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2024-03-29T15:31:18Z
From 2010.igem.org
MediaWiki 1.16.5
http://2010.igem.org/Team:Northwestern/Notebook
Team:Northwestern/Notebook
2010-10-28T02:38:16Z
<p>Bzhang89: /* Notebook */</p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
='''Notebook'''=<br />
<br />
[[Brainstorming April-June 2010]]<br />
<br />
NOTE: All work done by the undergraduate students of NU iGEM.<br />
=='''June'''==<br />
[[Week1 6/13/10-6/19/10]]<br />
<br />
[[Week2 6/20/10-6/26/10]]<br />
<br />
[[Week3 6/27/10-7/3/10]]<br />
<br />
<br />
=='''July'''==<br />
[[Week4 7/4/10-7/10/10]]<br />
<br />
[[Week5 7/11/10-7/17/10]]<br />
<br />
[[Week6 7/18/10-7/24/10]]<br />
<br />
[[Week7 7/25/10-7/31/10]]<br />
<br />
<br />
=='''August'''==<br />
[[Week8 8/1/10-8/7/10]]<br />
<br />
[[Week9 8/8/10-8/14/10]]<br />
<br />
[[Week10 8/15/10-8/21/10]]<br />
<br />
[[Week11 8/22/10-8/28/10]]<br />
<br />
[[Week12 8/29/10-9/4/10]]<br />
<br />
<br />
=='''September'''==<br />
[[Week13 9/5/10-9/11/10]]<br />
<br />
[[Week14 9/12/10-9/18/10]]<br />
<br />
[[Week15 9/19/10-9/25/10]]<br />
<br />
[[Week16 9/26/10-10/2/10]]<br />
<br />
<br />
=='''October'''==<br />
[[Week17 10/3/10-10/9/10]]<br />
<br />
[[Week18 10/10/10-10/16/10]]<br />
<br />
[[Week19 10/17/10-10/23/10]]<br />
<br />
[[Week20 10/24/10-10/30/10]]<br />
<br />
<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Lac
Team:Northwestern/Project/Lac
2010-10-23T18:57:22Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
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<!--- The Mission, Experiments ---><br />
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!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
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<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
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<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
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<td align="center">Modeling</td><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
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<br />
|-<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
=='''Induction'''==<br />
<br />
===Induction System===<br />
For the induction system, our team decided to use the lac-operon/iptg construct because of its widespread use and the availability of information. This system was assembled using standard biobricks parts. To induce our system, we used a IPTG spray of two and five millimolar concentrations, and one millimolar solutions for liquid cultures.<br />
<br />
===Parts and Assembly===<br />
The induction construct consisted of a constitutive promoter (J23100, J23104, or J23105), a combination part of Ribosome Binding Site, Lac Repressor, double Terminators, and Lac Promoter (Q01121, Q04121), and Ribosome Binding Sequence (B0034, B0031, B0032). Various combinations of these parts were assembled to create varying induction speeds for Chitin Synthase and apoptosis. See the parts section for more information.<br />
<br />
===Diffusion and Modeling===<br />
To induce our system, IPTG is sprayed onto the biofilm, diffusing through the top layer of the bacteria. This diffusion through the bacterial membrane is detailed in the modeling section. <br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Lac
Team:Northwestern/Project/Lac
2010-10-23T18:27:29Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
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<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
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<br />
|-<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
===Induction System===<br />
For the induction system, our team decided to use the lac-operon/iptg construct because of its widespread use and the availability of information. This system was assembled using standard biobricks parts. To induce our system, we used a IPTG spray of two and five millimolar concentrations, and one millimolar solutions for liquid cultures.<br />
<br />
===Parts and Assembly===<br />
<br />
The induction construct consisted of a constitutive promoter (J23100, J23104, or J23105), a combination part of Ribosome Binding Site, Lac Repressor, double Terminators, and Lac Promoter (Q01121, Q04121), and Ribosome Binding Sequence (B0034, B0031, B0032). See the parts section for more information.<br />
<br />
Multiple versions of each part were used to generate a wide range of repressor concentrations, so as to allow for variation between the induction time-delay and degree of Apoptosis protein and Chitin Synthase synthesis.<br />
<br />
The effectiveness of these constructs were tested in the modeling section.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Apoptosis
Team:Northwestern/Project/Apoptosis
2010-10-23T16:28:35Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
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!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
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<br />
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<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
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<tr><br />
<td align="center">Modeling</td><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
</tr><br />
</table><br />
</html><br />
<br />
|-<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
<br />
We used the Apoptosis Cassette by Brown '08 iGEM team (K124017).<br />
<br />
The bacteriophage cassette includes S105 protein (Holin), R protein (Endolysin), and Rz protein, all of which act in combination to lyse the bacteria.<br />
<br />
Holin is a small membrane protein that produces holes in the membrane. <br />
<br />
R is an endolysin that digests and cleaves the cell wall. <br />
<br />
Rz protein, a periplasmic protein, through reasons that are not yet totally clear, carries out the final step of host lysis.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Chitin_Synthesis
Team:Northwestern/Project/Chitin Synthesis
2010-10-23T16:28:17Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
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|colspan="2"|<br />
<br />
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<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
</tr><br />
<tr><br />
<td align="center">Modeling</td><br />
<td align="center">Chassis</td><br />
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<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
</tr><br />
</table><br />
</html><br />
<br />
|-<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
<br />
Chitin Synthase 3 (CHS3) was cloned out of Saccharomyces Cerevisiae (S.C.) cDNA.<br />
<br />
CHS3 from S.C. was chosen because the the protein does not require cofactors or activation factors and also because it was determined to be the most active of the Chitin Synthase family.<br />
<br />
Chitin Synthase polymerizes N-Acetyl-D-Glucosamine, also known as Chitin, with substrate as UDP-N-Acetyl-D-Glucosamine.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Lac
Team:Northwestern/Project/Lac
2010-10-23T16:27:24Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
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|colspan="2"|<br />
<br />
<html><br />
<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
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</tr><br />
<tr><br />
<td align="center">Modeling</td><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
</tr><br />
</table><br />
</html><br />
<br />
|-<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
<br />
For the induction system, our team decided to use the lac-operon/iptg construct because of its widespread use and the availability of information.<br />
<br />
The induction construct consisted of a constitutive promoter (J23100, J23104, or J23105), a combination part of Ribosome Binding Site, Lac Repressor, double Terminators, and Lac Promoter (Q01121, Q04121), and Ribosome Binding Sequence (B0034, B0031, B0032).<br />
<br />
Multiple versions of each part were used to generate a wide range of repressor concentrations, so as to allow for variation between the induction time-delay and degree of Apoptosis protein and Chitin Synthase synthesis.<br />
<br />
The effectiveness of these constructs were tested in the modeling section.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Chassis
Team:Northwestern/Project/Chassis
2010-10-23T16:26:50Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
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|colspan="2"|<br />
<br />
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<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
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<td align="center">Chassis</td><br />
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<td align="center">Apoptosis</td><br />
</tr><br />
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</html><br />
<br />
|-<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
<br />
Our team primarily used the high transformation efficiency top10 cells from invitrogen for most protocols.<br />
<br />
In order to ensure lawn formation, the TqsA (also known as the YdgG) knockout were taken from a copy of the Keio Collection with permission from Professor Margaret Saks of Northwestern University. The ΔTqsA strain increases the thickness of biofilm by interfering with the quorum sensing mechanism (more specifically, the autoinducer-2 transport system).<br />
<br />
To prevent bacteria from digesting synthesized Chitin, as it normally would, the ΔChiA strain was also taken from the Keio Collection. Because this strain lacks Chitinase, a digestive enzyme that breaks the glycosidic bonds in Chitin.<br />
<br />
<br />
<br />
<br />
<br />
===Invitrogen Top10 Cells:===<br />
<br />
Purchase and Description: http://products.invitrogen.com/ivgn/product/C404010<br />
<br />
===TqsA aka YdgG Knockouts:===<br />
<br />
http://jb.asm.org/cgi/content/short/188/2/587<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=106356<br />
<br />
===ChiA Knockouts:===<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=100308<br />
<br />
http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW3300<br />
<br />
===MAGE Protocol===<br />
<br />
http://www.wired.com/wiredscience/2009/07/cellfactories/<br />
<br />
http://www.nature.com/nature/journal/v460/n7257/full/nature08187.html<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Modeling
Team:Northwestern/Project/Modeling
2010-10-23T16:26:28Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
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<br />
<html><br />
<head><br />
<style><br />
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background: #EFCDF8; <!-- EEDCC8 url(https://static.igem.org/mediawiki/2010/3/38/BG1.jpg) repeat-y; --><br />
}<br />
</style><br />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
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{| align="center" border="0" width="75%"<br />
|colspan="2"|<br />
<br />
<html><br />
<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
</tr><br />
<tr><br />
<td align="center">Modeling</td><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
</tr><br />
</table><br />
</html><br />
<br />
|-<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
<br />
<br />
Using simple enzyme kinetics equations, we elected to mathematically simulate the following model:<br />
<br />
[[Image:SuperModeling.jpg|500px|center]]<br />
<br />
add kkkkkkkk<br />
<br />
Matlab was used to generate a theoretical model where IPTG would diffuse down the biofilm as according to Fick's Law of Diffusion.<br />
<br />
The extracellular substrate concentration was assumed to be much greater than the uptake/use, and so would diffuse in at a constant rate.<br />
<br />
This model was fitted with empirical data using cp-lacpi-gfp to estimate the effect of varying cp, lacpi, and rbs on enzyme and final product production.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Contact
Team:Northwestern/Contact
2010-10-23T16:22:28Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
<br />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
If you have any questions or remarks, please let us know by e-mailing us at [mailto:nuigem10@gmail.com nuigem10@gmail.com]<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Media
Team:Northwestern/Media
2010-10-23T16:20:01Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
<br />
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<html><br />
<style><br />
/* Wiki Hacks - START */<br />
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/* Wiki Hacks - END */<br />
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</head><br />
</html><br />
<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
'''Spring 2010''': NU iGEM in Centerpiece Article (a Northwestern Quarterly by the Office for Research): [http://www.biosci.northwestern.edu/documents/CenterpieceArticle-Spring2010.pdf link]<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/References
Team:Northwestern/References
2010-10-23T16:19:29Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
<br />
<br />
<html><br />
<style><br />
/* Wiki Hacks - START */<br />
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<br />
<br />
/* Wiki Hacks - END */<br />
<br />
<br />
#content {<br />
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<br />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
=== Lac Operon Control ===<br />
<br />
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG<br />
<br />
===Chitin===<br />
<br />
Adding Glucosamine in medium: http://ec.asm.org/cgi/reprint/2/5/886<br />
<br />
Chitin synthesis Pathway (image): [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg]<br />
<br />
Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long <br />
<br />
Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html<br />
<br />
=== Chitin Synthesis ===<br />
<br />
Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311<br />
<br />
CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465<br />
<br />
===Chitin Staining (Calcofluor)===<br />
<br />
Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf<br />
<br />
Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za<br />
<br />
Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/<br />
<br />
Data sheet: http://tinyurl.com/283wax2<br />
<br />
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html<br />
<br />
=== Apoptosis ===<br />
<br />
partsregistry: http://partsregistry.org/Cell_death<br />
<br />
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===<br />
<br />
DMAO(Live), EtD-III(Dead)<br />
*http://www.promokine.info/products/cell-analysis/cell-staining-reagents-related-products/<br />
*http://www.biotium.com/product/product_info/Protocol/30027.pdf<br />
<br />
===Keio Collection - KnockOuts===<br />
<br />
Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html <br />
<br />
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp<br />
<br />
Method: http://www.pnas.org/content/97/12/6640.full.pdf+html<br />
<br />
Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html<br />
<br />
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls<br />
<br />
=== ChiA (Chitinase) Knockout ===<br />
<br />
Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts<br />
<br />
Chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300<br />
<br />
===ydgg/tqsA (AI2-Transporter) Knockout===<br />
<br />
Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf<br />
<br />
=== BIF (Biological Imaging Facility)===<br />
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br /><br />
Methods: http://www.northwestern.edu/bioimaging/methods.html<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Links
Team:Northwestern/Links
2010-10-23T16:18:46Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
===Basic iGEM Resources===<br />
Digestion & Ligations: http://ginkgobioworks.com/support/<br />
<br />
Openwetware: http://openwetware.org/wiki/Protocols<br />
<br />
Medal Requirements: https://2010.igem.org/Judging/Judging_Criteria<br />
<br />
Parts Registry: http://partsregistry.org/Part_Types<br />
<br />
===Protocol-Related===<br />
<br />
Plasmid Naming Convention: http://partsregistry.org/Help:Plasmids/Nomenclature<br />
<br />
Part Types: http://partsregistry.org/Part_Types<br />
<br />
PCR Primer Design: http://perlprimer.sourceforge.net/<br />
<br />
Plate Reader: http://www.biotek.com/resources/articles/beta-galactosidase-plate-reader.html<br />
<br />
===Research Resources===<br />
<br />
Friendly Pubmed: http://www.hubmed.org/<br />
<br />
E.Coli Genotypes: http://openwetware.org/wiki/E._coli_genotypes<br />
<br />
===Wikipedia Editing Resources===<br />
<br />
http://www.mediawiki.org/wiki/Help:Formatting<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Safety
Team:Northwestern/Safety
2010-10-23T16:17:59Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
==Safety==<br />
<br />
Please use this page to answer the safety questions posed on the [[Safety | safety page]].<br />
<br />
1. '''Would any of your project ideas raise safety issues in terms of:'''<br />
* researcher safety,<br />
* public safety, or<br />
* environmental safety?<br />
2. '''Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,'''<br />
* did you document these issues in the Registry?<br />
* how did you manage to handle the safety issue?<br />
* How could other teams learn from your experience?<br />
3. '''Is there a local biosafety group, committee, or review board at your institution?'''<br />
* If yes, what does your local biosafety group think about your project?<br />
* If no, which specific biosafety rules or guidelines do you have to consider in your country?<br />
4. '''Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions?'''<br />
'''How could parts, devices and systems be made even safer through biosafety engineering?'''<br />
<br />
<br />
'''Would any of your project ideas raise safety issues in terms of researcher safety, public safety or environmental safety?'''<br /><br />
<br />
We can pinpoint three possible negative consequences of our project:<br />
<br />
1. The strain produces some toxin related to chitin in addition to the chitin itself.<br><br />
2. The strain produces pure chitin, and the extraction thereof results in a high incidence of allergic reaction among those that work with it.<br><br />
3. The strain becomes airborne, resulting in lung infection and chitin deposition in the airways.<br><br />
<br />
<br />
'''Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?'''<br /><br />
<br />
No.<br />
<br />
'''If yes, did you document these issues in the Registry?'''<br /><br />
<br />
'''How did you manage to handle the safety issue?'''<br /><br />
<br />
'''How could other teams learn from your experience?'''<br /><br />
<br />
'''Is there a local biosafety group, committee, or review board at your institution?'''<br /><br />
<br />
Yes.<br />
<br />
'''If yes, what does your local biosafety group think about your project?'''<br /><br />
<br />
<br />
<br />
'''If no, which specific biosafety rules or guidelines do you have to consider in your country?'''<br /><br />
<br />
'''Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions?'''<br /><br />
<br />
When pursuing a project, an iGEM team should attempt to think ahead of any dangerous consequences of their pursuits. If there are any concerns, the team should consider drafting recommendations for any group that might desire to utilize their devices. If infection is a concern, appropriate apoptotic signals should be considered.<br />
<br />
'''How could parts, devices and systems be made even safer through biosafety engineering?'''<br />
<br />
Parts might be programmed with an apoptotic signal so that the bacteria dies when separated from culture. In addition, certain "key" systems may be desirable. If parts provided are of a somewhat "black box" format, it may be possible to program in killswitches so that if a strain is not treated with a particular nutrient or other molecule, transformed strains either apoptose or do not have the proper function. If these keys are sent with the desired part, it may make it more difficult to "hack" dangerous parts for illicit use.<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Protocol
Team:Northwestern/Protocol
2010-10-23T16:17:42Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
== '''DNA''' ==<br />
<br />
[[Team:Northwestern/Protocol/PDNA|Prepping DNA from the kit plates]]<br />
<br />
[[Team:Northwestern/Protocol/Quikchange (from primers to colonies!|Quikchange: Primers to Colonies]]<br />
<br />
[[Team:Northwestern/Protocol/Kit to Stock Plasmid|Kit to Stock Plasmid]]<br />
<br />
[[Team:Northwestern/Protocol/Ethanol Precipitation|Ethanol Precipitation]]<br />
<br />
[[Team:Northwestern/Protocol/New Part Design(PCR)|New Part Design]]<br />
<br />
=='''Bacterial Work'''==<br />
<br />
[[Team:Northwestern/Protocol/Transformation|Transformation]]<br />
<br />
[[Team:Northwestern/Protocol/O/N Culture|Overnight Cultures]]<br />
<br />
[[Team:Northwestern/Protocol/Preparation of Competent Cells|Preparation of Competent Cells]]<br />
<br />
[[Team:Northwestern/Protocol/LB Media|LB Media]]<br />
<br />
[[Team:Northwestern/Protocol/Preparing Plates|Preparing Plates]]<br />
<br />
[[Team:Northwestern/Protocol/Glycerol Stocks|Glycerol Stocks]]<br />
<br />
=='''Assembly'''==<br />
<br />
[[Team:Northwestern/Protocol/Restriction Enzyme Digests|Restriction Enzyme Digests]]<br />
<br />
[[Team:Northwestern/Protocol/Plasmid Construction|Plasmid Construction]]<br />
<br />
[[Team:Northwestern/Protocol/3A Assembly|3A Assembly]]<br />
<br />
[[Team:Northwestern/Protocol/Ligations|Ligations]]<br />
<br />
[[Team:Northwestern/Protocol/Mini Prep|Qiagen Mini Prep]]<br />
<br />
=='''Microscopy'''==<br />
<br />
[[Team:Northwestern/Protocol/Confocal Microscopy|Confocal Microscopy]]<br />
<br />
[[Team:Northwestern/Protocol/Fluorescence Microscopy|Fluorescence Microscopy]]<br />
<br />
=='''Reagents'''==<br />
<br />
[[Team:Northwestern/Protocol/Reagents|Reagents]]<br />
<br />
=='''Cell Staining'''==<br />
<br />
[[Team:Northwestern/Protocol/Rhodamine-Conjugated Chitin Probe|Rhodamine-Conjugated Chitin Probe]]<br />
<br />
[[Team:Northwestern/Protocol/Methanol Fixation|Methanol Fixation]]<br />
<br />
[[Team:Northwestern/Protocol/LIVE/DEAD® BacLight - Bacterial Viability Kit|Live/Dead Baclight]]<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Calendar
Team:Northwestern/Calendar
2010-10-23T16:17:17Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
<html><br />
<div align="center"><br />
<iframe src="https://www.google.com/calendar/embed?title=Northwestern%20iGEM%202010&amp;height=600&amp;wkst=1&amp;bgcolor=%23FFFFFF&amp;src=nuigem10%40gmail.com&amp;color=%23853104&amp;ctz=America%2FChicago" style=" border-width:0 " width="933" height="600" frameborder="0" scrolling="no"></iframe><br />
</div><br />
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<br />
<div align="right"><br />
click on ^<br />
<br />
nuigem10//igem2010 @g<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Notebook
Team:Northwestern/Notebook
2010-10-23T16:16:48Z
<p>Bzhang89: </p>
<hr />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
[[Brainstorming April-June 2010]]<br />
<br />
[[Week1 6/13/10-6/19/10]]<br />
<br />
[[Week2 6/20/10-6/26/10]]<br />
<br />
[[Week3 6/27/10-7/3/10]]<br />
<br />
[[Week4 7/4/10-7/10/10]]<br />
<br />
[[Week5 7/11/10-7/17/10]]<br />
<br />
[[Week6 7/18/10-7/24/10]]<br />
<br />
[[Week7 7/25/10-7/31/10]]<br />
<br />
[[Week8 8/1/10-8/7/10]]<br />
<br />
[[Week9 8/8/10-8/14/10]]<br />
<br />
[[Week10 8/15/10-8/21/10]]<br />
<br />
[[Week11 8/22/10-8/28/10]]<br />
<br />
[[Week12 8/29/10-9/4/10]]<br />
<br />
[[Week13 9/5/10-9/11/10]]<br />
<br />
[[Week14 9/12/10-9/18/10]]<br />
<br />
[[Week15 9/19/10-9/25/10]]<br />
<br />
[[Week16 9/26/10-10/2/10]]<br />
<br />
[[Week17 10/3/10-10/9/10]]<br />
<br />
[[Week18 10/10/10-10/16/10]]<br />
<br />
[[Week19 10/17/10-10/23/10]]<br />
<br />
[[Week20 10/24/10-10/30/10]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
===10/3/10===<br />
Timi miniprepped the CP-LacPI-GFP cultures and digested them with E/P. She then poured a big and a small gel.<br />
<br />
Kevin came in and ran the digested CP-LacPI-GFP, digested CP-LacPI with digested Cp and digested LacPI parts.<br />
----<br />
<br />
===10/4/10===<br />
Timi and Kevin decided to take a day off :)<br />
----<br />
<br />
===10/5/10===<br />
Timi and Kevin came in to discuss why their gels were running strangely. We believe there is something wrong with our buffer, so we are swapping everything out with a fresh batch of Prof. Mordacq's 0.5x TBE buffer. Timi poured a large gel that we will be using tomorrow.<br />
----<br />
===10/6/10===<br />
----<br />
===10/7/10===<br />
Timi- took part 2-17F out of the DNA kit. Transformed into T10 cells to grow overnight.<br />
----<br />
<br />
===10/8/10===<br />
Kevin- ran gel of the CP-LacPI parts. Gel results are still inconclusive. Also put in an overnight culture of the 2-17F part into the incubator for Timi.<br />
----<br />
<br />
===10/9/10===<br />
Timi- Miniprepped the 2-17F part. Digested the DNA with E/P and ligated the 2-17F GFP part into Chlor and Tet backbone.<br />
----<br />
<br />
===10/10/10===<br />
Timi- Transformed and plated part 2-17F onto Chlor and Tet plates. Will be ready for miniprepping tomorrow.<br />
----<br />
<br />
===10/11/10===<br />
----<br />
===10/12/10===<br />
Matt - digested LacP-RBS with SpeI in preparation for standard assembly with ES digested CHS3<br />
----<br />
<br />
===10/13/10===<br />
----<br />
===10/14/10===<br />
Kevin transformed T10 cells with CP-LacPI parts that we did not have much digest of left. He plated them onto TET plates.<br />
----<br />
<br />
===10/15/10===<br />
Kevin took out the CP-LacPI plates and put them into the 4 degree for Timi. Timi inoculated overnight cultures at 7pm.<br />
----<br />
<br />
===10/16/10===<br />
Team meeting at 12pm to work on our wiki. We made the discouraging discovery that our CHS3 DNA that Ben had worked super hard for actually contained XbaI restriction sites. This complicates our assembly and might jeopardize the success of our project. We will talk to the advisors about this to see if things can still work out.<br />
<br />
Timi and Kevin miniprepped the CP-LacPI inoculations, digested them with E&P, and ligated them to GFP.<br />
----<br />
<br />
===10/17/10===<br />
Timi phosphotase-treated the newly digested chlor backbone and ligated a second set of CP-LacPI.<br />
Kevin transformed and plated this new set of phosophotase treated Cp-LacPI.<br />
<br />
Kevin inoculated the first set of non-phosphotase treated CP-LacPI inoculations.<br />
<br />
----<br />
<br />
===10/18/10===<br />
Matt miniprepped 31GFP, 21GFP (old), and 32GFP (old). He digested the miniprepped DNA with E/P for Kevin to run on a gel. He also reinoculated all 9 CP-LacPI combinations.<br />
<br />
Matt inoculated the phosophotase-treated ligations at 9pm.<br />
----<br />
<br />
===10/19/10===<br />
Plan: Timi miniprepped the phosphotase-treated CP-LacPI and ran them on a gel. But Mordacq's class was using the thermocycler so Timi just sat and read.<br />
<br />
Plate reader fun with Kevin @ 3pm.<br />
<br />
Sean - ran CHS3(pMAL+SDM) digest, pMAL digest, and ligation on a gel -> CHS3 exhibited incorrect bands (there are 2, when there should be 1) ligation showed nothing -> plan to run CHS3 undigested and rerun the above 3.<br />
----<br />
<br />
===10/20/10===<br />
Timi and Kevin ligated the old 212, 312, and 322 parts into a phosophotase-treated Chlor backbone for submission into the registry. They transformed and plated for inoculation tomorrow night.<br />
<br />
They inoculated cultures for the plate reader.<br />
----<br />
<br />
===10/21/10===<br />
Timi/Kevin: Early morning plate reader protocol entering.<br />
<br />
Weekly lab meeting with advisors.<br />
----<br />
<br />
===10/22/10===<br />
PCR'ed out CHS3 with pMAL ends and Gel extracted<br />
----<br />
<br />
===10/23/10===<br />
----<br />
===10/24/10===<br />
----<br />
===10/25/10===<br />
----<br />
===10/26/10===<br />
----<br />
===10/27/10===<br />
----<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Parts
Team:Northwestern/Parts
2010-10-23T16:16:20Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
===Parts===<br />
<br />
<groupparts>iGEM010 Northwestern</groupparts></div>
Bzhang89
http://2010.igem.org/Team:Northwestern/SideProject
Team:Northwestern/SideProject
2010-10-23T16:15:56Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
==Human Practices Essay==<br />
Ragan, put the essay here.<br />
----<br />
==Ethics==<br />
Prompt: Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
<br />
Resources: <br />
<br />
* http://bioethics.northwestern.edu/faculty/zoloth.html<br />
<br />
* http://www.feinberg.northwestern.edu/research/cores/units/ethics<br />
<br />
* http://en.wikipedia.org/wiki/Medical_ethics<br />
<br />
* http://en.wikipedia.org/wiki/Bioethics<br />
<br />
* http://en.wikipedia.org/wiki/Synthetic_biology#Social_and_Ethical<br />
<br />
==Abstract==<br />
Ethics oriented Analysis of synthetic biology in general and in relation to the NU2010 Bacterial Skin project.<br />
==Outline==<br />
===Preamble or Historical Perspective===<br />
Aversion to synthetic life, religious, uncanny valley, Frankensteinian fears <br />
http://en.wikipedia.org/wiki/History_of_biotechnology<br />
http://en.wikipedia.org/wiki/Asilomar_Conference_on_Recombinant_DNA<br />
http://en.wikipedia.org/wiki/Timeline_of_biotechnology<br />
http://www.wired.com/magazine/2010/07/pl_backstory_timemachine/<br />
===Medical (Societal) Ethics===<br />
Beneficence, Non-maleficence, autonomy (zoloth principle=fidelity), Justice, (Dignity, Truthfulness)<br />
===Moral (Individual) Ethics===<br />
Kant(Categorical Imperative, ends) vs Mill(Utilitarianism) vs Aristotle(Character)<br />
===Unique Ethical Problems===<br />
Ontological<br />
Epistemic<br />
===Project specific problems===<br />
application specific analysis<br />
<br />
<br />
==Magnetite Production==<br />
<br />
Siderophore<br />
<br />
TonB<br />
<br />
Oxireductases<br />
<br />
FeCl2,Fecl3 reinforced media<br />
<br />
mms6<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project
Team:Northwestern/Project
2010-10-23T16:15:11Z
<p>Bzhang89: </p>
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<!--- The Mission, Experiments ---><br />
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!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
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!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
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<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
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<td align="center">Modeling</td><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
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<br />
Our main project is to simulate mammalian skin using chitin in E. Coli. This process involves four major components: Lawn Formation, Chitin Synthesis, Bacterial Apoptosis, and lac-Operon Signaling.<br />
<br />
A thick bacterial lawn is generated by plating Keio Collection ydgG knock-out mutants in an enriched agar plate. The protein product of ydgG plays an integral role in AI-2 transport. ydgG knock-outs exhibit increased motility which should ultimately allow for a thick and level lawn.<br />
<br />
The 3.5kbp Chitin Synthase III gene is extracted from the Saccharomyces Cerevisiae genome. Chitin Synthase III catalyzes the polymerization of chitin.<br />
<br />
Apoptosis of cells is achieved by using the bacteriophage lysis cassette built by the Brown '08 iGEM Team. The cassette includes Holin, Endolysin, and Rz Protein genes. These enzymes puncture and degrade the cell membrane which results in lysing of the cell and the release of synthesized chitin.<br />
<br />
Once the lawn is established, an IPTG solution is sprayed over the lawn to induce chitin synthesis (fast response) and apoptosis (slow response). IPTG mimics allolactose which binds to the LacI repressor, allowing for a build-up in chitin followed by apoptosis and subsequent release into the extracellular environment. Thus, any abrasions to the chitinous surface can be repaired by spraying IPTG.<br />
<br />
In mammalian skin, mitosis occurs in the basal layer of the epithelial cells and cells travel outwards towards the surface of the skin as they mature. As the cells move further away from the basal layer, they die and their cytoplasm is released and the cells are filled with keratin, thus forming a continuously regenerating protective layer on the outer-most part of epithelial layer; our project is modeled after this. The bacterial lawn is externally controlled to produce chitin only at the top-most layer and these cells then undergo apoptosis to result in the formation of a chitinous layer at the surface of the lawn.<br />
<br />
<br />
'''SIGNIFICANCE OF CHITIN''':<br />
<br />
<u>Medicinal Use</u>:<br />
<br />
*Wound and burn treatment/healing<br />
*Hemostasis for orthopedic treatment of broken bones<br />
*Viscoelastic solutions for ophthamology and orthopedic surgery<br />
*Abdominal adhesion treatment<br />
*Antibacterial and antifungal agents <br />
*Tumor therapies<br />
*Microsurgery and neurosurgery<br />
*Treatment of chronic wounds, ulcers and bleeding (chitin powder) <br />
<br />
<u>Industrial Use</u>:<br />
<br />
*Food/Pharmaceutical/Agricultural/Cosmetic thickener, stabilizer<br />
*Agricultural protection<br />
*Water resistant properties<br />
*Dietary supplement<br />
*Water purification<br />
*Biodegradable<br />
*Edible microcrystalline films used to preserve food<br />
*Sequestering of particles (i.e. oil)<br />
<br />
||[[Image:PosterChild.jpg|400px|center]]<br />
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<br />
<br />
==Strategy==<br />
<br />
===Obtaining Chitin Synthase 3 Gene===<br />
First, the Chitin Synthase 3 (CHS3) gene is subcloned out of Saccharomyces Cerevisiae (Baker’s Yeast) cDNA (complementary DNA – contains no introns, thus can be used in prokaryotes) with biobrick restriction sites (EcoR1, Xbal1 on one end, and Spe1, Pst1 on the other). CHS3 was chosen as it was found to be the major enzyme (knockouts had 80% reduced Chitin) in its family and requires no co-enzyme or activating compounds. Upon running CHS3 through NEB Cutter V2.0, we found a PST1 restriction site which is incompatible with the biobrick standard (EcoR1, Xbal, Spe1, Pst1). To remove this Pst1 site, we insert CHS3 into a biobrick vector plasmid, and performed site-directed mutagenesis (SDM).<br />
<br />
===pMAL Vector===<br />
Research revealed that chitin synthase is a transmembrane enzyme, and in order to simulate similar conditions, we decided to use the pMAL vector by NEB which contains a periplasmic membrane signal sequence. CHS3 is subcloned in to the pMAL-p5x NEB vector by first PCR’ing it out of the biobrick vector plasmid - on which it must undergo SDM - with pMAL restriction sites (Nde1 and EcoR1) and ligated into the pMAL-p5x vector. Then, the CHS3 is again amplified with biobrick sites, but this time, with the periplasmic signal sequence native to the pMAL-p5x plasmid, and inserted into a standard biobrick vector. The entire part is then sequenced and submitted to the registry of standard parts.<br />
A bacterial apoptosis cassette made by the Brown iGEM team in ‘08 is taken from the iGEM 2010 distribution kit and colony amplified.<br />
<br />
===Constitutive Promoters & Lac Operon===<br />
3 constitutive promoters and 2 lac-inhibitor/lac-operon combination parts are taken from the registry and ligated in all 6 combinations through 3A Assembly. These combinations express different levels of lacI, thus exhibiting variable inductivity. These 6 constructs are then ligated with a reporter protein - green fluorescent protein - and characterized via an automated fluorescent microplate reader; fluorescence is used to determine the construct inductivity and expression level.<br />
<br />
===IPTG Activation===<br />
The data is used to fit our own theoretical kinetics model that accounts for IPTG diffusion through biofilm, external IPTG concentration, internal IPTG concentration, lac repressor concentration, repressor bound gene (DNA) concentration, unbound gene (DNA) concentration, mRNA concentration, enzyme concentration, substrate concentration, enzyme-substrate complex concentration, and final product concentration, as well as all the rate constants involved. Using the data acquired from the microplate reader, a final semi-empirical kinetics model is generated. Using this model, two different constructs are chosen; both with similar inductivity, but one with and the other without time delay.<br />
<br />
===Chitin Synthesis Production===<br />
The fast expression construct is ligated with Chitin Synthase, while the slow expression construct is ligated with the apoptosis cassette. Both plasmids are then transformed into a chiA and tqsA double knockout strain of K12 Escherichia Coli. ChiA knockouts lack Chitinase, which is an enzyme that catabolizes chitin. tqsA knockouts have a disrupted quorum sensing mechanism that allows them to grow very thick lawns. The mutants are acquired from Keio collection (one from Northwestern, and the other from Yale respectively).<br />
<br />
===MAGE===<br />
<br />
<br />
===Mechanism===<br />
The double knockout colonies with both constructs are then sprayed with IPTG, which first induces the fast chitin synthesis construct, causi a buildup of chitin in cells in the top layer of the bacterial lawn. Then the slow apoptosis construct is induced, which then lyses the cells, and releases a layer of chitin in the top layer of the bacterial lawn. This construct is then stained with a chitin-specific rhodamine probe by NEB as well as Baclight by Invitrogen in order to ensure that the cells are producing chitin and lysing. The lawn is then imaged through a fluorescent confocal microscope.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Acknowledgements
Team:Northwestern/Acknowledgements
2010-10-23T16:14:30Z
<p>Bzhang89: </p>
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{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
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!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
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<br />
=='''Sponsors'''==<br />
'''EMD CHEMICALS - Shou Wong'''<br />
<br />
Corresponded with Shou who promised to meet with team in August and to potentially set up sponsorship with EMD Millipore.<br />
<br />
'''EPOCH LIFE SCIENCES - XueNong Zhang'''<br />
<br />
Sponsorship of 1000 DNA Spin Columns<br />
<br />
'''NEB - Lori Tonello'''<br />
<br />
Sponsorship of Biobrick Kits, Antarctic Phosphotase, Chitin Rhodamine, Taq polymerase, 1kb DNA ladder, DpnI and pMAL<br />
<br />
'''PROMEGA - Sara Mann'''<br />
<br />
Nominal amount of free products and additional discounts on petri dishes, pipet tips, Nova Blue cells, T4 DNA Ligase, pour boats, nuclease free water, gloves, biohazard bags, delicate wipers, serological pipets, 1.7 mL tubes, and agar.<br />
<br />
'''QIAGEN - Jackie Ciardo'''<br />
<br />
Discounts on miniprep kits, gel extraction kits, and PCR purification kits.<br />
<br />
'''VWR - Amy Vanarsdale'''<br />
<br />
Additional discounts on petri dishes, pipet tips, Nova Blue cells, T4 DNA Ligase, pour boats, nuclease free water, gloves, biohazard bags, delicate wipers, serological pipets, 1.7 mL tubes, and agar.<br />
<br />
=='''Advisors'''==<br />
<br />
'''John Mordacq''' <br><br />
Distinguished Senior Lecturer<br><br />
Program in Biological Sciences<br><br />
Email: j-mordacq@northwestern.edu<br> <br />
<br />
'''Joshua Leonard'''<br><br />
Department of Chemical and Biological Engineering<br><br />
Email: j-leonard@northwestern.edu<br> <br />
<br />
'''Michael Jewett'''<br><br />
Department of Chemical and Biological Engineering<br><br />
Email: m-jewett@northwestern.edu<br />
<br />
=='''NU Faculty and Affiliates'''==<br />
'''Debora Boetcher''' <br /> McCormick Biological and Chemical Engineering, Office Assistant <br /> Email: d-boetcher@northwestern.edu <br /> Contribution: Assisted with logistics such as billing and receiving of products. <br /><br />
<br />
'''Paul Brannon''' <br /> Biological Imaging Facilities, Confocal Specialist <br /> Biology, University of Chicago <br /> Email: p-brannon@northwestern.edu <br /> Room: Hogan 5-150 <br /> Contribution: Trained team members for confocal microscopy operation and made suggestions on how to integrate confocal microscopy into our project. <br /><br />
<br />
'''Jamie Bufkin''' <br /> Biological Imaging Facilities, Program Assistant <br /> Sociology & History, University of San Diego <br /> Email: j-bufkin@northwestern.edu <br /> Room: Hogan 5-150 <br /> Contribution: Set up confocal training for team members. <br /><br />
<br />
'''Sara Fernandez Dunne''' <br /> High Throughput Analysis Lab, Research Technologist II <br /> <br />
Northwestern University <br /> Email: s-fernandez@northwestern.edu <br /> Room: Hogan 4-140 <br /> Contribution: trained team members for plate reader and made suggestions on how to integrate the plate reader into our project. <br /><br />
<br />
'''John F. Marko'''<br /> Professor <br /> Biochemistry, Molecular Biology & Cell Biology; Physics & Astronomy <br /> PhD, Massachusetts Institute of Technology <br /> Email: john-marko@northwestern.edu <br /> Phone: (847) 467-1276 <br /> Room: Pancoe Rm 4109 <br /> Contribution: Discussed using Keio knockout collection. <br /><br />
<br />
'''Linda Mattice''' <br /> Yale University Molecular, Cellular and Developmental Biology <br /> E. Coli Keio Knockout Collection Distributor <br /> Email: cgsc@yale.edu <br /> Contribution: Send us Keio Collection ydgG knockout cells. <br /><br />
<br />
'''William Russin'''<br /> Biological Imaging Facilities, Manager <br /> PhD, University of Wisconsin - Madison <br /> Email: w-russin@northwestern.edu <br /> Phone: (847) 491-6657 <br /> Room: Hogan 5-150 <br /> Contribution: Discussed microscopy options for our project and integrated confocal microscopy into our project. <br /><br />
<br />
'''Margaret (Peggy) Saks'''<br /> Research Professor, The Uhlenbeck Lab <br /> Biochemistry, Molecular Biology & Cell Biology <br /> Email: m-saks@northwestern.edu <br /> Phone: (847) 491-5624<br /> Room: Pancoe Rm 4113 <br /> Times: 10:30am-end <br /> Contribution: Discussed chiA, tqsA knockout procedures. <br /><br />
<br />
'''Wei Zhang''' <br /> Civil and Environmental Engineering, PhD Candidate <br /> Aaron Packman Lab <br /> Interests: Flow and biofilm interaction and microbial communities in biofilms. <br /> Email: w-zhang@u.northwestern.edu <br /> Contribution: Discussed potential use of flow cells to form a biofilm. <br /><br />
<br />
'''Laurie Zoloth''' <br /> Northwestern University Feinberg School of Medicine <br /> Professor of Medical Humanities & Bioethics and Religion <br /> Director of Center for Bioethics, Science and Society <br /> Interests: Ethics in Genetic Medicine, in Stem Cell Research, Justice in health care allocation <br /> Email: lzoloth@northwestern.edu <br /> Contribution: Discussed ethics of synthetic biology and made suggestions on potential essay topics. <br /><br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Team
Team:Northwestern/Team
2010-10-23T16:14:08Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
{|border = "0" align="center" cellspacing="20" cellpadding="0" width="900px"<br />
|+'''ADVISORS'''<br />
----<br />
|-<br />
|width="33%" align="center"| [[Image: Jewett.jpg|center|150px]]'''Professor Michael Jewett'''<br />
|width="34%" align="center"| [[Image: Leonard.jpg|center|150px]]'''Professor Joshua Leonard'''<br />
|width="33%" align="center"| [[Image: Mordacq.jpg|center|178px]]'''Professor John Mordacq'''<br />
|-<br />
|Department of Chemical and Biological Engineering <br />
<br />
Tel: (847) 467-5007<br />Fax: (847) 491-3728<br />Email: m-jewett@northwestern.edu<br />
||Department of Chemical and Biological Engineering <br />
<br />
tel: 847/491-7455<br />fax: 847/491-3728<br />Email: j-leonard@northwestern.edu<br />
||Distinguished Senior Lecturer <br />
Program in Biological Sciences<br />
<br />
Tech MG79<br />Tel: 847-491-7835<br />Email: j-mordacq@northwestern.edu <br />
|}<br />
<br />
<br />
{|border = "0" align="center" cellspacing="20"<br />
|+'''TEAM MEMBERS'''<br />
----<br />
|-<br />
|align="center"|[[Image: Ben.jpg|center|100px]]'''Ben Zhang'''||'''Benjamin Zhang'''<br />Northwestern University, MEAS 2011<br />Biomedical Engineering<br />(405) 397-3817<br />xuzhang2007@u.northwestern.edu<br /> Weird Fact: Ben insists that he digested fetal pigs during bio lab in high school instead of dissecting them. <br />
<br />
He also has ears of a cat. <br /><br />
|-<br />
|align="center"|[[Image: Kevin.jpg|center|100px]]'''Kevin Rogacki'''|| '''Kevin Rogacki''' <br /> Northwestern University, MEAS 2011<br />Biomedical Engineering<br />(708) 373-9388<br /> krr@u.northwestern.edu<br /> Weird Fact: Kevin pronounces the word "carbonyl" strangely...and thinks he's right. <br /><br />
|-<br />
|align="center"|[[Image: Matt.jpg|center|100px]]'''Matt Tong'''|| '''Matthew Tong''' <br /> Northwestern University, WCAS 2011<br />Biological Sciences<br />(516) 554-2333<br /> matttong@u.northwestern.edu<br /> Weird Fact: Matt once gave a delivery man a $22 dollar tip for an $18 pizza order. <br /><br />
|-<br />
|align="center"|[[Image: Ragan.jpg|center|100px]]'''Ragan Pitner'''||'''Ragan Pitner'''<br />Northwestern University, MEAS 2011<br />Biomedical Engineering<br />raganpitner2007@u.northwestern.edu<br /> Weird Fact: Ragan locked himself out of the lab once. <br />
<br />
Funny story. Ask him about it. <br /><br />
|-<br />
|align="center"|[[Image: Sean.jpg|center|100px]]'''Sean Yu'''||'''Sean Chonghwan Yu'''<br />Northwestern University, MEAS 2011<br />Biomedical Engineering<br />(440) 655-1759<br />cyu286@u.northwestern.edu <br /> Weird Fact: All this kid wants to do is liquify meat. <br />
<br />
Seriously, don't you think your time could be better spent? <br /><br />
|-<br />
|align="center"|[[Image: Timi.jpg|center|100px]]'''Timi Chu'''||'''Timi Chu'''<br /> Northwestern University, MEAS 2013<br />Biomedical Engineering<br />(347) 671-1239<br />timi@u.northwestern.edu<br /> Weird Fact: Timi insists she is not a picky eater. <br />
<br />
Pineapple and shrimp just make her head itch. <br /><br />
|-<br />
<br />
{|border = "0" align="center" cellspacing="20" cellpadding="0" width="900px"<br />
|+'''FOUNDERS'''<br />
----<br />
|-<br />
|width="50%" align="center"| [[Image: avi.jpg|center|100px]]'''Avi Samelson'''<br />
|width="50%" align="center"| [[Image: Jeremy.jpg|center|100px]]'''Jeremy Schifberg'''<br />
|-<br />
<br />
|-<br />
|align="center"|University of California, Berkeley <br /> Molecular and Cell Biology <br /> Northwestern Class of 2010 <br /> asamelson@gmail.com<br />
<br />
|align="center"|Northwestern Class of 2010 <br /> Biological Sciences, Integrated Science Program <br /> jeremyschifberg2007@u.northwestern.edu<br />
|-<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Brainstorm
Team:Northwestern/Brainstorm
2010-10-23T16:12:43Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
==Round 1: Group Brainstorming Session==<br />
<br />
<br />
'''Health/Medicine'''<br />
Release in presence of wound signal (pH) Factor VIII<br />
Symbiosis with human body<br />
Selective phagocytosis (absorb toxin)<br />
Selective phagocytosis (lead)<br />
Phagocytosis for drug overdoses<br />
Drug sensing bactera<br />
Bacterial spermicide <br />
Drug delivery method through WBC<br />
Apoptosis with drug delivery when disease is recognized<br />
Vitamin and mineral delivery<br />
Bacteria that takes up excess ions in the body<br />
Self Healing material: growth factor<br />
Apoptosis in presence of a particular disease<br />
Swine Flu testing on site<br />
Target bad cells selectively based on offset in circadian rythmn<br />
Cure celiac’s with bacteria<br />
Ethrypoeitin production in e. coli<br />
Thrombolytics in presence in LDL<br />
Thrombolytics in precense of clots (macrophages)<br />
Bacterial pacemakers<br />
<br />
<br />
'''Food/Energy'''<br />
Supplementary vitamin and minerals to be grown on produce<br />
Removable pesticide bacterial film<br />
Cheese reservatrol<br />
Splitting Hydrogen from water<br />
Electrogenesis: produce voltage from bacteria<br />
<br />
'''Environment'''<br />
Consume gases in the air (ozone)<br />
Consume (CFCs)<br />
On site radiation testing (make it click like a Geiger counter) <br />
Breaking down plastics (look at past presentation)<br />
Photo-driven battery<br />
<br />
'''Manufacturing/Industrial'''<br />
Trace explosive Bacteria<br />
EXPLODING BACTERIA<br />
Bacterial Superglue<br />
Resistors<br />
Capacitors (Storing charge)<br />
Phagocytosis for water in shoes<br />
Bacterial barometer<br />
Bacterial paper to print on <br />
Active pH buffer for e. coli (target pH) <br />
pH meter<br />
Cilia creating fluid flow, generating fluid current<br />
Create ferrofluuid to create magnetism<br />
Bacteria to regulate the temperature of a surface (endothermic and exothermic reaction)<br />
Long lasting bacterial sunblock<br />
Bacterial Clothing <br />
Thermal heating for toes<br />
Adjusting Young’s Modulus<br />
Contracting group of cells<br />
Thermometer<br />
Bacterial film that responds to laser so you can sketch on it. (express GFP light induced promoter)<br />
Bacterial Gears <br />
<br />
'''Miscellaneous'''<br />
ELISA for DNA<br />
ELISA for mRNA<br />
Magnetic Bacteria <br />
Faster biodegradation (Signal activated ) (isn't this environmental?)<br />
Oncoprotein expressed on the outside missing ligand binding portion<br />
Cytoskeleton in bacteria<br />
Engineering current flow intracellularly<br />
Bacterial gyroscope<br />
Bacterias that produce primers<br />
Proteosome into e. coli design system to keep at steady state to keep e. coli alive<br />
Nail polish (grow back or fade away)<br />
Tight junctions into bacteria<br />
Synthetic Apoptotic signal (and isn't this medical?)<br />
Music Playing Bacteria: loudspeaker<br />
Clock using bacterial gears<br />
Non Newtonian fluid bacteria (using force)<br />
Bacteria piston using sinking and floating mechanism<br />
Gap junction music playing<br />
Rotifers: surviving without water mechanism (protein protection)<br />
Engineering signal glycoproteins into bacteria (integration of virus disrupts reporter gene)<br />
<br />
==Round 2: Official 2010 iGEM Draft==<br />
<br />
Each member chose 3 favorite topics to research<br />
<br />
'''Sean''' - Opsin, Electrogenesis, Tight Junction<br />
<br />
'''Avi''' - Proteosome, Storing Charge, Magnetic Field<br />
<br />
'''Ben''' - Pacemaker, Factor8, Excess Ion uptake<br />
<br />
'''Matt''' - Self Healing Material, WBC, Bacterial Thermometer<br />
<br />
'''Timi''' - Splitting Water, Primer Production, Oncoprotein Express<br />
<br />
'''Jeremy''' - Circadian Rhythm, pH meter, Cytoskeleton<br />
<br />
'''Ragan''' - Selective Phagocytosis, Erythropoietin Production, Inducible Apoptosis<br />
<br />
==Round 3: Presentation and Voting==<br />
<br />
<u>Voted on the basis of</u>: Sexiness, Available Parts, Feasibility, and Applications<br />
<br />
<u>Narrowed Down to</u>: Cytoskeleton, Magnetic Bacteria, and Self Healing Armor<br />
<br />
==Round 4: Group Discussion==<br />
<br />
Cytoskeleton Discarded<br />
<br />
Self-Healing Armor altered to Bacterial Skin<br />
<br />
B-Cell/T-Cell Response Modeling Introduced<br />
<br />
Magnetic Bacteria relegated to side project<br />
<br />
==Round 5: Presentation and Final Voting==<br />
<br />
Main Project: Bacterial Skin<br />
<br />
Side Project: Magnetic Bacteria (Magnetite Synthesis)<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern
Team:Northwestern
2010-10-23T16:11:46Z
<p>Bzhang89: </p>
<hr />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #EFCDF8; color: #FFFFFF" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#000000">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#000000">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#000000">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#000000">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#000000">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#000000">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#000000">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#000000">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#000000">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#000000">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#000000">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#000000">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#000000">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#000000">'''Contact'''</font>]]<br />
|}<br />
{| align="center" border="0" width="75%" style="background:#FFFFFF"<br />
|style="padding: 5" valign="top" width="60%"|<br />
<br />
{|cellspacing="30" border="0"<br />
|'''SCIN - Self-regenerating Chitin INduction'''<br />
<br />
Chitin, found in the exoskeletons of insects and crustaceans, is one of the most abudant substances in nature. Like keratin in skin, it comprises the protective outer layer of these animals. Our chitin expression platform involves generating a layer of chitin from a lawn of bacteria in response to an external molecular cue. This cue induces chitin synthesis (fast) and cell lysis (slow). This system allows for a build-up of chitin followed by cell lysis and subsequent release into the top layer of the lawn. Abrasions expose cells to the external cue for self-repair. In this way, we create a regenerative chitin biolayer with potential medical and industrial applications.<br />
|}<br />
<br />
{|<br />
|align="center"|To find out more, click the links below:<br />
<br />
<html><br />
<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project"><img width="220" class="icon" src="https://static.igem.org/mediawiki/2010/e/ee/Projectoverview_copy.jpg"></a></td><br />
</tr><br />
</table><br />
</html><br />
<br />
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<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
</tr><br />
<tr><br />
<td align="center">Modeling</td><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
</tr><br />
</table><br />
</html><br />
|}<br />
|[[Image:PosterChild.jpg|330px|center]]<br />
<br />
| align = "center" width="15%"|<br />
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<div><iframe frameborder="0" width="200" height="305" src="http://www2.cbox.ws/box/?boxid=2063485&amp;boxtag=jl56tn&amp;sec=main" marginheight="2" marginwidth="2" scrolling="auto" allowtransparency="yes" name="cboxmain" style="border:#ababab 1px solid;" id="cboxmain"></iframe></div><br />
<div><iframe frameborder="0" width="200" height="75" src="http://www2.cbox.ws/box/?boxid=2063485&amp;boxtag=jl56tn&amp;sec=form" marginheight="2" marginwidth="2" scrolling="no" allowtransparency="yes" name="cboxform" style="border:#ababab 1px solid;border-top:0px" id="cboxform"></iframe></div><br />
</html><br />
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<a href="http://www2.clustrmaps.com/counter/maps.php?url=https://2010.igem.org/Team:Northwestern" id="clustrMapsLink" style="text-align: center; line-height: 0"><img src="http://www2.clustrmaps.com/counter/index2.php?url=https://2010.igem.org/Team:Northwestern" style="text-align: center;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onerror="this.onerror=null; this.src='http://clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://clustrmaps.com';" /><br />
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<br />
|-<br />
|colspan="3"|<br />
<br />
== '''Northwestern University''' ==<br />
Northwestern University in Evanston, IL, combines innovative teaching and pioneering research in a highly collaborative environment that transcends traditional academic boundaries.<br />
<br />
Our lab facilities are located at: Technological Institute 2145 Sheridan Road, Evanston, IL 60208<br />
<br />
Find out more about [http://www.northwestern.edu Northwestern University]<br />
<br />
Find out more about [http://www.mccormick.northwestern.edu/ McCormick School of Engineering]<br />
<br />
Find out more about [http://www.weinberg.northwestern.edu/ Weinberg College of Arts and Sciences]<br />
<br />
=='''Sponsors'''==<br />
<br />
[[image:NU.jpg|200px]] [[image:NEB.jpg|200px]] [[image:Promega.jpg|200px]] [[image:invitrogen.jpg|200px]] [[image:VWR.jpg|200px]] [[image:Picture1.jpg|200px]] [[image:BIF.jpg|200px]] [[image:EPOCH.jpg|200px]]<br />
<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Chassis
Team:Northwestern/Project/Chassis
2010-10-23T03:48:32Z
<p>Bzhang89: </p>
<hr />
<div>[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<html><br />
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background: #EFCDF8;<br />
}<br />
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<!--- The Mission, Experiments ---><br />
{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"<br />
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]<br />
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]<br />
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]<br />
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]<br />
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]<br />
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]<br />
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]<br />
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]<br />
|}<br />
<br />
Our team primarily used the high transformation efficiency top10 cells from invitrogen for most protocols.<br />
<br />
In order to ensure lawn formation, the TqsA (also known as the YdgG) knockout were taken from a copy of the Keio Collection with permission from Professor Margaret Saks of Northwestern University. The ΔTqsA strain increases the thickness of biofilm by interfering with the quorum sensing mechanism (more specifically, the autoinducer-2 transport system).<br />
<br />
To prevent bacteria from digesting synthesized Chitin, as it normally would, the ΔChiA strain was also taken from the Keio Collection. Because this strain lacks Chitinase, a digestive enzyme that breaks the glycosidic bonds in Chitin.<br />
<br />
<br />
<br />
<br />
<br />
===Invitrogen Top10 Cells:===<br />
<br />
Purchase and Description: http://products.invitrogen.com/ivgn/product/C404010<br />
<br />
===TqsA aka YdgG Knockouts:===<br />
<br />
http://jb.asm.org/cgi/content/short/188/2/587<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=106356<br />
<br />
===ChiA Knockouts:===<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=100308<br />
<br />
http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW3300<br />
<br />
===MAGE Protocol===<br />
<br />
http://www.wired.com/wiredscience/2009/07/cellfactories/<br />
<br />
http://www.nature.com/nature/journal/v460/n7257/full/nature08187.html</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Chassis
Team:Northwestern/Project/Chassis
2010-10-23T03:34:22Z
<p>Bzhang89: </p>
<hr />
<div>[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<html><br />
<head><br />
<style><br />
body {<br />
background: #EFCDF8;<br />
}<br />
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<!--- The Mission, Experiments ---><br />
{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"<br />
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]<br />
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]<br />
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]<br />
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]<br />
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]<br />
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]<br />
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]<br />
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]<br />
|}<br />
<br />
Our team primarily used the high transformation efficiency top10 cells from invitrogen for most protocols.<br />
<br />
In order to ensure lawn formation, the TqsA (also known as the YdgG) knockout were taken from a copy of the Keio Collection with permission from Professor Margaret Saks of Northwestern University. The ΔTqsA strain increases the thickness of biofilm by interfering with the quorum sensing mechanism (more specifically, the autoinducer-2 transport system).<br />
<br />
To prevent bacteria from digesting synthesized Chitin, as it normally would, the ΔChiA strain was also taken from the Keio Collection. Because this strain lacks Chitinase, a digestive enzyme that breaks the glycosidic bonds in Chitin.<br />
<br />
<br />
<br />
<br />
<br />
===Invitrogen Top10 Cells:===<br />
<br />
http://products.invitrogen.com/ivgn/product/C404010<br />
<br />
===TqsA aka YdgG Knockouts:===<br />
<br />
http://jb.asm.org/cgi/content/short/188/2/587<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=106356<br />
<br />
===ChiA Knockouts:===<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=100308<br />
<br />
http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW3300<br />
<br />
===MAGE Protocol===<br />
<br />
http://www.wired.com/wiredscience/2009/07/cellfactories/<br />
<br />
http://www.nature.com/nature/journal/v460/n7257/full/nature08187.html</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Apoptosis
Team:Northwestern/Project/Apoptosis
2010-10-23T02:51:34Z
<p>Bzhang89: </p>
<hr />
<div>[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<html><br />
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<style><br />
body {<br />
background: #EFCDF8<br />
}<br />
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<!--- The Mission, Experiments ---><br />
{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"<br />
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]<br />
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]<br />
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]<br />
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]<br />
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]<br />
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]<br />
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]<br />
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]<br />
|}<br />
<br />
We used the Apoptosis Cassette by Brown '08 iGEM team (K124017).<br />
<br />
The bacteriophage cassette includes S105 protein (Holin), R protein (Endolysin), and Rz protein, all of which act in combination to lyse the bacteria.<br />
<br />
Holin is a small membrane protein that produces holes in the membrane. <br />
<br />
R is an endolysin that digests and cleaves the cell wall. <br />
<br />
Rz protein, a periplasmic protein, through reasons that are not yet totally clear, carries out the final step of host lysis.</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Chitin_Synthesis
Team:Northwestern/Project/Chitin Synthesis
2010-10-23T02:51:19Z
<p>Bzhang89: </p>
<hr />
<div>[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<html><br />
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<style><br />
body {<br />
background: #EFCDF8<br />
}<br />
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</head><br />
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<!--- The Mission, Experiments ---><br />
{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"<br />
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]<br />
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]<br />
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<span style="col#000000;">'''Notebook'''</span>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]<br />
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]<br />
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]<br />
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]<br />
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]<br />
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]<br />
|}<br />
<br />
Chitin Synthase 3 (CHS3) was cloned out of Saccharomyces Cerevisiae (S.C.) cDNA.<br />
<br />
CHS3 from S.C. was chosen because the the protein does not require cofactors or activation factors and also because it was determined to be the most active of the Chitin Synthase family.<br />
<br />
Chitin Synthase polymerizes N-Acetyl-D-Glucosamine, also known as Chitin, with substrate as UDP-N-Acetyl-D-Glucosamine.</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Lac
Team:Northwestern/Project/Lac
2010-10-23T02:51:03Z
<p>Bzhang89: </p>
<hr />
<div>[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<html><br />
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<style><br />
body {<br />
background: #EFCDF8<br />
}<br />
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<!--- The Mission, Experiments ---><br />
{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"<br />
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]<br />
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]<br />
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]<br />
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]<br />
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]<br />
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]<br />
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]<br />
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]<br />
|}<br />
<br />
For the induction system, our team decided to use the lac-operon/iptg construct because of its widespread use and the availability of information.<br />
<br />
The induction construct consisted of a constitutive promoter (J23100, J23104, or J23105), a combination part of Ribosome Binding Site, Lac Repressor, double Terminators, and Lac Promoter (Q01121, Q04121), and Ribosome Binding Sequence (B0034, B0031, B0032).<br />
<br />
Multiple versions of each part were used to generate a wide range of repressor concentrations, so as to allow for variation between the induction time-delay and degree of Apoptosis protein and Chitin Synthase synthesis.<br />
<br />
The effectiveness of these constructs were tested in the modeling section.</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project/Chassis
Team:Northwestern/Project/Chassis
2010-10-23T02:50:23Z
<p>Bzhang89: </p>
<hr />
<div>[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<html><br />
<head><br />
<style><br />
body {<br />
background: #EFCDF8;<br />
}<br />
</style><br />
</head><br />
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<!--- The Mission, Experiments ---><br />
{|- style="background:#FFFFFF; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="97%" align="center"<br />
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]<br />
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]<br />
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Side Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]<br />
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]<br />
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]<br />
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]<br />
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]<br />
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]<br />
|}<br />
<br />
Our team primarily used the high transformation efficiency top10 cells from invitrogen for most protocols.<br />
<br />
In order to ensure lawn formation, the TqsA (also known as the YdgG) knockout were taken from a copy of the Keio Collection with permission from Professor Margaret Saks of Northwestern University. The ΔTqsA strain increases the thickness of biofilm by interfering with the quorum sensing mechanism (more specifically, the autoinducer-2 transport system).<br />
<br />
To prevent bacteria from digesting synthesized Chitin, as it normally would, the ΔChiA strain was also taken from the Keio Collection. Because this strain lacks Chitinase, a digestive enzyme that breaks the glycosidic bonds in Chitin.<br />
<br />
<br />
<br />
<br />
<br />
''Invitrogen Top10 Cells:''<br />
<br />
http://products.invitrogen.com/ivgn/product/C404010<br />
<br />
''TqsA aka YdgG Knockouts:''<br />
<br />
http://jb.asm.org/cgi/content/short/188/2/587<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=106356<br />
<br />
''ChiA Knockouts:''<br />
<br />
http://cgsc2.biology.yale.edu/Mutation.php?ID=100308<br />
<br />
http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW3300<br />
<br />
''MAGE Protocol''<br />
<br />
http://www.wired.com/wiredscience/2009/07/cellfactories/<br />
<br />
http://www.nature.com/nature/journal/v460/n7257/full/nature08187.html</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Contact
Team:Northwestern/Contact
2010-10-23T02:49:26Z
<p>Bzhang89: </p>
<hr />
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<br />
<html><br />
<head><br />
<style><br />
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background: #EFCDF8; <!-- EEDCC8 url(https://static.igem.org/mediawiki/2010/3/38/BG1.jpg) repeat-y; --><br />
}<br />
</style><br />
</head><br />
</html><br />
<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#2B3856">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
If you have any questions or remarks, please let us know by e-mailing us at [mailto:nuigem10@gmail.com nuigem10@gmail.com]<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Media
Team:Northwestern/Media
2010-10-23T02:48:57Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
<br />
<br />
<html><br />
<style><br />
/* Wiki Hacks - START */<br />
#globalWrapper {<br />
background-color: transparent;<br />
padding-bottom:0px;<br />
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}<br />
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}<br />
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<br />
<br />
/* Wiki Hacks - END */<br />
<br />
<br />
#content {<br />
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</style><br />
</html><br />
<br />
<html><br />
<head><br />
<style><br />
body {<br />
background: #EFCDF8; <!-- EEDCC8 url(https://static.igem.org/mediawiki/2010/3/38/BG1.jpg) repeat-y; --><br />
}<br />
</style><br />
</head><br />
</html><br />
<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#2B3856">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
'''Spring 2010''': NU iGEM in Centerpiece Article (a Northwestern Quarterly by the Office for Research): [http://www.biosci.northwestern.edu/documents/CenterpieceArticle-Spring2010.pdf link]<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/References
Team:Northwestern/References
2010-10-23T02:48:37Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
<br />
<br />
<html><br />
<style><br />
/* Wiki Hacks - START */<br />
#globalWrapper {<br />
background-color: transparent;<br />
padding-bottom:0px;<br />
border: none;<br />
}<br />
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height: 0px;<br />
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top: 100px;<br />
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<br />
<br />
/* Wiki Hacks - END */<br />
<br />
<br />
#content {<br />
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</style><br />
</html><br />
<br />
<html><br />
<head><br />
<style><br />
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background: #EFCDF8; <!-- EEDCC8 url(https://static.igem.org/mediawiki/2010/3/38/BG1.jpg) repeat-y; --><br />
}<br />
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</html><br />
<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#2B3856">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
=== Lac Operon Control ===<br />
<br />
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG<br />
<br />
===Chitin===<br />
<br />
Adding Glucosamine in medium: http://ec.asm.org/cgi/reprint/2/5/886<br />
<br />
Chitin synthesis Pathway (image): [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg]<br />
<br />
Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long <br />
<br />
Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html<br />
<br />
=== Chitin Synthesis ===<br />
<br />
Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311<br />
<br />
CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465<br />
<br />
===Chitin Staining (Calcofluor)===<br />
<br />
Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf<br />
<br />
Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za<br />
<br />
Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/<br />
<br />
Data sheet: http://tinyurl.com/283wax2<br />
<br />
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html<br />
<br />
=== Apoptosis ===<br />
<br />
partsregistry: http://partsregistry.org/Cell_death<br />
<br />
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===<br />
<br />
DMAO(Live), EtD-III(Dead)<br />
*http://www.promokine.info/products/cell-analysis/cell-staining-reagents-related-products/<br />
*http://www.biotium.com/product/product_info/Protocol/30027.pdf<br />
<br />
===Keio Collection - KnockOuts===<br />
<br />
Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html <br />
<br />
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp<br />
<br />
Method: http://www.pnas.org/content/97/12/6640.full.pdf+html<br />
<br />
Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html<br />
<br />
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls<br />
<br />
=== ChiA (Chitinase) Knockout ===<br />
<br />
Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts<br />
<br />
Chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300<br />
<br />
===ydgg/tqsA (AI2-Transporter) Knockout===<br />
<br />
Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf<br />
<br />
=== BIF (Biological Imaging Facility)===<br />
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br /><br />
Methods: http://www.northwestern.edu/bioimaging/methods.html<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Links
Team:Northwestern/Links
2010-10-23T02:48:13Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
<br />
<br />
<html><br />
<style><br />
/* Wiki Hacks - START */<br />
#globalWrapper {<br />
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border: none;<br />
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/* Wiki Hacks - END */<br />
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</style><br />
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<br />
<html><br />
<head><br />
<style><br />
body {<br />
background: #EFCDF8; <!-- EEDCC8 url(https://static.igem.org/mediawiki/2010/3/38/BG1.jpg) repeat-y; --><br />
}<br />
</style><br />
</head><br />
</html><br />
<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#2B3856">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
===Basic iGEM Resources===<br />
Digestion & Ligations: http://ginkgobioworks.com/support/<br />
<br />
Openwetware: http://openwetware.org/wiki/Protocols<br />
<br />
Medal Requirements: https://2010.igem.org/Judging/Judging_Criteria<br />
<br />
Parts Registry: http://partsregistry.org/Part_Types<br />
<br />
===Protocol-Related===<br />
<br />
Plasmid Naming Convention: http://partsregistry.org/Help:Plasmids/Nomenclature<br />
<br />
Part Types: http://partsregistry.org/Part_Types<br />
<br />
PCR Primer Design: http://perlprimer.sourceforge.net/<br />
<br />
Plate Reader: http://www.biotek.com/resources/articles/beta-galactosidase-plate-reader.html<br />
<br />
===Research Resources===<br />
<br />
Friendly Pubmed: http://www.hubmed.org/<br />
<br />
E.Coli Genotypes: http://openwetware.org/wiki/E._coli_genotypes<br />
<br />
===Wikipedia Editing Resources===<br />
<br />
http://www.mediawiki.org/wiki/Help:Formatting<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Safety
Team:Northwestern/Safety
2010-10-23T02:47:55Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
<br />
<br />
<html><br />
<style><br />
/* Wiki Hacks - START */<br />
#globalWrapper {<br />
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<br />
/* Wiki Hacks - END */<br />
<br />
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}<br />
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</style><br />
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<br />
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<head><br />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#2B3856">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
==Safety==<br />
<br />
Please use this page to answer the safety questions posed on the [[Safety | safety page]].<br />
<br />
1. '''Would any of your project ideas raise safety issues in terms of:'''<br />
* researcher safety,<br />
* public safety, or<br />
* environmental safety?<br />
2. '''Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,'''<br />
* did you document these issues in the Registry?<br />
* how did you manage to handle the safety issue?<br />
* How could other teams learn from your experience?<br />
3. '''Is there a local biosafety group, committee, or review board at your institution?'''<br />
* If yes, what does your local biosafety group think about your project?<br />
* If no, which specific biosafety rules or guidelines do you have to consider in your country?<br />
4. '''Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions?'''<br />
'''How could parts, devices and systems be made even safer through biosafety engineering?'''<br />
<br />
<br />
'''Would any of your project ideas raise safety issues in terms of researcher safety, public safety or environmental safety?'''<br /><br />
<br />
We can pinpoint three possible negative consequences of our project:<br />
<br />
1. The strain produces some toxin related to chitin in addition to the chitin itself.<br><br />
2. The strain produces pure chitin, and the extraction thereof results in a high incidence of allergic reaction among those that work with it.<br><br />
3. The strain becomes airborne, resulting in lung infection and chitin deposition in the airways.<br><br />
<br />
<br />
'''Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?'''<br /><br />
<br />
No.<br />
<br />
'''If yes, did you document these issues in the Registry?'''<br /><br />
<br />
'''How did you manage to handle the safety issue?'''<br /><br />
<br />
'''How could other teams learn from your experience?'''<br /><br />
<br />
'''Is there a local biosafety group, committee, or review board at your institution?'''<br /><br />
<br />
Yes.<br />
<br />
'''If yes, what does your local biosafety group think about your project?'''<br /><br />
<br />
<br />
<br />
'''If no, which specific biosafety rules or guidelines do you have to consider in your country?'''<br /><br />
<br />
'''Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions?'''<br /><br />
<br />
When pursuing a project, an iGEM team should attempt to think ahead of any dangerous consequences of their pursuits. If there are any concerns, the team should consider drafting recommendations for any group that might desire to utilize their devices. If infection is a concern, appropriate apoptotic signals should be considered.<br />
<br />
'''How could parts, devices and systems be made even safer through biosafety engineering?'''<br />
<br />
Parts might be programmed with an apoptotic signal so that the bacteria dies when separated from culture. In addition, certain "key" systems may be desirable. If parts provided are of a somewhat "black box" format, it may be possible to program in killswitches so that if a strain is not treated with a particular nutrient or other molecule, transformed strains either apoptose or do not have the proper function. If these keys are sent with the desired part, it may make it more difficult to "hack" dangerous parts for illicit use.<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Protocol
Team:Northwestern/Protocol
2010-10-23T02:47:32Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#2B3856">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
== '''DNA''' ==<br />
<br />
[[Team:Northwestern/Protocol/PDNA|Prepping DNA from the kit plates]]<br />
<br />
[[Team:Northwestern/Protocol/Quikchange (from primers to colonies!|Quikchange: Primers to Colonies]]<br />
<br />
[[Team:Northwestern/Protocol/Kit to Stock Plasmid|Kit to Stock Plasmid]]<br />
<br />
[[Team:Northwestern/Protocol/Ethanol Precipitation|Ethanol Precipitation]]<br />
<br />
[[Team:Northwestern/Protocol/New Part Design(PCR)|New Part Design]]<br />
<br />
=='''Bacterial Work'''==<br />
<br />
[[Team:Northwestern/Protocol/Transformation|Transformation]]<br />
<br />
[[Team:Northwestern/Protocol/O/N Culture|Overnight Cultures]]<br />
<br />
[[Team:Northwestern/Protocol/Preparation of Competent Cells|Preparation of Competent Cells]]<br />
<br />
[[Team:Northwestern/Protocol/LB Media|LB Media]]<br />
<br />
[[Team:Northwestern/Protocol/Preparing Plates|Preparing Plates]]<br />
<br />
[[Team:Northwestern/Protocol/Glycerol Stocks|Glycerol Stocks]]<br />
<br />
=='''Assembly'''==<br />
<br />
[[Team:Northwestern/Protocol/Restriction Enzyme Digests|Restriction Enzyme Digests]]<br />
<br />
[[Team:Northwestern/Protocol/Plasmid Construction|Plasmid Construction]]<br />
<br />
[[Team:Northwestern/Protocol/3A Assembly|3A Assembly]]<br />
<br />
[[Team:Northwestern/Protocol/Ligations|Ligations]]<br />
<br />
[[Team:Northwestern/Protocol/Mini Prep|Qiagen Mini Prep]]<br />
<br />
=='''Microscopy'''==<br />
<br />
[[Team:Northwestern/Protocol/Confocal Microscopy|Confocal Microscopy]]<br />
<br />
[[Team:Northwestern/Protocol/Fluorescence Microscopy|Fluorescence Microscopy]]<br />
<br />
=='''Reagents'''==<br />
<br />
[[Team:Northwestern/Protocol/Reagents|Reagents]]<br />
<br />
=='''Cell Staining'''==<br />
<br />
[[Team:Northwestern/Protocol/Rhodamine-Conjugated Chitin Probe|Rhodamine-Conjugated Chitin Probe]]<br />
<br />
[[Team:Northwestern/Protocol/Methanol Fixation|Methanol Fixation]]<br />
<br />
[[Team:Northwestern/Protocol/LIVE/DEAD® BacLight - Bacterial Viability Kit|Live/Dead Baclight]]<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Calendar
Team:Northwestern/Calendar
2010-10-23T02:47:03Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#2B3856">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
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<iframe src="https://www.google.com/calendar/embed?title=Northwestern%20iGEM%202010&amp;height=600&amp;wkst=1&amp;bgcolor=%23FFFFFF&amp;src=nuigem10%40gmail.com&amp;color=%23853104&amp;ctz=America%2FChicago" style=" border-width:0 " width="933" height="600" frameborder="0" scrolling="no"></iframe><br />
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<div align="right"><br />
click on ^<br />
<br />
nuigem10//igem2010 @g<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Notebook
Team:Northwestern/Notebook
2010-10-23T02:46:43Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#2B3856">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
[[Brainstorming April-June 2010]]<br />
<br />
[[Week1 6/13/10-6/19/10]]<br />
<br />
[[Week2 6/20/10-6/26/10]]<br />
<br />
[[Week3 6/27/10-7/3/10]]<br />
<br />
[[Week4 7/4/10-7/10/10]]<br />
<br />
[[Week5 7/11/10-7/17/10]]<br />
<br />
[[Week6 7/18/10-7/24/10]]<br />
<br />
[[Week7 7/25/10-7/31/10]]<br />
<br />
[[Week8 8/1/10-8/7/10]]<br />
<br />
[[Week9 8/8/10-8/14/10]]<br />
<br />
[[Week10 8/15/10-8/21/10]]<br />
<br />
[[Week11 8/22/10-8/28/10]]<br />
<br />
[[Week12 8/29/10-9/4/10]]<br />
<br />
[[Week13 9/5/10-9/11/10]]<br />
<br />
[[Week14 9/12/10-9/18/10]]<br />
<br />
[[Week15 9/19/10-9/25/10]]<br />
<br />
[[Week16 9/26/10-10/2/10]]<br />
<br />
[[Week17 10/3/10-10/9/10]]<br />
<br />
[[Week18 10/10/10-10/16/10]]<br />
<br />
[[Week19 10/17/10-10/23/10]]<br />
<br />
[[Week20 10/24/10-10/30/10]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
===10/3/10===<br />
Timi miniprepped the CP-LacPI-GFP cultures and digested them with E/P. She then poured a big and a small gel.<br />
<br />
Kevin came in and ran the digested CP-LacPI-GFP, digested CP-LacPI with digested Cp and digested LacPI parts.<br />
----<br />
<br />
===10/4/10===<br />
Timi and Kevin decided to take a day off :)<br />
----<br />
<br />
===10/5/10===<br />
Timi and Kevin came in to discuss why their gels were running strangely. We believe there is something wrong with our buffer, so we are swapping everything out with a fresh batch of Prof. Mordacq's 0.5x TBE buffer. Timi poured a large gel that we will be using tomorrow.<br />
----<br />
===10/6/10===<br />
----<br />
===10/7/10===<br />
Timi- took part 2-17F out of the DNA kit. Transformed into T10 cells to grow overnight.<br />
----<br />
<br />
===10/8/10===<br />
Kevin- ran gel of the CP-LacPI parts. Gel results are still inconclusive. Also put in an overnight culture of the 2-17F part into the incubator for Timi.<br />
----<br />
<br />
===10/9/10===<br />
Timi- Miniprepped the 2-17F part. Digested the DNA with E/P and ligated the 2-17F GFP part into Chlor and Tet backbone.<br />
----<br />
<br />
===10/10/10===<br />
Timi- Transformed and plated part 2-17F onto Chlor and Tet plates. Will be ready for miniprepping tomorrow.<br />
----<br />
<br />
===10/11/10===<br />
----<br />
===10/12/10===<br />
Matt - digested LacP-RBS with SpeI in preparation for standard assembly with ES digested CHS3<br />
----<br />
<br />
===10/13/10===<br />
----<br />
===10/14/10===<br />
Kevin transformed T10 cells with CP-LacPI parts that we did not have much digest of left. He plated them onto TET plates.<br />
----<br />
<br />
===10/15/10===<br />
Kevin took out the CP-LacPI plates and put them into the 4 degree for Timi. Timi inoculated overnight cultures at 7pm.<br />
----<br />
<br />
===10/16/10===<br />
Team meeting at 12pm to work on our wiki. We made the discouraging discovery that our CHS3 DNA that Ben had worked super hard for actually contained XbaI restriction sites. This complicates our assembly and might jeopardize the success of our project. We will talk to the advisors about this to see if things can still work out.<br />
<br />
Timi and Kevin miniprepped the CP-LacPI inoculations, digested them with E&P, and ligated them to GFP.<br />
----<br />
<br />
===10/17/10===<br />
Timi phosphotase-treated the newly digested chlor backbone and ligated a second set of CP-LacPI.<br />
Kevin transformed and plated this new set of phosophotase treated Cp-LacPI.<br />
<br />
Kevin inoculated the first set of non-phosphotase treated CP-LacPI inoculations.<br />
<br />
----<br />
<br />
===10/18/10===<br />
Matt miniprepped 31GFP, 21GFP (old), and 32GFP (old). He digested the miniprepped DNA with E/P for Kevin to run on a gel. He also reinoculated all 9 CP-LacPI combinations.<br />
<br />
Matt inoculated the phosophotase-treated ligations at 9pm.<br />
----<br />
<br />
===10/19/10===<br />
Plan: Timi miniprepped the phosphotase-treated CP-LacPI and ran them on a gel. But Mordacq's class was using the thermocycler so Timi just sat and read.<br />
<br />
Plate reader fun with Kevin @ 3pm.<br />
<br />
Sean - ran CHS3(pMAL+SDM) digest, pMAL digest, and ligation on a gel -> CHS3 exhibited incorrect bands (there are 2, when there should be 1) ligation showed nothing -> plan to run CHS3 undigested and rerun the above 3.<br />
----<br />
<br />
===10/20/10===<br />
Timi and Kevin ligated the old 212, 312, and 322 parts into a phosophotase-treated Chlor backbone for submission into the registry. They transformed and plated for inoculation tomorrow night.<br />
<br />
They inoculated cultures for the plate reader.<br />
----<br />
<br />
===10/21/10===<br />
Timi/Kevin: Early morning plate reader protocol entering.<br />
<br />
Weekly lab meeting with advisors.<br />
----<br />
<br />
===10/22/10===<br />
PCR'ed out CHS3 with pMAL ends and Gel extracted<br />
----<br />
<br />
===10/23/10===<br />
----<br />
===10/24/10===<br />
----<br />
===10/25/10===<br />
----<br />
===10/26/10===<br />
----<br />
===10/27/10===<br />
----<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Parts
Team:Northwestern/Parts
2010-10-23T02:46:23Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#2B3856">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
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!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
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!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
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<br />
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|<br />
<br />
<br />
===Parts===<br />
<br />
<groupparts>iGEM010 Northwestern</groupparts></div>
Bzhang89
http://2010.igem.org/Team:Northwestern/SideProject
Team:Northwestern/SideProject
2010-10-23T02:46:02Z
<p>Bzhang89: </p>
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<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#2B3856">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
==Human Practices Essay==<br />
Ragan, put the essay here.<br />
----<br />
==Ethics==<br />
Prompt: Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
<br />
Resources: <br />
<br />
* http://bioethics.northwestern.edu/faculty/zoloth.html<br />
<br />
* http://www.feinberg.northwestern.edu/research/cores/units/ethics<br />
<br />
* http://en.wikipedia.org/wiki/Medical_ethics<br />
<br />
* http://en.wikipedia.org/wiki/Bioethics<br />
<br />
* http://en.wikipedia.org/wiki/Synthetic_biology#Social_and_Ethical<br />
<br />
==Abstract==<br />
Ethics oriented Analysis of synthetic biology in general and in relation to the NU2010 Bacterial Skin project.<br />
==Outline==<br />
===Preamble or Historical Perspective===<br />
Aversion to synthetic life, religious, uncanny valley, Frankensteinian fears <br />
http://en.wikipedia.org/wiki/History_of_biotechnology<br />
http://en.wikipedia.org/wiki/Asilomar_Conference_on_Recombinant_DNA<br />
http://en.wikipedia.org/wiki/Timeline_of_biotechnology<br />
http://www.wired.com/magazine/2010/07/pl_backstory_timemachine/<br />
===Medical (Societal) Ethics===<br />
Beneficence, Non-maleficence, autonomy (zoloth principle=fidelity), Justice, (Dignity, Truthfulness)<br />
===Moral (Individual) Ethics===<br />
Kant(Categorical Imperative, ends) vs Mill(Utilitarianism) vs Aristotle(Character)<br />
===Unique Ethical Problems===<br />
Ontological<br />
Epistemic<br />
===Project specific problems===<br />
application specific analysis<br />
<br />
<br />
==Magnetite Production==<br />
<br />
Siderophore<br />
<br />
TonB<br />
<br />
Oxireductases<br />
<br />
FeCl2,Fecl3 reinforced media<br />
<br />
mms6<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Acknowledgements
Team:Northwestern/Acknowledgements
2010-10-23T02:45:47Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
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<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#2B3856">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
<br />
=='''Sponsors'''==<br />
'''EMD CHEMICALS - Shou Wong'''<br />
<br />
Corresponded with Shou who promised to meet with team in August and to potentially set up sponsorship with EMD Millipore.<br />
<br />
'''EPOCH LIFE SCIENCES - XueNong Zhang'''<br />
<br />
Sponsorship of 1000 DNA Spin Columns<br />
<br />
'''NEB - Lori Tonello'''<br />
<br />
Sponsorship of Biobrick Kits, Antarctic Phosphotase, Chitin Rhodamine, Taq polymerase, 1kb DNA ladder, DpnI and pMAL<br />
<br />
'''PROMEGA - Sara Mann'''<br />
<br />
Nominal amount of free products and additional discounts on petri dishes, pipet tips, Nova Blue cells, T4 DNA Ligase, pour boats, nuclease free water, gloves, biohazard bags, delicate wipers, serological pipets, 1.7 mL tubes, and agar.<br />
<br />
'''QIAGEN - Jackie Ciardo'''<br />
<br />
Discounts on miniprep kits, gel extraction kits, and PCR purification kits.<br />
<br />
'''VWR - Amy Vanarsdale'''<br />
<br />
Additional discounts on petri dishes, pipet tips, Nova Blue cells, T4 DNA Ligase, pour boats, nuclease free water, gloves, biohazard bags, delicate wipers, serological pipets, 1.7 mL tubes, and agar.<br />
<br />
=='''Advisors'''==<br />
<br />
'''John Mordacq''' <br><br />
Distinguished Senior Lecturer<br><br />
Program in Biological Sciences<br><br />
Email: j-mordacq@northwestern.edu<br> <br />
<br />
'''Joshua Leonard'''<br><br />
Department of Chemical and Biological Engineering<br><br />
Email: j-leonard@northwestern.edu<br> <br />
<br />
'''Michael Jewett'''<br><br />
Department of Chemical and Biological Engineering<br><br />
Email: m-jewett@northwestern.edu<br />
<br />
=='''NU Faculty and Affiliates'''==<br />
'''Debora Boetcher''' <br /> McCormick Biological and Chemical Engineering, Office Assistant <br /> Email: d-boetcher@northwestern.edu <br /> Contribution: Assisted with logistics such as billing and receiving of products. <br /><br />
<br />
'''Paul Brannon''' <br /> Biological Imaging Facilities, Confocal Specialist <br /> Biology, University of Chicago <br /> Email: p-brannon@northwestern.edu <br /> Room: Hogan 5-150 <br /> Contribution: Trained team members for confocal microscopy operation and made suggestions on how to integrate confocal microscopy into our project. <br /><br />
<br />
'''Jamie Bufkin''' <br /> Biological Imaging Facilities, Program Assistant <br /> Sociology & History, University of San Diego <br /> Email: j-bufkin@northwestern.edu <br /> Room: Hogan 5-150 <br /> Contribution: Set up confocal training for team members. <br /><br />
<br />
'''Sara Fernandez Dunne''' <br /> High Throughput Analysis Lab, Research Technologist II <br /> <br />
Northwestern University <br /> Email: s-fernandez@northwestern.edu <br /> Room: Hogan 4-140 <br /> Contribution: trained team members for plate reader and made suggestions on how to integrate the plate reader into our project. <br /><br />
<br />
'''John F. Marko'''<br /> Professor <br /> Biochemistry, Molecular Biology & Cell Biology; Physics & Astronomy <br /> PhD, Massachusetts Institute of Technology <br /> Email: john-marko@northwestern.edu <br /> Phone: (847) 467-1276 <br /> Room: Pancoe Rm 4109 <br /> Contribution: Discussed using Keio knockout collection. <br /><br />
<br />
'''Linda Mattice''' <br /> Yale University Molecular, Cellular and Developmental Biology <br /> E. Coli Keio Knockout Collection Distributor <br /> Email: cgsc@yale.edu <br /> Contribution: Send us Keio Collection ydgG knockout cells. <br /><br />
<br />
'''William Russin'''<br /> Biological Imaging Facilities, Manager <br /> PhD, University of Wisconsin - Madison <br /> Email: w-russin@northwestern.edu <br /> Phone: (847) 491-6657 <br /> Room: Hogan 5-150 <br /> Contribution: Discussed microscopy options for our project and integrated confocal microscopy into our project. <br /><br />
<br />
'''Margaret (Peggy) Saks'''<br /> Research Professor, The Uhlenbeck Lab <br /> Biochemistry, Molecular Biology & Cell Biology <br /> Email: m-saks@northwestern.edu <br /> Phone: (847) 491-5624<br /> Room: Pancoe Rm 4113 <br /> Times: 10:30am-end <br /> Contribution: Discussed chiA, tqsA knockout procedures. <br /><br />
<br />
'''Wei Zhang''' <br /> Civil and Environmental Engineering, PhD Candidate <br /> Aaron Packman Lab <br /> Interests: Flow and biofilm interaction and microbial communities in biofilms. <br /> Email: w-zhang@u.northwestern.edu <br /> Contribution: Discussed potential use of flow cells to form a biofilm. <br /><br />
<br />
'''Laurie Zoloth''' <br /> Northwestern University Feinberg School of Medicine <br /> Professor of Medical Humanities & Bioethics and Religion <br /> Director of Center for Bioethics, Science and Society <br /> Interests: Ethics in Genetic Medicine, in Stem Cell Research, Justice in health care allocation <br /> Email: lzoloth@northwestern.edu <br /> Contribution: Discussed ethics of synthetic biology and made suggestions on potential essay topics. <br /><br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Team
Team:Northwestern/Team
2010-10-23T02:45:30Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#2B3856">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
{|border = "0" align="center" cellspacing="20" cellpadding="0" width="900px"<br />
|+'''ADVISORS'''<br />
----<br />
|-<br />
|width="33%" align="center"| [[Image: Jewett.jpg|center|150px]]'''Professor Michael Jewett'''<br />
|width="34%" align="center"| [[Image: Leonard.jpg|center|150px]]'''Professor Joshua Leonard'''<br />
|width="33%" align="center"| [[Image: Mordacq.jpg|center|178px]]'''Professor John Mordacq'''<br />
|-<br />
|Department of Chemical and Biological Engineering <br />
<br />
Tel: (847) 467-5007<br />Fax: (847) 491-3728<br />Email: m-jewett@northwestern.edu<br />
||Department of Chemical and Biological Engineering <br />
<br />
tel: 847/491-7455<br />fax: 847/491-3728<br />Email: j-leonard@northwestern.edu<br />
||Distinguished Senior Lecturer <br />
Program in Biological Sciences<br />
<br />
Tech MG79<br />Tel: 847-491-7835<br />Email: j-mordacq@northwestern.edu <br />
|}<br />
<br />
<br />
{|border = "0" align="center" cellspacing="20"<br />
|+'''TEAM MEMBERS'''<br />
----<br />
|-<br />
|align="center"|[[Image: Ben.jpg|center|100px]]'''Ben Zhang'''||'''Benjamin Zhang'''<br />Northwestern University, MEAS 2011<br />Biomedical Engineering<br />(405) 397-3817<br />xuzhang2007@u.northwestern.edu<br /> Weird Fact: Ben insists that he digested fetal pigs during bio lab in high school instead of dissecting them. <br />
<br />
He also has ears of a cat. <br /><br />
|-<br />
|align="center"|[[Image: Kevin.jpg|center|100px]]'''Kevin Rogacki'''|| '''Kevin Rogacki''' <br /> Northwestern University, MEAS 2011<br />Biomedical Engineering<br />(708) 373-9388<br /> krr@u.northwestern.edu<br /> Weird Fact: Kevin pronounces the word "carbonyl" strangely...and thinks he's right. <br /><br />
|-<br />
|align="center"|[[Image: Matt.jpg|center|100px]]'''Matt Tong'''|| '''Matthew Tong''' <br /> Northwestern University, WCAS 2011<br />Biological Sciences<br />(516) 554-2333<br /> matttong@u.northwestern.edu<br /> Weird Fact: Matt once gave a delivery man a $22 dollar tip for an $18 pizza order. <br /><br />
|-<br />
|align="center"|[[Image: Ragan.jpg|center|100px]]'''Ragan Pitner'''||'''Ragan Pitner'''<br />Northwestern University, MEAS 2011<br />Biomedical Engineering<br />raganpitner2007@u.northwestern.edu<br /> Weird Fact: Ragan locked himself out of the lab once. <br />
<br />
Funny story. Ask him about it. <br /><br />
|-<br />
|align="center"|[[Image: Sean.jpg|center|100px]]'''Sean Yu'''||'''Sean Chonghwan Yu'''<br />Northwestern University, MEAS 2011<br />Biomedical Engineering<br />(440) 655-1759<br />cyu286@u.northwestern.edu <br /> Weird Fact: All this kid wants to do is liquify meat. <br />
<br />
Seriously, don't you think your time could be better spent? <br /><br />
|-<br />
|align="center"|[[Image: Timi.jpg|center|100px]]'''Timi Chu'''||'''Timi Chu'''<br /> Northwestern University, MEAS 2013<br />Biomedical Engineering<br />(347) 671-1239<br />timi@u.northwestern.edu<br /> Weird Fact: Timi insists she is not a picky eater. <br />
<br />
Pineapple and shrimp just make her head itch. <br /><br />
|-<br />
<br />
{|border = "0" align="center" cellspacing="20" cellpadding="0" width="900px"<br />
|+'''FOUNDERS'''<br />
----<br />
|-<br />
|width="50%" align="center"| [[Image: avi.jpg|center|100px]]'''Avi Samelson'''<br />
|width="50%" align="center"| [[Image: Jeremy.jpg|center|100px]]'''Jeremy Schifberg'''<br />
|-<br />
<br />
|-<br />
|align="center"|University of California, Berkeley <br /> Molecular and Cell Biology <br /> Northwestern Class of 2010 <br /> asamelson@gmail.com<br />
<br />
|align="center"|Northwestern Class of 2010 <br /> Biological Sciences, Integrated Science Program <br /> jeremyschifberg2007@u.northwestern.edu<br />
|-<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Brainstorm
Team:Northwestern/Brainstorm
2010-10-23T02:44:33Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#2B3856">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
==Round 1: Group Brainstorming Session==<br />
<br />
<br />
'''Health/Medicine'''<br />
Release in presence of wound signal (pH) Factor VIII<br />
Symbiosis with human body<br />
Selective phagocytosis (absorb toxin)<br />
Selective phagocytosis (lead)<br />
Phagocytosis for drug overdoses<br />
Drug sensing bactera<br />
Bacterial spermicide <br />
Drug delivery method through WBC<br />
Apoptosis with drug delivery when disease is recognized<br />
Vitamin and mineral delivery<br />
Bacteria that takes up excess ions in the body<br />
Self Healing material: growth factor<br />
Apoptosis in presence of a particular disease<br />
Swine Flu testing on site<br />
Target bad cells selectively based on offset in circadian rythmn<br />
Cure celiac’s with bacteria<br />
Ethrypoeitin production in e. coli<br />
Thrombolytics in presence in LDL<br />
Thrombolytics in precense of clots (macrophages)<br />
Bacterial pacemakers<br />
<br />
<br />
'''Food/Energy'''<br />
Supplementary vitamin and minerals to be grown on produce<br />
Removable pesticide bacterial film<br />
Cheese reservatrol<br />
Splitting Hydrogen from water<br />
Electrogenesis: produce voltage from bacteria<br />
<br />
'''Environment'''<br />
Consume gases in the air (ozone)<br />
Consume (CFCs)<br />
On site radiation testing (make it click like a Geiger counter) <br />
Breaking down plastics (look at past presentation)<br />
Photo-driven battery<br />
<br />
'''Manufacturing/Industrial'''<br />
Trace explosive Bacteria<br />
EXPLODING BACTERIA<br />
Bacterial Superglue<br />
Resistors<br />
Capacitors (Storing charge)<br />
Phagocytosis for water in shoes<br />
Bacterial barometer<br />
Bacterial paper to print on <br />
Active pH buffer for e. coli (target pH) <br />
pH meter<br />
Cilia creating fluid flow, generating fluid current<br />
Create ferrofluuid to create magnetism<br />
Bacteria to regulate the temperature of a surface (endothermic and exothermic reaction)<br />
Long lasting bacterial sunblock<br />
Bacterial Clothing <br />
Thermal heating for toes<br />
Adjusting Young’s Modulus<br />
Contracting group of cells<br />
Thermometer<br />
Bacterial film that responds to laser so you can sketch on it. (express GFP light induced promoter)<br />
Bacterial Gears <br />
<br />
'''Miscellaneous'''<br />
ELISA for DNA<br />
ELISA for mRNA<br />
Magnetic Bacteria <br />
Faster biodegradation (Signal activated ) (isn't this environmental?)<br />
Oncoprotein expressed on the outside missing ligand binding portion<br />
Cytoskeleton in bacteria<br />
Engineering current flow intracellularly<br />
Bacterial gyroscope<br />
Bacterias that produce primers<br />
Proteosome into e. coli design system to keep at steady state to keep e. coli alive<br />
Nail polish (grow back or fade away)<br />
Tight junctions into bacteria<br />
Synthetic Apoptotic signal (and isn't this medical?)<br />
Music Playing Bacteria: loudspeaker<br />
Clock using bacterial gears<br />
Non Newtonian fluid bacteria (using force)<br />
Bacteria piston using sinking and floating mechanism<br />
Gap junction music playing<br />
Rotifers: surviving without water mechanism (protein protection)<br />
Engineering signal glycoproteins into bacteria (integration of virus disrupts reporter gene)<br />
<br />
==Round 2: Official 2010 iGEM Draft==<br />
<br />
Each member chose 3 favorite topics to research<br />
<br />
'''Sean''' - Opsin, Electrogenesis, Tight Junction<br />
<br />
'''Avi''' - Proteosome, Storing Charge, Magnetic Field<br />
<br />
'''Ben''' - Pacemaker, Factor8, Excess Ion uptake<br />
<br />
'''Matt''' - Self Healing Material, WBC, Bacterial Thermometer<br />
<br />
'''Timi''' - Splitting Water, Primer Production, Oncoprotein Express<br />
<br />
'''Jeremy''' - Circadian Rhythm, pH meter, Cytoskeleton<br />
<br />
'''Ragan''' - Selective Phagocytosis, Erythropoietin Production, Inducible Apoptosis<br />
<br />
==Round 3: Presentation and Voting==<br />
<br />
<u>Voted on the basis of</u>: Sexiness, Available Parts, Feasibility, and Applications<br />
<br />
<u>Narrowed Down to</u>: Cytoskeleton, Magnetic Bacteria, and Self Healing Armor<br />
<br />
==Round 4: Group Discussion==<br />
<br />
Cytoskeleton Discarded<br />
<br />
Self-Healing Armor altered to Bacterial Skin<br />
<br />
B-Cell/T-Cell Response Modeling Introduced<br />
<br />
Magnetic Bacteria relegated to side project<br />
<br />
==Round 5: Presentation and Final Voting==<br />
<br />
Main Project: Bacterial Skin<br />
<br />
Side Project: Magnetic Bacteria (Magnetite Synthesis)<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project
Team:Northwestern/Project
2010-10-23T02:43:59Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#2B3856">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
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|align="left" valign="top" width="80%" style="padding: 5"|<br />
<br />
Our main project is to simulate mammalian skin using chitin in E. Coli. This process involves four major components: Lawn Formation, Chitin Synthesis, Bacterial Apoptosis, and lac-Operon Signaling.<br />
<br />
A thick bacterial lawn is generated by plating ydgG knock-out mutants (acquired from the Keio Collection) in an enriched agar plate. The protein product of ydgG plays an integral role in AI-2 transport. ydgG knock-outs exhibit increased motility which should ultimately allow for a thick and level lawn.<br />
<br />
The 3.5kbp Chitin Synthase III gene is extracted from the Saccharomyces Cerevisiae genome. Chitin Synthase III catalyzes the polymerization of chitin by transferring UDP-N-acetyl-D-glucosamine to an N(1,4 N-Acetyl-beta-D-glucosaminyl) to produce N+1(1,4 N-Acetyl-beta-D-glucosaminyl).<br />
<br />
Apoptosis of cells is achieved by using the bacteriophage lysis cassette built by the Brown '08 iGEM Team. The cassette includes Holin, Endolysin, and Rz Protein genes. These enzymes puncture and degrade the cell membrane which results in lysing of the cell and the release of synthesized chitin.<br />
<br />
Once the lawn is established, an IPTG solution is sprayed over the lawn to induce chitin synthesis (fast response) and apoptosis (slow response). IPTG mimics allolactose which binds to the LacI repressor, causing LacI to detach from DNA and allowing RNA Polymerase to begin transcription. This will allow for a build-up in chitin followed by apoptosis and subsequent release into the extracellular environment. Thus, any abrasions to the chitinous surface can be repaired by spraying IPTG.<br />
<br />
In mammalian skin, mitosis occurs in the basal layer of the epithelial cells and cells travel outwards towards the surface of the skin as they mature. As the cells move further away from the basal layer, they begin to die due to lack of nutrients. As they die, their cytoplasm is released and the cells are filled with keratin, thus forming a continuously regenerating protective layer on the outer-most part of epithelial layer. Our project is modeled after this. The bacterial lawn produces chitin only at the top-most layer and these cells then undergo apoptosis to result in the formation of a chitinous layer at the surface of the lawn. The critical difference is that the bacterial colony is not internally controlled (controlled by IPTG spray), but this is something that can be remedied and a possible goal for future teams.<br />
<br />
<br />
'''SIGNIFICANCE OF CHITIN''':<br />
<br />
<u>Medicinal Use</u>:<br />
<br />
*Wound and burn treatment/healing<br />
*Hemostasis for orthopedic treatment of broken bones<br />
*Viscoelastic solutions for ophthamology and orthopedic surgery<br />
*Abdominal adhesion treatment<br />
*Antibacterial and antifungal agents <br />
*Tumor therapies<br />
*Microsurgery and neurosurgery<br />
*Treatment of chronic wounds, ulcers and bleeding (chitin powder) <br />
<br />
<u>Industrial Use</u>:<br />
<br />
*Food/Pharmaceutical/Agricultural/Cosmetic thickener, stabilizer<br />
*Water resistant properties<br />
*Dietary supplement<br />
*Water purification<br />
*Biodegradable<br />
*Edible microcrystalline films used to preserve food<br />
*Sequestering of particles (i.e. oil)<br />
<br />
||[[Image:PosterChild.jpg|400px|center]]<br />
|-<br />
|colspan="2"|<br />
<br />
<br />
<html><br />
<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
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<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
<td align="center">Modeling</td><br />
</tr><br />
</table><br />
</html><br />
<br />
|-<br />
|colspan="2"|<br />
<br />
<br />
==Strategy==<br />
<br />
===Obtaining Chitin Synthase 3 Gene===<br />
First, the Chitin Synthase 3 (CHS3) gene was subcloned out of Saccharomyces Cerevisiae (Baker’s Yeast) cDNA (complementary DNA – contains no introns, thus can be used in prokaryotes) with biobrick restriction sites (EcoR1, Xbal1 on one end, and Spe1, Pst1 on the other). CHS3 was chosen as it was found to be the major enzyme (knockouts had 80% reduced Chitin) in its family and requires no co-enzyme or activating compounds. Upon running CHS3 through NEB Cutter V2.0, we found a PST1 restriction site which is incompatible with the biobrick standard (EcoR1, Xbal, Spe1, Pst1). To remove this Pst1 site, we inserted CHS3 into a biobrick vector plasmid, and performed site-directed mutagenesis (SDM).<br />
<br />
===pMAL Vector===<br />
Research revealed that chitin synthase is a transmembrane enzyme, and in order to simulate similar conditions, we decided to use the pMAL vector by NEB which contains a periplasmic membrane signal sequence. CHS3 was subcloned in to the pMAL-p5x NEB vector by first PCR’ing it out of the biobrick vector plasmid - on which it underwent SDM - with pMAL restriction sites (Nde1 and EcoR1) and ligated into the pMAL-p5x vector. Then, the CHS3 was again amplified with biobrick sites, but this time, with the periplasmic signal sequence native to the pMAL-p5x plasmid, and inserted into a standard biobrick vector. The entire part was then sequenced and submitted to the registry of standard parts.<br />
A bacterial apoptosis cassette made by the Brown iGEM team in ‘08 was taken from the igem 2010 distribution kit and colony amplified.<br />
<br />
===Constitutive Promoters & Lac Operon===<br />
3 constitutive promoters and 2 lac-inhibitor/lac-operon combination parts were taken from the registry and ligated in all 6 combinations through 3A Assembly. These combinations would express different levels of laci, thus exhibiting variable inductivity. These 6 constructs were then ligated with a reporter protein - green fluorescent protein - and characterized via an automated fluorescent microplate reader; fluorescence was used to determine the construct inductivity and expression level.<br />
<br />
===IPTG Activation===<br />
Then the data was used to fit our own theoretical kinetics model that accounts for IPTG diffusion through biofilm, external IPTG concentration, internal IPTG concentration, lac repressor concentration, repressor bound gene (DNA) concentration, unbound gene (DNA) concentration, mRNA concentration, enzyme concentration, substrate concentration, enzyme-substrate complex concentration, and final product concentration, as well as all the rate constants involved. Using the data acquired from the microplate reader, a final semi-empirical kinetics model was generated. Using this model, two different constructs were chosen; both with similar inductivity, but one with and the other without time delay.<br />
<br />
===Chitin Synthesis Production===<br />
The fast expression construct was ligated with Chitin Synthase, while the slow expression construct was ligated with the apoptosis cassette. Both plasmids were then transformed into a ChiA and tqsA double knockout strain of K12 Escherichia Coli. ChiA knockouts lack Chitinase, which is an enzyme that catabolizes chitin. tqsA knockouts have a disrupted quorum sensing mechanism that allows them to grow very thick lawns. The mutants were acquired from Keio collection (one from Northwestern, and the other from Yale respectively), and the Multiplex Automated Genome Engineering (MAGE) protocol developed by H. H. Wang. et al. was used to acquire double knockouts. The MAGE protocol is an accelerated evolution procedure where oligonucleotides are electroporated into the cells in order to introduce mutations in the genome during replication by binding as lagging strand primers.<br />
<br />
===Mechanism===<br />
The double knockout colonies with both constructs were then sprayed with IPTG, which first induced the fast chitin synthesis construct, which caused a buildup of chitin in cells in the top layer of the bacterial lawn. Then the slow apoptosis construct was induced, which then lysed the cells, and released a layer of chitin in the top layer of the bacterial lawn. This construct was then stained with Chitin-specific rhodamine probe by NEB as well as baclight by Invitrogen in order to ensure that the cells were producing chitin and lysing. The lawn was then imaged through a fluorescent confocal microscope.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/Project
Team:Northwestern/Project
2010-10-23T02:43:31Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#2B3856">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|align="left" valign="top" width="80%" style="padding: 5"|<br />
<br />
Our main project is to simulate mammalian skin using chitin in E. Coli. This process involves four major components: Lawn Formation, Chitin Synthesis, Bacterial Apoptosis, and lac-Operon Signaling.<br />
<br />
A thick bacterial lawn is generated by plating ydgG knock-out mutants (acquired from the Keio Collection) in an enriched agar plate. The protein product of ydgG plays an integral role in AI-2 transport. ydgG knock-outs exhibit increased motility which should ultimately allow for a thick and level lawn.<br />
<br />
The 3.5kbp Chitin Synthase III gene is extracted from the Saccharomyces Cerevisiae genome. Chitin Synthase III catalyzes the polymerization of chitin by transferring UDP-N-acetyl-D-glucosamine to an N(1,4 N-Acetyl-beta-D-glucosaminyl) to produce N+1(1,4 N-Acetyl-beta-D-glucosaminyl).<br />
<br />
Apoptosis of cells is achieved by using the bacteriophage lysis cassette built by the Brown '08 iGEM Team. The cassette includes Holin, Endolysin, and Rz Protein genes. These enzymes puncture and degrade the cell membrane which results in lysing of the cell and the release of synthesized chitin.<br />
<br />
Once the lawn is established, an IPTG solution is sprayed over the lawn to induce chitin synthesis (fast response) and apoptosis (slow response). IPTG mimics allolactose which binds to the LacI repressor, causing LacI to detach from DNA and allowing RNA Polymerase to begin transcription. This will allow for a build-up in chitin followed by apoptosis and subsequent release into the extracellular environment. Thus, any abrasions to the chitinous surface can be repaired by spraying IPTG.<br />
<br />
In mammalian skin, mitosis occurs in the basal layer of the epithelial cells and cells travel outwards towards the surface of the skin as they mature. As the cells move further away from the basal layer, they begin to die due to lack of nutrients. As they die, their cytoplasm is released and the cells are filled with keratin, thus forming a continuously regenerating protective layer on the outer-most part of epithelial layer. Our project is modeled after this. The bacterial lawn produces chitin only at the top-most layer and these cells then undergo apoptosis to result in the formation of a chitinous layer at the surface of the lawn. The critical difference is that the bacterial colony is not internally controlled (controlled by IPTG spray), but this is something that can be remedied and a possible goal for future teams.<br />
<br />
<br />
'''SIGNIFICANCE OF CHITIN''':<br />
<br />
<u>Medicinal Use</u>:<br />
<br />
*Wound and burn treatment/healing<br />
*Hemostasis for orthopedic treatment of broken bones<br />
*Viscoelastic solutions for ophthamology and orthopedic surgery<br />
*Abdominal adhesion treatment<br />
*Antibacterial and antifungal agents <br />
*Tumor therapies<br />
*Microsurgery and neurosurgery<br />
*Treatment of chronic wounds, ulcers and bleeding (chitin powder) <br />
<br />
<u>Industrial Use</u>:<br />
<br />
*Food/Pharmaceutical/Agricultural/Cosmetic thickener, stabilizer<br />
*Water resistant properties<br />
*Dietary supplement<br />
*Water purification<br />
*Biodegradable<br />
*Edible microcrystalline films used to preserve food<br />
*Sequestering of particles (i.e. oil)<br />
<br />
||[[Image:PosterChild.jpg|400px|center]]<br />
|-<br />
|colspan="2"|<br />
<br />
<br />
<html><br />
<table align="center"><br />
<tr><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="100" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
</tr><br />
<tr><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
<td align="center">Modeling</td><br />
</tr><br />
</table><br />
</html><br />
<br />
|-<br />
|colspan="2"|<br />
<br />
<br />
==Strategy==<br />
<br />
===Obtaining Chitin Synthase 3 Gene===<br />
First, the Chitin Synthase 3 (CHS3) gene was subcloned out of Saccharomyces Cerevisiae (Baker’s Yeast) cDNA (complementary DNA – contains no introns, thus can be used in prokaryotes) with biobrick restriction sites (EcoR1, Xbal1 on one end, and Spe1, Pst1 on the other). CHS3 was chosen as it was found to be the major enzyme (knockouts had 80% reduced Chitin) in its family and requires no co-enzyme or activating compounds. Upon running CHS3 through NEB Cutter V2.0, we found a PST1 restriction site which is incompatible with the biobrick standard (EcoR1, Xbal, Spe1, Pst1). To remove this Pst1 site, we inserted CHS3 into a biobrick vector plasmid, and performed site-directed mutagenesis (SDM).<br />
<br />
===pMAL Vector===<br />
Research revealed that chitin synthase is a transmembrane enzyme, and in order to simulate similar conditions, we decided to use the pMAL vector by NEB which contains a periplasmic membrane signal sequence. CHS3 was subcloned in to the pMAL-p5x NEB vector by first PCR’ing it out of the biobrick vector plasmid - on which it underwent SDM - with pMAL restriction sites (Nde1 and EcoR1) and ligated into the pMAL-p5x vector. Then, the CHS3 was again amplified with biobrick sites, but this time, with the periplasmic signal sequence native to the pMAL-p5x plasmid, and inserted into a standard biobrick vector. The entire part was then sequenced and submitted to the registry of standard parts.<br />
A bacterial apoptosis cassette made by the Brown iGEM team in ‘08 was taken from the igem 2010 distribution kit and colony amplified.<br />
<br />
===Constitutive Promoters & Lac Operon===<br />
3 constitutive promoters and 2 lac-inhibitor/lac-operon combination parts were taken from the registry and ligated in all 6 combinations through 3A Assembly. These combinations would express different levels of laci, thus exhibiting variable inductivity. These 6 constructs were then ligated with a reporter protein - green fluorescent protein - and characterized via an automated fluorescent microplate reader; fluorescence was used to determine the construct inductivity and expression level.<br />
<br />
===IPTG Activation===<br />
Then the data was used to fit our own theoretical kinetics model that accounts for IPTG diffusion through biofilm, external IPTG concentration, internal IPTG concentration, lac repressor concentration, repressor bound gene (DNA) concentration, unbound gene (DNA) concentration, mRNA concentration, enzyme concentration, substrate concentration, enzyme-substrate complex concentration, and final product concentration, as well as all the rate constants involved. Using the data acquired from the microplate reader, a final semi-empirical kinetics model was generated. Using this model, two different constructs were chosen; both with similar inductivity, but one with and the other without time delay.<br />
<br />
===Chitin Synthesis Production===<br />
The fast expression construct was ligated with Chitin Synthase, while the slow expression construct was ligated with the apoptosis cassette. Both plasmids were then transformed into a ChiA and tqsA double knockout strain of K12 Escherichia Coli. ChiA knockouts lack Chitinase, which is an enzyme that catabolizes chitin. tqsA knockouts have a disrupted quorum sensing mechanism that allows them to grow very thick lawns. The mutants were acquired from Keio collection (one from Northwestern, and the other from Yale respectively), and the Multiplex Automated Genome Engineering (MAGE) protocol developed by H. H. Wang. et al. was used to acquire double knockouts. The MAGE protocol is an accelerated evolution procedure where oligonucleotides are electroporated into the cells in order to introduce mutations in the genome during replication by binding as lagging strand primers.<br />
<br />
===Mechanism===<br />
The double knockout colonies with both constructs were then sprayed with IPTG, which first induced the fast chitin synthesis construct, which caused a buildup of chitin in cells in the top layer of the bacterial lawn. Then the slow apoptosis construct was induced, which then lysed the cells, and released a layer of chitin in the top layer of the bacterial lawn. This construct was then stained with Chitin-specific rhodamine probe by NEB as well as baclight by Invitrogen in order to ensure that the cells were producing chitin and lysing. The lawn was then imaged through a fluorescent confocal microscope.<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern
Team:Northwestern
2010-10-23T01:59:41Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#2B3856">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#FFFFFF">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
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|style="padding: 5" valign="top" width="60%"|<br />
<br />
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|'''SCIN - Self-regenerating Chitin INduction'''<br />
<br />
Chitin, found in the exoskeletons of insects and crustaceans, is one of the most abudant substances in nature. Like keratin in skin, it comprises the protective outer layer of these animals. Our chitin expression platform involves generating a layer of chitin from a lawn of bacteria in response to an external molecular cue. This cue induces chitin synthesis (fast) and cell lysis (slow). This system allows for a build-up of chitin followed by cell lysis and subsequent release into the top layer of the lawn. Abrasions expose cells to the external cue for self-repair. In this way, we create a regenerative chitin biolayer with potential medical and industrial applications.<br />
<br />
|}<br />
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<td><a href="https://2010.igem.org/Team:Northwestern/Project"><img width="220" class="icon" src="https://static.igem.org/mediawiki/2010/e/ee/Projectoverview_copy.jpg"></a></td><br />
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<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chassis"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/a/a6/Nuchassis.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Lac"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/1/18/Nulac.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Chitin Synthesis"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/4/4e/Nuchitin.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Apoptosis"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/c/cb/Nuapop.jpg"></a></td><br />
<td><a href="https://2010.igem.org/Team:Northwestern/Project/Modeling"><img width="65" class="icon" src="https://static.igem.org/mediawiki/2010/a/a7/NU_modeling.jpg"></a></td><br />
</tr><br />
<tr><br />
<td align="center">Chassis</td><br />
<td align="center">Induction</td><br />
<td align="center">Chitin</td><br />
<td align="center">Apoptosis</td><br />
<td align="center">Modeling</td><br />
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</table><br />
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|[[Image:PosterChild.jpg|330px|center]]<br />
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<br />
<br />
|-<br />
|colspan="3"|<br />
<br />
== '''Northwestern University''' ==<br />
Northwestern University in Evanston, IL, combines innovative teaching and pioneering research in a highly collaborative environment that transcends traditional academic boundaries.<br />
<br />
Our lab facilities are located at: Technological Institute 2145 Sheridan Road, Evanston, IL 60208<br />
<br />
Find out more about [http://www.northwestern.edu Northwestern University]<br />
<br />
Find out more about [http://www.mccormick.northwestern.edu/ McCormick School of Engineering]<br />
<br />
Find out more about [http://www.weinberg.northwestern.edu/ Weinberg College of Arts and Sciences]<br />
<br />
=='''Sponsors'''==<br />
<br />
[[image:NU.jpg|200px]] [[image:NEB.jpg|200px]] [[image:Promega.jpg|200px]] [[image:invitrogen.jpg|200px]] [[image:VWR.jpg|200px]] [[image:Picture1.jpg|200px]] [[image:BIF.jpg|200px]] [[image:EPOCH.jpg|200px]]<br />
<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/References
Team:Northwestern/References
2010-10-23T01:20:19Z
<p>Bzhang89: </p>
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#2B3856">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
=== Lac Operon Control ===<br />
<br />
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG<br />
<br />
===Chitin===<br />
<br />
Adding Glucosamine in medium: http://ec.asm.org/cgi/reprint/2/5/886<br />
<br />
Chitin synthesis Pathway (image): [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg]<br />
<br />
Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long <br />
<br />
Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html<br />
<br />
=== Chitin Synthesis ===<br />
<br />
Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311<br />
<br />
CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465<br />
<br />
===Chitin Staining (Calcofluor)===<br />
<br />
Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf<br />
<br />
Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za<br />
<br />
Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/<br />
<br />
Data sheet: http://tinyurl.com/283wax2<br />
<br />
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html<br />
<br />
=== Apoptosis ===<br />
<br />
partsregistry: http://partsregistry.org/Cell_death<br />
<br />
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===<br />
<br />
DMAO(Live), EtD-III(Dead)<br />
*http://www.promokine.info/products/cell-analysis/cell-staining-reagents-related-products/<br />
*http://www.biotium.com/product/product_info/Protocol/30027.pdf<br />
<br />
===Keio Collection - KnockOuts===<br />
<br />
Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html <br />
<br />
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp<br />
<br />
Method: http://www.pnas.org/content/97/12/6640.full.pdf+html<br />
<br />
Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html<br />
<br />
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls<br />
<br />
=== ChiA (Chitinase) Knockout ===<br />
<br />
Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts<br />
<br />
Chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300<br />
<br />
===ydgg/tqsA (AI2-Transporter) Knockout===<br />
<br />
Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf<br />
<br />
=== BIF (Biological Imaging Facility)===<br />
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br /><br />
Methods: http://www.northwestern.edu/bioimaging/methods.html<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/References
Team:Northwestern/References
2010-10-23T01:19:30Z
<p>Bzhang89: </p>
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[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<font color="#FFFFFF">'''Calendar'''</font>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
!align="center"|[[Team:Northwestern/References|<font color="#2B3856">'''References'''</font>]]<br />
!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
=== Lac Operon Control ===<br />
<br />
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG<br />
<br />
<br />
<br />
<br />
<br />
===Chitin===<br />
<br />
Adding Glucosamine in medium: http://ec.asm.org/cgi/reprint/2/5/886<br />
<br />
Chitin synthesis Pathway (image): [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg]<br />
<br />
Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long <br />
<br />
Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html<br />
<br />
=== Chitin Synthesis ===<br />
<br />
Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311<br />
<br />
CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465<br />
<br />
<br />
===Chitin Staining (Calcofluor)===<br />
<br />
Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf<br />
<br />
Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za<br />
<br />
Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/<br />
<br />
Data sheet: http://tinyurl.com/283wax2<br />
<br />
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html<br />
<br />
=== Apoptosis ===<br />
<br />
partsregistry: http://partsregistry.org/Cell_death<br />
<br />
<br />
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===<br />
<br />
DMAO(Live), EtD-III(Dead)<br />
*http://www.promokine.info/products/cell-analysis/cell-staining-reagents-related-products/<br />
*http://www.biotium.com/product/product_info/Protocol/30027.pdf<br />
<br />
===Keio Collection - KnockOuts===<br />
<br />
Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html <br />
<br />
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp<br />
<br />
Method: http://www.pnas.org/content/97/12/6640.full.pdf+html<br />
<br />
Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html<br />
<br />
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls<br />
<br />
<br />
<br />
=== ChiA (Chitinase) Knockout ===<br />
<br />
Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts<br />
<br />
Chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300<br />
<br />
===ydgg/tqsA (AI2-Transporter) Knockout===<br />
<br />
Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf<br />
<br />
=== BIF (Biological Imaging Facility)===<br />
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br /><br />
Methods: http://www.northwestern.edu/bioimaging/methods.html<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/References
Team:Northwestern/References
2010-10-23T01:17:31Z
<p>Bzhang89: </p>
<hr />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="font-size: 87%; background: #AFC7C7; color: #000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<font color="#FFFFFF">'''Home'''</font>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<font color="#FFFFFF">'''Brainstorm'''</font>]]<br />
!align="center"|[[Team:Northwestern/Team|<font color="#FFFFFF">'''Team'''</font>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<font color="#FFFFFF">'''Acknowledgements'''</font>]]<br />
!align="center"|[[Team:Northwestern/Project|<font color="#FFFFFF">'''Project'''</font>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<font color="#FFFFFF">'''Human Practices'''</font>]]<br />
!align="center"|[[Team:Northwestern/Parts|<font color="#FFFFFF">'''Parts'''</font>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<font color="#FFFFFF">'''Notebook'''</font>]]<br />
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!align="center"|[[Team:Northwestern/Protocol|<font color="#FFFFFF">'''Protocol'''</font>]]<br />
!align="center"|[[Team:Northwestern/Safety|<font color="#FFFFFF">'''Safety'''</font>]]<br />
!align="center"|[[Team:Northwestern/Links|<font color="#FFFFFF">'''Links'''</font>]]<br />
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!align="center"|[[Team:Northwestern/Media|<font color="#FFFFFF">'''Media'''</font>]]<br />
!align="center"|[[Team:Northwestern/Contact|<font color="#FFFFFF">'''Contact'''</font>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
== Lac Operon Control ==<br />
<br />
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG<br />
<br />
<br />
<br />
<br />
<br />
==Chitin==<br />
<br />
Adding Glucosamine in medium: http://ec.asm.org/cgi/reprint/2/5/886<br />
<br />
Chitin synthesis Pathway (image): http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg<br />
<br />
Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production: http://www.jbc.org/content/268/26/19858.long <br />
<br />
Uses for Chitin: http://www.gmp-chitosan.com/en/products-services/chitin.html<br />
<br />
=== Chitin Synthesis ===<br />
<br />
Chitin Synthase Gene (CHS3): http://www.ncbi.nlm.nih.gov/gene/852311<br />
<br />
CHS3 polymerizes: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465<br />
<br />
<br />
===Chitin Staining (Calcofluor)===<br />
<br />
Effect on e. coli: http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf<br />
<br />
Staining of Biofilm Polysaccharides- http://tinyurl.com/36pn4za<br />
<br />
Inhibition of Chitin Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/<br />
<br />
Data sheet: http://tinyurl.com/283wax2<br />
<br />
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html<br />
<br />
== Apoptosis ==<br />
<br />
partsregistry: http://partsregistry.org/Cell_death<br />
<br />
<br />
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===<br />
<br />
DMAO(Live), EtD-III(Dead)<br />
*http://www.promokine.info/products/cell-analysis/cell-staining-reagents-related-products/<br />
*http://www.biotium.com/product/product_info/Protocol/30027.pdf<br />
<br />
==Keio Collection - KnockOuts==<br />
<br />
Keio Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html <br />
<br />
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp<br />
<br />
Method: http://www.pnas.org/content/97/12/6640.full.pdf+html<br />
<br />
Journal Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html<br />
<br />
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls<br />
<br />
<br />
<br />
=== ChiA (Chitinase) Knockout ===<br />
<br />
Summary of e. coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts<br />
<br />
Chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300<br />
<br />
===ydgg/tqsA (AI2-Transporter) Knockout===<br />
<br />
Knockout biofilm formation: http://jb.asm.org/cgi/content/short/188/2/587, http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf<br />
<br />
== BIF (Biological Imaging Facility)==<br />
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br /><br />
Methods: http://www.northwestern.edu/bioimaging/methods.html<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Team:Northwestern/References
Team:Northwestern/References
2010-10-23T00:50:09Z
<p>Bzhang89: </p>
<hr />
<div>__NOTOC__<br />
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<br />
[[Image:LOGOBANNER1.jpg|936px|center|link=http://wikipedia.org|Tech Institute]]<br />
<br />
<!--- The Mission, Experiments ---><br />
{|- style="background: "transparent"; style="font-size: 87%;" color:#000000" cellpadding="1" cellspacing="1" bordercolor="#000000" width="75%" align="center"<br />
!align="center"|[[Team:Northwestern|<span style="color:#000000;">'''Home'''</span>]]<br />
!align="center"|[[Team:Northwestern/Brainstorm|<span style="color:#000000;">'''Brainstorm'''</span>]]<br />
!align="center"|[[Team:Northwestern/Team|<span style="color:#000000;">'''Team'''</span>]]<br />
!align="center"|[[Team:Northwestern/Acknowledgements|<span style="color:#000000;">'''Acknowledgements'''</span>]]<br />
!align="center"|[[Team:Northwestern/Project|<span style="color:#000000;">'''Project'''</span>]]<br />
!align="center"|[[Team:Northwestern/SideProject|<span style="color:#000000;">'''Human Practices'''</span>]]<br />
!align="center"|[[Team:Northwestern/Parts|<span style="color:#000000;">'''Parts'''</span>]]<br />
!align="center"|[[Team:Northwestern/Notebook|<span style="color:#000000;">'''Notebook'''</span>]]<br />
!align="center"|[[Team:Northwestern/Calendar|<span style="color:#000000;">'''Calendar'''</span>]]<br />
!align="center"|[[Team:Northwestern/Protocol|<span style="color:#000000;">'''Protocol'''</span>]]<br />
!align="center"|[[Team:Northwestern/Safety|<span style="color:#000000;">'''Safety'''</span>]]<br />
!align="center"|[[Team:Northwestern/Links|<span style="color:#000000;">'''Links'''</span>]]<br />
!align="center"|[[Team:Northwestern/References|<span style="color:#000000;">'''References'''</span>]]<br />
!align="center"|[[Team:Northwestern/Media|<span style="color:#000000;">'''Media'''</span>]]<br />
!align="center"|[[Team:Northwestern/Contact|<span style="color:#000000;">'''Contact'''</span>]]<br />
|}<br />
<br />
{| align="center" border="0" width="75%"<br />
|<br />
<br />
== Lac Operon Control ==<br />
<br />
Lac Operon induction and IPTG: http://openwetware.org/wiki/IPTG<br />
<br />
<br />
<br />
== Ara Operon Control (pbad promoter)==<br />
<br />
http://partsregistry.org/wiki/index.php?title=Part:BBa_R0080<br />
<br />
http://partsregistry.org/wiki/index.php/Part:BBa_I0500<br />
<br />
arabinose information: http://openwetware.org/wiki/Arabinose<br />
<br />
pbad info: http://openwetware.org/wiki/Titratable_control_of_pBAD_and_lac_promoters_in_individual_E._coli_cells#pBAD_promotersOpenWetWare<br />
<br />
pbad family (only wildtype available) - http://partsregistry.org/PBAD_Promoter_Family<br />
<br />
<br />
==Chitin==<br />
<br />
Adding Glucosamine to growth medium boosts chitin production in Yeast (S.C.)- http://ec.asm.org/cgi/reprint/2/5/886<br />
<br />
Chitin synthesis Pathway (image) - [http://www.mekarn.org/msc2005-07/thesis07/latslrimage002.jpg] (Figure.1. Biosynthesis of chitin in insects. The pathway starts with trehalose, the main hemolymph sugar in most insects, and ends with the chitin polymer. The diagrammatic representation is based on previously published pathways (Kramer and Koga, 1986; Cohen, 2001).)<br />
<br />
Chitin Precursor (UDP-N-Acetyl-Glucosamine) is used for Endotoxin (Lipid A) production - http://www.jbc.org/content/268/26/19858.long - possible safety issue - "When bacterial cells arelysed by the immune system, fragments of membrane containing lipid A are released into the circulation, causing fever, diarrhea, and possible fatal endotoxic shock (also called septic shock)." - thus spake wikipedia<br />
<br />
Chitin Uses: http://www.gmp-chitosan.com/en/products-services/chitin.html<br />
<br />
=== Chitin Synthesis ===<br />
<br />
chitin synthase gene (chs3): http://www.ncbi.nlm.nih.gov/gene/852311<br />
<br />
CHS3 does polymerization (Chitin-UDP acetyl-glucosaminyl transferase is just another name for CHS3) - http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004835, http://www.uniprot.org/uniprot/P29465<br />
<br />
http://tools.neb.com/NEBcutter2/cutshow.php?name=cb3c5ddc-<br />
<br />
===Chitin Staining (Calcofluor)===<br />
<br />
Does not stain E Coli - http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.pdf<br />
<br />
Stains Biofilm Polysaccharides? - http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6V73-3YKKH2J-4S-1&_cdi=5831&_user=965532&_pii=0043135494003399&_orig=search&_coverDate=08%2F31%2F1995&_sk=999709991&view=c&wchp=dGLbVzz-zSkzS&md5=fedcb287ed9c9dafca2dbb4f2bc053a4&ie=/sdarticle.pdf<br />
<br />
Inhibits Synthase - http://www.ncbi.nlm.nih.gov/pmc/articles/instance/40653/<br />
<br />
Data sheet: https://docs.google.com/viewer?url=http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/18909dat.Par.0001.File.tmp/18909dat.pdf&pli=1<br />
<br />
Excitation/Emission: http://www.olympusmicro.com/primer/techniques/fluorescence/fluorotable2.html<br />
<br />
== Apoptosis ==<br />
<br />
registry: http://partsregistry.org/Cell_death<br />
<br />
<br />
===Control===<br />
<br />
*Adjust genetic order<br />
*RBS of varying strengths<br />
*OmpR Binding Site (to detect extracellular glucose)<br />
**http://partsregistry.org/wiki/index.php?title=Part:BBa_I761001<br />
**http://partsregistry.org/wiki/index.php/Part:BBa_I761011<br />
*PhoB<br />
<br />
=== Live/Dead Staining aka Viability/Cytotoxicity Assay===<br />
<br />
DMAO(Live), EtD-III(Dead)<br />
*http://www.promokine.info/products/cell-analysis/cell-staining-reagents-related-products/<br />
*http://www.biotium.com/product/product_info/Protocol/30027.pdf<br />
<br />
==Keio Collection - KnockOuts==<br />
<br />
Website: http://ecoli.naist.jp/gb6/Resources/deletion/deletion.html <br />
<br />
Ordering: http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp<br />
<br />
Method: http://www.pnas.org/content/97/12/6640.full.pdf+html<br />
<br />
Paper: http://www.nature.com/msb/journal/v2/n1/full/msb4100050.html<br />
<br />
Primer Extensions: http://www.biomedsearch.com/attachments/00/16/73/85/16738554/msb4100050-s4.xls<br />
<br />
<br />
<br />
=== ChiA(Chitinase) Knockout (may not be necessary) ===<br />
<br />
summary of e coli knockouts: http://openwetware.org/wiki/Escherichia_coli/Knockouts<br />
<br />
chitinase gene (chiA): http://www.ncbi.nlm.nih.gov/gene/947837<br />
<br />
chiA-knockout strain e coli: http://ecoli.naist.jp/GB6/info.jsp?id=JW3300<br />
<br />
===ydgg/tqsA (AI2-Transporter) Knockout===<br />
<br />
KO -> ~7000x biofilm thickness, ~500x biomass - http://jb.asm.org/cgi/content/short/188/2/587<br />
<br />
http://ecoli.aist-nara.ac.jp/GB5/info.jsp?id=JW1593<br />
<br />
more info: http://www.open-access-biology.com/biofilms/biofilmsch7.pdf<br />
<br />
== BIF (Biological Imaging Facility)==<br />
List of Equipment: http://www.northwestern.edu/bioimaging/equip.html <br /><br />
Methods: http://www.northwestern.edu/bioimaging/methods.html<br />
<br />
<br />
|}</div>
Bzhang89
http://2010.igem.org/Mini_Prep
Mini Prep
2010-10-16T21:29:29Z
<p>Bzhang89: </p>
<hr />
<div>==Materials==<br />
<br />
For purifying plasmid DNA from ''Escherichia coli'' cells, the [http://www1.qiagen.com/Products/Plasmid/QIAprepMiniprepSystem/QIAprepSpinMiniprepKit.aspx Qiagen Spin Miniprep Kit] produces quite reliable results.<br />
<br />
<br />
Do not autoclave solutions containing isopropanol or MOPS; use sterile filtration if necessary.<br />
<br />
Buffer P1<br />
<br />
* 50 mM Tris-HCl pH 8.0<br />
* 10 mM EDTA<br />
* 100 &mu;g/ml RNaseA<br />
<br />
The buffer and RNaseA can also be ordered from Qiagen separately (catalog numbers 19051 and 19101).<br />
<br />
Buffer P2<br />
* 200 mM NaOH<br />
* 1% SDS<br />
<br />
Buffer P3 (not for spin columns, but for Qiatips, midi, maxi, giga kits)<br />
* 3.0 M potassium acetate pH 5.5<br />
<br />
Buffer N3<br />
* 4.2 M Gu-HCl<br />
* 0.9 M potassium acetate<br />
* pH 4.8<br />
<br />
Buffer PB<br />
* 5 M Gu-HCl<br />
* 30% ethanol<br />
*(maybe add 10mM Tris-HCL PH 6.6, and that is better)<br />
<br />
Buffer PE<br />
* 10 mM Tris-HCl pH 7.5<br />
* 80% ethanol<br />
<br />
Buffer QBT equilibration buffer<br />
* 750 mM NaCl<br />
* 50 mM MOPS pH 7.0<br />
* 15% isopropanol<br />
* 0.15% triton X-100<br />
<br />
Buffer QC wash buffer<br />
* 1.0M NaCl<br />
* 50 mM MOPS pH 7.0<br />
* 15% isopropanol<br />
<br />
Buffer QF elution buffer<br />
* 1.25M NaCl<br />
* 50 mM Tris-HCl pH 8.5<br />
* 15% isopropanol<br />
<br />
Buffer QN<br />
* 1.6M NaCl<br />
* 50 mM MOPS pH 7.0<br />
* 15% isopropanol<br />
<br />
<br />
Buffer FWB2<br />
* 1M potassium acetate, pH 5.0<br />
<br />
<br />
(Source: [http://methodsandreagents.pbwiki.com/], [[media:US6383393.pdf | US Patent 6,383,393]])<br />
<br />
The LyseBlue indicator dye added to some of the buffers is Thymophthalein, pH shift from colorless to blue at pH 9.3<br />
<br />
==Protocol==<br />
<br />
See [http://www1.qiagen.com/literature/handbooks/PDF/PlasmidDNAPurification/PLS_QP_Miniprep/1027678_HB_QP_0504_WW_LR.pdf here] or [http://www1.qiagen.com/literature/protocols/QIAprepMiniprep.aspx here] for the handbook for the Qiagen Spin Miniprep Kit. If you have never done this protocol before, read the the background information in the handbook (like the Important Notes section). It contains useful information. The following has been reproduced from the handbook and annotated based on experience with the kit.<br />
<br />
'''Protocol: QIAprep Spin Miniprep Kit Using a Microcentrifuge'''<br />
<br />
This protocol is designed for purification of up to 20 &mu;g of high-copy plasmid DNA from<br />
1–5 ml overnight cultures of ''E. coli'' in LB (Luria-Bertani) medium. For purification of<br />
low-copy plasmids and cosmids, large plasmids (>10 kb), and DNA prepared using<br />
other methods, refer to the recommendations on page 37.<br />
Please read “Important Notes” on pages 19–21 before starting.<br />
Note: All protocol steps should be carried out at room temperature.<br />
<br />
Procedure<br />
<br />
#Add 1ml of overnight culture to a microcentrifuge tube. Spin for 10 minutes at 13,000 rpm. Pour off supernatant.<br />
#Add another 1ml of overnight culture. Spin for 10 minutes at 13,000 rpm. Pour off supernatant.<br />
#Resuspend pelleted bacterial cells in 250 µl Buffer P1 (kept at 4 &deg;C)<br> Ensure that RNase A has been added to Buffer P1. No cell clumps should be visible after resuspension of the pellet.<br />
#Add 250 &mu;l Buffer P2 and gently invert the tube 4–6 times to mix.<br> Mix gently by inverting the tube. Do not vortex, as this will result in shearing of genomic DNA. If necessary, continue inverting the tube until the solution becomes viscous and slightly clear. Do not allow the lysis reaction to proceed for more than 5 min.<br />
#Add 350 &mu;l Buffer N3 and invert the tube immediately but gently 4–6 times. <br> To avoid localized precipitation, mix the solution gently but thoroughly, immediately after addition of Buffer N3. The solution should become cloudy.<br />
#Centrifuge for 10 min at 13,000 rpm (~17,900 x g) in a table-top microcentrifuge.<br> A compact white pellet will form.<br />
#Apply the supernatants from step 4 to the QIAprep spin column by decanting or pipetting.<br />
#Centrifuge for 30–60 s. Discard the flow-through. <br> ''Spinning for 60 seconds produces good results.''<br />
#(Optional): Wash the QIAprep spin column by adding 0.5 ml Buffer PB and centrifuging for 30–60 s. Discard the flow-through.<br>This step is necessary to remove trace nuclease activity when using endA+ strains such as the JM series, HB101 and its derivatives, or any wild-type strain, which have high levels of nuclease activity or high carbohydrate content. Host strains such as XL-1 Blue and DH5&alpha;™ do not require this additional wash step.<br>''Although they call this step optional, it does not really hurt your yield and you may think you are working with an endA- strain when in reality you are not. Again for this step, spinning for 60 seconds produces good results.''<br />
#Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifuging for 30–60 s. <br> ''Spinning for 60 seconds produces good results.''<br />
#Discard the flow-through, and centrifuge for an additional 1 min to remove residual wash buffer.<br> IMPORTANT: Residual wash buffer will not be completely removed unless the flow-through is discarded before this additional centrifugation. Residual ethanol from Buffer PE may inhibit subsequent enzymatic reactions. ''They are right about this.''<br />
#Place the QIAprep column in a clean 1.5 ml microcentrifuge tube. Evaporate off any residual alcohol at 37 &deg;C for 1 minute.<br />
#To elute DNA, add 50 &mu;l '''Buffer EB''' (10 mM Tris·Cl, pH 8.5) or water to the center of each QIAprep spin column, let stand for 5-10 min, and centrifuge for 1 min.<br>''If you are concerned about the concentration of the DNA, you can alternatively add 30 &mu;L water to the center of the column, incubate at room temperature on the bench for 5-10 mins and then centrifuge for 5-10 min. This will increase the concentration of DNA in your final sample which can be useful in some cases. <br />
<br />
See notes below for why you should elute in water rather than the Buffer EB they recommend if you plan to sequence your sample. Even if you are not sequencing, it may be beneficial to elute in water. For instance, if you elute in buffer EB and you are using this DNA in a restriction digest, then the additional salts in your sample can affect the salt content of your digest. This may matter with some finicky enzymes.''<br />
<br />
==Notes==<br />
<br />
*If you are doing more than ~10 minipreps simultaneously, it can save time to switch to the vacuum manifold version of this protocol since you eliminate having to load and unload samples into the centrifuge.<br />
*The sequencing center has begun using new machines and as a result you may want to consider eluting in water rather than EB. See [[Optimizing Sample for Sequencing|note]] from sequencing center.<br> The elution is dependent on pH, however measuring the pH of unbuffered water is [http://www.eutechinst.com/techtips/tech-tips48.htm difficult]. However, anecdotally we have been able to get good yields using the water from the stock room. Eluting in deionized water from the Knight lab has also produced good results.<br />
*I use the "mini-fuge" for the binding and washing steps. You still have to do the drying step after the <b>PE</b> wash in a "real" microfuge though.<br />
*Passing the lysate over the column twice increases yield by about 20%.<br />
*Contaminating salt from the initial lysate or the <b>PB</b> will ruin a sequencing reaction more frequently than eluting in the <b>EB</b> (10 mM Tris as a small component of the total sequencing reaction is negligible). I always elute with <b>EB</b> and my reactions sequence just dandy. There are two major sources of salt contamination: the inside upper edge of the spin column and the residual <b>PB</b> mixing with the <b>PE</b> wash. When you add the initial <b>PE</b>, it mixes with the leftover junk in the column. Spinning this through can only lower the salt to a level that was present after mixing. To get around these problems, I do two <b>PE</b> washes of about 300-500 &mu;L. For the the first, I dispense the liquid from the pipette tip along the inner ledge of the spin column in a circular motion to wash off the residue there. I follow the first <b>PE</b> wash with a second to further de-salt the sample before the drying spin. Yes, it adds a step, but the time spend here is far less than waiting three days only to find out your sequencing didn't work.<br />
*Heating the elution buffer to 55&deg;C prior to loading on the column can slightly increase yields.<br />
*Similarly, doing the elution in two steps (first a 30 &mu;L elution and then a 20 &mu;L dilution) can also slightly increase yields.<br />
<br />
<br />
Back to [[Team:Northwestern/Protocol|<span style="color:#4B088A;">Protocol</span>]]<br />
<br />
[[Category:Protocol]]</div>
Bzhang89
http://2010.igem.org/Ligations
Ligations
2010-10-16T21:28:45Z
<p>Bzhang89: </p>
<hr />
<div>'''Reagents'''<br />
*T4 DNA ligase<br />
*10x T4 DNA Ligase Buffer<br />
*Deionized, sterile H2O<br />
*Purified, linearized vector (likely in H2O or EB)<br />
*Purified, linearized insert (likely in H2O or EB) <br />
<br />
'''Equipment''' <br /><br />
*Vortex<br />
<br />
<u> '''Procedure''' </u> <br /><br />
'''10μL Ligation Mix''' <br /><br />
Note: Larger ligation mixes are also commonly used <br /><br />
*1.0 μL 10X T4 ligase buffer<br />
*6:1 molar ratio of insert to vector (~10ng vector)<br />
*Add (8.5 - vector and insert volume)μl ddH2O<br />
*0.5 μL T4 Ligase<br />
<br />
<br /><br />
<br />
'''Calculating Insert Amount'''<br />
[[Image: insert.jpg|left|450px]] <br />
<br /><br />
<br /><br />
<br /><br />
<i>The insert to vector molar ratio can have a significant effect on the outcome of a ligation and subsequent transformation step. Molar ratios can vary from a 1:1 insert to vector molar ratio to 10:1. It may be necessary to try several ratios in parallel for best results.</i> <br /><br />
<br />
'''Method'''<br />
#Add appropriate amount of deionized H2O to sterile 0.6 mL tube<br />
#Add 1 μL ligation buffer to the tube. <br /> Vortex buffer before pipetting to ensure that it is well-mixed. <br /> Remember that the buffer contains ATP so repeated freeze, thaw cycles can degrade the ATP thereby decreasing the efficiency of ligation.<br />
#Add appropriate amount of insert to the tube.<br />
#Add appropriate amount of vector to the tube.<br />
#Add 0.5 μL ligase. <br /> Vortex ligase before pipetting to ensure that it is well-mixed. <br /> Also, the ligase, like most enzymes, is in some percentage of glycerol which tends to stick to the sides of your tip. To ensure you add only 0.5 μL, just touch your tip to the surface of the liquid when pipetting.<br />
#Let the 10 μL solution sit at 22.5°C for 30 mins<br />
#Denature the ligase at 65°C for 10min<br />
#Dialyze for 20 minutes if electroporating<br />
#Use disks shiny side up<br />
#Store at -20°C<br />
<br />
<br /><br />
<br />
Adapted from: http://openwetware.org/wiki/DNA_ligation<br />
<br />
Back to [[Team:Northwestern/Protocol|<span style="color:#4B088A;">Protocol</span>]]<br />
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Bzhang89