IGEM:Berkeley/2010

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Current revision (15:29, 2 December 2010) (view source)
 
(21 intermediate revisions not shown.)
Line 4: Line 4:
<div id="about">
<div id="about">
{|
{|
-
| rowspan=2 | [[Image:berkeleyCampanile01.jpg|left|200px]]'''Project Name'''
+
| rowspan=2 | [[Image:berkeleyCampanile01.jpg|left|200px]]'''Choa Choa's Delivery Service'''
-
Project Summary  <br>  
+
   
 +
The ability to manipulate the DNA of an organism is vital to many modern fields of biology. While we have perfected this in common research species such as E. coli, yeast and mouse cells, it is still impossible to transform many other species researchers study. Our project is an attempt to develop transgenics ) techniques for a family of single celled organisms called choanoflagellates. These species are interesting to researchers because they are the closest living relative to our microbial ancestor that became the first multicellular animal. Nicole King, here at UC Berkeley, and other researchers across the globe who study these little creatures are hindered by the inability to genetically manipulate them.
 +
The Berkeley iGEM 2010 team is applying synthetic biology to this problem. We are engineering bacteria that can deliver DNA into the choano. Choanos are predatory, which makes our job a bit simpler. Once our bacteria is engulfed by the choano, it is programmed to burst using a self-lysis device. Proteins we have placed inside the bacteria will then go into action. First, we have designed a vacuole-buster device that will burst the small food membrane holding the bacteria inside the choano, spewing the contents into the cytoplasm of the cell. In the cytoplasm, a transposon/transposase device tagged with a nuclear localization device will move to the nucleus. In the nucleus, the transposase will splice the transposon into the choanoflagellate DNA.
|-
|-
Line 26: Line 28:
[http://openwetware.org/wiki/User:Amy_N._Kristofferson Amy Kristofferson] <br>
[http://openwetware.org/wiki/User:Amy_N._Kristofferson Amy Kristofferson] <br>
[[Conor McClune]] <br>
[[Conor McClune]] <br>
-
[[Tahoura]] <br>
+
[http://openwetware.org/wiki/User:Tahoura_Samad Tahoura Samad] <br>
[http://openwetware.org/wiki/User:Daniela_Mehech Daniela] <br>
[http://openwetware.org/wiki/User:Daniela_Mehech Daniela] <br>
[http://openwetware.org/wiki/User:Christoph_Neyer Christoph Neyer] <br>
[http://openwetware.org/wiki/User:Christoph_Neyer Christoph Neyer] <br>
Line 40: Line 42:
[[Chris Anderson]] <br>
[[Chris Anderson]] <br>
[http://www.openwetware.org/wiki/PP_-_Terry Terry Johnson] <br>
[http://www.openwetware.org/wiki/PP_-_Terry Terry Johnson] <br>
 +
[[Image:Ladder pic.png]]
Line 52: Line 55:
<!-- END TOOLS HEADER with edit link-->
<!-- END TOOLS HEADER with edit link-->
-
[[Berk2010 | Lab calendar]]
+
 
 +
'''Extremely Important Material'''<br>
 +
[[Quotes]] <br>
 +
[[Nicknames]] <br>
 +
 
'''Lab Notebooks'''
'''Lab Notebooks'''
Line 63: Line 70:
[[Berk2010-Christoph | Christoph]]<br>
[[Berk2010-Christoph | Christoph]]<br>
[[Berk2010-Tim | Tim]]<br>
[[Berk2010-Tim | Tim]]<br>
 +
 +
'''The Details'''  
'''The Details'''  
-
[[Berk2010-Oligos | Oligonucleotides]]<br>
+
[https://spreadsheets1.google.com/ccc?key=tCL7NVstt-4T_wcRbwe-kWg&hl=en#gid=8 Oligonucleotides]<br>
[[Berk2010-Gel Pictures | Gel Pictures]]<br>
[[Berk2010-Gel Pictures | Gel Pictures]]<br>
[[Berk2010-Sequencing | Sequencing]]<br>
[[Berk2010-Sequencing | Sequencing]]<br>
[[Berk2010-Constructs | Construction Files]]<br>
[[Berk2010-Constructs | Construction Files]]<br>
-
[[Berk2010-StockBoxes | -80 Stocks]]<br>
+
[https://spreadsheets1.google.com/ccc?key=tCL7NVstt-4T_wcRbwe-kWg&hl=en#gid=13 -80 Stocks]<br>
[[Berk2010-Assembly | Assembly Trees]]<br>
[[Berk2010-Assembly | Assembly Trees]]<br>
[[Berk2010-New Composite Parts | New Composite Parts]]<br>
[[Berk2010-New Composite Parts | New Composite Parts]]<br>
-
 
+
[[Berk2010-Robot CSV Files | Robot CSV Files]]<br>
-
 
+
Line 94: Line 102:
[[Template:SBB-Protocols_Enz1 | EcoRI/BamHI Digest of Wobble Products]]<br>
[[Template:SBB-Protocols_Enz1 | EcoRI/BamHI Digest of Wobble Products]]<br>
[[Template:SBB-Protocols_Enz2 | EcoRI/BamHI Digest of PCR Products]]<br>
[[Template:SBB-Protocols_Enz2 | EcoRI/BamHI Digest of PCR Products]]<br>
 +
[[Manual 2ab Assembly Digest]] <br>
[[Template:SBB-Protocols_Enz3 | BglII Digest of EIPCR Products]]<br>
[[Template:SBB-Protocols_Enz3 | BglII Digest of EIPCR Products]]<br>
[[Template:SBB-Protocols_Enz4 | Ligation of EcoRI/BamHI digests]]<br>
[[Template:SBB-Protocols_Enz4 | Ligation of EcoRI/BamHI digests]]<br>
Line 104: Line 113:
[[Template:SBB-Protocols_Micro3 | Miniprep purification of DNA]]<br>
[[Template:SBB-Protocols_Micro3 | Miniprep purification of DNA]]<br>
[[Template:SBB-Protocols_Micro4 | Macherey-Nagel Miniprep]]<br>
[[Template:SBB-Protocols_Micro4 | Macherey-Nagel Miniprep]]<br>
 +
[[Template:8-Strip Machery Nagel Miniprep | 8-Strip Machery Nagel Miniprep]] <br>
 +
[[Genomic Miniprep]]<br>
[[-80 Glycerol Stocks]]<br>
[[-80 Glycerol Stocks]]<br>
[[Making Competent Cells]]<br>
[[Making Competent Cells]]<br>
 +
[[Small Scale Electrocompetent Prep-Generic ]]<br>
''Other''<br>
''Other''<br>
Line 113: Line 125:
[[Template:SBB-Protocols_SmallScaleCompetent | Small Scale Competent Cell Transformation]]<br>
[[Template:SBB-Protocols_SmallScaleCompetent | Small Scale Competent Cell Transformation]]<br>
[[Template:SBB-Protocols_ELISA | ELISA]]<br>
[[Template:SBB-Protocols_ELISA | ELISA]]<br>
-
[[2ab Assembly]]
+
[[2ab Assembly]]<br>
 +
[[Gibson Assembly]]<br>
 +
[[Choano Food Preperation]]
Line 136: Line 150:
'''Subgroup Strategies, Overview'''
'''Subgroup Strategies, Overview'''
 +
 +
 +
[http://2010.igem.org/Team:Berkeley '''iGEM Wiki for Berkeley''']
|}
|}

Current revision


Choa Choa's Delivery Service

The ability to manipulate the DNA of an organism is vital to many modern fields of biology. While we have perfected this in common research species such as E. coli, yeast and mouse cells, it is still impossible to transform many other species researchers study. Our project is an attempt to develop transgenics ) techniques for a family of single celled organisms called choanoflagellates. These species are interesting to researchers because they are the closest living relative to our microbial ancestor that became the first multicellular animal. Nicole King, here at UC Berkeley, and other researchers across the globe who study these little creatures are hindered by the inability to genetically manipulate them.

The Berkeley iGEM 2010 team is applying synthetic biology to this problem. We are engineering bacteria that can deliver DNA into the choano. Choanos are predatory, which makes our job a bit simpler. Once our bacteria is engulfed by the choano, it is programmed to burst using a self-lysis device. Proteins we have placed inside the bacteria will then go into action. First, we have designed a vacuole-buster device that will burst the small food membrane holding the bacteria inside the choano, spewing the contents into the cytoplasm of the cell. In the cytoplasm, a transposon/transposase device tagged with a nuclear localization device will move to the nucleus. In the nucleus, the transposase will splice the transposon into the choanoflagellate DNA.


Resources The Team


Undergrads

Amy Kristofferson
Conor McClune
Tahoura Samad
Daniela
Christoph Neyer

Graduate Students
Tim Hsiau

Postdocs

Insert names here

Advisors
Chris Anderson
Terry Johnson
Image:Ladder pic.png


News Tools



Extremely Important Material
Quotes
Nicknames


Lab Notebooks

Group
Amy
Conor
Daniela
Tahoura
Christoph
Tim


The Details

Oligonucleotides
Gel Pictures
Sequencing
Construction Files
-80 Stocks
Assembly Trees
New Composite Parts
Robot CSV Files


Procedures

Polymerase Reactions
Wobble Reaction
Cloning by PCR
SOEing PCR
PCA Gene Synthesis
QuikChange
Colony PCR

Cleanup Reactions
Regular Zymo Cleanup
Small-Frag Zymo Cleanup
Zymo Gel Purification

Digestions Reactions
EcoRI/BamHI Digest of Wobble Products
EcoRI/BamHI Digest of PCR Products
Manual 2ab Assembly Digest
BglII Digest of EIPCR Products
Ligation of EcoRI/BamHI digests
Ligation of EIPCR digests
Analytical digests (Mapping)

Bacteria Manipulations
Transformation by heat-shock
Picking of colonies
Miniprep purification of DNA
Macherey-Nagel Miniprep
8-Strip Machery Nagel Miniprep
Genomic Miniprep
-80 Glycerol Stocks
Making Competent Cells
Small Scale Electrocompetent Prep-Generic

Other
LR Gateway Transfers
EcoRI/BamHI Part Transfers
What do I do with my sequencing data?
Small Scale Competent Cell Transformation
ELISA
2ab Assembly
Gibson Assembly
Choano Food Preperation


Subgroup Notebooks



Resources Project



Useful Links


Subgroup Strategies, Overview


iGEM Wiki for Berkeley

Personal tools