Difference between revisions of "Team:UCopenhagen/Notebook"

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    <h1>Scrolling Sidebar</h1>
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                        <a href="#week27" class="list-group-item active">Week 27</a>
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    <p>By <a href="http://css-tricks.com"><strong>CSS</strong>-Tricks</a></p>
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                        <a href="#week28" class="list-group-item">Week 28</a>
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                        <a href="#week29" class="list-group-item">Week 29</a>
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                        <a href="#week30" class="list-group-item">Week 30</a>
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                        <a href="#week32" class="list-group-item">Week 32</a>
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                        <a href="#week33" class="list-group-item">Week 33</a>
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  <p>Scroll down and watch the sidebar on the right follow.</p>
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                        <a href="#week34" class="list-group-item">Week 34</a>
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                        <a href="#week35" class="list-group-item">Week 35</a>
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                        <a href="#week36" class="list-group-item">Week 36</a>
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                        <a href="#week42" class="list-group-item">Week 42</a>
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<a href="#week43" class="list-group-item">Week 43</a>
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                        <a href="#week43" class="list-group-item">Week 44</a>
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  <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus</p>
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  <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus</p>
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  <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus</p>
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  <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus</p>
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Ordered primers, checked cell stocks and prepared LB plates
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<!----------------------------- Week 27 -------------------------------------------->
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Making plates, initial transformations, ordered more primers.
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Made glycerol stock of MG1655. Designed primers: yddG +/- his-tag, and pointmutations in trpE and aroG
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Inoculation and creation of glycerol stocks and streaking on LB plates of 8 bacterial cultures: Micrococcus luteus, Staphylococcus epidermis, Bacillus Cereus, Bacillus licheniformis, Serratia marcescens, Pseudomonas putida and Rhizobium meliloti.
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Preparation of additional LB plates without antibiotica.
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Creation of competent Mach1 cells and fast transformation with pRSET A to test efficiency. 
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Started making plates and initial transformations
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PCR from MG1655 stock. Amplified aroG #1 and #2 in first attempt, and trpE #2 at a higher annealing temp, then began optimizing the PCR for yddG and trpE#2 using gradient temperatures without success.
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Fluorescent microscopy of S. marascens, E. coli and S. epidermis stained with bodipu.
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Removal of XbaI sites in pRSET A mod, PCR amplification and gel-extraction of the plasmid.
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Transformation of competent cells with pRSET amod 1, and test of XbaI site removal by digestion.
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Started work on pRSETjin and pRSETjin CPP vectors from the pRSET vector without XbaI site.
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Started making plates and initial transformations
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Continued work on PCR optimization of yddG and trpE#1. Continuous attempts with gradient temperatures. Extracted genomic DNA from MG1655 - one where RNAase was forgotten, so we did two. Successfull PCR of yddG-stop and yddG-his. Started amplification of the whole trpE gene.
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Continued working on pRSETjin vectors. Attempted to optimize PCR amplification of pRSETjin vector. Adjusted temperatires, template dilutions, tested digestion of unknown bands, retested primers, redid template, tried different templates, template volumes, primer concentrations, annealing temperatures, redoing templates.
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<!----------------------------- Week 30 -------------------------------------------->
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<h3 id="week30">Week 30 (July 24 - 30)</h3>
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Successfull amplification of whole trpE gene from gDNA, after many attempts due to wrong buffers. Amplified and gel-extracted trpE whole gene to be used as template. Unsuccessfull amplification of trpE#1. Got new fusion primers for trpE#1: Finally succes!
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Continued working on pRSETjin vectors. Transformation with BFP, YFP and RFP biobricks
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<!----------------------------- Week 31 -------------------------------------------->
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<h3 id="week31">Week 31 (July 31 - August 6)</h3>
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Well deserved vacations were held, so nothing happened this week.
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Extraction of BFP, YFP and RFP from transformations. Amplification of pET102 Trx, to remove Trx domain, then amplification, DPN1 digestion of template. Gelextraction of DPN1 digested, then USER cloned (phosphorylated and ligated). Transformation with the new pRSET vector, and miniprep to extract the vector.
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<!----------------------------- Week 32 -------------------------------------------->
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<h3 id="week32">Week 32 (August 7 - 13)</h3>
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<h4 class="media heading">Wet Lab Overview</h4>
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<p>
+
−
Txt
+
−
</p>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/f/fd/Interdependency_small.jpg ">
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−
<div class="media-body">
+
−
<h4 class="media heading">Interdependency</h4>
+
−
<p>
+
−
Text
+
−
</p>
+
−
</div>
+
−
</div>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/8/89/Numbercontrol_small.jpeg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Number Control</h4>
+
−
<p>
+
−
Text
+
−
</p>
+
−
</div>
+
−
</div>
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/a/a6/Proteinimport_small.jpg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Protein Import</h4>
+
−
<p>
+
−
Verification of pET102 iGEM with digestion and sequencing.
+
−
 
+
−
</p>
+
−
</div>
+
−
</div>
+
−
</ul>
+
−
<br><br>
+
−
<!----------------------------- Week 33 -------------------------------------------->
+
−
<h3 id="week33">Week 33 (August 14 - 20)</h3>
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−
<hr>
+
−
<ul class="media-list">
+
−
<li class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Wet Lab Overview</h4>
+
−
<p>
+
−
Txt
+
−
</p>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/f/fd/Interdependency_small.jpg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Interdependency</h4>
+
−
<p>
+
−
Amplification of trpE#1 and trpE#2, aroG#1 and aroG#2, yddGhis and yddG-stop with different template dilutions to find the optimal, then amplification of all, and gel-extraction of trpE#1 and #2.
+
−
</p>
+
−
</div>
+
−
</div>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/8/89/Numbercontrol_small.jpeg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Number Control</h4>
+
−
<p>
+
−
Text
+
−
</p>
+
−
</div>
+
−
</div>
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/a/a6/Proteinimport_small.jpg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Protein Import</h4>
+
−
<p>
+
−
Gelextraction of minipreps to remove chromosomal DNA. Minipreps of inoculated cells with correct vector. Start optimization for BFP and YFP PCR amplifications.
+
−
 
+
−
</p>
+
−
</div>
+
−
</div>
+
−
</ul>
+
−
<br><br>
+
−
<!----------------------------- Week 34 -------------------------------------------->
+
−
<h3 id="week34">Week 34 (August 21 - 27)</h3>
+
−
<hr>
+
−
<ul class="media-list">
+
−
<li class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Wet Lab Overview</h4>
+
−
<p>
+
−
Txt
+
−
</p>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/f/fd/Interdependency_small.jpg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Interdependency</h4>
+
−
<p>
+
−
Amplification and gelextraction of yddG (both versions), aroG#1 and aroG#2. First attempt at growing E.coli in minimal yeast medium - no growth.
+
−
</p>
+
−
</div>
+
−
</div>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/8/89/Numbercontrol_small.jpeg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Number Control</h4>
+
−
<p>
+
−
Text
+
−
</p>
+
−
</div>
+
−
</div>
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/a/a6/Proteinimport_small.jpg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Protein Import</h4>
+
−
<p>
+
−
Linearization of pET102 iGEM. Attempted amplification of pET102 iGEM with CPP primers. In both cases, issues - maybe due to damaged template? Finally managed to linearize the vector. PCR Amplification and gelextraction of YFP
+
−
 
+
−
</p>
+
−
</div>
+
−
</div>
+
−
</ul>
+
−
<br><br>
+
−
<!----------------------------- Week 35 -------------------------------------------->
+
−
<h3 id="week35">Week 35 (August 28 - September 3)</h3>
+
−
<hr>
+
−
<ul class="media-list">
+
−
<li class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Wet Lab Overview</h4>
+
−
<p>
+
−
Txt
+
−
</p>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/f/fd/Interdependency_small.jpg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Interdependency</h4>
+
−
<p>
+
−
Transformation with trpE, aroG, yddG and YFP using linearized pET102 iGEM plasmid. Parts #1 and #2 of trpE and aroG used, combining the two parts give the point mutation. Succesfull growth. Miniprep of the transformed DNA, and digestion of plasmids. Initial failure due to low concentration of DNA in the mini-prep samples.
+
−
</p>
+
−
</div>
+
−
</div>
+
−
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/8/89/Numbercontrol_small.jpeg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Number Control</h4>
+
−
<p>
+
−
Text
+
−
</p>
+
−
</div>
+
−
</div>
+
−
<div class="media">
+
−
<img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/a/a6/Proteinimport_small.jpg ">
+
−
<div class="media-body">
+
−
<h4 class="media heading">Protein Import</h4>
+
−
<p>
+
−
Transformation and amplification of YFP done in interdependency. Amplification and gelextraction of BFP.
+
−
 
+
−
</p>
+
−
</div>
+
−
</div>
+
−
</ul>
+
−
<br><br>
+
−
</div>
+
−
 
+
−
<!----------------------------- Week 36 -------------------------------------------->
+
−
<!----------------------------- Week 37 -------------------------------------------->
+
−
<!----------------------------- Week 38 -------------------------------------------->
+
−
<!----------------------------- Week 39 -------------------------------------------->
+
−
<!----------------------------- Week 40 -------------------------------------------->
+
−
<!----------------------------- Week 41 -------------------------------------------->
+
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<!----------------------------- Week 42 -------------------------------------------->
+
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<!----------------------------- Week 43 -------------------------------------------->
+
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<!----------------------------- Week 44 -------------------------------------------->
+
  
  
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</div>
 
 
 
 
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Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus

Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus

Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus