BU06:Team A

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{{BU06}}
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back to the [[:Category: Boston University 2006|BU iGEM main page]]
back to the [[:Category: Boston University 2006|BU iGEM main page]]
[[Category: Boston University 2006| Team A]]
[[Category: Boston University 2006| Team A]]
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== Members ==
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== '''Members''' ==
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{| width="600"
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|- style="background:#E1E1E1;"
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| <font face="century gothic">'''Mac Cowell'''
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| <font face="century gothic">[mailto:macowell@bu.edu macowell@bu.edu]   
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| <font face="century gothic"> aim: cxmac2
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|-
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| <font face="century gothic">'''Christine Woods'''
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| <font face="century gothic">[mailto:cwoods@bu.edu cwoods@bu.edu]
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| <font face="century gothic">aim: xoptopinope
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|
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|- style="background:#E1E1E1;"
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| <font face="century gothic">'''Nancy Mendonca Davis'''
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| <font face="century gothic">[mailto:nancymd@bu.edu nancymd@bu.edu]
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| <font face="century gothic">
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|-
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| <font face="century gothic">'''Nadav Ivzan'''
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| <font face="century gothic">[mailto:nivzan@bu.edu nivzan@bu.edu]
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| <font face="century gothic">aim:kingos82 msn:kingos19@hotmail.com
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|}
== Meeting Schedule ==
== Meeting Schedule ==
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Next meeting:
== Current Progress ==
== Current Progress ==
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===Making ''E. coli'' Glow===
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===Photosystem parts===
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'''Preliminary Design: ''-Light Sensing Inhibitor- -> -Light emission device-'' '''
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''Light Sensing Inhibitor:''  
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* [http://partsregistry.org/Part:BBa_I15008 BBa_I15008] (well: 21A  plate: iGEM2006 DNA-2)
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* [http://partsregistry.org/Part:BBa_I15009 BBa_I15009] (well: 21C  plate: iGEM2006 DNA-2)
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* [http://partsregistry.org/Part:BBa_I15010 BBa_I15010] (Note: Must be used in E.coli deficient in natural EnvZ.  Also, not in 2006 iGEM dna distribution)
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* [http://partsregistry.org/Part:BBa_R0082 BBa_R0082] (well: 15P  plate: iGEM2006 DNA-1)
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''Light Sensing Inihibitor:'' [http://partsregistry.org/Part:BBa_I15008 BBa_I15008] , [http://partsregistry.org/Part:BBa_I15009 BBa_I15009] , [http://partsregistry.org/Part:BBa_I15010 BBa_I15010] , [http://partsregistry.org/Part:BBa_R0082 BBa_R0082]
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'''[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=BU BU's temporary parts]'''
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''Light Emission Device:'' (from lux [http://en.wikipedia.org/wiki/Operon operon]) THIS IS WHAT WE NEED TO DO. [[Lux_operon| Lux Operon]]
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===Assembly of parts===
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* [[Biobrick delivery]] - overview of the the 2006 iGEM DNA distribution plates.
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Point Mutation: Lamda Red - Datsenko, Wanner... or by PCR: look for protocol on OpenWetWare\
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* [http://partsregistry.org/Help:How_to_make_agar Color-codes] that indicate the corresponding biobrick's antibiotic resistance. (Each brick has a certain antibiotic resistance. Biobricks stored in Plate 1 are all Ampicilin resistant.  Those in Plate 2 have a color-code).
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Codon Usage Bias Database: http://www.kazusa.or.jp/codon/
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* [http://openwetware.org/wiki/BioBricks_construction_tutorial biobrick construction tutoral] and related protocols.
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** [http://openwetware.org/wiki/Silver:_BB_Strategy Summary] of biobrick construction from the Silver lab.
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** [http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly 3A assembly] is an interesting alternative that avoids the gel purification step.
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Light Sensor Parts: http://partsregistry.org/Featured_Parts:Light_Sensor and paper : http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html (this paper simply explains how the device works!)
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==Questions==
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It seems to repress gene expression by having red light inhibit phosphorylation which would activate a promoter. We would replace the LacZ protein coding region with our lux [http://en.wikipedia.org/wiki/Operon operon].  
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* What strain of e. coli should we use?  How do we make those cells competent? 
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Part: BBa_F1610 codes for LuxI, should we need it...
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* How do we find out which antibiotic a particular DNA on Plate 2 is resistant to?  The [[Biobrick delivery|Biobrick Delivery instructions]] say that we should use the [http://partsregistry.org/cgi/assembly/libraries.cgi?id=6 Registry Repository] to find out, but it doens't seem to list each part's antibiotic resistance on there.
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** The bottom of each well is [http://partsregistry.org/Help:How_to_make_agar color-coded] to indicate the antibiotic resistance.
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* How do we obtain part I15010?
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**  Email Meagan at the registry (meaganl AT mit DOT edu) and copy James Brown (jrb62 AT cam.ac.uk)
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== References ==
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* How do we obtain EnvZ- e. coli?
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**  Ask frank - he seems to know. 
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=== Techniques ===
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* Who knows what we can buy now and what general lab supplies are available for our use?
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<br><br>
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=== Protocols ===
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==Protocols==
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== References ==
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* [http://openwetware.org/wiki/Synthetic_Biology:BioBricks Synthetic_Biology:BioBricks] TONS of overlooked info & protocols on OWW.
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* The [http://partsregistry.org/cgi/assembly/libraries.cgi index] of the 384-well plates.
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* The [http://partsregistry.org/Featured_Parts:Light_Sensor Light Sensing System].
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* [http://openwetware.org/wiki/Protocols Protocols]
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* [http://partsregistry.org/Part:BBa_M30109 Reference Part M30109]
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* Bacterial Photography [http://openwetware.org/wiki/BE.109:Systems_engineering/Basic_bacterial_photography:_black_and_white Lab] w/M30109 part.
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* [http://www.hamline.edu/depts/biology/courses/biocon2/luxback.html Background] on the lux operon
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* [http://encyclopedia.laborlawtalk.com/bioluminescence Bioluminescence. Interesting.]

Latest revision as of 01:31, 31 July 2006

BU06.jpg
Schedule Research Fundraising Resources Members Contact
Team Goal: Photography System Assembly and Testing


back to the BU iGEM main page

Contents

Members

Mac Cowell macowell@bu.edu aim: cxmac2
Christine Woods cwoods@bu.edu aim: xoptopinope
Nancy Mendonca Davis nancymd@bu.edu
Nadav Ivzan nivzan@bu.edu aim:kingos82 msn:kingos19@hotmail.com

Meeting Schedule

Next meeting:

Current Progress

Photosystem parts

Light Sensing Inhibitor:

  • [http://partsregistry.org/Part:BBa_I15008 BBa_I15008] (well: 21A plate: iGEM2006 DNA-2)
  • [http://partsregistry.org/Part:BBa_I15009 BBa_I15009] (well: 21C plate: iGEM2006 DNA-2)
  • [http://partsregistry.org/Part:BBa_I15010 BBa_I15010] (Note: Must be used in E.coli deficient in natural EnvZ. Also, not in 2006 iGEM dna distribution)
  • [http://partsregistry.org/Part:BBa_R0082 BBa_R0082] (well: 15P plate: iGEM2006 DNA-1)

[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=BU BU's temporary parts]

Assembly of parts

  • [http://partsregistry.org/Help:How_to_make_agar Color-codes] that indicate the corresponding biobrick's antibiotic resistance. (Each brick has a certain antibiotic resistance. Biobricks stored in Plate 1 are all Ampicilin resistant. Those in Plate 2 have a color-code).
  • [http://openwetware.org/wiki/BioBricks_construction_tutorial biobrick construction tutoral] and related protocols.
    • [http://openwetware.org/wiki/Silver:_BB_Strategy Summary] of biobrick construction from the Silver lab.
    • [http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly 3A assembly] is an interesting alternative that avoids the gel purification step.

Questions

  • What strain of e. coli should we use? How do we make those cells competent?
  • How do we find out which antibiotic a particular DNA on Plate 2 is resistant to? The Biobrick Delivery instructions say that we should use the [http://partsregistry.org/cgi/assembly/libraries.cgi?id=6 Registry Repository] to find out, but it doens't seem to list each part's antibiotic resistance on there.
    • The bottom of each well is [http://partsregistry.org/Help:How_to_make_agar color-coded] to indicate the antibiotic resistance.
  • How do we obtain part I15010?
    • Email Meagan at the registry (meaganl AT mit DOT edu) and copy James Brown (jrb62 AT cam.ac.uk)
  • How do we obtain EnvZ- e. coli?
    • Ask frank - he seems to know.
  • Who knows what we can buy now and what general lab supplies are available for our use?

Protocols

References

  • [http://openwetware.org/wiki/Synthetic_Biology:BioBricks Synthetic_Biology:BioBricks] TONS of overlooked info & protocols on OWW.
  • The [http://partsregistry.org/cgi/assembly/libraries.cgi index] of the 384-well plates.
  • The [http://partsregistry.org/Featured_Parts:Light_Sensor Light Sensing System].
  • [http://openwetware.org/wiki/Protocols Protocols]
  • [http://partsregistry.org/Part:BBa_M30109 Reference Part M30109]
  • Bacterial Photography [http://openwetware.org/wiki/BE.109:Systems_engineering/Basic_bacterial_photography:_black_and_white Lab] w/M30109 part.
  • [http://www.hamline.edu/depts/biology/courses/biocon2/luxback.html Background] on the lux operon
  • [http://encyclopedia.laborlawtalk.com/bioluminescence Bioluminescence. Interesting.]

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