Project Timeline

January

• 2013-01-15 Budget completed
• 2013-01-29 Human Practices: Workshop for highschool students

February

• 2013-02-25 Project selected: Conversion of ammonia to nitrous oxide in E. coli

March

• 2013-03-11 Biobrick workshop hosted for KU and SDU
• 2013-03-13 Project kickoff meeting with supervisors

April

• 2013-04-15 Team contract written and signed
• 2013-04-28 Human Practices: Held second workshop for highschool students

May

• 2013-05-29 Hello World pilot project kicked off

June

• 2013-06-04 Team competency mapping
• 2013-06-09 Work on wiki started
• 2013-06-29 Team BBQ

July

Week 27

• Hello World project complete and successful. From a cytoplasmic extraction, we have observed GFP in the periplasm and RFP in the cytoplasm.
• Conducted the toxicity experiment and completed data analysis: average ammonia concentrations in wastewater are not toxic to E. coli.

Week 28

• Designed, ordered and received primers to extract genes from Nitrosomonas and Pseudomonas
• Began work on cloning genes out of Nitrosomonas europaea and Pseudomonas aeruginosa. All isolations successful so far except for Nir.

Week 29

• Performed first experiment to investigate the anaerobic stability of nitrite in native E. coli

Week 30

• Ordered new primers to extract Nir gene in two pieces.
• Despite successful PCR and transformation of AMO, HAO and cytochromes, we only have viable colonies for the cytochromes. Expect that this is due to the fact that we are expressing periplasmic and membrane proteins, which is causing excessive stress on the cells.
• Began work on pBAD synthetic promoter library so that we will be able to induce a low level of expression of our periplasmic genes.

Week 31

• The week no PCR worked -- ran 96 PCRs with varying conditions to debug what is not working
• Saturday BBQ with KU

August

Week 32

• Conducted the experiment to characterize anaerobic production of N₂O in native E. coli
• Began work on kinetic models of the aerobic and anaerobic pathways
• Began putting together our presentation

Week 33

• Began having daily meetings
• Transformed arabinose inducible promoter for use with pBAD synthetic promoter library
• Amplified one Nir fragment with USER primers (changed DMSO, Mg, temperature, etc), one left to go
• Repeated the experiment to characterize anaerobic production of N₂O to try to reproduce results

Week 34

• Ran first biolector experiment to characterize pBAD synthetic promoter library
• Completed first draft of presentation
• Completed first draft of poster

Week 35

• Attended Scandinavian meetup in Odense hosted by SDU team. Thank you SDU for a great weekend!
• Conducted another set of biolector experiments to characterize more colonies from the pBAD synthetic promoter library
• Sent pBAD SPL samples for sequencing
• Conducted experiment to characterize AMO and HAO transformants
• Decided on project title: Reqiuem for a Stream
• Wrote the project abstract
• Reviewed presentation with Julie, who gave us very good advice on pitching our project

September

Week 36

• Made biobricks for AMO and cytochromes (are going to sequence these), the others are pending.
• Completed biolector experiments for the pBAD synthetic promoter library
• Began constructing a page to describe the pBAD SPL in the parts registry
• Began modelling the design of a reactor using a continuous stirred tank reactor
• Began researching physical reactor design

Week 37

• biobricks -- have 2 that are fine: AMO and cytochromes
• redo colony pcr with sequencing primers to verify
• Nir experiment on friday
• Planning for bioreactor experiment
• Human Practices: Attended BioPeople event "The Basics and the Best" on IP and patent law

Week 38

• Filmed "Bricks of Knowledge" video on USER cloning for KU team
• Biobricks mailed
  • tat signal peptide
  • amo
  • cytochromes
• arabinose promoter biobrick not made -- Kristian and Henrike will make this in the next few days
• Bioreactor experiment started this morning, will finish at 10pm tonight.

Week 39

• Hackathon intensive to complete wiki 28th of Sept
• Nir experiment -- Kasia and Ariadne will do this on Thursday
• Video in progress
• Reviewed poster v2

October

Week 40

• Wiki complete!