Difference between revisions of "IGEM:Harvard/2006/Cyanobacteria"

From OpenWetWare
Jump to: navigation, search
(Presentations)
(Presentations)
 
Line 89: Line 89:
 
*[[:Image:Cyano presentation.ppt | Jamboree presentation]] (in progress)
 
*[[:Image:Cyano presentation.ppt | Jamboree presentation]] (in progress)
 
**[[:Image:Cyano_presentation_script.doc|Script]] (in progress)
 
**[[:Image:Cyano_presentation_script.doc|Script]] (in progress)
*[[:Media:Cyano poster.ppt | Cyano poster]] (in progress)
+
*[[:Image:Cyano poster.ppt | Cyano poster]] (in progress)
  
 
==Team Members==
 
==Team Members==

Latest revision as of 03:28, 3 November 2006

<html><style type='text/css'> .tabs {

 font-size:80%;
 font-weight:none;
 width: 100%;
 color: #FFFFFF;
 background:#FFFFFF url("/images/5/54/DarkgreenTab-bg.gif") repeat-x bottom;

}

.tabs li {

 background:url("/images/3/36/DarkgeenTab-left.gif") no-repeat left top;

}

.tabs a,.tabs strong {

 background:url("/images/d/d3/DarkgreenTab-right.gif") no-repeat right top;
 color:#FFFFFF;
 padding: 3px 10px 3px 4px;

}

.tabs strong{

 color:#CCFF00;
 background-image:url("/images/b/b1/DarkgreenTab-right_on.gif");

}

.tabs a:hover{

 color:#66FF00;

}


</style></html>


Introduction

Welcome to the lab notebook for the Cyanobacteria oscillator 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:

  1. 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.
  2. 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.

For more background information on the ciracadian system, please check out our "Literature" section. Otherwise, day-to-day work can be found under the "Lab Notebook" tab; we will post major results of our work and links to the days as they become available. If you have questions or comments, feel free to contact us: information is located at the main Harvard iGEM 2006 page. Thanks!


Sincerely,
Zhipeng, Hetmann, Dave, and Jeff


Update 10/27/06: We believe we can express the three proteins into e. coli, and that there is interaction between A+C and possible interaction between B+C. See the Lab Notebook for more information.

102706 cyanoresult.jpg

Outline of Findings and Signifigant Dates

  • 07/05/06: The incubator for growing up our cyanobacteria is complete; we have cultures growing! Link
  • 07/10/06: Some computer modeling has been done to see the effect of multiple unsyncronized clocks on phosphorylation state output. Link
  • 07/21/06: Upon having trouble with site-specific mutagenesis on the KaiA and KaiBC operons from the cyanobacterial genome, we have decided to pursue synthesis of the constructs in parallel with continued extraction attempts. Link
  • 08/01/06: Preliminary success with site-specific mutagenesis. Link
  • 08/05/06: Promoter leakness tests come out negative. May have to use low-copy plasmids if we want good control of protein expression in Top10F. Link
  • 08/11/06: We are moving to the synthetic KaiA, KaiB, and KaiC for future work. Link
  • 08/30/06: We successfully made the first construct, Lac+RBS+KaiC. Link
  • 09/01/06: Using the newly developed ligation protocol, we have successfully repeated Lac+RBS+KaiC from 08/30/06 and made Lac+RBS+KaiA. Link
  • 10/21/06: Successfully made Lac+RBS+KaiB and Lac+RBS+KaiA+Lac+RBS+KaiC. Link
  • 10/24/06: Successfully made Lac+RBS+KaiB+Lac+RBS+KaiC. Link
  • 10/25/06: Constructs for Stage I have been completed; ready to move to Stage I of Western Blotting, to verify expression of KaiC and interaction of KaiA and KaiB with KaiC. Link
  • 10/27/06: Preliminary data indicates that the Kai proteins are being expressed in e. coli and that there is interaction between the three proteins! Link

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


Agenda

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

Long-term project outline

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

10 December 2017

     23:07 

Lee:Lab Members‎‎ (2 changes | history) . . (+223). . [Wooin Lee‎ (2×)]

     

23:07

(cur | prev) . . (+106). . Wooin Lee (talk | contribs) (Graduate students)

     

23:03

(cur | prev) . . (+117). . Wooin Lee (talk | contribs) (Alumni)

     21:55 

Yeo lab:Lab Members‎‎ (2 changes | history) . . (+156). . [Yoonyeo‎ (2×)]

     

21:55

(cur | prev) . . (+82). . Yoonyeo (talk | contribs) (Lab photo archive)

     

21:24

(cur | prev) . . (+74). . Yoonyeo (talk | contribs) (Lab photo archive)

     21:24 

User:Rollinsr‎‎ (5 changes | history) . . (+875). . [Rollinsr‎ (5×)]

     

21:24

(cur | prev) . . (+25). . Rollinsr (talk | contribs) (SHERLOCK)

     

21:22

(cur | prev) . . (0). . Rollinsr (talk | contribs) (SHERLOCK)

     

21:22

(cur | prev) . . (+829). . Rollinsr (talk | contribs) (SHERLOCK)

     

16:29

(cur | prev) . . (+7). . Rollinsr (talk | contribs) (Rick Rollins Discussion Page)

     

16:28

(cur | prev) . . (+14). . Rollinsr (talk | contribs) (Rick Rollins Discussion Page)

 m   20:59 

Pea Database Collaboration Project‎‎ (11 changes | history) . . (+570). . [Andrew Barney‎ (11×)]

 m   

20:59

(cur | prev) . . (-31). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

 m   

20:54

(cur | prev) . . (+53). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

 m   

14:10

(cur | prev) . . (+51). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

 m   

13:20

(cur | prev) . . (+140). . Andrew Barney (talk | contribs)

 m   

09:52

(cur | prev) . . (+39). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

 m   

09:51

(cur | prev) . . (+114). . Andrew Barney (talk | contribs)

 m   

09:45

(cur | prev) . . (+1). . Andrew Barney (talk | contribs)

 m   

09:45

(cur | prev) . . (+100). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

 m   

08:46

(cur | prev) . . (-1). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

 m   

08:45

(cur | prev) . . (+52). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

 m   

08:24

(cur | prev) . . (+52). . Andrew Barney (talk | contribs) (Pea Varieties By Phenotype)

N    20:58 

Pea Database Collaboration Project/Mighty Midget‎‎ (3 changes | history) . . (+663). . [Andrew Barney‎ (3×)]

 m   

20:58

(cur | prev) . . (+84). . Andrew Barney (talk | contribs) (Mighty Midget)

 m   

20:57

(cur | prev) . . (+6). . Andrew Barney (talk | contribs)

N    

20:56

(cur | prev) . . (+573). . Andrew Barney (talk | contribs) (Created page with "==Mighty Midget== UDSA GRIN:PI 635173 Pisum sativum L. 'MIGHTY MIDGET' Donated from: Minnesota United States Maintained by: Western Regional PI Station NPGS received: 01-...")

     17:41  Helab:Publications‎ (diff | hist) . . (+21). . Xiaoming He (talk | contribs)

N    14:28 

Pea Database Collaboration Project/Golden Sweet‎‎ (8 changes | history) . . (+693). . [Andrew Barney‎ (8×)]

 m   

14:28

(cur | prev) . . (+11). . Andrew Barney (talk | contribs)

 m   

14:27

(cur | prev) . . (+5). . Andrew Barney (talk | contribs) (Tendrils)

 m   

14:27

(cur | prev) . . (+15). . Andrew Barney (talk | contribs) (Pods)

 m   

14:25

(cur | prev) . . (+24). . Andrew Barney (talk | contribs)

 m   

14:22

(cur | prev) . . (+158). . Andrew Barney (talk | contribs)

 m   

08:35

(cur | prev) . . (-41). . Andrew Barney (talk | contribs) (Golden Sweet)

 m   

08:33

(cur | prev) . . (+451). . Andrew Barney (talk | contribs)

N    

08:29

(cur | prev) . . (+70). . Andrew Barney (talk | contribs) (Created page with "File:Golden Sweet.jpg File:Golden Sweet Seeds Søren Holt.jpg")

     14:20 

(Upload log). .

[Andrew Barney‎ (9×)]

     

14:20

. . Andrew Barney (talk | contribs) uploaded File:Golden Sweet pod3.jpg(Golden Sweet Pod(s). Photo by Andrew Barney.)

     

14:18

. . Andrew Barney (talk | contribs) uploaded File:Golden Sweet pod2.jpg(Golden Sweet Pod(s). Photo by Andrew Barney.)

     

14:16

. . Andrew Barney (talk | contribs) uploaded File:Golden Sweet pod1.jpg(Golden Sweet Pod(s). Photo by Andrew Barney.)

     

14:14

. . Andrew Barney (talk | contribs) uploaded File:Golden Sweet Tendril.jpg(Yellow Tendril of Golden Sweet / Golden Podded Pea. Photo by Andrew Barney.)

     

14:05

. . Andrew Barney (talk | contribs) uploaded File:Jonis-taxi.jpg(Joni's Taxi Pea Pod. Large Yellow. Photo by Greg Muller, Useful Seeds, Bendigo, Australia.)

     

14:00

. . Andrew Barney (talk | contribs) uploaded File:Ossi header small.jpg(OSSI Open Source Seed Initiative Logo small)

     

13:59

. . Andrew Barney (talk | contribs) uploaded File:Ossi header.png(OSSI Open Source Seed Initiative Logo)

     

08:28

. . Andrew Barney (talk | contribs) uploaded File:Golden Sweet Seeds Søren Holt.jpg(Golden Sweet Pea Seeds. Photo by Søren Holt.)

     

08:25

. . Andrew Barney (talk | contribs) uploaded File:Golden Sweet.jpg(Seeds of Golden Sweet Pea. Pisum Sativum. Photo by Rebsie Fairholm.)

N    14:09 

Pea Database Collaboration Project/Joni's Taxi‎‎ (7 changes | history) . . (+1,426). . [Andrew Barney‎ (7×)]

 m   

14:09

(cur | prev) . . (+23). . Andrew Barney (talk | contribs) (Description)

 m   

14:08

(cur | prev) . . (+38). . Andrew Barney (talk | contribs)

 m   

14:07

(cur | prev) . . (+102). . Andrew Barney (talk | contribs)

 m   

14:01

(cur | prev) . . (+32). . Andrew Barney (talk | contribs) (Description)

 m   

13:56

(cur | prev) . . (+572). . Andrew Barney (talk | contribs) (Information)

 m   

13:24

(cur | prev) . . (+17). . Andrew Barney (talk | contribs)

N    

13:23

(cur | prev) . . (+642). . Andrew Barney (talk | contribs) (Created page with "'''*Crop:''' Snow Pea '''*Latin name:''' Pisum sativum '''*Plant Breeder:''' Greg Muller, Useful Seeds, Bendigo, Australia '''*Known Supplier(s):''' Useful Seeds '''*Date Ple...")

     10:01  Pecinka lab:Group meeting‎ (diff | hist) . . (-35). . Fen Yang (talk | contribs) (date - agenda - speaker)
     09:17  User:Raul Montanez‎ (diff | hist) . . (+29). . Raul Montanez (talk | contribs) (Research Interests)