Team:Yale/Notebook

From 2014.igem.org

(Difference between revisions)
 
(26 intermediate revisions not shown)
Line 118: Line 118:
-
<table style="width:1100px" align="center" style="margin-top:0px;">
+
<table style="border:none; width:1100px" align="center" style="margin-top:0px;">
<tr>
<tr>
<td style="border:none; width:1100px" colspan="12" align="center">
<td style="border:none; width:1100px" colspan="12" align="center">
-
<div class = "callout">
+
 
-
<h1 style="margin-top:70px; font-size:50px;"><FONT COLOR="#00B585">Lab Notebook</h1>
+
<div style="margin-top:50px"> </div>
-
</div>
+
<div class="callout">
-
+
<h1 style="margin-top:22px; font-size:44px;">Notebook</h1>
</td>
</td>
</tr>
</tr>
<!-- end welcome box -->
<!-- end welcome box -->
-
      <li style="list-style-type:square">
 
-
<tr>
 
-
<td colspan="12">
 
-
<div class = "tinycall">
 
-
<h1>Outline of Our Project</h1>
 
-
</div>
 
-
<div class = "well">
 
-
<p>
 
-
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
 
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 
-
<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/><meta name="exporter-version" content="Evernote Mac 5.5.1 (402628)"/><meta name="author" content="Ariel Hernandez-Leyva"/><meta name="created" content="2014-07-03 15:59:33 +0000"/><meta name="updated" content="2014-07-03 18:11:47 +0000"/><title>Outline of Our Project</title></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
 
-
Goal: Create a recombinant protein using a dopamine surface anchor and an anti-fouling head-domain that can be expressed in recoded E. Coli.
 
-
<div><br/></div>
 
-
<div>
 
-
<ul>
 
-
<li>Create an expression system</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>Creating theT7 Riboregulated System</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>First, create a construct that places the gene for T7 RNA polymerase in the backbone of a plasmid with a cis-repressing and trans-activating RNA.</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>Obtain T7 RNA Pol: from team strain #5.</li>
 
-
<li>Obtain pZE21 backbone: from Ryan</li>
 
-
<li>Design primers for PCR and Gibson Assembly (191, 192, 193, 194, 195)</li>
 
-
<li>PCR amplify T7 RNA Pol an pZE21 using primers.</li>
 
-
<li>DPN1 Digest template DNA.</li>
 
-
<li>Run fragments on a gel green Gel</li>
 
-
<li>Gel Purification of fragments.</li>
 
-
<li>Gibson Assembly of fragments into plasmid construct.</li>
 
-
<li>Transform plasmid construct into K12 derivative, ECNR2. Plate on Kan Plates.</li>
 
-
<li>Pick colonies from Kan Plates, inoculate liquid culture.</li>
 
-
<li>From liquid culture make a frozen stock.</li>
 
-
<li>Screen colonies for presence of plasmid of interest</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>First find which colonies have T7 and pZE21.</li>
 
-
<li>Use sequencing primers to amplify sequence of interest. Sequence for verification.</li>
 
-
</ul>
 
-
</li>
 
-
<li>Integrate into genome of ECNR2 or BL21.</li>
 
-
</ul>
 
-
</li>
 
-
</ul>
 
-
</li>
 
-
<li>Create Promoter for T7 Riboregulated System</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>Create a construct that installs sfGFP behind promoter for T7.</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>Obtained T7 promoter from registry and Life Technologies.</li>
 
-
<li>obtained sfGFP gene from laboratory stock.</li>
 
-
<li>Approach 1: T7 Overhangs Approach</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>amplify standard pZE21::sfGFP plasmid with primers designed by Stephanie that have T7 as overhangs. Amplification of this plasmid will situate the T7 promoter in front of sfGFP.</li>
 
-
<li>DPN1 digest.</li>
 
-
<li>Gibson Assemble to circularize into plasmid.</li>
 
-
<li>Drop Dialysis to minimize salt.</li>
 
-
<li>transform into ECNR2/BL21</li>
 
-
<li>Screening for Plasmid</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>Insert plasmid into BL21 DE3 and screen for expression of sfGFP. BL21 DE3 is a strain that contains the gene for T7 RNA Polymerase.</li>
 
-
</ul>
 
-
</li>
 
-
</ul>
 
-
</li>
 
-
<li>Approach 2: Insert sfGFP into T7 containing plasmid.</li>
 
-
<li style="list-style: none; display: inline">
 
-
<ul>
 
-
<li>Using psB1A2 with T7 promoter from registry. Transform bacteria to make stock of pSB1AC2.</li>
 
-
<li>Using primers designed by Ariel amplify pSB1AC2 to have overhangs with sfGFP.</li>
 
-
<li>Amplify sfGFP from pZE21::sfGFP with primers designed by Ariel to have overhangs with pSB1A2 with T7 Promoter.</li>
 
-
<li>DPN1 Digest</li>
 
-
<li>Gibson Assemble.</li>
 
-
<li>Drop Dialysis.</li>
 
-
<li>Transform into BL21/576</li>
 
-
<li>Screen for ampicillin/carbenicillin resistance.</li>
 
-
<li>Insert plasmid into BL21 DE3 and screen for sfGFP expression.<span style="-evernote-last-insertion-point:true;"/></li>
 
-
</ul>
 
-
</li>
 
-
</ul>
 
-
</li>
 
-
</ul>
 
-
</li>
 
-
</ul>
 
-
</li>
 
-
<li>Create constructs</li>
 
-
<li>Express Constructs in rE.Coli</li>
 
-
<li>Test Constructs using Antimicrobial Assays</li>
 
-
<li>Test Constructs using Adhesion Assays.</li>
 
-
<br /> </p> </tr> </ul>
 
<tr>
<tr>
-
<td colspan="12">
+
<td colspan="8">  
-
<div class = "tinycall">
+
<embed src="https://static.igem.org/mediawiki/2014/f/f2/Evernote.pdf#view=FitH" width="100%" height="900"></embed></td>
-
<h1>TroubleShooting (T7)</h1>
+
</tr>
-
</div>
+
</table>
-
<div class = "well">
+
</html>
-
<p>
+
-
Okay, so we’re currently having some issues with the transformations, so let’s take a step back and look at what can go wrong, and how we can fix them: 
+
-
<div><br/></div>
+
-
<div>Template generation: For T7 RNA pol+pZE21 with the cr/ta system, the hairpins on the primers limit the efficacy of PCR and Gibson assembly.</div>
+
-
<div><br/></div>
+
-
<div>Solutions: First, we should screen the plasmids we have to check and see if they do in fact contain T7. Ariel has designed primers for the test already, and if necessary we can use the pZE21 with CAT as a control, since the band would be a significantly shorter length. </div>
+
-
<div>     We can also try a different method of assembly: restriction enzyme digest (may be difficult because there are none that anneal EXACTLY to the spots we want, some are a few base pairs off), or deactivating CAT’s start codon and placing T7 a little ways downstream of the crRNA sequence, INSIDE CAT (which, without the start codon, would not be translated).</div>
+
-
<div><br/></div>
+
-
<div>Transformation: We need to drop dialyze longer. Our bacteria doesn’t seem to like the high salt concentration. Do duplicate plates. </div>
+
-
<div>Quality control on plates: be sure to streak a non-transformed plate every time to make sure the antibiotic is working.</div>
+
-
<div>Transform into a hardier strain/one better suited for transformations?</div>
+
-
<div><br/></div>
+
-
</p>
+
-
</div>
+
-
<div class = "tinycall">
+
-
<h1>Construct Idea: DOPA + Spider silk</h1>
+
-
</div>
+
-
<div class = "well">
+
-
<p>
+
-
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
-
<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/><meta name="exporter-version" content="Evernote Mac 5.5.1 (402628)"/><meta name="author" content="stephanie_mao"/><meta name="created" content="2014-07-13 02:52:05 +0000"/><meta name="updated" content="2014-07-13 16:50:00 +0000"/><title>Construct Idea: DOPA + Spider silk</title></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Here’s an idea: what if we attach spider silk in between two mussel foot proteins, and then coat a surface with it?</span></p>
+
-
(Stephanie’s idea)<br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">1. Spider silk has been shown to be</span> <a href="http://www.academia.edu/3223021/The_Antimicrobial_Properties_of_Spider_Silk" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">antimicrobial</span></a></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">2. Spider silk is strong and resistant to degradation.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">3. Spider silk is a structural polymer and does not require terminal specificity.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">4. Spider silk has been produced with a conjugated protein before by</span> <a href="https://2013.igem.org/Team:Utah_State/Parts" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">a former iGEM team</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
5. Spider silk loses its stickiness over time, and its antimicrobial effects are decreased when exposed to water…DOPA can help <br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Spider silk is in the</span> <a href="http://parts.igem.org/Part:BBa_K844004" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">iGEM registry</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">, and sequences can also be found</span> <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000514" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">here</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
<div>The idea then is to generate spider-silk DOPA peptides that, in coating a surface, creates a mesh on which biofilms cannot form. This may be a good alternative in looking at medical applications, since spider silk is NOT toxic in mammals.
+
-
</div>
+
-
<div><br/></div>
+
-
 
+
-
</p>
+
-
</div>
+
-
<div class = "tinycall">
+
-
<h1>Construct Idea: DOPA + Spider silk</h1>
+
-
</div>
+
-
<div class = "well">
+
-
<p>
+
-
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
-
<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/><meta name="exporter-version" content="Evernote Mac 5.5.1 (402628)"/><meta name="author" content="stephanie_mao"/><meta name="created" content="2014-07-13 02:52:05 +0000"/><meta name="updated" content="2014-07-13 16:50:00 +0000"/><title>Construct Idea: DOPA + Spider silk</title></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Here’s an idea: what if we attach spider silk in between two mussel foot proteins, and then coat a surface with it?</span></p>
+
-
(Stephanie’s idea)<br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">1. Spider silk has been shown to be</span> <a href="http://www.academia.edu/3223021/The_Antimicrobial_Properties_of_Spider_Silk" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">antimicrobial</span></a></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">2. Spider silk is strong and resistant to degradation.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">3. Spider silk is a structural polymer and does not require terminal specificity.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">4. Spider silk has been produced with a conjugated protein before by</span> <a href="https://2013.igem.org/Team:Utah_State/Parts" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">a former iGEM team</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
5. Spider silk loses its stickiness over time, and its antimicrobial effects are decreased when exposed to water…DOPA can help <br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Spider silk is in the</span> <a href="http://parts.igem.org/Part:BBa_K844004" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">iGEM registry</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">, and sequences can also be found</span> <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000514" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">here</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
<div>The idea then is to generate spider-silk DOPA peptides that, in coating a surface, creates a mesh on which biofilms cannot form. This may be a good alternative in looking at medical applications, since spider silk is NOT toxic in mammals.
+
-
</div>
+
-
<div><br/></div>
+
-
 
+
-
</p>
+
-
</div>
+
-
<div class = "tinycall">
+
-
<h1>Construct Idea: DOPA + Spider silk</h1>
+
-
</div>
+
-
<div class = "well">
+
-
<p>
+
-
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
-
<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/><meta name="exporter-version" content="Evernote Mac 5.5.1 (402628)"/><meta name="author" content="stephanie_mao"/><meta name="created" content="2014-07-13 02:52:05 +0000"/><meta name="updated" content="2014-07-13 16:50:00 +0000"/><title>Construct Idea: DOPA + Spider silk</title></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Here’s an idea: what if we attach spider silk in between two mussel foot proteins, and then coat a surface with it?</span></p>
+
-
(Stephanie’s idea)<br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">1. Spider silk has been shown to be</span> <a href="http://www.academia.edu/3223021/The_Antimicrobial_Properties_of_Spider_Silk" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">antimicrobial</span></a></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">2. Spider silk is strong and resistant to degradation.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">3. Spider silk is a structural polymer and does not require terminal specificity.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">4. Spider silk has been produced with a conjugated protein before by</span> <a href="https://2013.igem.org/Team:Utah_State/Parts" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">a former iGEM team</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
5. Spider silk loses its stickiness over time, and its antimicrobial effects are decreased when exposed to water…DOPA can help <br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Spider silk is in the</span> <a href="http://parts.igem.org/Part:BBa_K844004" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">iGEM registry</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">, and sequences can also be found</span> <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000514" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">here</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
<div>The idea then is to generate spider-silk DOPA peptides that, in coating a surface, creates a mesh on which biofilms cannot form. This may be a good alternative in looking at medical applications, since spider silk is NOT toxic in mammals.
+
-
</div>
+
-
<div><br/></div>
+
-
 
+
-
</p>
+
-
</div>
+
-
<div class = "tinycall">
+
-
<h1>Construct Idea: DOPA + Spider silk</h1>
+
-
</div>
+
-
<div class = "well">
+
-
<p>
+
-
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
-
<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/><meta name="exporter-version" content="Evernote Mac 5.5.1 (402628)"/><meta name="author" content="stephanie_mao"/><meta name="created" content="2014-07-13 02:52:05 +0000"/><meta name="updated" content="2014-07-13 16:50:00 +0000"/><title>Construct Idea: DOPA + Spider silk</title></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Here’s an idea: what if we attach spider silk in between two mussel foot proteins, and then coat a surface with it?</span></p>
+
-
(Stephanie’s idea)<br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">1. Spider silk has been shown to be</span> <a href="http://www.academia.edu/3223021/The_Antimicrobial_Properties_of_Spider_Silk" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">antimicrobial</span></a></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">2. Spider silk is strong and resistant to degradation.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">3. Spider silk is a structural polymer and does not require terminal specificity.</span></p>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">4. Spider silk has been produced with a conjugated protein before by</span> <a href="https://2013.igem.org/Team:Utah_State/Parts" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">a former iGEM team</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
5. Spider silk loses its stickiness over time, and its antimicrobial effects are decreased when exposed to water…DOPA can help <br/>
+
-
<p dir="ltr" style="line-height:1.15;"><span style="vertical-align: baseline; white-space: pre-wrap;">Spider silk is in the</span> <a href="http://parts.igem.org/Part:BBa_K844004" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">iGEM registry</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">, and sequences can also be found</span> <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000514" style="text-decoration:none;"><span style="color: rgb(17, 85, 204); text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">here</span></a><span style="vertical-align: baseline; white-space: pre-wrap;">.</span></p>
+
-
<div>The idea then is to generate spider-silk DOPA peptides that, in coating a surface, creates a mesh on which biofilms cannot form. This may be a good alternative in looking at medical applications, since spider silk is NOT toxic in mammals.
+
-
</div>
+
-
<div><br/></div>
+
{{Template:Team:Yale2014/Templates/Footer}}
{{Template:Team:Yale2014/Templates/Footer}}

Latest revision as of 02:52, 18 October 2014

Notebook

Main Campus:
Molecular, Cellular & Developmental Biology
219 Prospect Street
P.O. Box 208103
New Haven, CT 06520
Phone: 203.432.3783
igem@yale.edu
natalie.ma@yale.edu (Graduate Advisor)
Copyright (c) 2014 Yale IGEM

Retrieved from "http://2014.igem.org/Team:Yale/Notebook"