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Team:Freiburg Bioware/NoteBook/Labjournal/April
From 2010.igem.org
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<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 - | + | <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 | + | <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/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> | + | <li><a href="https://2010.igem.org/Team:Freiburg_Bioware/NoteBook/Labjournal/Cellculture">Cellculture</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
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<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 | + | |
| - | 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]] | ||
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<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> | ||
| - | |||
<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 | ||
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<p><b>Investigators: Adrian, Chris W., Hanna, Bea</b></p><br> | <p><b>Investigators: Adrian, Chris W., Hanna, Bea</b></p><br> | ||
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*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> | ||
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===<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>=== | ||
Latest revision as of 21:39, 27 October 2010
- March (labday 1)
- April (labday 2 - 5)
- May (labday 6 - 17)
- June (labday 18 - 45)
- July (labday 46 - 75)
- August part 1 (labday 76 - 92)
- August part 2 (labday 93 - 106)
- September part 1 (labday 107 - 123)
- September part 2 (labday 124 - 135)
- October part 1 (labday 136 - 149 )
- October part 2 (labday 150 - 166 )
- November (labday 167 - 170 )
- Cellculture
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)
