Team:LMU-Munich/Team

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{{:Team:LMU-Munich/Templates/Page Header}}
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<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
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==<font color="#9933CC">'''Team LMU iGEM 2010'''</font>==
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[[Image:LMU-Munich_team.png|center|600px|Our team picture]]
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[[Image:TeamLMU.JPG|center|600px|Also our team]]
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<html>
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<!-- {|align="justify" -->
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<div id="box" style="margin: 0 137px; padding: 5px; border: 3px solid #000; background-color: #fe2b33;">
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<!-- |You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing. -->
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<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;">
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<!-- |[[Image:LMU-Munich_logo.png|200px|right|frame]] -->
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This is a template page. READ THESE INSTRUCTIONS.
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<!-- |- -->
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<!-- | -->
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<!-- ''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)'' -->
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<!-- |[[Image:LMU-Munich_team.png|right|frame|Your team picture]] -->
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<!-- |- -->
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<!-- | -->
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<!-- |align="center"|[[Team:LMU-Munich | Team Example]] -->
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-->
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<!--- The Mission, Experiments --->
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<!--{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center" -->
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<!--!align="center"|[[Team:LMU-Munich|Home]] -->
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<!--!align="center"|[[Team:LMU-Munich/Team|Team]] -->
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<!--!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=LMU-Munich Official Team Profile] -->
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<!--!align="center"|[[Team:LMU-Munich/Project|Project]] -->
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<!--!align="center"|[[Team:LMU-Munich/Parts|Parts Submitted to the Registry]] -->
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<!--!align="center"|[[Team:LMU-Munich/Modeling|Modeling]] -->
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<!--!align="center"|[[Team:LMU-Munich/Notebook|Notebook]] -->
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<!--!align="center"|[[Team:LMU-Munich/Safety|Safety]] -->
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<!--|} -->
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== '''Who we are''' ==
 +
 
 +
We are a team constisting of biologists, biochemists, chemists and bioinformatics and four faculty advisors... The LMU team is competing for the first time.
 +
 
 +
=== Advisors ===
 +
 
 +
<div align="center">
 +
<gallery>
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Image: Böttger.jpg|'''<span style="color:#0000CD"> Prof. Dr. Angelika Böttger</span>:''' Department Biologie II/ Cell and Developmental Biology
 +
Image:Jung.jpg|'''<span style="color:#0000CD"> Prof. Dr. Kirsten Jung</span>:''' Head of the Division of Microbiology
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Image:Mascher.jpg|'''<span style="color:#0000CD"> Prof. Dr. Thorsten Mascher</span>:''' Department Biologie I/ Microbiology
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</gallery>
</div>
</div>
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<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
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<div align="center">
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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki. You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
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<gallery>
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Image:Tresch.jpg|'''<span style="color:#0000CD"> Dr. Achim Tresch</span>:''' Computational Biology and Regulatory Networks
 +
Image:Akman.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/KemalAkman Kemal Akman]:''' Bioinformatics
 +
</gallery>
</div>
</div>
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<div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;">
 
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You <strong>MUST</strong> have a team description page, a project abstract, a complete project description, a lab notebook, and a safety page.  PLEASE keep all of your pages within your teams namespace. 
 
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</div>
 
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</div>
 
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</html>
 
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<!-- *** End of the alert box *** -->
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=== Undergrads ===
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{|align="justify"
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<div align="center">
-
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.
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<gallery>
-
|[[Image:LMU-Munich_logo.png|200px|right|frame]]
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Image:Julia3.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Julia Julia Bartels]:'''        expected BSc Biology, ApoControl, Pathway
 +
Image:Tobi.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Tobi Tobias Bauer]:'''      BSc Biology, Pathway
 +
Image:Alexander Buschle.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Alex Alexander Buschle]:'''        BSc Biology, ApoControl
 +
Image:Benny.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Benny Benjamin Clanner]:'''        Chemistry and Biochemistry, pharmaceutical sciences, Pathway
 +
</gallery>
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<gallery>
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Image:Maria.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Maria Maria Katharina Drexler]:'''        BSc Biology, ApoControl
 +
Image:ErikFumi.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Erik Erik Fumi]:'''        Chemistry and Biochemistry, Pathway
 +
Image:Tatyana.jpg|'''[https://2010.igem.org/User:Tatyana Tatyana Goldberg]:'''      BSc Bioinformatics, ApoControl
 +
Image:Franzi.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Franzi Franziska Häfele]:'''        expected BSc Biology, ApoControl
 +
</gallery>
 +
<gallery>
 +
Image:Corinna.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Corinna Corinna Hofer]:'''        BSc Biology, ApoControl
 +
Image:Nicolas.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Nicky Nicolas Keller]:'''        Biology, Law, ApoControl, Pathway
 +
Image:Laura2.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Laura Laura Kleinknecht]:'''      BSc Biology, ApoControl
 +
Image:Christina.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Christina Christina Krönauer]:'''      expected BSc Biology, Pathway
 +
</gallery>
 +
<gallery>
 +
Image:Marisa.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Marisa Marisa Kurz]:'''        Chemistry and Biochemistry, Pathway
 +
Image:Jens Popken.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Jens Jens Popken]:'''        Biology, Pathway
 +
Image:Jara2.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Jara Jara Radeck]:'''        Biology, ApoControl
 +
Image:Emanuel.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Emanuel Emanuel Stiegeler]:'''        BSc Biology, Pathway
 +
</gallery>
 +
<gallery>
 +
Image:Geli.jpg‎|'''[https://2010.igem.org/Team:LMU-Munich/Team/Geli Angelika Vetter]:'''        Biology, ApoControl
 +
Image:Sabine Wagner.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Bine Sabine Wagner]:'''        Biology, ApoControl, Pathway
 +
Image:Grace.jpg|'''[https://2010.igem.org/Team:LMU-Munich/Team/Grace Mengzhe Wang (Grace)]:'''        Biology, ApoControl
 +
</gallery>
 +
</div>
 +
 
 +
== '''Who is in charge of what''' ==
 +
 
 +
{|
 +
| Press
 +
| Nicolas Keller, Marisa Kurz
|-
|-
-
|
+
| Sponsoring
-
''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
+
| Sabine Wagner, Franziska Haefele
-
|[[Image:LMU-Munich_team.png|right|frame|Your team picture]]
+
|-
|-
-
|
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| Pathway
-
|align="center"|[[Team:LMU-Munich | Team Example]]
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| Tobias Bauer, Emanuel Stiegeler, Benny Clanner
 +
|-
 +
| ApoControl
 +
| Julia Bartels, Jara Radeck, Mengzhe Grace Wang
 +
|-
 +
| Homepage
 +
| Tatyana Goldberg, Jens Popken
 +
|-
 +
| Coordination/Organisation
 +
|  Jara Radeck, Angelika Vetter
 +
|-
 +
| Contact
 +
| igemlmu(at)yahoo(dot)de
|}
|}
 +
== '''What we did''' ==
-
<!--- The Mission, Experiments --->
+
<b>Short description of our work, our results and our supporters</b>
-
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
 
-
!align="center"|[[Team:LMU-Munich|Home]]
 
-
!align="center"|[[Team:LMU-Munich/Team|Team]]
 
-
!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=LMU-Munich Official Team Profile]
 
-
!align="center"|[[Team:LMU-Munich/Project|Project]]
 
-
!align="center"|[[Team:LMU-Munich/Parts|Parts Submitted to the Registry]]
 
-
!align="center"|[[Team:LMU-Munich/Modeling|Modeling]]
 
-
!align="center"|[[Team:LMU-Munich/Notebook|Notebook]]
 
-
!align="center"|[[Team:LMU-Munich/Safety|Safety]]
 
-
|}
 
 +
The creation of certain constructs was necessary for our two systems for cell selection by means of apoptosis: “Cut’N’Survive” and “Jump-Or-Die”. We searched for sources of the DNA sequences we needed and found several supporters which are listed below.
 +
Most genes and promoters were amplificated via PCR with overhang-primers with the BioBrick prefix or suffix. If the sequence contained a EcoR1-, Pst1-, Xba1-, Spe1- or Not1- restriction site, we used mutagenesis primers and fusioned both DNA parts by fusion PCR. All PCRs worked out, even the fusion PCRs.
-
== '''Who we are''' ==
+
The length of the PCR products were tested by agarose gel electrophoresis. We tried to sequence our PCR products, but obtained poor results and resorted to sequencing the plasmids.
-
{|border = "0"
+
-
|-
+
-
|rowspan="3"|
+
 +
In parallel, we made competent cells and multiplied ccdB (death gene)-vectors with different antibiotic resistances. All components were digested with the appropriate restriction enzymes. The samples were cleaned with a PCR clean up kit or dephosphorylated to reduce false ligations.
 +
We ligated our constructs and several interim stages with the 3A-assembly according to our schedule. The ligations were transformed to E.coli DH5α strains and selected by antibiotics. Afterwards, some colonies were picked and we tested the insertion of the construct by colony PCR.
 +
If the colony PCR resulted in bands of the right size, we extracted the plasmids from overnight cultures and sequenced the samples with forward and reverse BioBrick primers.
 +
Unfortunately, not all BioBricks were cloned succesfully. However, we were able to produce 4 BioBricks, one of which represents a full construct while the other three are intermediates. The system wasn't completed on time, so we weren´t able to test them in eukarytic cell lines.
-
'''Advisors:'''
+
Besides, we found out that the CMV-promoter we ordered from the BioBrick registry (<html><a href="http://partsregistry.org/Part:BBa_J52034">BBa_J52034</a href></html>) was in fact a lacI gene, which resulted in the procrastination of our plan. We have sent the correction to the registry to facilitate future teams.
-
*'''Thorsten Mascher''':    Mentor for all
 
-
*'''Kirsten Jung''':        Mentor for all
 
-
*'''Angelika Böttger''':    Mentor for Apo-Control
 
-
*'''Grad Student 1''':    Our leader 
+
<b>Our notebook with detailed descriptions can be found here:</b> [[Team:LMU-Munich/Notebook/Apoptosis|ApoControl notebook]]
 +
<b>The protocols we used are listed here: </b> [[Team:LMU-Munich/Notebook#Protocols|Protocols]]
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'''Undergrads:'''
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<b>The Biobricks we submitted: </b>
-
*'''Student 1''':   Sleepyhead
+
*BBa_K368004: attP+eGFP+SV40PA
 +
*BBa_K368011: eGFP+SV40PA
 +
*BBa_K368016: TEVrecognition site+N-degron+SF3b155
 +
*BBa_K368019: TEV-Protease+p14*+TEVrecognition site
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*'''Bartels Julia''': Pathway, Apo-Control     
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<b>Supervisors</b>
-
*'''Bauer Tobias''': Pathway   
+
-
*'''Buschle Alexander''': Apo-Control
+
-
*'''Clanner Benjamin''': Pathway
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-
*'''Drexler Maria''': Apo-Control
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-
*'''Fumi Erik''': Pathway       
+
-
*'''Goldberg Tatyana''': Apo-Control
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*'''Häfele Franziska''': Apo-Control     
+
-
*'''Hofer Corinna''': Apo-Control   
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*'''Keller Nicolas''': Apo-Control, Pathway       
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*'''Kleinknecht Laura''': Apo-Control
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-
*'''Krönauer Christina''': Pathway   
+
-
*'''Kurz Marisa''': Pathway         
+
-
*'''Popken Jens''': Apo-Control         
+
-
*'''Radeck Jara''': Apo-Control         
+
-
*'''Stiegeler Emanuel''': Pathway
+
-
*'''Vetter Angelika''':Apo-Control     
+
-
*'''Wagner Sabine''':Apo-Control       
+
-
*'''Wang Mengzhe (Grace)''': Apo-Control
+
-
*'''Zink Lisa-Maria''': Apo-Control     
+
 +
* Prof. Dr. Angelika Böttger :
 +
** prevTRE (tet-on CMV promoter; inducible by doxycycline in special cell lines)
 +
** supported the construction ideas and would have given us the cells and mediums we would have needed
 +
** SV40PA (Polyadenylation site): gave us a vector containing it
 +
** Human Bak:  her assistant Erika Clement gave us appropriate cDNA
 +
* Prof. Dr. Thorsten Mascher:
 +
** Helped with primer design, agarose gel electrophoresis apparatuses and trouble shooting
 +
* Prof. Dr. Kirsten Jung:
 +
** Helped with ideas and fundraising
 +
* Dr. Susanne Gebhard:
 +
** Helped with trouble-shooting and materials
 +
* Kemal Akman
 +
** Helped and supported our sub-project ProSearch
-
|
+
<b> Plasmid and sequence sources </b>
-
<gallery>
+
-
Image:LMU-Munich_Team_member_1.png|Team member 1
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Image:LMU-Munich_Team_member_2.png|Team member 2
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Image:LMU-Munich_Team_member_3.png|Team member 3
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Image:LMU-Munich_Team_member_4.png|Team member 4
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Image:LMU-Munich_Team_member_5.png|Team member 5
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Image:LMU-Munich_Team_member_6.png|Team member 6
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Image:LMU-Munich_Team_member_7.png|Team member 7
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-
</gallery>
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|}
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-
== '''What we did''' ==
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* Dr. Arnim Weber: provided us with human Bak plasmid
 +
* Dr. Philipe Soriano: <html>
 +
<a href="http://www.ncbi.nlm.nih.gov/pubmed/17225864?dopt=Abstract"> (Raymond CS et al: High-Efficiency FLP and PhiC31 Site-Specific Recombination in Mammalian Cells (2007))</a>
 +
</html>
 +
** Sequences of attB and attP site
 +
** PhiC31o was bought via Addgene
 +
* Dr. Michael Knop:(Heidelberg): <html>
 +
<a href ="http://www.ncbi.nlm.nih.gov/pubmed?term=Efficient%20protein%20depletion%20by%20genetically%20controlled%20deprotection%20of%20a%20dormant%20N-degron">(Knop et al.: Efficient protein depletion by genetically controlled deprotection of a dormant N-degron (2009))</a>
 +
</html>
 +
** provided us with:
 +
** TEVrecognition site+N-degron+SF3b155
 +
** TEV-Protease+p14*+TEVrecognition site
 +
* Prof. Dr. Andreas Brachmann:
 +
** Sequenced our samples
 +
* Partsregistry provided us with:
 +
** eGFP (BBa_I714891)
 +
** CMV-Promoter (BBa_J52034: this part was wrong: its lacI !!!)
 +
** ccdB amp, cam, tet, kan in E.coli DH3
-
(Provide proper attribution for all work)
 
-
Organigram
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As our project for human practice, we carried out a survey about synthetic biology on the general public at the Oktoberfest, LMU Munich and the Municipal Secretary: [[Team:LMU-Munich/HumanPractice|Human practice]]
-
<p>Responsibilities for:</p>
+
== '''Where we are from''' ==
-
<p>Press: Nicolas Keller,  Marisa Kurz</p>
+
-
<p>Sponsors: Sabine Wagner</p>
+
-
<p>Pathway: Tobias Bauer, Emanuel Stiegeler,  Benjamin Clanner</p>
+
-
<p>Apo-Control: Mengzhe Wang („Grace“),  Julia Bartels</p>
+
-
<p>Homepage: Tatyana Goldberg,  Jens Popken</p>
+
-
<p>Coordination/Organisation: Jara Radeck</p>
+
-
<p>Contact: igemlmu(at)yahoo(dot)de</p>
+
-
== '''Where we're from''' ==
+
We are students at Ludwigs-Maximilians-University in Munich, Germany.
 +
 
 +
 
 +
 
 +
[[Image:lmu2.jpg|center|760px|Biozentrum]]our bio-center (photos courtesy of www.stbam2.bayern.de)
 +
 
 +
There's a second University in our beautiful Munich, even though it is "only" a technical University. Also check out their
 +
<html><a href="https://2010.igem.org/Team:TU_Munich">wiki</a href></html>.
 +
 
 +
[[Image:Tu.jpg]]
 +
 
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<html>
 +
<!-- hitwebcounter Code START -->
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<br>
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<br>
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<div align="center">
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<a href="http://www.hitwebcounter.com/internetcountercontact.php" target="_blank">
 +
<img src="http://hitwebcounter.com/counter/counter.php?page=102444&style=0006&nbdigits=5&type=page&initCount=0" title="Statistics Counters" Alt="Statistics Counters"  border="0" >
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<br>
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<a href="http://www.hitwebcounter.com/" title="Our Web Counter"
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target="_blank" style="font-family: Geneva, Arial, Helvetica, sans-serif;
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font-size: 11px; color: #8A8A8A; text-decoration: none;"><strong>Our Web Counter</strong>
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</a> <!-- hitwebcounter.com --> 
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</html>
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we are from Munich
 
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Latest revision as of 21:10, 10 January 2011


Team LMU iGEM 2010

Our team picture
Also our team


-->

Who we are

We are a team constisting of biologists, biochemists, chemists and bioinformatics and four faculty advisors... The LMU team is competing for the first time.

Advisors

Prof. Dr. Angelika Böttger: Department Biologie II/ Cell and Developmental Biology

Prof. Dr. Kirsten Jung: Head of the Division of Microbiology

Prof. Dr. Thorsten Mascher: Department Biologie I/ Microbiology

Dr. Achim Tresch: Computational Biology and Regulatory Networks

Kemal Akman: Bioinformatics

Undergrads

Julia Bartels: expected BSc Biology, ApoControl, Pathway

Tobias Bauer: BSc Biology, Pathway

Alexander Buschle: BSc Biology, ApoControl

Benjamin Clanner: Chemistry and Biochemistry, pharmaceutical sciences, Pathway

Maria Katharina Drexler: BSc Biology, ApoControl

Erik Fumi: Chemistry and Biochemistry, Pathway

Tatyana Goldberg: BSc Bioinformatics, ApoControl

Franziska Häfele: expected BSc Biology, ApoControl

Corinna Hofer: BSc Biology, ApoControl

Nicolas Keller: Biology, Law, ApoControl, Pathway

Laura Kleinknecht: BSc Biology, ApoControl

Christina.jpg

Christina Krönauer: expected BSc Biology, Pathway

Marisa Kurz: Chemistry and Biochemistry, Pathway

Jens Popken: Biology, Pathway

Jara Radeck: Biology, ApoControl

Emanuel Stiegeler: BSc Biology, Pathway

Angelika Vetter: Biology, ApoControl

Sabine Wagner: Biology, ApoControl, Pathway

Mengzhe Wang (Grace): Biology, ApoControl

Who is in charge of what

Press Nicolas Keller, Marisa Kurz
Sponsoring Sabine Wagner, Franziska Haefele
Pathway Tobias Bauer, Emanuel Stiegeler, Benny Clanner
ApoControl Julia Bartels, Jara Radeck, Mengzhe Grace Wang
Homepage Tatyana Goldberg, Jens Popken
Coordination/Organisation Jara Radeck, Angelika Vetter
Contact igemlmu(at)yahoo(dot)de

What we did

Short description of our work, our results and our supporters


The creation of certain constructs was necessary for our two systems for cell selection by means of apoptosis: “Cut’N’Survive” and “Jump-Or-Die”. We searched for sources of the DNA sequences we needed and found several supporters which are listed below.

Most genes and promoters were amplificated via PCR with overhang-primers with the BioBrick prefix or suffix. If the sequence contained a EcoR1-, Pst1-, Xba1-, Spe1- or Not1- restriction site, we used mutagenesis primers and fusioned both DNA parts by fusion PCR. All PCRs worked out, even the fusion PCRs.

The length of the PCR products were tested by agarose gel electrophoresis. We tried to sequence our PCR products, but obtained poor results and resorted to sequencing the plasmids.

In parallel, we made competent cells and multiplied ccdB (death gene)-vectors with different antibiotic resistances. All components were digested with the appropriate restriction enzymes. The samples were cleaned with a PCR clean up kit or dephosphorylated to reduce false ligations.

We ligated our constructs and several interim stages with the 3A-assembly according to our schedule. The ligations were transformed to E.coli DH5α strains and selected by antibiotics. Afterwards, some colonies were picked and we tested the insertion of the construct by colony PCR.

If the colony PCR resulted in bands of the right size, we extracted the plasmids from overnight cultures and sequenced the samples with forward and reverse BioBrick primers.

Unfortunately, not all BioBricks were cloned succesfully. However, we were able to produce 4 BioBricks, one of which represents a full construct while the other three are intermediates. The system wasn't completed on time, so we weren´t able to test them in eukarytic cell lines.

Besides, we found out that the CMV-promoter we ordered from the BioBrick registry (BBa_J52034) was in fact a lacI gene, which resulted in the procrastination of our plan. We have sent the correction to the registry to facilitate future teams.


Our notebook with detailed descriptions can be found here: ApoControl notebook

The protocols we used are listed here: Protocols

The Biobricks we submitted:

  • BBa_K368004: attP+eGFP+SV40PA
  • BBa_K368011: eGFP+SV40PA
  • BBa_K368016: TEVrecognition site+N-degron+SF3b155
  • BBa_K368019: TEV-Protease+p14*+TEVrecognition site

Supervisors

  • Prof. Dr. Angelika Böttger :
    • prevTRE (tet-on CMV promoter; inducible by doxycycline in special cell lines)
    • supported the construction ideas and would have given us the cells and mediums we would have needed
    • SV40PA (Polyadenylation site): gave us a vector containing it
    • Human Bak: her assistant Erika Clement gave us appropriate cDNA
  • Prof. Dr. Thorsten Mascher:
    • Helped with primer design, agarose gel electrophoresis apparatuses and trouble shooting
  • Prof. Dr. Kirsten Jung:
    • Helped with ideas and fundraising
  • Dr. Susanne Gebhard:
    • Helped with trouble-shooting and materials
  • Kemal Akman
    • Helped and supported our sub-project ProSearch

Plasmid and sequence sources


As our project for human practice, we carried out a survey about synthetic biology on the general public at the Oktoberfest, LMU Munich and the Municipal Secretary: Human practice

Where we are from

We are students at Ludwigs-Maximilians-University in Munich, Germany.


Biozentrum
our bio-center (photos courtesy of www.stbam2.bayern.de)

There's a second University in our beautiful Munich, even though it is "only" a technical University. Also check out their wiki.

Tu.jpg



 

Retrieved from "http://2010.igem.org/Team:LMU-Munich/Team"