Team:BostonU/Workflow

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         <th scope="col">For phase III of our hybridized workflow, we will put together the new transcriptional units according to regulatory arcs and test them individually. To do that, using Raven and Eugene will be very beneficial as they can generate designs and assembly plans for very large devices. Testing several pairs of units with varying concentrations of small molecule induction is always a good idea so that a large range of data can be collected. This data will then be analyzed to gauge the efficacy of the device. </th>
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Revision as of 15:46, 25 September 2014



Workflow

Phase I - Build and test basic parts.

Key software tools: TASBE Tools, Eugene (optional), Raven (optional)

General Chimera Workflow

Case Study: BU Priority Encoder

general I • Add parts to MoClo library. These parts were found to be necessary for our priority encoder:

• 3 MoClo level 1 and 3 MoClo level 2 backbones, each with a different origin of replication:

• ColE1
• p15A
• pSC101

• 4 MoClo level 0 fusion proteins:

• TetR_GFP
• TetR_YFP
• AraC_YFP
• AraC_GFP


• X MoClo level 0 tandem promoters:

• pTet_pBad
• pBad_pTet

These parts were cloned into a E. coli Bioline strain using our MoClo and transformation protocols. They were purified, sequenced, and tested using our FACS Workflow. These parts were then cloned into appropriate vectors and tested in our Fortessa flow cytometer. The TASBE Tools were then employed to characterize their expression.

Phase II - Build and characterize TU behavior.

Key software tools: TASBE Tools, Eugene, Raven

General Chimera Workflow

Case Study: BU Priority Encoder

general II • Run one-pot Multiplexing MoClo reaction. We initially multiplexed 5' UTIs and Terminators

• Eugene was employed to visualize all possible part substitutions.
• Raven was employed to optimize the assembly of these combinations.



• Clone multiplexed reactions into Pro strain of E. coli using Pro Transformation protocol.

• Pick 20 colonies per plate, purify, and sequence.

• Test using flow cytometry workflow and analyze data using the TASBE Tools.

Phase III - Test regulatory arcs and assemble final device.

Key software tools: TASBE Tools, Eugene, Raven

General Chimera Workflow

Case Study: BU Priority Encoder

For phase III of our hybridized workflow, we will put together the new transcriptional units according to regulatory arcs and test them individually. To do that, using Raven and Eugene will be very beneficial as they can generate designs and assembly plans for very large devices. Testing several pairs of units with varying concentrations of small molecule induction is always a good idea so that a large range of data can be collected. This data will then be analyzed to gauge the efficacy of the device. • Test individual TU regulatory arcs:

• ...

• Use Eugene to plan final device topology.

• Use Raven to guide MoClo assembly of encoder.

• Clone multiplexed reactions into Pro strain of E. coli using Pro Transformation protocol.

• Pick colonies, purify, and sequence.

• Test using flow cytometry workflow and analyze data using the TASBE Tools.







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