Team:Gothenburg/Calendar

From 2014.igem.org

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                 </table>
                 </table>
             </div>
             </div>
-
         </div>
+
         </div> <!-- End Calendar -->
 +
 +
<div id="calendar-data">
 +
<div class="summary" id="6-10">
 +
<h1>10/6/2014</h1>       
 +
<h2 align="center">Safety Instructions</h2>
 +
<h4 align="center"> <p> The team received mandatory safety training and general lab routine information.
 +
<br> </p><p> A really cool video about Chalmers' chemical safety routine (recorded at our very own lab!) can be seen in http://www.chalmers.se/insidan/EN/about-chalmers/environmental-work/policies/chemical-safety-routine</p></h4>
 +
</div>
 +
 +
== 6 ==
 +
=== 10 ===
 +
==== Titles ====
 +
<div>
 +
*Training
 +
*Wiki
 +
</div>
 +
====Details====
 +
<div>
 +
====Training====
 +
 
 +
The teams split into small groups to discuss individual themes. They did some research into multiple aspects of the project including: wiki layout, t-shirt design and possible team logos. We also looked at past iGEM team wikis for inspirational ideas.
 +
 
 +
[[File:P1050457.JPG|frameless|300px]],[[File:P1050459.JPG|frameless|300px]]
 +
 
 +
A talk on Computational Modelling and BioBrick concepts was given. This talk led the team to start building the biophysical model of the lipid membrane of ''Bacillus subtilis'' and modelling of lipid synthetic pathway. Later in the day, the team met to discuss initial aims and progress of our work so far.
 +
 
 +
[[File:P1050460.JPG|frameless|300px]]
 +
 
 +
====Wiki====
 +
 
 +
Initial designs for the wiki have been created and uploaded. Currently all style sheets and javascript pages are stored externally until the design has been ratified by the team. Front-page image carousel has been created and initialised with blank colours to demonstrate what it shall look like until actual photographs have been taken and edited.
 +
</div>
 +
 
 +
<!-->
 +
<div class="summary" id="6-17">
 +
<h1>17/6/2014</h1>       
 +
<h2 align="center">Introduction to centrifuges and autoclaves</h2>
 +
<h4 align="center"> <p> As a part of the mandatory training required by the SysBio group, the team received instructions on how to operate the centrifuges and autoclaves of the labs.
 +
<br>We also worked on our risk declaration; a mandatory document containing our experiments descriptions and information about the chemicals we are going to use, their handling, storage and associated risk, as well as waste handling. </p></h4>
 +
</div>
 +
 +
<div class="summary" id="6-20">
 +
<h1>20/6/2014</h1>       
 +
<h2 align="center">Finished mandatory training</h2>
 +
<h4 align="center">Our Risk Declaration was approved by the lab manager and our supervisors. We also sign a safety certificate stating that we are aware of the safety instructions and with that, completed the mandatory "check-in list for new incomers" of the lab.</h4>
 +
</div>
 +
 +
<div class="summary" id="6-23">
 +
<h1>2/6/2014</h1>       
 +
<h2 align="center">Media Preparation</h2>
 +
<h4 align="center">On the first day of laboration, we prepared LB, YPD and SC-Ura/His/Trp-Leu and YPD media.
 +
<br>
 +
Click here to see the protocol.  [[PUT METHOD]]!
 +
<br>
 +
[[File:20140623_103124.jpg]],[[File:20140623_115809.jpg|frameless|300px]]</h4>
 +
</div>
 +
 +
<div class="summary" id="6-25">
 +
<h1>2/6/2014</h1>       
 +
<h2 align="center">Amplification and Purification of non-synthetic parts</h2>
 +
<h4 align="center"> Succesfully PCR amplified five out of the seven parts from yeast genome via a Phusion High-Fidelity DNA Polymerase. Click here to see the protocol.<br>
 +
The PCR program used was: <br>
 +
1. 3 min at 98ºC <br>
 +
2. 10s at 98ºC <br>
 +
3. Gradient from 52 to 61ºC for 30s <br>
 +
4. 1 min at 72ºC <br>
 +
5. Go to step 2 (repeat 39 times) <br>
 +
6. 10 min at 72ºC. <br>
 +
 
 +
A diagnostic gel was performed and the result was as follows:
 +
[[File: Bio-Rad 2014-06-25 15hr 34min.jpg|frameless|300px]] <br>
 +
 
 +
The purification of the succesfully amplified parts was done using a PCR Purification Kit from GenJet following the instructions of the manufacture's manual but with no addition of isopropanol. <br> </h4>
 +
</div>
 +
 +
<div class="summary" id="6-26">
 +
<h1>10/6/2014</h1>       
 +
<h2 align="center">Plasmid Purification</h2>
 +
<h4 align="center"> <p> Performed plasmid purification on E. coli cells containing plasmids p413, p414, p415, p416, p2055 and a plasmid containig our Cas9 sequence (pTPG1-dCas9-UPGP)via a GenJet Plasmid Purification Kit. The manufacter's instructions were followed, except the elution buffer was subtituted by water on the last step.
 +
<br>  </p></h4>
 +
<h2 align="center">Amplification and purification of parts</h2>
 +
<h4 align="center"> Performed a PCR amplification of the non-synthetic parts that failed on the day before and on the dCas9 sequence and the three fluorecent proteins -Yellow, Cyano and Red (YFP, CFP and RFP, respectively).
 +
<br>
 +
The PCR was done using the Phusion High-Fidelity DNA Polymerase (see protocol here) and the program used was:
 +
<br>
 +
1. 3 min at 98ºC
 +
<br>
 +
2. 10s at 98ºC
 +
<br>
 +
3. Gradient from 50 to 55ºC for 30s
 +
<br>
 +
4. 30s at 60ºC
 +
<br>
 +
5. 2min 15s at 72ºC
 +
<br>
 +
5. Go to step 2 (repeat 39 times)
 +
<br>
 +
6. 10 min at 72ºC.
 +
<br>
 +
A diagnostic gel was performed and the result is as follows: <br>
 +
[[File: Bio-Rad 2014-06-26 17hr 53min.jpg|frameless|300px]]
 +
<br></h4>
 +
</div></!-->
 +
</div> <!-- End Calender-data -->
     </div>
     </div>
     </body>
     </body>
</html>
</html>

Revision as of 11:27, 31 July 2014

TemplateUp

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10/6/2014

Safety Instructions

The team received mandatory safety training and general lab routine information.

A really cool video about Chalmers' chemical safety routine (recorded at our very own lab!) can be seen in http://www.chalmers.se/insidan/EN/about-chalmers/environmental-work/policies/chemical-safety-routine

== 6 == === 10 === ==== Titles ====
*Training *Wiki
====Details====
====Training==== The teams split into small groups to discuss individual themes. They did some research into multiple aspects of the project including: wiki layout, t-shirt design and possible team logos. We also looked at past iGEM team wikis for inspirational ideas. [[File:P1050457.JPG|frameless|300px]],[[File:P1050459.JPG|frameless|300px]] A talk on Computational Modelling and BioBrick concepts was given. This talk led the team to start building the biophysical model of the lipid membrane of ''Bacillus subtilis'' and modelling of lipid synthetic pathway. Later in the day, the team met to discuss initial aims and progress of our work so far. [[File:P1050460.JPG|frameless|300px]] ====Wiki==== Initial designs for the wiki have been created and uploaded. Currently all style sheets and javascript pages are stored externally until the design has been ratified by the team. Front-page image carousel has been created and initialised with blank colours to demonstrate what it shall look like until actual photographs have been taken and edited.

17/6/2014

Introduction to centrifuges and autoclaves

As a part of the mandatory training required by the SysBio group, the team received instructions on how to operate the centrifuges and autoclaves of the labs.
We also worked on our risk declaration; a mandatory document containing our experiments descriptions and information about the chemicals we are going to use, their handling, storage and associated risk, as well as waste handling.

20/6/2014

Finished mandatory training

Our Risk Declaration was approved by the lab manager and our supervisors. We also sign a safety certificate stating that we are aware of the safety instructions and with that, completed the mandatory "check-in list for new incomers" of the lab.

2/6/2014

Media Preparation

On the first day of laboration, we prepared LB, YPD and SC-Ura/His/Trp-Leu and YPD media.
Click here to see the protocol. [[PUT METHOD]]!
[[File:20140623_103124.jpg]],[[File:20140623_115809.jpg|frameless|300px]]

2/6/2014

Amplification and Purification of non-synthetic parts

Succesfully PCR amplified five out of the seven parts from yeast genome via a Phusion High-Fidelity DNA Polymerase. Click here to see the protocol.
The PCR program used was:
1. 3 min at 98ºC
2. 10s at 98ºC
3. Gradient from 52 to 61ºC for 30s
4. 1 min at 72ºC
5. Go to step 2 (repeat 39 times)
6. 10 min at 72ºC.
A diagnostic gel was performed and the result was as follows: [[File: Bio-Rad 2014-06-25 15hr 34min.jpg|frameless|300px]]
The purification of the succesfully amplified parts was done using a PCR Purification Kit from GenJet following the instructions of the manufacture's manual but with no addition of isopropanol.

10/6/2014

Plasmid Purification

Performed plasmid purification on E. coli cells containing plasmids p413, p414, p415, p416, p2055 and a plasmid containig our Cas9 sequence (pTPG1-dCas9-UPGP)via a GenJet Plasmid Purification Kit. The manufacter's instructions were followed, except the elution buffer was subtituted by water on the last step.

Amplification and purification of parts

Performed a PCR amplification of the non-synthetic parts that failed on the day before and on the dCas9 sequence and the three fluorecent proteins -Yellow, Cyano and Red (YFP, CFP and RFP, respectively).
The PCR was done using the Phusion High-Fidelity DNA Polymerase (see protocol here) and the program used was:
1. 3 min at 98ºC
2. 10s at 98ºC
3. Gradient from 50 to 55ºC for 30s
4. 30s at 60ºC
5. 2min 15s at 72ºC
5. Go to step 2 (repeat 39 times)
6. 10 min at 72ºC.
A diagnostic gel was performed and the result is as follows:
[[File: Bio-Rad 2014-06-26 17hr 53min.jpg|frameless|300px]]

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