IGEM:Harvard/2009/Notebook/Harvard iGEM 2010/2010/06/18: Difference between revisions

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|style="background-color: #EEE"|[[Image:igem-logo-150px.png|150px]]<span style="font-size:22px;"> iGEM Project name 1</span>
|style="background-color: #EEE"|[[Image:igem-logo-150px.png|150px]]<span style="font-size:22px;"> iGEM iGarden</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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==Entry title==
==Week 1 Summary (6/18/2010)==
* Insert your content here.
==Team Vector==
<html>
Aim: To biobrick agrobacteria vectors<br /><br />


We obtained the following pORE agrobacteria vectors from TAIR.<br /><br />
<table>
<tr>
<td>Name</td>
<td>Original Name</td>
<td>Description</td>
<td>Plant Resistance</td>
</tr>
<tr>
<td>V1</td>
<td>pORE_O1</td>
<td>Agrobacterium vector open series</td>
<td>pat</td>
</tr>
<tr>
<td>V2</td>
<td>pORE_O2</td>
<td>Agrobacterium vector open series</td>
<td>nptll</td>
</tr>
<tr>
<td>V3</td>
<td>pORE_E3</td>
<td>Agrobacterium vector with ENTCUP2 promoter</td>
<td>pat</td>
</tr>
<tr>
<td>V4</td>
<td>pORE_E4</td>
<td>Agrobacterium vector with ENTCUP2 promoter</td>
<td>nptll</td>
</tr>
<tr>
<td>V5</td>
<td>pORE_R1</td>
<td>Agrobacterium vector with gusA reporter</td>
<td>nptll</td>
</tr>
<tr>
<td>V6</td>
<td>pORE_R3</td>
<td>Agrobacterium vector with smgfp reporter</td>
<td>nptll</td>
</tr>
</table><br />
<p>To create the vector backbones we digested the E and R plasmids with HindIII and SpeI, and the O plasmids with SacII and SpeI. We ran the digested backbones on a gel and purified using the Qiaquick Gel Extraction kit. IMAGE HERE</p>
<p>To create the vector insert for the E plasmids, we designed primers such that we could amplify the promotor sequence present in the original plasmid and attach it to the biobrick multiple cloning site, bracketed with the appropriate restriction sites such that we could insert it into our digested backbone. The forward primer started with the HindIII restriction site to match the backbone, then included the biobrick cloning site, then the beginning of the promotor sequence to be amplified. The reverse primer started with the NheI restriction site (so that when ligated to the SpeI site in the backbone, a scar site would be created), then the end of the promotor sequence to be amplified.</p>
<p>We then ran a PCR reaction on the plasmids with these primers to obtain the vector insert, and digested with HindIII and NheI to prepare the inserts for insertion into the backbone</p>
<p>We plan to use annealed oligos to create the inserts for the O1 and O2 vectors.</p>
<p>We ligated the inserts with the backbones using T4 ligase. We transformed into NEB Turbo Competent E. coli cells and plated on LB and Kanamycin (50ug/ml). We picked colonies from each plate and made cultures.</p>


</html>
==Team Flavor==
==Team Allergy==
'''Progress'''
# Identified allergens in arabidopsis, strawberries,tomatoes, and carrots and created primers for amplifying out these allergens [http://openwetware.org/wiki/IGEM:Harvard/2010/Team_Allergy| (see primers and sequences)]
# Extracted cDNA (rna extraction followed by rt-pcr) from strawberries and tried to PCR out our strawberry allergen (Fra a 1), but were unble ato do so
# Looked to find introns ~ 800 bp to use to create our hairpins since it was difficult to acquire pHannibal vector w/ the pdk intron
'''Future Directions'''
# Look towards ordering [[Media:Aimrna.pdf|amiRNA]]for silencing
# Waiting on arabidopsis plants to grow to extract genomic DNA (mon)
# Look to find introns to use in creation of hairpin DNA
# Cloning (digesting/ligating our sense/antisense/intron sequences necessary for hairpin creation into one vector to create biobricks)
==Team Fence==
===LacI+NLS PCR===
LacI+NLS primers arrived in mail
spun at 14,000 rpm for 10 minutes
diluted stocks to 100 μM
    LacIn.BB.Rev (1.7nM) diluted with 17μL DH<sub>2</sub>O
    LacIn.BB.Fwd (1.5nM) diluted with 1011μL DH<sub>2</sub>O
    NLS.BB.Rev (4.2nM) diluted with 42μL DH<sub>2</sub>O
    LacIn.BB.Fwd (101.1nM) diluted with 15μL DH<sub>2</sub>O
PCR recipe
*20μL per reaction
*1μL template plasmid
*1μL R primer
*1μL F primer
*4μL HF buffer 5X
*2μL DNTPs
*0.5μL pFU polymerase
*rest H2O to make the volume per tube 20μL
used LACIN program in phusion PCR machine to perform PCR


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Revision as of 08:41, 21 June 2010

iGEM iGarden <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

Week 1 Summary (6/18/2010)

Team Vector

<html> Aim: To biobrick agrobacteria vectors<br /><br />

We obtained the following pORE agrobacteria vectors from TAIR.<br /><br /> <table> <tr> <td>Name</td> <td>Original Name</td> <td>Description</td> <td>Plant Resistance</td> </tr> <tr> <td>V1</td> <td>pORE_O1</td> <td>Agrobacterium vector open series</td> <td>pat</td> </tr> <tr> <td>V2</td> <td>pORE_O2</td> <td>Agrobacterium vector open series</td> <td>nptll</td> </tr> <tr> <td>V3</td> <td>pORE_E3</td> <td>Agrobacterium vector with ENTCUP2 promoter</td> <td>pat</td> </tr> <tr> <td>V4</td> <td>pORE_E4</td> <td>Agrobacterium vector with ENTCUP2 promoter</td> <td>nptll</td> </tr> <tr> <td>V5</td> <td>pORE_R1</td> <td>Agrobacterium vector with gusA reporter</td> <td>nptll</td> </tr> <tr> <td>V6</td> <td>pORE_R3</td> <td>Agrobacterium vector with smgfp reporter</td> <td>nptll</td> </tr> </table><br /> <p>To create the vector backbones we digested the E and R plasmids with HindIII and SpeI, and the O plasmids with SacII and SpeI. We ran the digested backbones on a gel and purified using the Qiaquick Gel Extraction kit. IMAGE HERE</p> <p>To create the vector insert for the E plasmids, we designed primers such that we could amplify the promotor sequence present in the original plasmid and attach it to the biobrick multiple cloning site, bracketed with the appropriate restriction sites such that we could insert it into our digested backbone. The forward primer started with the HindIII restriction site to match the backbone, then included the biobrick cloning site, then the beginning of the promotor sequence to be amplified. The reverse primer started with the NheI restriction site (so that when ligated to the SpeI site in the backbone, a scar site would be created), then the end of the promotor sequence to be amplified.</p> <p>We then ran a PCR reaction on the plasmids with these primers to obtain the vector insert, and digested with HindIII and NheI to prepare the inserts for insertion into the backbone</p> <p>We plan to use annealed oligos to create the inserts for the O1 and O2 vectors.</p> <p>We ligated the inserts with the backbones using T4 ligase. We transformed into NEB Turbo Competent E. coli cells and plated on LB and Kanamycin (50ug/ml). We picked colonies from each plate and made cultures.</p>


</html>

Team Flavor

Team Allergy

Progress

  1. Identified allergens in arabidopsis, strawberries,tomatoes, and carrots and created primers for amplifying out these allergens (see primers and sequences)
  2. Extracted cDNA (rna extraction followed by rt-pcr) from strawberries and tried to PCR out our strawberry allergen (Fra a 1), but were unble ato do so
  3. Looked to find introns ~ 800 bp to use to create our hairpins since it was difficult to acquire pHannibal vector w/ the pdk intron

Future Directions

  1. Look towards ordering amiRNAfor silencing
  2. Waiting on arabidopsis plants to grow to extract genomic DNA (mon)
  3. Look to find introns to use in creation of hairpin DNA
  4. Cloning (digesting/ligating our sense/antisense/intron sequences necessary for hairpin creation into one vector to create biobricks)

Team Fence

LacI+NLS PCR

LacI+NLS primers arrived in mail

spun at 14,000 rpm for 10 minutes diluted stocks to 100 μM 

   LacIn.BB.Rev (1.7nM) diluted with 17μL DH2O
   LacIn.BB.Fwd (1.5nM) diluted with 1011μL DH2O
   NLS.BB.Rev (4.2nM) diluted with 42μL DH2O
   LacIn.BB.Fwd (101.1nM) diluted with 15μL DH2O

PCR recipe

  • 20μL per reaction
  • 1μL template plasmid
  • 1μL R primer
  • 1μL F primer
  • 4μL HF buffer 5X
  • 2μL DNTPs
  • 0.5μL pFU polymerase
  • rest H2O to make the volume per tube 20μL


used LACIN program in phusion PCR machine to perform PCR


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