IGEM:Harvard/2006/Cyanobacteria

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Introduction

Welcome to the lab notebook for the Cyanobacteria project! The goal of our team, composed of four members, is to reconstruct the cyanobacterial circadian oscillator system into E. coli. Three proteins, KaiA, B, and C, have been shown to have an in-vitro phosphorylation state oscillation (Nakajima et al. 2005) by transcriptional-translational independent methods. If this system can be reconstituted in E. coli, there are two important applications:

    • Synthetic Biology: Creating a functional, oscillating set of proteins is the next logical step from the synthetic "repressilator" system engineered by Elowitz et al. (2000). Although a good proof of concept, the "repressilator" lacks the stability needed from a robust oscillator such as the naturally evolved cyanobacterial oscillator. This robust oscillator could prove useful in an eventual biocircuit.
    • Circadian Biology: Cyanobacteria are the simplest model organisms for the study of circadian oscillation. Although circadian oscillation has been fairly well characterized, less is understood at the molecular level. By porting the oscillation system into E. coli, one can begin to understand more precisely the pathways involved in the genomic oscillation of cyanobacteria.

Construct Planning

Constructs we plan to create.


Lengths

From VF2 to VR (BioBrick primers):

  • KaiA + J04500: 1406 bp
  • KaiB + J04500: 859 bp
  • KaiC + J04500: 2110 bp

Synthesis

Synthesis

Agenda

See image at right for our long-term project outline.

Long-term project outline

Click here for our current agenda

Kai Gene sizes

  • KaiA size: 855bp
    • 903bp with BioBrick ends
  • KaiB: 309bp
    • 357bp with BioBrick ends
  • KaiC: 1560bp

BioBricks Used

  • <bbpart>BBa_J04450</bbpart>
    • RFP device
    • Insert size: 1069bp
    • [pSB1A2]
      • High-copy, AmpR
      • Size: 2079bp
  • <bbpart>BBa_J04500</bbpart>
    • Lac promoter + RBS
    • Insert size: 220bp
    • [pSB1AK3]
      • High-copy, AmpR, KanR
      • Insert size: 3189bp
  • [pSB4A3]
    • Low-copy, AmpR
    • Insert size: 3339 bp
  • <bbpart>BBa_R0010</bbpart> + <bbpart>BBa_E0241</bbpart>
    • GFP device
    • Insert size: 995 bp

Presentations

Team Members

Recent Changes

18 June 2018

     16:40 

Hoatlin:BMB seminar series 2017-2018‎‎ (3 changes | history) . . (+51). . [Maureen E. Hoatlin‎ (⧼ntimes⧽)]

     

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(cur | prev) . . (-2). . Maureen E. Hoatlin (talk | contribs) (Seminar Series Planning 2018-2019)

     

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(cur | prev) . . (+3). . Maureen E. Hoatlin (talk | contribs) (Seminar Series Planning 2018-2019)

     

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(cur | prev) . . (+50). . Maureen E. Hoatlin (talk | contribs) (Seminar Series Planning 2018-2019)

     09:05  McClean:LabMtgSchedule‎ (diff | hist) . . (+518). . Megan N McClean (talk | contribs)
     05:36  Lauffenburger:Brian Joughin‎ (diff | hist) . . (+55). . Bjoughin (talk | contribs) (Publications)

     05:32 

User:Etienne Robillard/Notebook/Research‎‎ (4 changes | history) . . (+976). . [Etienne Robillard‎ (⧼ntimes⧽)]

     

05:32

(cur | prev) . . (+208). . Etienne Robillard (talk | contribs)

     

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(cur | prev) . . (+719). . Etienne Robillard (talk | contribs) (sync page with master server)

     

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(cur | prev) . . (+26). . Etienne Robillard (talk | contribs) (minor update)

     

05:10

(cur | prev) . . (+23). . Etienne Robillard (talk | contribs)

 m   01:49  Forster Lab‎ (diff | hist) . . (+186). . Anthony C. Forster (talk | contribs) (new publications)
     00:44  Pecreaux‎ (diff | hist) . . (+7). . Jacques Pecreaux (talk | contribs)

17 June 2018

     23:31 

Pecreaux‎‎ (2 changes | history) . . (+115). . [Jacques Pecreaux‎ (⧼ntimes⧽)]

     

23:31

(cur | prev) . . (+45). . Jacques Pecreaux (talk | contribs) (News!)

     

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(cur | prev) . . (+70). . Jacques Pecreaux (talk | contribs) (News!)

     23:31 

(Upload log). .

[Jacques Pecreaux‎ (⧼ntimes⧽)]

     

23:31

. . Jacques Pecreaux (talk | contribs) uploaded File:Master LC 2018-2019 dynamique-mécanique-fuseau+.pdf

     

23:25

. . Jacques Pecreaux (talk | contribs) uploaded File:Stage microtubules CeDRE master2018-2019 FR.pdf

     18:38  OpenSourceTB‎ (diff | hist) . . (-905). . Matthew Todd (talk | contribs)
     18:03  OpenSourceTB:Compound Series‎ (diff | hist) . . (+94). . Matthew Todd (talk | contribs)

     18:02 

OpenSourceTB:OSTB Series 1‎‎ (6 changes | history) . . (-2,153). . [Matthew Todd‎ (⧼ntimes⧽)]

     

18:02

(cur | prev) . . (-209). . Matthew Todd (talk | contribs) (Data for this Page)

     

18:01

(cur | prev) . . (-231). . Matthew Todd (talk | contribs) (Preliminary Work on the Series Outside GSK)

     

17:58

(cur | prev) . . (-87). . Matthew Todd (talk | contribs) (Other Sources of These, or Similar, Compounds)

     

17:57

(cur | prev) . . (-461). . Matthew Todd (talk | contribs) (Project 3)

     

17:52

(cur | prev) . . (-730). . Matthew Todd (talk | contribs) (Project 1)

     

17:47

(cur | prev) . . (-435). . Matthew Todd (talk | contribs) (Project 2)

15 June 2018

     16:52  User:Gareth Trubl‎ (diff | hist) . . (+66). . Gtrubl (talk | contribs)

N    13:44 

The Essential Unknowns/Set Theories‎‎ (3 changes | history) . . (+149). . [Koeng‎ (⧼ntimes⧽)]

     

13:44

(cur | prev) . . (-19). . Koeng (talk | contribs)

     

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(cur | prev) . . (+79). . Koeng (talk | contribs)

N    

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(cur | prev) . . (+89). . Koeng (talk | contribs) (Created page with "A placeholder for thoughts and framing of how to figure out what the essential genes are.")

     13:35 

The Essential Unknowns‎‎ (10 changes | history) . . (+137). . [Koeng‎ (⧼ntimes⧽)]

     

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(cur | prev) . . (-1). . Koeng (talk | contribs) (How to participate)

     

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(cur | prev) . . (+83). . Koeng (talk | contribs)

     

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(cur | prev) . . (-55). . Koeng (talk | contribs)

     

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(cur | prev) . . (-41). . Koeng (talk | contribs)

     

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(cur | prev) . . (+44). . Koeng (talk | contribs)

     

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(cur | prev) . . (+26). . Koeng (talk | contribs)

     

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(cur | prev) . . (+81). . Koeng (talk | contribs)

     

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(cur | prev) . . (+353). . Koeng (talk | contribs)

     12:57 (Upload log) . . Koeng (talk | contribs) uploaded File:JCVI-syn3-cells.jpg(A picture of the JCVI syn3 cell line)
     07:57  Hoatlin:BMB seminar series 2017-2018‎ (diff | hist) . . (+50). . Millejef (talk | contribs)

14 June 2018

     19:47  X-Lab‎ (diff | hist) . . (+80). . ChanEngr (talk | contribs)

N    17:57 

The Essential Unknowns‎‎ (4 changes | history) . . (+445). . [Koeng‎ (⧼ntimes⧽)]

     

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(cur | prev) . . (-1,217). . Koeng (talk | contribs)

     

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(cur | prev) . . (+1,395). . Koeng (talk | contribs)

     

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(cur | prev) . . (+81). . Koeng (talk | contribs)

N    

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(cur | prev) . . (+186). . Koeng (talk | contribs) (Created page with "This is a placeholder for The Essential Unknowns wiki project. ==Background== [https://example.com The Essential gene set and the Minimal organism?]<br> [https://example.co...")

 m   16:51  User:Korey Griffin‎ (diff | hist) . . (+272). . Korey Griffin (talk | contribs)
     16:37 (User creation log) . . User account Millejef (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     13:24 

User:JernejTurnsek‎‎ (3 changes | history) . . (+142). . [Jernej Turnsek‎ (⧼ntimes⧽)]

     

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(cur | prev) . . (+127). . Jernej Turnsek (talk | contribs) (Resources)

     

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(cur | prev) . . (-2). . Jernej Turnsek (talk | contribs)

     

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(cur | prev) . . (+17). . Jernej Turnsek (talk | contribs)