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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 Saturday 7/27/13 54 Monday 7/29/13 55 Tuesday 7/30/13 56 Wednesday 7/31/13 57 Thursday 8/1/13 58 Friday 8/2/13 59 Monday 8/5/13 60 Tuesday 8/6/13 61 Monday 8/12/13 62 Tuesday 8/13/13 63 Thursday 8/15/13 64 Friday 8/16/13 65 Wednesday 8/21/13 66 Thursday 8/22/13 67 Wednesday 8/28/13 68 Tuesday 9/3/13 69 Wednesday 9/4/13 70 Wednesday 9/18/13 71 Monday 9/24/13 72 Wednesday 9/25/13 73 Thursday 9/26/13 74 Friday 9/27/13

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
• Consider heavy metal project and its feasibility

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
• Consider ligands that induce signal transduction pathways in E. coli

Monday 6/10/13

• Read papers about surface sensing and adhesion of E. coli
• Look into pathways that could work with PI3K when binding to ligand

Tuesday 6/11/13

• Made BL21 competent E. coli cells

Wednesday 6/12/13

• Meeting with Dr. Kishmairer about yeast polarization project
• Consider GPCR and beta-arrestin to use to polarize cell when bound to surface

Thursday 6/13/13

• Studied TU Delft’s project about GPCRs in yeast
• Learned about yeast and Ras signaling with yeast

Friday 6/14/13

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

Monday 6/17/13

• Met to discuss how to prevent yeast from shmooing
• Looked into cdc42 and g-proteins to see if can activate cdc42 and use that to localize within the cell

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

• Assess the level of characterization of parts already in the Parts Registry

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
• Interview with Exponent
• Emailed Vivek Mutalik for achieving BCDs and restriction site location

Tuesday 7/2/13

• Meeting with Jill about using the Flow Cytometer in Bindley
• HP meeting with Ryan, Swetha, Betsy and Amanda
• Received plasmids, control strains from Jess Walter for yeast project
• Review RFC[10]

Wednesday 7/3/13

• Team meeting about project
• Communication with other teams

Thursday 7/4/13

• Find BB yeast expression vector

Friday 7/5/13

• Learned Golden Gate Assembly with BB standard
• Choose BCD parts: BCD7,BCD18,BCD22 and BCD23

Monday 7/8/13

• Exec meeting with Amanda, Chris, and Jim to discuss lab work
• Work on protocol for turning Biobricks into BCDs

Tuesday 7/9/13

• Meeting with Rouxi about using the Coulter Counter
• HP meeting with Swetha, Betsy and Amanda
• Research for assemble BCD using RFC[25]

Wednesday 7/10/13

• Meeting with exponent
• Modeling yeast project

Thursday 7/11/13

• Received respond from Vivek Mutalik for scar.

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
• Figured out plasmid details
• Working on Microryze

Wednesday 7/17/13

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

Thursday 7/18/13

• Writed code on data sheet

Friday 7/19/13

• Team meeting for making BCDs with oligos compatible to Golden Gate assembly.

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

• Write letter to Mitch Daniels
• Video tape with staff from ABE department

Wednesday 7/24/13

• Miniprep BCD parts go get better concentration

Thursday 7/25/13

• Transformed Ptrc* and GFP

Friday 7/26/13

• Transformed B0031
• Miniprep Ptrc*

Saturday 7/27/13

• Coding for data sheet

Monday 7/29/13

• Put E.coli with PRS414 into 5ml ampicillin LB to grow up for miniprep
• Modified BCD design
• Modified GOI: MRFP1 to decrease hairpins within synthesis with IDT

Tuesday 7/30/13

• Write Background for BCDs
• Miniprep GFP and PRS414

Wednesday 7/31/13

• SURF presentations
• Transformed B0015 and RFP

Thursday 8/1/13

• Miniprep PRS414 & GFP for Taguchi method

Friday 8/2/13

• Transformed BBa_K775000, BBa_B0037, BBa_B0015

Monday 8/5/13

• Send Boston University a screencast of our "proof-of-concept" code

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

Thursday 8/22/13

• Digested of miniprep of E.coli with BBa_B0075

Wednesday 8/28/13

• Discuss travel plans
• Continue planning pancake breakfast
• Resuspended lyopholized Ptrc*, BCD7,BCD18,BCD22 and BCD23 DNA in 20 ul TE buffer.
• Digest mix for IDT gblocks.

=== Sunday 9/1/13

• Digestion for Ptrc* and BCD7,BCD18,BCD22,BCD23, mistaken using restriction enzyme EcoRI and PstI (should be SpecI)
• Decided to etOH purify to digestions and redo digestion using EcoRI and SpecI
• Ligated the BCDs and Ptrc* cut at EcoRI and PstI with PSB1C3: using 1.83 ul Ptrc*, 13.35 ul for PSB1C3 and 6.74 ul for all BCDs
• etOH purified the ligation

Tuesday 9/3/13

• Digest Mix of BCD7
• Transformed E.coli with the BCD + plasmids (PSB1C3)

Wednesday 9/4/13

• ligation of BCDs, B0075 and PSB1C3

Wednesday 9/18/13

• Distribute different sections within the wiki to write
• Overview of which diagrams will be included on wiki

Monday 9/24/13

• Continue organizing the wiki information

Wednesday 9/25/13

• Golden Gate assembly for all BCDs
• Finalized the presenters at the competition
• Revised the wiki as a team

Thursday 9/26/13

• Performed growth rate assay on BL21, Prtc*, and pSB1C3
• Transformed BCD 7, 13, 22, 23 in E. coli

Friday 9/27/13

• Make final changes on the wiki
• Take entire team photo to display on the team page of the wiki
• Finalize Parts Registry page