Difference between revisions of "Team:Penn/Notebook"
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+ | <title>University of Pennsylvania iGEM</title> | ||
+ | <link href='http://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'> | ||
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+ | </head> | ||
− | < | + | <body> |
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+ | <div id="redbox"> | ||
+ | <div style = "text-align: center;"><img width="300px" src="https://static.igem.org/mediawiki/2014/1/1d/Timeline-header.png"></div><br> | ||
+ | <div id="textbox"> | ||
+ | <h3 style= "text-align: center;">Week 1</h3> | ||
+ | <ol> | ||
+ | <li>Molecolar Biology Training Workshop</li> | ||
+ | <li>Practiced the basics of molecular cloning</li> | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 2</h3> | ||
+ | <ol> | ||
+ | <li>Idea Brainstorming and Generation</li> | ||
+ | <li>Compiled a preliminary list of potential ideas</li> | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 3</h3> | ||
+ | <ol> | ||
+ | <li>Settled on two main ideas: 1. Quorum sensing with antibiotics 2. Heavy metal removal with Magnetotactic bacteria</li> | ||
+ | <li>Learned how to use Geneious to design cloning process</li> | ||
+ | <li>Practiced extracting biobricks and transforming NEB Turbo cells with plasmids</li> | ||
− | < | + | <li>Human Practices</li> |
− | < | + | <li>Visited Biomeme to get the portable qPCR machine</li> |
− | <li> | + | </ol> |
− | <li> | + | <h3 style= "text-align: center;">Week 4</h3> |
− | <li> | + | <ol> |
− | <li> | + | <li>Decided on the project idea: Heavy metal removal with Magnetotactic bacteria |
− | < | + | <li>Identified primers and promoters in AMB-1 strain |
+ | <li>Identified AMB-1 transformation vector | ||
+ | <li>Extracted smtA biobrick gene and made glycerol stock | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 5</h3> | ||
+ | <ol> | ||
+ | <li>Developed three goals to accomplish for the project | ||
+ | <li>Determined the constructs to clone into AMB-1 | ||
+ | <li>Designed two fast-fail experiments | ||
+ | <li> Created a workflow for the construction of plasmid | ||
+ | <li> Human Practices | ||
+ | <li>Planned outreach events at high school summer programs | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 6</h3> | ||
+ | <ol> | ||
+ | <li>Ordered chemicals for AMB-1 growth medium | ||
+ | <li>Completed primer design | ||
+ | <li>Obtained AMB-1 strain from Dr.Goolian | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 7</h3> | ||
+ | <ol> | ||
+ | <li>Determined the OD600 plate reading conversion formola experimentally | ||
+ | <li>Attempted to do E.Coli and AMB-1 cadmium tolerance test | ||
+ | <li>Designed all construct on Geneious | ||
− | < | + | <li>Human Practices |
− | < | + | <li>Met with Dr.Rizk to discuss presenting to incoming bioengineering freshmen |
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 8</h3> | ||
+ | <ol> | ||
+ | <li>Ordered DNAs from Genscript and IDT | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 9</h3> | ||
+ | <ol> | ||
+ | <li>Redid E.Coli Cadmium Tolerance Test in M9 media | ||
+ | <li>Learned to do cell count for AMB-1 | ||
+ | <li>Attempted to make AMB-1 chemically competent | ||
− | < | + | <li>Human Practices |
− | <li>< | + | <li>Presented to high school students at Penn M&T program |
− | < | + | <li>Planned a synthetic biology preceptorial |
− | <li>< | + | <li>Contacted Schuylkill Action Network |
− | <li> | + | </ol> |
− | + | <h3 style= "text-align: center;">Week 10</h3> | |
+ | <ol> | ||
+ | <li>Completed AMB-1 growth curve under different media | ||
+ | <li>Determined cell count and OD600 conversion formola for AMB-1 experimentally | ||
+ | <li>Completed E.Coli Cadmium Tolerance Test in LB media | ||
− | </div> | + | <li>Human Practices |
+ | <li> Volunteered at SEA Science Carnival | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 11</h3> | ||
+ | <ol> | ||
+ | <li>Addressed EMSGM growth problem with pH | ||
+ | <li>Make new recovery media with adjusted pH for optimal AMB-1 growth | ||
+ | <li>Chemical Transformation with different recovery broths | ||
+ | <li>Attempted PCR assembly with synthesized parts | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 12</h3> | ||
+ | <ol> | ||
+ | <li>Used anaerobic chambers to grow plates | ||
+ | <li>Troubleshooted lack of magnetism with new iron maleate solution | ||
+ | <li>Troubleshooted AMB-1 electroporation experiment with plating at every step | ||
+ | <li>Began cloning successfolly assembled PCRed constructs into PYMB essentials | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 13</h3> | ||
+ | <ol> | ||
+ | <li>Finished cloning flurescent protein with smtA and mCherry into PYMB essentials | ||
+ | <li>Transform AMB-1 with this construct to test for successfol transformation with fluorescence test | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 14</h3> | ||
+ | <ol> | ||
+ | <li>Make new E-MSGM media | ||
+ | <li>Re-designed construct | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 15</h3> | ||
+ | <ol> | ||
+ | <li>Troubleshooted cloning E. coli construct for cadmium tolerance | ||
+ | <li>Sequence verified finished constructs on PYMB | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 16</h3> | ||
+ | <ol> | ||
+ | <li>Built the prototype of a portable spectrophotometer for cell recovery experiment | ||
+ | <li>Designed primers for Gibson Assembly of final construct | ||
+ | |||
+ | <li>Human Practices | ||
+ | <li>Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers. | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 17</h3> | ||
+ | <ol> | ||
+ | <li>Tested AMB-1 aerobic colture and anaerobic colture with magnetometer | ||
+ | <li>Troubleshooted and retried cloning E. coli construct | ||
+ | <li>PCRed up parts we received for construction of shuttle vector | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 18</h3> | ||
+ | <ol> | ||
+ | <li>Tested AMB-1 aerobic colture and anaerobic colture with magnetometer | ||
+ | <li>Finished PCRing parts we received from IDT | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 19</h3> | ||
+ | <ol> | ||
+ | <li> Measured the magnetic strength indicator T2 for various concentration of AMB-1 colture and attempted to develop a trendline | ||
+ | <li> Counted folly grown sample of aerobic AMB-1 and made a trendline converting OD to cell concentration | ||
+ | <li>Cloned all biobricks into PSB1C3 backbone | ||
+ | </ol> | ||
+ | <h3 style= "text-align: center;">Week 20</h3> | ||
+ | <ol> | ||
+ | <li>compiled all data and graphics for wiki | ||
+ | |||
+ | |||
+ | </ol><div id="textbox"> | ||
+ | </body> | ||
</html> | </html> |
Revision as of 04:42, 26 August 2015
Week 1
- Molecolar 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
- Human Practices
- 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
- Human Practices
- 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.Goolian
Week 7
- Determined the OD600 plate reading conversion formola experimentally
- Attempted to do E.Coli and AMB-1 cadmium tolerance test
- Designed all construct on Geneious
- Human Practices
- 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
- Human Practices
- 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 formola for AMB-1 experimentally
- Completed E.Coli Cadmium Tolerance Test in LB media
- Human Practices
- 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 successfolly 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 successfol 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
- Human Practices
- Presented to Penn BE 100 lecture to intriduce synthetic biology to freshman bioengineers.
Week 17
- Tested AMB-1 aerobic colture and anaerobic colture 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 colture and anaerobic colture with magnetometer
- Finished PCRing parts we received from IDT
Week 19
- Measured the magnetic strength indicator T2 for various concentration of AMB-1 colture and attempted to develop a trendline
- Counted folly 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