Team:Penn/Notebook

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Notebook

Week 1
- Molecular Biology Training Workshop
- Practiced the basics of molecular cloning
Week 2
- Idea Brainstorming and Generation
- Compiled a preliminary list of potential ideas
Week 3
- Settled on two main ideas: 1. quorum sensing with antibiotics 2. Heavy metal removal with Magnetotactic bacteria
- Learned how to use Geneious to design cloning process
- Practiced extracting biobricks and transforming NEB Turbo cells with plasmids
- Visited Biomeme to get the portable qPCR machine
Week 4
- Decided on the project idea: Heavy metal removal with Magnetotactic bacteria
- Identified primers and promoters in AMB-1 strain
- Identified AMB-1 transformation vector
- Extracted smtA biobrick gene and made glycerol stock
Week 5
- Developed three goals to accomplish for the project
- Determined the constructs to clone into AMB-1
- Designed two fast-fail experiments
- Created a workflow for the construction of plasmid
- Planned outreach events at high school summer programs
Week 6
- Ordered chemicals for AMB-1 growth medium
- Completed primer design
- Obtained AMB-1 strain from Dr.Goulian
Week 7
- Determined the OD600 plate reading conversion formula experimentally
- Attempted to do E.Coli and AMB-1 cadmium tolerance test
- Designed all construct on Geneious
- Met with Dr.Rizk to discuss presenting to incoming bioengineering freshmen
Week 8
- Ordered DNAs from Genscript and IDT
Week 9
- Redid E.Coli Cadmium Tolerance Test in M9 media
- Learned to do cell count for AMB-1
- Attempted to make AMB-1 chemically competent
- Presented to high school students at Penn M&T program
- Planned a synthetic biology preceptorial
- Contacted Schuylkill Action Network
Week 10
- Completed AMB-1 growth curve under different media
- Determined cell count and OD600 conversion formula for AMB-1 experimentally
- Completed E.Coli Cadmium Tolerance Test in LB media
- Volunteered at SEA Science Carnival
Week 11
- Addressed EMSGM growth problem with pH
- Make new recovery media with adjusted pH for optimal AMB-1 growth
- Chemical Transformation with different recovery broths
- Attempted PCR assembly with synthesized parts
Week 12
- Used anaerobic chambers to grow plates
- Troubleshooted lack of magnetism with new iron maleate solution
- Troubleshooted AMB-1 electroporation experiment with plating at every step
- Began cloning successfully assembled PCRed constructs into PYMB essentials
Week 13
- Finished cloning flurescent protein with smtA and mCherry into PYMB essentials
- Transform AMB-1 with this construct to test for successful transformation with fluorescence test
Week 14
- Make new E-MSGM media
- Re-designed construct
Week 15
- Troubleshooted cloning E. coli construct for cadmium tolerance
- Sequence verified finished constructs on PYMB
Week 16
- Built the prototype of a portable spectrophotometer for cell recovery experiment
- Designed primers for Gibson Assembly of final construct
- Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers.
Week 17
- Tested AMB-1 aerobic culture and anaerobic culture with magnetometer
- Troubleshooted and retried cloning E. coli construct
- PCRed up parts we received for construction of shuttle vector
Week 18
- Tested AMB-1 aerobic culture and anaerobic culture with magnetometer
- Finished PCRing parts we received from IDT
Week 19
- Measured the magnetic strength indicator T2 for various concentration of AMB-1 culture and attempted to develop a trendline
- Counted fully grown sample of aerobic AMB-1 and made a trendline converting OD to cell concentration
- Cloned all biobricks into PSB1C3 backbone
Week 20
- compiled all data and graphics for wiki