Team:DTU-Denmark/Timeline

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{{:Team:DTU-Denmark/Templates/StartPage|Timeline}}
{{:Team:DTU-Denmark/Templates/StartPage|Timeline}}
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==Project Timeline==
==Project Timeline==
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===January===
===January===
-
* 2013-01-15 Budget completed
+
* 2013-01-15 Budget completed.
-
* 2013-01-29 Human Practices: [[Team:DTU-Denmark/High_School_Outreach|Workshop for highschool students]]
+
* 2013-01-29 Human Practices: [[Team:DTU-Denmark/High_School_Outreach|Workshop for highschool students]].
===February===
===February===
-
* 2013-02-25 Project selected: Conversion of ammonia to nitrous oxide in ''E. coli''
+
* 2013-02-25 Project selected: Conversion of ammonia to nitrous oxide in ''E. coli''.
===March===
===March===
-
* 2013-03-11 [[Team:DTU-Denmark/Biobrick_Workshop|Biobrick workshop]] hosted for KU and SDU
+
* 2013-03-11 [[Team:DTU-Denmark/Biobrick_Workshop|Biobrick workshop]] hosted for KU and SDU.
-
* 2013-03-13 Project kickoff meeting with supervisors
+
* 2013-03-13 Project kickoff meeting with supervisors.
===April===
===April===
-
* 2013-04-15 Team contract written and signed
+
* 2013-04-15 Team contract written and signed.
-
* 2013-04-28 Human Practices: Held second [[Team:DTU-Denmark/High_School_Outreach|workshop for highschool students]]
+
* 2013-04-28 Human Practices: Held second [[Team:DTU-Denmark/High_School_Outreach|workshop for highschool students]].
===May===
===May===
-
* 2013-05-29 [[Team:DTU-Denmark/HelloWorld|Hello World]] pilot project kicked off
+
* 2013-05-29 [[Team:DTU-Denmark/HelloWorld|Hello World]] pilot project kicked off.
===June===
===June===
-
* 2013-06-04 Team competency mapping
+
* 2013-06-04 Team competency mapping.
-
* 2013-06-09 Work on wiki started
+
* 2013-06-09 Work on wiki started.
-
* 2013-06-29 Team BBQ
+
* 2013-06-29 Team BBQ.
===July===
===July===
Line 41: Line 39:
'''Week 28'''
'''Week 28'''
-
* Designed, ordered and received primers to extract genes from ''Nitrosomonas'' and ''Pseudomonas''
+
* 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.
* Began work on cloning genes out of ''Nitrosomonas europaea'' and ''Pseudomonas aeruginosa''.  All isolations successful so far except for Nir.
 +
* Held the first hackaton to work on the wiki.
'''Week 29'''
'''Week 29'''
-
* Performed first [[Team:DTU-Denmark/Experiment1a| experiment to investigate the anaerobic stability of nitrite in native ''E. coli'']]
+
* Performed first [[Team:DTU-Denmark/Experiment1a| experiment to investigate the anaerobic stability of nitrite in native ''E. coli'']].
'''Week 30'''
'''Week 30'''
-
* Ordered new primers to extract Nir gene in two pieces.
+
* Ordered new primers to extract Nir gene in two pieces. [[File:Dtu-Mutant2.png|right]].
* 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.  
* 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 [[Team:DTU-Denmark/pBAD_SPL | pBAD synthetic promoter library]] so that we will be able to induce a low level of expression of our periplasmic genes.  
* Began work on [[Team:DTU-Denmark/pBAD_SPL | pBAD synthetic promoter library]] so that we will be able to induce a low level of expression of our periplasmic genes.  
'''Week 31'''
'''Week 31'''
-
* Saturday BBQ with KU
+
* The week no PCR worked -- ran 96 PCRs with varying conditions to debug what is not working.
 +
* Saturday BBQ with KU.
===August===
===August===
'''Week 32'''
'''Week 32'''
-
* The week no PCR worked -- ran 96 PCRs with varying conditions to debug what is not working
+
* Conducted the [[Team:DTU-Denmark/Experiment2|experiment to characterize anaerobic production of N<sub>2</sub>O]] in native ''E. coli''.
-
* Conducted the [[Team:DTU-Denmark/Experiment2|experiment to characterize anaerobic production of N<sub>2</sub>O]] in native ''E. coli''
+
* Began work on [[Team:DTU-Denmark/Kinetic_Model|kinetic models of the aerobic and anaerobic pathways]].
-
* Began work on [[Team:DTU-Denmark/Kinetic_Model|kinetic models of the aerobic and anaerobic pathways]]
+
* Began putting together our presentation.
-
* Began putting together our presentation
+
'''Week 33'''
'''Week 33'''
-
* Began having daily meetings
+
* Began having daily meetings.
-
* Transformed arabinose inducible promoter for use with [[Team:DTU-Denmark/pBAD_SPL|pBAD synthetic promoter library]]
+
* Transformed arabinose inducible promoter for use with [[Team:DTU-Denmark/pBAD_SPL|pBAD synthetic promoter library]].
-
* One Nir fragment has been amplified with USER primers (changed DMSO, Mg, temperature, etc), one to go
+
* Amplified one Nir fragment with USER primers (changed DMSO, Mg, temperature, etc), one left to go.
-
* [[Team:DTU-Denmark/Experiment2|Experiment to characterize anaerobic production of N<sub>2</sub>O]] will be repeated this week
+
* Repeated the [[Team:DTU-Denmark/Experiment2|experiment to characterize anaerobic production of N<sub>2</sub>O]] to try to reproduce results.
 +
* Held the second hackathon.
'''Week 34'''
'''Week 34'''
-
* Decided on final human practices event
+
* Ran first biolector experiment to characterize [[Team:DTU-Denmark/pBAD_SPL|pBAD synthetic promoter library]].
-
* Ran first biolector experiment to characterize [[Team:DTU-Denmark/pBAD_SPL|pBAD synthetic promoter library]]
+
* Completed first draft of presentation.
 +
* Completed first draft of poster.
'''Week 35'''
'''Week 35'''
-
* Attended Scandinavian meetup in Odense hosted by SDU team
+
* Attended Scandinavian meetup in Odense hosted by SDU team.  Thank you SDU for a great weekend!
-
* Biobricks in progress
+
* Conducted another set of biolector experiments to characterize more colonies from the [[Team:DTU-Denmark/pBAD_SPL|pBAD synthetic promoter library]].
-
* Biolector for SPL in progress
+
* Sent [[Team:DTU-Denmark/pBAD_SPL|pBAD SPL]] samples for sequencing.
-
* sequencing for SPL in progress
+
* Conducted [[Team:DTU-Denmark/Experiment4 | experiment to characterize AMO and HAO transformants]].  Found that the AMO transformant is using ammonia faster than a nontransformed ''E. coli'' control! [[File:Dtu-Mutant1.png|right]].
-
* first draft of presentation
+
* Decided on project title: Requiem for a Stream.
-
* first draft of poster
+
* Wrote the project [[Team:DTU-Denmark/Project|abstract]].
-
* measure Nir, AMO, HAO transformants
+
* Reviewed presentation with Julie, who gave us very good advice on pitching our project.
-
* modelling of kinetics and design of a reactor: Vanessa
+
* Completed [[Team:DTU-Denmark/Safety|safety]] form.
-
* Title and abstract finished; Title: Requiem for a Stream
+
-
* Reviewed presentation with Julie, who gave us very good advice on pitching our project
+
-
* measure AMO, HAO transformants complete
+
===September===
===September===
'''Week 36'''
'''Week 36'''
-
* Have biobricks for AMO and cytochromes (are going to sequence these), the others are coming.
+
* Made biobricks for AMO and cytochromes (are going to sequence these), the others are pending.
-
* Running last biolector experiment today
+
* Completed biolector experiments for the [[Team:DTU-Denmark/pBAD_SPL|pBAD synthetic promoter library]].  We have constructed promoters that when induced, show higher activity than the constitutive promoter, and when not induced show very low activity.
-
* sequencing for SPL is in progress
+
* Began constructing a page to describe the [http://parts.igem.org/PBAD_SPL pBAD SPL in the parts registry].
-
* Kristian is working on a page in the parts registry for the parts registry
+
* Began modelling the [[Team:DTU-Denmark/Reactor_Model|design of a reactor using a continuous stirred tank reactor]].
-
* first draft of presentation completed
+
* Began researching physical reactor design.
-
* first draft of poster complete
+
-
* modelling of kinetics and design of a reactor: using Continuous Stirred Tank Reactor
+
-
* Began reactor design -- ask Mikael Rordham in 223 for 2 1L chemostats
+
'''Week 37'''
'''Week 37'''
-
* biobricks -- have 2 that are fine: AMO and cytochromes
+
* Verified biobricks with colony pcr using the sequencing primers.
-
* redo colony pcr with sequencing primers to verify
+
* Human Practices: [[Team:DTU-Denmark/IP_and_Synthetic_Biology| Attended BioPeople event "The Basics and the Best" on IP and patent law]] to discuss the impact of the US Supreme Court ruling on Myriad Genetics on synthetic biology.
-
* 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'''
'''Week 38'''
-
* Filmed "Bricks of Knowledge" video on USER cloning for KU team
+
* Filmed "Bricks of Knowledge" [https://www.youtube.com/watch?v=7EiVttJpXH4 video on USER cloning] for KU team.
-
* Biobricks mailed
+
* Mailed Biobricks! (tat signal peptide, AMO, cytochromes).
-
** tat signal peptide
+
* Conducted [[Team:DTU-Denmark/Bioreactor|Bioreactor experiment]].
-
** 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'''
'''Week 39'''
-
* Hackathon intensive to complete wiki 28th of Sept
+
* Held hackathon to complete wiki.
-
* Nir experiment -- Kasia and Ariadne will do this on Thursday
+
* Conducted [[Team:DTU-Denmark/Experiment2|experiment to characterize Nir transformant]].
-
* Video in progress
+
-
* Reviewed poster v2
+
-
=== October ===
+
===October===
'''Week 40'''
'''Week 40'''
-
* Wiki complete!
+
*Safety forms were approved on September 29, 2013 by the iGEM Safety Committee.
-
 
+
* Completed wiki.
{{:Team:DTU-Denmark/Templates/EndPage}}
{{:Team:DTU-Denmark/Templates/EndPage}}

Latest revision as of 17:49, 4 October 2013

Timeline

Contents

Project Timeline

January

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

May

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.
  • Held the first hackaton to work on the wiki.

Week 29

Week 30

  • Ordered new primers to extract Nir gene in two pieces.
    Dtu-Mutant2.png
    .
  • 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

Week 33

Week 34

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. Found that the AMO transformant is using ammonia faster than a nontransformed E. coli control!
    Dtu-Mutant1.png
    .
  • Decided on project title: Requiem for a Stream.
  • Wrote the project abstract.
  • Reviewed presentation with Julie, who gave us very good advice on pitching our project.
  • Completed safety form.

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. We have constructed promoters that when induced, show higher activity than the constitutive promoter, and when not induced show very low activity.
  • Began constructing a page to describe the [http://parts.igem.org/PBAD_SPL 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

Week 38

Week 39

October

Week 40

  • Safety forms were approved on September 29, 2013 by the iGEM Safety Committee.
  • Completed wiki.

Retrieved from "http://2013.igem.org/Team:DTU-Denmark/Timeline"