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Contents 1 Wednesday 5/15/13 2 Sunday 5/19/13 3 Monday 5/20/13 4 Tuesday 5/21/13 5 Wednesday 5/22/13 6 Thursday 5/23/13 7 Friday 5/24/13 8 Monday 5/27/13 9 Tuesday 5/28/13 10 Wednesday 5/29/13 11 Thursday 5/30/13 12 Friday 5/31/13 13 Monday 6/3/13 14 Tuesday 6/4/13 15 Wednesday 6/5/13 16 Thursday 6/6/13 17 Friday 6/7/13 18 Monday 6/10/13 19 Tuesday 6/11/13 20 Wednesday 6/12/13 21 Thursday 6/13/13 22 Friday 6/14/13 23 Monday 6/17/13 24 Tuesday 6/18/13 25 Wednesday 6/19/13 26 Thursday 6/20/13 27 Friday 6/21/13 28 Monday 6/24/13 29 Tuesday 6/25/13 30 Wednesday 6/26/13 31 Thursday 6/27/13 32 Friday 6/28/13 33 Monday 7/1/13 34 Tuesday 7/2/13 35 Wednesday 7/3/13 36 Thursday 7/4/13 37 Friday 7/5/13 38 Monday 7/8/13 39 Tuesday 7/9/13 40 Wednesday 7/10/13 41 Thursday 7/11/13 42 Friday 7/12/13 43 Monday 7/15/13 44 Tuesday 7/16/13 45 Wednesday 7/17/13 46 Thursday 7/18/13 47 Friday 7/19/13 48 Monday 7/22/13 49 Tuesday 7/23/13 50 Wednesday 7/24/13 51 Thursday 7/25/13 52 Friday 7/26/13 53 Monday 7/29/13 54 Tuesday 7/30/13 55 Wednesday 7/31/13 56 Thursday 8/1/13 57 Friday 8/2/13 58 Monday 8/5/13 59 Tuesday 8/6/13 60 Monday 8/12/13 61 Tuesday 8/13/13 62 Thursday 8/15/13 63 Friday 8/16/13 64 Wednesday 8/21/13

Wednesday 5/15/13

• Amanda met with iGEM faculty advisor Prof. Clase about advisors, HHMI student (Austin) and wetlab involvement.
• Amanda met with Prof. Tao about project modeling.

Sunday 5/19/13

• James, Peter, Brenda Gonzalez and Arizona Fox went to Greenfield HS for Girl Scouts synthetic biology workshop.
• Chris and Amanda met to talk about week and the summer.

Monday 5/20/13

• Charlotte and Nidhi completed required lab training.
• Chris and Charlotte met with the business office and filled out the required payroll forms.

Tuesday 5/21/13

• Chris created all of the social media pages for the team, including Facebook, Twitter, Google+, Gmail, and the blog.
• Everyone did general research about the different types of post-translational modifications.

Wednesday 5/22/13

• Team Meeting (Biomakers assemble!!)
  • Post-Translational Modifications
  • Social media
  • iGEM wiki (Alec)
  • iGEm website
• James and Xiuyuan met with Prof. Tao to discuss project modeling task outline.

Thursday 5/23/13

• Meeting with Prof. Rickus
  • Taguchi statistical methods for design optimization
  • Changed project from PTMs to quality control and Taguchi methods
• Austin arrived on campus... Good times...

Friday 5/24/13

• Team Meeting
  • PTMs and biobricks
  • Robustness and quality control
  • Different assembly methods
  • Ways to measure gene expression
  • Create plan for next week
• Started wiki design

Monday 5/27/13

• Memorial Day

Tuesday 5/28/13

• Team Meeting
  • Gave everyone a variable to research for quality control
  • Talked about public relations
• Team researched generally for quality control project

Wednesday 5/29/13

• Amanda met with Peter to discuss the project budget
• Team researched into past iGEM project relating to quality control

Thursday 5/30/13

• Exec meeting with Amanda, Chris and Jim to discuss project feasibility
• Team meeting to discuss background research

Friday 5/31/13

• Meeting with whole team, Janie, and Dr. Tao about project ideas
• Created a 3 week plan

Monday 6/3/13

• Meeting with Dr. Rickus, Austin and Amanda about Austin’s project for HHMI

* Discussed details of Taguchi method applied to genetic circuitry

Tuesday 6/4/13

• Team meeting to further discuss yeast polarization project idea

Wednesday 6/5/13

• Meeting with Dr. Rickus, Dr. Clase, Soo and Janie to discuss multiple project ideas, which are feasible and what direction to work in

Thursday 6/6/13

• Meeting with Dr. Mosier to discuss the use of yeast and lab space
• Meeting with Jenn to catch her up with project details

Friday 6/7/13

• Meeting with Amanda and Tarun to discuss project ideas

Monday 6/10/13

Tuesday 6/11/13

• Made BL21 competent E. coli cells

Wednesday 6/12/13

• Meeting with Dr. Kishmairer about yeast polarization project

Thursday 6/13/13

Friday 6/14/13

• Meeting with Larisa to discuss working with yeast cells in Bindley Bioscience Center

Monday 6/17/13

Tuesday 6/18/13

• Meeting with Amanda and Austin to discuss progress on HHMI Robustness project

Wednesday 6/19/13

• Lunch meeting with whole team
• Met with Dr. Hazbun about yeast polarization

Thursday 6/20/13

• Brainstormed fundraising ideas
• Meeting with Dr. Briggs to discuss the use of yeast in lab and polarization project

Friday 6/21/13

• Meeting with Dr. Clase to discuss presentation with teachers
• Team meeting

Monday 6/24/13

• Created a project outline and plan for the Taguchi Robustness project

Tuesday 6/25/13

Wednesday 6/26/13

• Human Practices meeting with Ryan, Swetha, Betsy and Amanda

Thursday 6/27/13

• Time line for Taguchi project with Mike

Friday 6/28/13

• Team meeting with Mike to discuss project deadlines for the protein overexpression (BCD)

Monday 7/1/13

• Meeting with Mike to discuss project deadlines for standardization of characterization

Tuesday 7/2/13

• Meeting with Jill about using the Flow Cytometer in Bindley
• HP meeting with Ryan, Swetha, Betsy and Amanda

Wednesday 7/3/13

• Team meeting about project

Thursday 7/4/13

Friday 7/5/13

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Monday 7/8/13

• Exec meeting with Amanda, Chris, and Jim to discuss lab work
• Team meeting

Tuesday 7/9/13

• Meeting with Rouxi about using the Coulter Counter
• HP meeting with Swetha, Betsy and Amanda

Wednesday 7/10/13

• Meeting with exponent

Thursday 7/11/13

Friday 7/12/13

• Austin’s HHMI presentation

Monday 7/15/13

• Amanda meeting with Dr. Mosier about presentation to teachers
• Dr. Chapell’s presentation on synthetic biology with aradopsis plants
• Meeting with Dr. Clase about presentation to teachers

Tuesday 7/16/13

• Mapped out timeline for HP activities

Wednesday 7/17/13

• Transformation of cells
• Amanda presentation of Modeling in AP Biology Classes

Thursday 7/18/13

Friday 7/19/13

• Team meeting

Monday 7/22/13

• Meeting with Amanda, Janie and Jim to discuss synthesis of BCDs
• Cleaned out lab space
• Meeting with Dr. Rickus and Amanda
• Team meeting to discuss goals, lab rules, summer fundraising

Tuesday 7/23/13

Wednesday 7/24/13

Thursday 7/25/13

Friday 7/26/13

Monday 7/29/13

Tuesday 7/30/13

Wednesday 7/31/13

• SURF presentations

Thursday 8/1/13

Friday 8/2/13

Monday 8/5/13

Tuesday 8/6/13

• BBa_K775000 was miniprepped from E. coli with a concentration of 295.7 ng/ul.
• PRS414 was miniprepped from E. coli with a concentration of 317.7 ng/ul.
• Digested BBa_K775000 (1.67 ul) and PRS414 (158 ul) with EcoRI and PstI according to Knight Restriction Digest Protocol for later ligation together and transformation into S. cerevisiae strain from Lim Lab.

Monday 8/12/13

• Received BBa_B0015 (double terminator) from iGEM HQ in E. coli stabbed into solid medium.
• BBa_B0015 will be assembled to end of BCD gBlocks from IDT to complete the BCD EOUs.

Tuesday 8/13/13

• Attempted etOH purification of of BBa_K775000 and PRS414 before ligation. Nanodrop results were 1.3 ng/ul and 18 ng/ul respectively.

Thursday 8/15/13

• The 1st supernatants of the failed etOH purification were electrophoresed through a 1% agarose gel.
• The digested BBa_K775000 and linearized PRS414 plasmid were extracted from the gel using the QIAquick gel extraction kit.
• According to nanodrop, 1130.5 total ng of PRS414 and 2145.5 ng of BBa_K775000 were extracted.

Friday 8/16/13

• Ligated K775000 into PRS414, change the ligation mix to 2X.
• Mass of K775000 for insertion is 35.44 ng and the volume is 1.317 ul. Mass of PRS414 for extraction is 20 ng with a volume of 0.746 ul.

Wednesday 8/21/13

• Miniprep(isolate & extract genomic DNA from transformed colonies)of liquid culture to get BBa_B0015
• According to nanodrop, 227.7 ng/ul is extracted