Team:Lethbridge Canada/notebook june

From 2013hs.igem.org

(Difference between revisions)
 
(35 intermediate revisions not shown)
Line 32: Line 32:
<ul>
<ul>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/project">Description</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/project">Description</a></li>
 +
                                                <li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/project#video_oxy">Visual Modeling</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/math">Math Model</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/math">Math Model</a></li>
 +
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/results">Results</a></li>
 +
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/wikifreeze">Wikifreeze</a></li>
</ul>
</ul>
</li>
</li>
Line 53: Line 56:
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/videos">Videos</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/videos">Videos</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/surveys">Parent Surveys</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/surveys">Parent Surveys</a></li>
 +
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/novel_study">Novel Study</a></li>
</ul>
</ul>
</li>
</li>
Line 70: Line 74:
<div id="notebook_header">
<div id="notebook_header">
<div id="notebook_links">
<div id="notebook_links">
-
<h1 id="notebook_links_header">Notebook Links</h1>
+
 +
<h1 id="notebook_links_header"> Notebook Links</h1>
 +
 
<ul id="notebook_march_links">
<ul id="notebook_march_links">
<li class="notebook_link_title"><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_march">March</a></li>
<li class="notebook_link_title"><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_march">March</a></li>
Line 165: Line 171:
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june#entry_six">June 13, 2013: Restricted and Ligated and Transformed</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june#entry_six">June 13, 2013: Restricted and Ligated and Transformed</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june#entry_seven">June 13, 2013: Picked Cells</a></li>
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june#entry_seven">June 13, 2013: Picked Cells</a></li>
 +
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june#entry_eight">June 15, 2013: Ni-Sepharose Purification</a></li>
 +
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june#entry_nine">June 18, 2013: Tris-Tricine PAGE</a></li>
 +
<li><a href="https://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june#entry_ten">June 21, 2013: Anti-His Slot Blot</a></li>
</ul>
</ul>
</div>
</div>
</div>
</div>
-
+
 
 +
<div class="pull_banner_left">
 +
<img src="https://static.igem.org/mediawiki/2013hs/2/21/Lethbridge_hs_igem_2013_banner_notebookjune.png">
 +
</div>
 +
 
<div id="notebook_body">
<div id="notebook_body">
<div class="notebook_entry">
<div class="notebook_entry">
Line 174: Line 187:
<h1 class="notebook_entry_header">Restrictions</h1>
<h1 class="notebook_entry_header">Restrictions</h1>
<ul class="notebook_entry_list">
<ul class="notebook_entry_list">
-
<li>Restricted (total 60µl DNA) K314100 in psb1c3 with Spec1 and Pst1</li>
+
<li>Restricted (total 60µL DNA) K314100 in pSB1C3 with Spe1 and Pst1</li>
-
<li>Restricted (total 60µl DNA) Oxytocin in puc19a with Xba1 and Pst1</li>
+
<li>Restricted (total 60µL DNA) Oxytocin in puc19a with Xba1 and Pst1</li>
-
<li>Restricted (total 60µl DNA) NEC1puc19a with Xba1 and Pst1</li>
+
<li>Restricted (total 60µL DNA) NEC1puc19a with Xba1 and Pst1</li>
-
<li>Set 12 µl aside from each reaction and gel extracted (GEX) the remaining  48µl</li>
+
<li>Set 12 µL aside from each reaction and gel extracted (GEX) the remaining  48µL</li>
<li>Combined heat killed restriction mixtures into ligation mix from NEB using NEB protocol, left at room temperature for 10 mins then heat killed for 20 mins at 80°C </li>
<li>Combined heat killed restriction mixtures into ligation mix from NEB using NEB protocol, left at room temperature for 10 mins then heat killed for 20 mins at 80°C </li>
-
<li>K314100 – psb1c3 (s,p), with: Oxytocin (x,p)</li>
+
<li>K314100 – pSB1C3 (s,p), with: Oxytocin (x,p)</li>
-
<li>K314100 – psb1c3 (s,p), with: NEC1 (x,p)</li>
+
<li>K314100 – pSB1C3 (s,p), with: NEC1 (x,p)</li>
-
<li>GEX K314100 – psb1c3 (s,p), with: GEX Oxytocin (x,p)</li>
+
<li>GEX K314100 – pSB1C3 (s,p), with: GEX Oxytocin (x,p)</li>
-
<li>GEX K314100 – psb1c3 (s,p), with: GEX NEC1 (x,p)</li>
+
<li>GEX K314100 – pSB1C3 (s,p), with: GEX NEC1 (x,p)</li>
</ul>
</ul>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
Line 192: Line 205:
<h1 class="notebook_entry_header">Transformation</h1>
<h1 class="notebook_entry_header">Transformation</h1>
<ul class="notebook_entry_list">
<ul class="notebook_entry_list">
-
<li class="notebook_nested_start">Transformed ligations into 20µl high efficiency DH5α cells and 50µl lab made competent DH5α</li>
+
<li class="notebook_nested_start">Transformed ligations into 20µL high efficiency DH5α cells and 50µL lab made competent DH5α</li>
<li><ul class="notebook_nested_list">
<li><ul class="notebook_nested_list">
-
<li>K314100 – psb1c3 (s,p), with: Oxytocin (x,p)</li>
+
<li>K314100 – pSB1C3 (s,p), with: Oxytocin (x,p)</li>
-
<li>K314100 – psb1c3 (s,p), with: NEC1 (x,p)</li>
+
<li>K314100 – pSB1C3 (s,p), with: NEC1 (x,p)</li>
-
<li>GEX K314100 – psb1c3 (s,p), with: GEX Oxytocin (x,p)</li>
+
<li>GEX K314100 – pSB1C3 (s,p), with: GEX Oxytocin (x,p)</li>
-
<li>GEX K314100 – psb1c3 (s,p), with: GEX NEC1 (x,p)</li>
+
<li>GEX K314100 – pSB1C3 (s,p), with: GEX NEC1 (x,p)</li>
</ul>
</ul>
</li>
</li>
<li>Plated on CAM plates</li>
<li>Plated on CAM plates</li>
-
<li>Results: Only the 20µl non gel extracted DH5α E. coli high efficiency cells grew</li>
+
<li>Results: Only the 20µL non gel extracted DH5α E. coli high efficiency cells grew</li>
</ul>
</ul>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
Line 214: Line 227:
<li>Picked 10 colonies from each plate</li>
<li>Picked 10 colonies from each plate</li>
<li>Grew over night in LB and mini prepped</li>
<li>Grew over night in LB and mini prepped</li>
-
<li>PCR-ed with Vf2 and Vr primers, no results as shown</li>
+
<li>PCR-ed with VF2 and VR primers, no results as shown</li>
-
<li><img src="leth_hs_2013_gel_extraction_06_02_2013_2.png" alt="Gel on June 4, 2013"></li>
+
<li><img src="https://static.igem.org/mediawiki/2013hs/b/bd/Leth_hs_igem_june_10_1_colonies.png" alt="Gel on June 4, 2013"></li>
<li>  Picked 6 Oxytocin colonies and 5 NEC1 colonies grew overnight in LB – mini prepped and restricted all colonies picked so far at E, P cute sites and ran on gel, results concluded as ligations did not work since a band is seen at ~500 bp size of the promoter construct K314100 but not with oxytocin or NEC1</li>
<li>  Picked 6 Oxytocin colonies and 5 NEC1 colonies grew overnight in LB – mini prepped and restricted all colonies picked so far at E, P cute sites and ran on gel, results concluded as ligations did not work since a band is seen at ~500 bp size of the promoter construct K314100 but not with oxytocin or NEC1</li>
-
<li><img src="leth_hs_2013_gel_extraction_06_02_2013_1.png" alt="Gel on June 4, 2013"></li>
+
<li><img src="https://static.igem.org/mediawiki/2013hs/7/77/Leth_hs_igem_june_10_2_colonies.png" alt="Gel on June 4, 2013"></li>
</ul>
</ul>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
Line 228: Line 241:
<ul class="notebook_entry_list">
<ul class="notebook_entry_list">
<li>Date: June 10, 2013</li>
<li>Date: June 10, 2013</li>
-
<li class="notebook_nested_start">Sent 10µl DNA with 5µl of 5µM vf2 primer to genewize</li>
+
<li class="notebook_nested_start">Sent 10µL DNA with 5µL of 5µM VF2 primer to genewize</li>
<li><ul class="notebook_nested_list">
<li><ul class="notebook_nested_list">
<li>J23100-J06702</li>
<li>J23100-J06702</li>
<li>J23108-J06702</li>
<li>J23108-J06702</li>
<li>J23113-J06702</li>
<li>J23113-J06702</li>
-
<li>K314100-oxytocin neurophysin1 </li>
+
<li>K314100-oxytocin neurophysin I </li>
</ul>
</ul>
</li>
</li>
Line 241: Line 254:
<li>J23108-J06702- positive for J06702 but no promoter found</li>
<li>J23108-J06702- positive for J06702 but no promoter found</li>
<li>J23113-J06702- positive for J06702 but no promoter found</li>
<li>J23113-J06702- positive for J06702 but no promoter found</li>
-
<li>K314100-oxytocin neurophysin1 – Positive results full sequence found</li>
+
<li>K314100-oxytocin neurophysin I – Positive results full sequence found</li>
</ul>
</ul>
</li>
</li>
Line 254: Line 267:
<ul class="notebook_entry_list">
<ul class="notebook_entry_list">
<li>Date: June 13, 2013</li>
<li>Date: June 13, 2013</li>
-
<li>Transform mini prepped plasmid DNA of K314100–Oxytocin Neurophysin1 in psb1c3 into 15µl of Bl21 E.coli cells </li>
+
<li>Transform mini prepped plasmid DNA of K314100–Oxytocin Neurophysin I in pSB1C3 into 15µL of Bl21 E.coli cells </li>
<li>Let grow over night at 37°C on CAM plates</li>
<li>Let grow over night at 37°C on CAM plates</li>
</ul>
</ul>
Line 266: Line 279:
<ul class="notebook_entry_list">
<ul class="notebook_entry_list">
<li>Date: June 13, 2013</li>
<li>Date: June 13, 2013</li>
-
<li>Restricted K314100 Spec1 and Pst1 and NEC1 at Xba1 and Pst1 for 1 hour at 37°C followed by 20 min heat kill at 80°C</li>
+
<li>Restricted K314100 Spe1 and Pst1 and NEC1 at Xba1 and Pst1 for 1 hour at 37°C followed by 20 min heat kill at 80°C</li>
-
<li>Mixed restrictions in ratio of 10µl NEC1 and 2µl k314100 in psb1c3 let sit in ligation mixture for 10 mins at room temperature followed by 20 min heat kill at 80°C</li>
+
<li>Mixed restrictions in ratio of 10µL NEC1 and 2µL k314100 in pSB1C3 let sit in ligation mixture for 10 mins at room temperature followed by 20 min heat kill at 80°C</li>
-
<li>Transformed 2µl into 20µl of DH5α E.coli highly competent cells, incubated overnight at 37°C</li>
+
<li>Transformed 2µL into 20µL of DH5α E.coli highly competent cells, incubated overnight at 37°C</li>
</ul>
</ul>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
Line 279: Line 292:
<ul class="notebook_entry_list">
<ul class="notebook_entry_list">
<li>Date: June 13, 2013</li>
<li>Date: June 13, 2013</li>
-
<li>K314100–Oxytocin neurophysin 1 in psb1c3 grew in Bl21 from last nights transformation, picked 4 colonies and grew up in 5ml of LB overnight at 37°C with shaking</li>
+
<li>K314100–Oxytocin neurophysin 1 in pSB1C3 grew in Bl21 from last nights transformation, picked 4 colonies and grew up in 5ml of LB overnight at 37°C with shaking</li>
 +
</ul>
 +
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
 +
</div>
 +
</div>
 +
 
 +
<div class="notebook_entry">
 +
<div id="entry_eight">
 +
<h1 class="notebook_entry_header">Ni-Sepharose Purification</h1>
 +
<ul class="notebook_entry_list">
 +
<li>Date: June 15, 2013</li>
 +
<li>Grew 250mL culture of K314100 – Oxytocin neurophysin in psb1c3 overnight at 37&deg;C with shaking (June 14)</li>
 +
<li>Purified preprooxyphysin with Ni-Sapharose beads according to Wieden Protocol</li>
 +
<li>Eluted overnight</li>
 +
<li>Will confirm with tris-tricine PAGE</li>
 +
</ul>
 +
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
 +
</div>
 +
</div>
 +
 +
<div class="notebook_entry">
 +
<div id="entry_nine">
 +
<h1 class="notebook_entry_header">Tris-Tricine PAGE</h1>
 +
<ul class="notebook_entry_list">
 +
<li>Date: June 18, 2013</li>
 +
<li>Prepro-oxyphysin can be seen at the bottom of lanes 5 and 7</li>
 +
<li>
 +
<table>
 +
<tr>
 +
<th>Lane</th>
 +
<th>Contents</th>
 +
<th>Volume</th>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>Protein Molecular Weight Marker</td>
 +
<td>20&mu;L</td>
 +
</tr>
 +
<tr>
 +
<td>2</td>
 +
<td>Cbf5-Nop10-Gar1</td>
 +
<td>20&mu;L</td>
 +
</tr>
 +
<tr>
 +
<td>3</td>
 +
<td>Buffer A wash</td>
 +
<td>30&mu;L</td>
 +
</tr>
 +
<tr>
 +
<td>4</td>
 +
<td>Buffer B wash</td>
 +
<td>30&mu;L</td>
 +
</tr>
 +
<tr>
 +
<td>5</td>
 +
<td>Buffer E Wash</td>
 +
<td>30&mu;L</td>
 +
</tr>
 +
<tr>
 +
<td>6</td>
 +
<td>S-30 s/N</td>
 +
<td>30&mu;L</td>
 +
</tr>
 +
<tr>
 +
<td>7</td>
 +
<td>Buffer E – Concentrated Preprooxyphysin</td>
 +
<td>30&mu;L</td>
 +
</tr>
 +
</table>
 +
</li>
 +
</ul>
 +
<img class="june_et_img" src="https://static.igem.org/mediawiki/2013hs/3/34/Leth_hs_2013_june_18_sheet_1.png" alt=" " />
 +
<img class="june_et_img" src="https://static.igem.org/mediawiki/2013hs/b/bc/Leth_hs_2013_june_18_sheet_2.png" alt=" " />
 +
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
 +
</div>
 +
</div>
 +
 
 +
<div class="notebook_entry">
 +
<div id="entry_ten">
 +
<h1 class="notebook_entry_header">Anti-His Slot Blot</h1>
 +
<ul class="notebook_entry_list">
 +
<li>Date: June 21, 2013</li>
 +
<div style="display:block">
 +
<li><table style="float:left;" width:242px; height:120px;>
 +
<tbody><tr>
 +
<th>Lane #</th>
 +
<th>Contents</th>
 +
</tr><tr>
 +
 +
</tr><tr>
 +
<td>Lane 1:</td>
 +
<td>100μL Oxytocin in 200μL TBS</td>
 +
</tr>
 +
 
 +
 +
<tr>
 +
<td>Lane 2:</td>
 +
<td>200μL Oxytocin in 100μL TBS</td>
 +
</tr>
 +
 
 +
 +
<tr>
 +
<td>Lane 3:</td>
 +
<td>250μL Oxytocin in 50μL TBS</td>
 +
</tr>
 +
 
 +
 +
<tr>
 +
<td>Lane 4:</td>
 +
<td>300μL Oxytocin</td>
 +
</tr>
 +
 
 +
 +
<tr>
 +
<td>Lane 5:</td>
 +
<td>25pM TruB-His positive control</td>
 +
</tr>
 +
</tbody></table>
 +
</li>
 +
<img class="june_et_img" src="https://static.igem.org/mediawiki/2013hs/a/a1/Leth_hs_2013_oxt_histag.png" alt=" "
 +
style="float:left; width:830px; height:135px; padding-left:10px;" />
 +
</div>
 +
 
 +
<p>We used a 25pM sample of the protein TruB with a histidine tag which is seen in lane 5. In lanes 1,2,3 and 4, faint bands are seen on the slot blot. This is indicative of the histidine tag attached to Oxytocin-NeurophysinI.</p>
 +
 
</ul>
</ul>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>
<p class="top_notebook"><a href="#wrapper">Back to Top</a></p>

Latest revision as of 03:56, 22 June 2013

Restrictions

  • Restricted (total 60µL DNA) K314100 in pSB1C3 with Spe1 and Pst1
  • Restricted (total 60µL DNA) Oxytocin in puc19a with Xba1 and Pst1
  • Restricted (total 60µL DNA) NEC1puc19a with Xba1 and Pst1
  • Set 12 µL aside from each reaction and gel extracted (GEX) the remaining 48µL
  • Combined heat killed restriction mixtures into ligation mix from NEB using NEB protocol, left at room temperature for 10 mins then heat killed for 20 mins at 80°C
  • K314100 – pSB1C3 (s,p), with: Oxytocin (x,p)
  • K314100 – pSB1C3 (s,p), with: NEC1 (x,p)
  • GEX K314100 – pSB1C3 (s,p), with: GEX Oxytocin (x,p)
  • GEX K314100 – pSB1C3 (s,p), with: GEX NEC1 (x,p)

Back to Top

Transformation

  • Transformed ligations into 20µL high efficiency DH5α cells and 50µL lab made competent DH5α
    • K314100 – pSB1C3 (s,p), with: Oxytocin (x,p)
    • K314100 – pSB1C3 (s,p), with: NEC1 (x,p)
    • GEX K314100 – pSB1C3 (s,p), with: GEX Oxytocin (x,p)
    • GEX K314100 – pSB1C3 (s,p), with: GEX NEC1 (x,p)
  • Plated on CAM plates
  • Results: Only the 20µL non gel extracted DH5α E. coli high efficiency cells grew

Back to Top

Picked Colonies

  • Date: June 4, 2013
  • Picked 10 colonies from each plate
  • Grew over night in LB and mini prepped
  • PCR-ed with VF2 and VR primers, no results as shown
  • Gel on June 4, 2013
  • Picked 6 Oxytocin colonies and 5 NEC1 colonies grew overnight in LB – mini prepped and restricted all colonies picked so far at E, P cute sites and ran on gel, results concluded as ligations did not work since a band is seen at ~500 bp size of the promoter construct K314100 but not with oxytocin or NEC1
  • Gel on June 4, 2013

Back to Top

Picked Colonies

  • Date: June 10, 2013
  • Sent 10µL DNA with 5µL of 5µM VF2 primer to genewize
    • J23100-J06702
    • J23108-J06702
    • J23113-J06702
    • K314100-oxytocin neurophysin I
  • June 12th results arrived
    • J23100-J06702- positive for J06702 but no promoter found
    • J23108-J06702- positive for J06702 but no promoter found
    • J23113-J06702- positive for J06702 but no promoter found
    • K314100-oxytocin neurophysin I – Positive results full sequence found

Back to Top

Transformation of OXY into BL21

  • Date: June 13, 2013
  • Transform mini prepped plasmid DNA of K314100–Oxytocin Neurophysin I in pSB1C3 into 15µL of Bl21 E.coli cells
  • Let grow over night at 37°C on CAM plates

Back to Top

Restricted and Ligated and Transformed

  • Date: June 13, 2013
  • Restricted K314100 Spe1 and Pst1 and NEC1 at Xba1 and Pst1 for 1 hour at 37°C followed by 20 min heat kill at 80°C
  • Mixed restrictions in ratio of 10µL NEC1 and 2µL k314100 in pSB1C3 let sit in ligation mixture for 10 mins at room temperature followed by 20 min heat kill at 80°C
  • Transformed 2µL into 20µL of DH5α E.coli highly competent cells, incubated overnight at 37°C

Back to Top

Picked Cells

  • Date: June 13, 2013
  • K314100–Oxytocin neurophysin 1 in pSB1C3 grew in Bl21 from last nights transformation, picked 4 colonies and grew up in 5ml of LB overnight at 37°C with shaking

Back to Top

Ni-Sepharose Purification

  • Date: June 15, 2013
  • Grew 250mL culture of K314100 – Oxytocin neurophysin in psb1c3 overnight at 37°C with shaking (June 14)
  • Purified preprooxyphysin with Ni-Sapharose beads according to Wieden Protocol
  • Eluted overnight
  • Will confirm with tris-tricine PAGE

Back to Top

Tris-Tricine PAGE

  • Date: June 18, 2013
  • Prepro-oxyphysin can be seen at the bottom of lanes 5 and 7
  • Lane Contents Volume
    1 Protein Molecular Weight Marker 20μL
    2 Cbf5-Nop10-Gar1 20μL
    3 Buffer A wash 30μL
    4 Buffer B wash 30μL
    5 Buffer E Wash 30μL
    6 S-30 s/N 30μL
    7 Buffer E – Concentrated Preprooxyphysin 30μL

Back to Top

Anti-His Slot Blot

  • Date: June 21, 2013
  • Lane # Contents
    Lane 1: 100μL Oxytocin in 200μL TBS
    Lane 2: 200μL Oxytocin in 100μL TBS
    Lane 3: 250μL Oxytocin in 50μL TBS
    Lane 4: 300μL Oxytocin
    Lane 5: 25pM TruB-His positive control

    • We used a 25pM sample of the protein TruB with a histidine tag which is seen in lane 5. In lanes 1,2,3 and 4, faint bands are seen on the slot blot. This is indicative of the histidine tag attached to Oxytocin-NeurophysinI.

Back to Top

Retrieved from "http://2013hs.igem.org/Team:Lethbridge_Canada/notebook_june"