Weekly Progress

Weekend/Monday

Initial chambers for testing cells & fluorescent beads

Continued coding image analysis / segmentation code.
Fabricated Microfluidics using resources from Kamm lab and Voldemann lab.
- PDMS poured & cured Monday afternoon
Moved microscope setup to larger breadboard.

2 Cultures of I13521 started from freezer stocks tubes 2&3. Aliquoted into 5mL of LB+Amp and left to grow overnight. ~12 hours of growth time should be sufficient for experimentation tomorrow.
Idea: potentially growing up KAF95 and miniprepping it may prove useful if we can BioBrick out the fliC273 gene.

Aligned microscope setup on the larger breadboard
Tested different perfusion chambers:
PDMS with microwell is too thick to be imaged with inverted microscope
Stick on perfusion chambers are reusable
Visualized RFP bacterial cells under BF and Fluoresence, pictures were taken for further analysis

Begin building stepper motor driver circuitry with Polulu and Arduino
Experimenting with serial communication in Python, wrapper for stage control
Arduino C language for firmware in microcontroller, buffers and interpret serial input in bytes, and output electrical pulses

Stage control code tested: stepper motor can run at different speeds with specified number of steps through python
Input as (X direction, X step, Y direction, Y step)
X-Y axes motors move simultaneously given input to desired location

Mutation plasmid from Liu's group acquired. Transformed and grew in spectinomycin, but antibiotic was too weak, redo over weekend.
Finalizing and committed stage code.
Meeting with another MIT group to discuss building the ablation laser.

David Liu has agreed to give us MP-QUR, pickup will be TBD, but we can hopefully just go over to Harvard and get the plasmid.
The Elowitz Repressilator can apparently be found on Add-Gene, will need to either find or figure out a good testing rig to put it in.
Cory has I13521 and I13522, although both are in pSB1A3, which might prove problematic if the KAF95 fliC is also on a pBR322 derived plasmid. Current backup is J04450 which can be found in pSB1C3 and would allow for a co-transformant.