Difference between revisions of "Team:Freiburg/Parts"

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<div class="kommentar">
 
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Hier fehlt auf jeden Fall noch die Nennung unseres Favorite Biobricks mit erklärung warum das so ist. Ich denke in unserem Fall wird das der pOP sein oder? (Stefan)</br>
 
Hier fehlt auf jeden Fall noch die Nennung unseres Favorite Biobricks mit erklärung warum das so ist. Ich denke in unserem Fall wird das der pOP sein oder? (Stefan)</br>
Erster Versuch das Fav-Biobrick etwas genauer zu erklären. Verbesserungsvorschläge willkommen :) (Lara)
 
 
Bitte auf Artnamen achten (Vorname Groß, Nachname klein, alles kursiv (Philipp)) Bezüglich pop: warum ist pSB1C3 ein doofes Backbone für die expression? warum wird iGEM viel mehr proteinexpression machen (in-vitro ist en vogue)? Warum habt ihr plötzlich angefangen ein anderes Backbone genutzt? (Resistenz, lacI etc). Kurz: Warum ist pOP cool?
 
Bitte auf Artnamen achten (Vorname Groß, Nachname klein, alles kursiv (Philipp)) Bezüglich pop: warum ist pSB1C3 ein doofes Backbone für die expression? warum wird iGEM viel mehr proteinexpression machen (in-vitro ist en vogue)? Warum habt ihr plötzlich angefangen ein anderes Backbone genutzt? (Resistenz, lacI etc). Kurz: Warum ist pOP cool?
 +
</br> neuer Versuch (9.9.15 Lara)
 
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We think that expression of proteins is a rather big topic for future iGEM teams, since working <em>in-vitro</em> is an upcoming issue of synthetic biology. (Beispiele?)
+
We think that expression of proteins is a rather big topic for future iGEM teams, since working <em>in-vitro</em> is an upcoming issue of synthetic biology. (Beispiele? kommt noch)
 
Expression of proteins is usually done in specialized expression strains, that in the case of <em>E. coli</em> often carry a resistence against chloramphenicol. That is why plasmids used for expression should have an additional resistance making selection of positively transformed clones possible. The iGEM standard backbone pSB1C3 only contains a chloramphenicol resistance making it difficult to use in combination with expression strains like <em>E. coli</em> BL21 or ?.
 
Expression of proteins is usually done in specialized expression strains, that in the case of <em>E. coli</em> often carry a resistence against chloramphenicol. That is why plasmids used for expression should have an additional resistance making selection of positively transformed clones possible. The iGEM standard backbone pSB1C3 only contains a chloramphenicol resistance making it difficult to use in combination with expression strains like <em>E. coli</em> BL21 or ?.
Since protein expression sometimes has negative consequences for the cell expressing the protein it is useful to have a tool, which allows induction of protein expression at a certain timepoint. One system which is often used is a lac inducible promoter,that can be induced (anderes Wort?) with IPTG. pSB1C3 uses a promoter (which one?) that is constitutively active, therefore it is a rather poor vector for expression.
+
Since protein expression sometimes has negative consequences for the cell expressing the protein it is useful to have a tool, which allows induction of protein expression at a certain timepoint. One system which is often used is a lac inducible promoter system,that can be started with IPTG. pSB1C3 does not have any default promotor inserted at all, making protein expression more difficult because an appropriate promotor has to be inserted every time.
Therefore an iGEM backbone adapted for protein expression seemed to be a quite good idea. We improved the pSB1C3 standard vector so that it can be used to express proteins in <em>E. coli</em>.
+
</br>
 +
One additional disadvantage of pSB1C3 is the high copy ori which is really useful for cloning, but disturbs protein expression.
 +
Therefore an iGEM backbone adapted for protein expression seemed to be a quite good idea. We improved the pSB1C3 standard vector in a way that it can be used to express proteins in <em>E. coli</em> but still exhibits all the properties of an iGEM standard vector.
 
</br>
 
</br>
 
Details on which parts of pSB1C3 we changed and how we did this can be found <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Project/pOP-vector" title="pop_-_protein_expression_meets_igem_standards">here</a>.
 
Details on which parts of pSB1C3 we changed and how we did this can be found <a class="wikilink1" href="https://2015.igem.org/Team:Freiburg/Project/pOP-vector" title="pop_-_protein_expression_meets_igem_standards">here</a>.

Revision as of 09:27, 9 September 2015

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Biobricks

Hier fehlt auf jeden Fall noch die Nennung unseres Favorite Biobricks mit erklärung warum das so ist. Ich denke in unserem Fall wird das der pOP sein oder? (Stefan)
Bitte auf Artnamen achten (Vorname Groß, Nachname klein, alles kursiv (Philipp)) Bezüglich pop: warum ist pSB1C3 ein doofes Backbone für die expression? warum wird iGEM viel mehr proteinexpression machen (in-vitro ist en vogue)? Warum habt ihr plötzlich angefangen ein anderes Backbone genutzt? (Resistenz, lacI etc). Kurz: Warum ist pOP cool?
neuer Versuch (9.9.15 Lara)

Since our project involved expression of many antigenic peptides we decided to share those antigen-sequences with the iGEM community. We obtained most of the sequences via paper research and we would like to give special thanks to the group of Prof. Dr. Michael Hust (TU Braunschweig) who provided us with expression plasmids for the Salmonella Typhimurium antigen and a corresponding single chain variable fragment. The codon optimization tool from Integrated DNA Technologies was used to improve most sequences for expression in E. coli. We also removed all restriction sites that are not allowed in RFC[10], so that all sequences are compatible with the submission vector pSB1C3. When we started working with our first plasmids for this project, we decided to use a specific nomenclature. Every plasmid name starts with “pIG15” which is short for “plasmid igem 2015”. According to this, we named the plasmids containing our biobricks in the shipping backbone pRIG15 (“pRIG” as in “brick”)

In the table below we listed all our biobricks and our biobrick improvement, pOP. We decided on pOP as our favorite biobrick because it provides the iGEM communitiy with an iGEM conform backbone for protein expression. When we started our project we faced the problem of pSB1C3 being a plasmid designated for cloning colliding with our need of a plasmid for expression of proteins.
We think that expression of proteins is a rather big topic for future iGEM teams, since working in-vitro is an upcoming issue of synthetic biology. (Beispiele? kommt noch) Expression of proteins is usually done in specialized expression strains, that in the case of E. coli often carry a resistence against chloramphenicol. That is why plasmids used for expression should have an additional resistance making selection of positively transformed clones possible. The iGEM standard backbone pSB1C3 only contains a chloramphenicol resistance making it difficult to use in combination with expression strains like E. coli BL21 or ?. Since protein expression sometimes has negative consequences for the cell expressing the protein it is useful to have a tool, which allows induction of protein expression at a certain timepoint. One system which is often used is a lac inducible promoter system,that can be started with IPTG. pSB1C3 does not have any default promotor inserted at all, making protein expression more difficult because an appropriate promotor has to be inserted every time.
One additional disadvantage of pSB1C3 is the high copy ori which is really useful for cloning, but disturbs protein expression. Therefore an iGEM backbone adapted for protein expression seemed to be a quite good idea. We improved the pSB1C3 standard vector in a way that it can be used to express proteins in E. coli but still exhibits all the properties of an iGEM standard vector.
Details on which parts of pSB1C3 we changed and how we did this can be found here.

biobrick short description detailed desription
BBa_K1621000 Rubella Virus specific antigenic epitopes derived from glycoprotein E1pRIG15_6
BBa_K1621001 Varicella Zoster Virus specific antigenic epitopes derived from glycoprotein EpRIG15_7
BBA_K1621002 Herpes Simplex specific antigenic epitopes derived from glycoprotein GpRIG15_8
BBa_K1621003 Clostridium tetani specific antigenic epitopes derived from tetanus neurotoxin (TeNT_Hc)pRIG15_11
BBa_K1621004 Human Immunodeficiency Virus specific antigenic epitopes derived from a polyprotein called gag/tat/pol/envpRIG15_17
BBa_K1621005 Treponema pallidum specific antigenic peptides derived from bacterioferritin (TpF1)pRIG15_18
BBa_K1621006 Salmonella Typhimurium specific antigenic protein (DHAD)pRIG15_15
BBa_K1621007 scFv binding specifically to the Salmonella Typhimurium derived antigenpRIG15_13
BBa_K1621009 Standardized plasmid backbone optimized for protein overexpressionpOP