Team:Freiburg Bioware/NoteBook/Labjournal/April

From 2010.igem.org

(Difference between revisions)
(→Theoretical cloning)
 
(9 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:Freiburg_Bioware/css}}
{{:Team:Freiburg_Bioware/css}}
-
{{:Team:Freiburg_Bioware/SubNoteBook}}
 
{{:Team:Freiburg_Bioware/Head}}
{{:Team:Freiburg_Bioware/Head}}
 +
{{:Team:Freiburg_Bioware/menu_notebook}}
 +
{{:Team:Freiburg_Bioware/jquery}}
<!-- Freiburg_bioware -->
<!-- Freiburg_bioware -->
Line 20: Line 21:
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/September">September part 1 (labday 107 - 123)</a></li>
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/September">September part 1 (labday 107 - 123)</a></li>
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/September2">September part 2 (labday 124 - 135)</a></li>
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/September2">September part 2 (labday 124 - 135)</a></li>
-
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/October">October part 1 (labday 136 - 145 )</a></li>
+
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/October">October part 1 (labday 136 - 149 )</a></li>
-
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/October2">October part 2 (labday 146 - 155 )</a></li>
+
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/October2">October part 2 (labday 150 - 166 )</a></li>
-
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/October3">October part 3 (labday 156 - 166 )</a></li>
+
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/November">November  (labday 167 - 170 )</a></li>
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/November">November  (labday 167 - 170 )</a></li>
 +
<li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/Cellculture">Cellculture</a></li>
</ul>
</ul>
</div>
</div>
Line 35: Line 36:
<p><b>Investigators: Chris W., Bea, Kira, Hanna, Julian, Anna, Jessica (Tobias,Sven, Kristian)</b></p><br>
<p><b>Investigators: Chris W., Bea, Kira, Hanna, Julian, Anna, Jessica (Tobias,Sven, Kristian)</b></p><br>
-
 
+
The BioBricks Foundation is dedicated to promoting and protecting open development, sharing, and reuse of BioBrick™ standard biological parts.<br>
-
 
+
-
The BioBricks Foundation is dedicated to promoting and protecting the open development, <br>
+
-
sharing, and reuse of BioBrick™ standard biological parts.<br>
+
Homepage: [[http://openwetware.org/wiki/The_BioBricks_Foundation:RFC]]
Homepage: [[http://openwetware.org/wiki/The_BioBricks_Foundation:RFC]]
Line 84: Line 82:
<br>
<br>
<li>function of the Beta-Globin intron ( pAAV MCS Vector): increases the expression rate in Vivo/ Vitro through several mechanisms ( i.a. increased m-RNA accumulation <br>
<li>function of the Beta-Globin intron ( pAAV MCS Vector): increases the expression rate in Vivo/ Vitro through several mechanisms ( i.a. increased m-RNA accumulation <br>
-
([[Media: Freigem10_Nott_et_al_A_quantitative_analysis_of_intron_effects_on_mammalian_gene_expression_2003.pdf?]]; <br> [[Media: Freigem10_Haddad_et_al_A_systematic_study_of_the_function_of_the_h-beta-globin_introns_on_the_expression_2009.pdf?]])<br>
 
<br>
<br>
<li> Thymidin Kinase : we received another modified thymídin kinase-sequence from Amor, to do: check for iGEM restriction sites and develop a cloning strategie  
<li> Thymidin Kinase : we received another modified thymídin kinase-sequence from Amor, to do: check for iGEM restriction sites and develop a cloning strategie  
Line 96: Line 93:
<p><b>Investigators: Adrian, Chris W., Hanna, Bea</b></p><br>
<p><b>Investigators: Adrian, Chris W., Hanna, Bea</b></p><br>
-
 
-
 
*tomorrow we will obtain the vector sequence for the thymidinkinase (WT) from Amor
*tomorrow we will obtain the vector sequence for the thymidinkinase (WT) from Amor
*call at Stratagene: #240071 AAV-Helper Free System, 1412 € (netto), available until next week ; we asked for a discount (Bea got Infos per E-mail)
*call at Stratagene: #240071 AAV-Helper Free System, 1412 € (netto), available until next week ; we asked for a discount (Bea got Infos per E-mail)
*next step (tomorrow, 10 am): modification of the  multiple cloning site
*next step (tomorrow, 10 am): modification of the  multiple cloning site
<br>
<br>
-
 
===<p style="font-size:17px; background-color:#00dd77;">5. Labday 23.04.2010</p>===
===<p style="font-size:17px; background-color:#00dd77;">5. Labday 23.04.2010</p>===
Line 122: Line 116:
*To do: gather information about the mutant thymidinkinase (TK30 + SR39)  
*To do: gather information about the mutant thymidinkinase (TK30 + SR39)  
-
<center>[https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/May '''=> Go to Labjournal April (labday 2 - 5)''']</center><br>
+
<center>[https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/May '''=> Go to Labjournal May (labday 6 - 17)''']</center><br>
<html>
<html>
</div>
</div>
</html>
</html>

Latest revision as of 21:39, 27 October 2010

=> Back to Notebook overview

NoteBook Navigator


Contents

2. Labday 13.04.2010

The Biobricks Foundation: RFC

Investigators: Chris W., Bea, Kira, Hanna, Julian, Anna, Jessica (Tobias,Sven, Kristian)


The BioBricks Foundation is dedicated to promoting and protecting open development, sharing, and reuse of BioBrick™ standard biological parts.
Homepage: http://openwetware.org/wiki/The_BioBricks_Foundation:RFC

Two important standards:

BBF RFC-10:
This standard defines the required sequence properties for a Biobrick(tm) standard biological part.
http://dspace.mit.edu/bitstream/handle/1721.1/45138/BBFRFC10.txt?sequence=1

BBF RFC-25: Fusion Protein (Freiburg) Biobrick assembly standard
This Request for Comments (RFC) describes an extension to the original BioBrick assembly standard (BBF RFC 10).
Media:Freiburg10 BBF RFC 25.pdf


Theoretical cloning
DNA- and protein-analyse:

  • Thymidin Kinase HSVI

Accesion: V00470 (Genebank) CDS without iGEM-restriction sites, unkown sequence in front of CDS with an EcoRI-restriction site, sequence from 1980! (There is a lot of X-ray crystallography analysis data available, but just to be on the safe side we should check the sequence again)

  • Cytosine Deaminase (see also FCY1) (S.cerevisae)

Accession number: AF005261 (Genebank) CDS without iGEM-restriction site, unkown in front of CDS with PstI-restriction site, sequence from 1997

  • pORF-CodA::upp (E.coli) [Vektor from InvivoGen]

CDS of the Cytosine Deaminase (E.coli) without iGEM-restriction site

  • Alignment of the amino acid-sequences of the cytosin deaminases of E.coli (Invivogen) and S.cerevisiae (Genebank)

no consensus found in the amino acid-sequence discussion at the next meeting

3. Labday 15.04.2010

Theoretical cloning

Investigators: Kira, Johannes, Bea


  • pAAV-MCS vector (Stratagene): we checked the vector for igEM-restiction sites: (RFC-25)
    EcoRI 1327; Xbal 1344; are inside the MCS
    NgoMIV 2254 are inside the V1 Ori region

  • function of the Beta-Globin intron ( pAAV MCS Vector): increases the expression rate in Vivo/ Vitro through several mechanisms ( i.a. increased m-RNA accumulation

  • Thymidin Kinase : we received another modified thymídin kinase-sequence from Amor, to do: check for iGEM restriction sites and develop a cloning strategie


4. Labday 22.04.2010

Theoretical cloning

Investigators: Adrian, Chris W., Hanna, Bea


  • tomorrow we will obtain the vector sequence for the thymidinkinase (WT) from Amor
  • call at Stratagene: #240071 AAV-Helper Free System, 1412 € (netto), available until next week ; we asked for a discount (Bea got Infos per E-mail)
  • next step (tomorrow, 10 am): modification of the multiple cloning site


5. Labday 23.04.2010

Theoretical cloning

Investiators: Adrian, Chris W., Hanna, Kerstin, Anissa, (Kristian, Tobias, Sven)


  • thymidin kinase from Amor: there is a PstI restriction site within the sequence (instead of this kinase we will probably use the TK30 + SR39 mutant -> we have to find their sequences )
  • analysis of the ITR secondary structure (pAAV MCS of Stratagene), to decide if we can introduce a point mutation to delete the PstI-restriction site :

Right ITR
Left ITR
http://www.molbiotech.uni-freiburg.de/iGEM/wiki2010/images/e/ef/Freiburg_10ITRleft.pdf
http://www.molbiotech.uni-freiburg.de/iGEM/wiki2010/images/b/b5/Freiburg_10ITRright_AAV2.pdf

  • sequence alignement of the beta-globin of the pAAV MCS Plasmid with human beta-globin:

Nucleotide alignment of the AAV
  • To do: gather information about the mutant thymidinkinase (TK30 + SR39)
=> Go to Labjournal May (labday 6 - 17)

Retrieved from "http://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/April"