factory===
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*Gene expression devices
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**Transcriptional parts
 +
**Translational parts (riboregulators)
 +
* Post-Translational device
 +
**Degradation
 +
**Phosphorylation logic
 +
*Biosynthetic devices
 +
**Engineered metabolic enzymes (malic acid to malic semi-aldehyde)
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* Sensing/actuating/signaling devices
 +
**Sensing/actuating parts
 +
**Assembly – assembly based logic
 +
**Riboregulators
 +
**Phosphorylation logic
 +
**Transporters
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* Chassis parts

Current revision

back to SynBERC on OWW

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!

Contents

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
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