http://2010.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=250&target=AndreasConstantinou&year=&month=2010.igem.org - User contributions [en]2024-03-28T21:52:52ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:Stockholm/Results/BioBricksTeam:Stockholm/Results/BioBricks2010-10-28T01:03:08Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==BioBricks==<br />
===''Trans''-Activating Transcriptional Activator (TAT)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380000 BBa_K380000]: Standard part====<br />
[[image:TAT_BioBrick.png]]<br />
<br />
:'''Part name:''' TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#TAT_cell_penetrating_peptide_.28TAT.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp1 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380001 BBa_K380001]: N-part====<br />
[[image:NTAT_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#TAT_cell_penetrating_peptide_.28TAT.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_12_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Low Molecular Weight Protamine (LMWP)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380002 BBa_K380002]: Standard part)====<br />
[[image:LMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Low_molecular_weight_protamine_.28LMWP.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp2 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380003 BBa_K380003]: N-part====<br />
[[image:nLMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Low_molecular_weight_protamine_.28LMWP.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_11_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Transportan 10 (Tp10)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380004 BBa_K380004]: Standard part====<br />
[[image:Tp10_BioBrick.png]]<br />
<br />
:'''Part name:''' Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Transportan_10_.28Tp10.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Cpp12 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380005 BBa_K380005]: N-part====<br />
[[image:nTp10_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Transportan_10_.28Tp10.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_5_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380006 BBa_K380006]: Human Basic Fibroblast Growth Factor (bFGF)===<br />
[[image:BFGF_BioBrick.png]]<br />
<br />
:'''Part name:''' Human basic fibroblast growth factor, bFGF<br /><br />
:'''Property:''' Growth factor ([[Team:Stockholm/Project_Idea/Proteins#Human_basic_fibroblast_growth_factor_.28bFGF.29|more]])<br /><br />
:'''Edited nucleotide(s):''' nt341 C &rarr; T<br />
:'''Removed restr. site(s):''' AgeI<br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.bFGF_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380007 BBa_K380007]: Superoxide dismutase 1 (SOD1)===<br />
[[image:SOD1_BioBrick.png]]<br />
<br />
:'''Part name:''' Superoxide dismutase 1 protein<br /><br />
:'''Property:''' Catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> → H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub> ([[Team:Stockholm/Project_Idea/Proteins#Superoxide_dismutase_1_.28SOD1.29|more]])<br /><br />
:'''Edited nucleotide(s):''' nt331 A &rarr; G<br />
:'''Removed restr. site(s):''' PfeI<br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.SOD_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380008 BBa_K380008]: Yeast Copper Chaperone (yCCS)===<br />
[[image:YCCS_BioBrick.png]]<br />
<br />
:'''Part name:''' Yeast copper chaperone protein<br /><br />
:'''Property:''' Mediates the delivery of copper ions to SOD1 ([[Team:Stockholm/Project_Idea/Proteins#Yeast_copper_chaperon_.28yCCS.29|more]])<br /><br />
:'''Edited nucleotide(s):''' nt257 T &rarr; C<br />
:'''Removed restr. site(s):''' EcoRI<br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.yCCS_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380009 BBa_K380009]: Protein A Z-domain (PtA-Z)===<br />
[[image:ProteinA_BioBrick.png]]<br />
<br />
:'''Part name:''' Protein A Z-domain<br /><br />
:'''Property:''' Immunoglobulin Fc region binding ([[Team:Stockholm/Project_Idea/Proteins#Protein_A.2C_z_domain|more]])<br /><br />
:'''Edited nucleotide(s):''' -<br />
:'''Removed restr. site(s):''' -<br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.ProtA VR premix fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380010 BBa_K380010]: Immunoglobulin G protease (IdeS)===<br />
[[image:IdeS_BioBrick.png]]<br />
<br />
:'''Part name:''' Immunoglobulin G protease (IdeS)<br /><br />
:'''Property:''' Immunoglobulin G protease ([[Team:Stockholm/Project_Idea/Proteins#IgG_protease_.28IdeS.29|more]])<br /><br />
:'''Edited nucleotide(s):''' -<br />
:'''Removed restr. site(s):''' -<br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.IgGp_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/BioBricksTeam:Stockholm/Results/BioBricks2010-10-28T00:49:49Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==BioBricks==<br />
===''Trans''-Activating Transcriptional Activator (TAT)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380000 BBa_K380000]: Standard part====<br />
[[image:TAT_BioBrick.png]]<br />
<br />
:'''Part name:''' TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#TAT_cell_penetrating_peptide_.28TAT.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp1 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380001 BBa_K380001]: N-part====<br />
[[image:NTAT_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#TAT_cell_penetrating_peptide_.28TAT.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_12_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Low Molecular Weight Protamine (LMWP)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380002 BBa_K380002]: Standard part)====<br />
[[image:LMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Low_molecular_weight_protamine_.28LMWP.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp2 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380003 BBa_K380003]: N-part====<br />
[[image:nLMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Low_molecular_weight_protamine_.28LMWP.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_11_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Transportan 10 (Tp10)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380004 BBa_K380004]: Standard part====<br />
[[image:Tp10_BioBrick.png]]<br />
<br />
:'''Part name:''' Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Transportan_10_.28Tp10.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Cpp12 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380005 BBa_K380005]: N-part====<br />
[[image:nTp10_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project_Idea/Proteins#Transportan_10_.28Tp10.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_5_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380006 BBa_K380006]: Human Basic Fibroblast Growth Factor (bFGF)===<br />
[[image:BFGF_BioBrick.png]]<br />
<br />
:'''Part name:''' Human basic fibroblast growth factor, bFGF<br /><br />
:'''Property:''' Growth factor ([[Team:Stockholm/Project_Idea/Proteins#Human_basic_fibroblast_growth_factor_.28bFGF.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.bFGF_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380007 BBa_K380007]: Superoxide dismutase 1 (SOD1)===<br />
[[image:SOD1_BioBrick.png]]<br />
<br />
:'''Part name:''' Superoxide dismutase 1 protein<br /><br />
:'''Property:''' Catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> → H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub> ([[Team:Stockholm/Project_Idea/Proteins#Superoxide_dismutase_1_.28SOD1.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.SOD_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380008 BBa_K380008]: Yeast Copper Chaperone (yCCS)===<br />
[[image:YCCS_BioBrick.png]]<br />
<br />
:'''Part name:''' Yeast copper chaperone protein<br /><br />
:'''Property:''' Mediates the delivery of copper ions to SOD1 ([[Team:Stockholm/Project_Idea/Proteins#Yeast_copper_chaperon_.28yCCS.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.yCCS_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380009 BBa_K380009]: Protein A Z-domain (PtA-Z)===<br />
[[image:ProteinA_BioBrick.png]]<br />
<br />
:'''Part name:''' Protein A Z-domain<br /><br />
:'''Property:''' Immunoglobulin Fc region binding ([[Team:Stockholm/Project_Idea/Proteins#Protein_A.2C_z_domain|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.ProtA VR premix fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380010 BBa_K380010]: Immunoglobulin G protease (IdeS)===<br />
[[image:IdeS_BioBrick.png]]<br />
<br />
:'''Part name:''' Immunoglobulin G protease (IdeS)<br /><br />
:'''Property:''' Immunoglobulin G protease ([[Team:Stockholm/Project_Idea/Proteins#IgG_protease_.28IdeS.29|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.IgGp_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/BioBricksTeam:Stockholm/Results/BioBricks2010-10-28T00:37:13Z<p>AndreasConstantinou: /* BBa_K380010: Immunoglobulin G protease (IdeS) */</p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==BioBricks==<br />
===''Trans''-Activating Transcriptional Activator (TAT)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380000 BBa_K380000]: Standard part====<br />
[[image:TAT_BioBrick.png]]<br />
<br />
:'''Part name:''' TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp1 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380001 BBa_K380001]: N-part====<br />
[[image:NTAT_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_12_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Low Molecular Weight Protamine (LMWP)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380002 BBa_K380002]: Standard part)====<br />
[[image:LMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp2 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380003 BBa_K380003]: N-part====<br />
[[image:nLMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_11_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Transportan 10 (Tp10)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380004 BBa_K380004]: Standard part====<br />
[[image:Tp10_BioBrick.png]]<br />
<br />
:'''Part name:''' Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Cpp12 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380005 BBa_K380005]: N-part====<br />
[[image:nTp10_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_5_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380006 BBa_K380006]: Human Basic Fibroblast Growth Factor (bFGF)===<br />
[[image:BFGF_BioBrick.png]]<br />
<br />
:'''Part name:''' Human basic fibroblast growth factor, bFGF<br /><br />
:'''Property:''' Growth factor ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.bFGF_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380007 BBa_K380007]: Superoxide dismutase 1 (SOD1)===<br />
[[image:SOD1_BioBrick.png]]<br />
<br />
:'''Part name:''' Superoxide dismutase 1 protein<br /><br />
:'''Property:''' Catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> → H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub> ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.SOD_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380008 BBa_K380008]: Yeast Copper Chaperone (yCCS)===<br />
[[image:YCCS_BioBrick.png]]<br />
<br />
:'''Part name:''' Yeast copper chaperone protein<br /><br />
:'''Property:''' Mediates the delivery of copper ions to SOD1 ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.yCCS_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380009 BBa_K380009]: Protein A Z-domain (PtA-Z)===<br />
[[image:ProteinA_BioBrick.png]]<br />
<br />
:'''Part name:''' Protein A Z-domain<br /><br />
:'''Property:''' Immunoglobulin Fc region binding ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.ProtA VR premix fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380010 BBa_K380010]: Immunoglobulin G protease (IdeS)===<br />
[[image:IdeS_BioBrick.png]]<br />
<br />
:'''Part name:''' Immunoglobulin G protease (IdeS)<br /><br />
:'''Property:''' Immunoglobulin G protease ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.IgGp_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/BioBricksTeam:Stockholm/Results/BioBricks2010-10-28T00:35:44Z<p>AndreasConstantinou: /* BBa_K380009: Protein A Z-domain (PtA-Z) */</p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==BioBricks==<br />
===''Trans''-Activating Transcriptional Activator (TAT)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380000 BBa_K380000]: Standard part====<br />
[[image:TAT_BioBrick.png]]<br />
<br />
:'''Part name:''' TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp1 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380001 BBa_K380001]: N-part====<br />
[[image:NTAT_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_12_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Low Molecular Weight Protamine (LMWP)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380002 BBa_K380002]: Standard part)====<br />
[[image:LMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:Cpp2 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380003 BBa_K380003]: N-part====<br />
[[image:nLMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_11_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Transportan 10 (Tp10)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380004 BBa_K380004]: Standard part====<br />
[[image:Tp10_BioBrick.png]]<br />
<br />
:'''Part name:''' Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Cpp12 premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380005 BBa_K380005]: N-part====<br />
[[image:nTp10_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_5_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380006 BBa_K380006]: Human Basic Fibroblast Growth Factor (bFGF)===<br />
[[image:BFGF_BioBrick.png]]<br />
<br />
:'''Part name:''' Human basic fibroblast growth factor, bFGF<br /><br />
:'''Property:''' Growth factor ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.bFGF_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380007 BBa_K380007]: Superoxide dismutase 1 (SOD1)===<br />
[[image:SOD1_BioBrick.png]]<br />
<br />
:'''Part name:''' Superoxide dismutase 1 protein<br /><br />
:'''Property:''' Catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> → H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub> ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.SOD_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380008 BBa_K380008]: Yeast Copper Chaperone (yCCS)===<br />
[[image:YCCS_BioBrick.png]]<br />
<br />
:'''Part name:''' Yeast copper chaperone protein<br /><br />
:'''Property:''' Mediates the delivery of copper ions to SOD1 ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.yCCS_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380009 BBa_K380009]: Protein A Z-domain (PtA-Z)===<br />
[[image:ProteinA_BioBrick.png]]<br />
<br />
:'''Part name:''' Protein A Z-domain<br /><br />
:'''Property:''' Immunoglobulin Fc region binding ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.ProtA VR premix fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380010 BBa_K380010]: Immunoglobulin G protease (IdeS)===<br />
[[image:IdeS_BioBrick.png]]<br />
<br />
:'''Part name:''' igg protease<br /><br />
:'''Property:''' - ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.IgGp_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Project_Idea/IntroductionTeam:Stockholm/Project Idea/Introduction2010-10-28T00:29:07Z<p>AndreasConstantinou: /* Spot on Treatment */</p>
<hr />
<div>{{Stockholm/Project_Idea}}<br />
<br />
{|<br />
|<br />[[image:SU_Planning_Icon.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
<div align="justify"><br />
==Introduction==<br />
Many different ideas were discussed during the startup of our iGEM project. We finally decided to focus on the skin disorder Vitiligo. We have discussed our project idea with two leading Vitiligo researchers in Sweden (Mats J. Olsson & Håkan Hedstrand, Uppsala University), both who have shown interest and encouraged us to go ahead with the project. We have also been given a grant from the [http://www.vitiligoforbundet.se Swedish Vitiligo Association].<br />
<br />
<br />
'''Vitiligo - in short'''<br />
[[Image:Vitiligohands.jpg|right|200px|Vitiligo hands. From Wikipedia, the free encyclopedia. Creative Commons Attribution-Share Alike 3.0 Unported License]]<br />
<br />
Vitiligo is a skin disorder causing affected parts of the skin to turn white. This is due to abnormal melanocyte function, resulting from the immune system mistakenly targeting the pigment cells, making Vitiligo an autoimmune disease. Vitiligo usually begins before the age of 20 and is estimated to affect 0.5-2 % of the world population. It is a very complex disorder and there is a lack of good treatments.<br />
<br />
<br />
'''<br />
== Spot on Treatment ==<br />
'''<br />
<br />
'''iGEM Stockholm on the Vitiligo project <br />
This article is an effort from us in the iGEM Stockholm team to explain our Vitiligo-treatment scientific project in words that anyone can understand, consequently we will keep the scientific explanations on a basic level. <br />
'''<br />
<br />
Our primary goal is to merge current scientific knowledge with an innovative new investigative approach known as Synthetic Biology, in order to hopefully help Vitiligo patients achieve faster and more efficient repigmentation of affected skin in the future. <br />
<br />
'''Background'''<br />
<br />
Vitiligo (leukoderma) is a skin disorder in which pigment cells known as melanocytes are destroyed, resulting in white patches of the skin1. Melanocytes are the cells responsible for creating skin color, so when these are destroyed, the normal shade of the skin turns white. Vitiligo is in itself not dangerous and does not lead to any severe health problems, but patients’ life quality may be seriously altered by the cosmetic appearance that is a result of the white spots from Vitiligo. Between 1-2 percent of the world population are estimated to be affected by Vitiligo, with varying levels of severity. The disorder is characterized by patches occurring on the skin in various parts of the body, hair growing on the patches may also turn white [1]. <br />
<br />
Population surveys have shown that Vitiligo patients first outbreak is seen before the age of 20 in 50 % of the cases, and 70-80 before the age of 30. So it is relatively uncommon with Vitiligo outbreaks in mid-age. Both sexes in adults and children are affected in equal weights; however studies have showed that females contact doctors in a larger number due to greater psychological and social impact [2].<br />
<br />
At first, vitiligo can be thought of as a minor disorder, however the effect on patient’s self-esteem and social interactions can be devastating, especially in patients with darker pigmented skin where the white patches can be more visible. There are two distinguished large sub-sets of vitiligo, called focal/segmental vitiligo and non-segmental vitiligo. The former is characterized by few numbers of small lesions while the second form by an asymmetric distribution of the skin surface. Non-segmental vitiligo is correlated to all generalized, symmetrical forms. The course of the outbreak of the disease is unpredictable with phases of stabilized depigmentation. White vitiligo patches that are in an enlarging manner or the development of new lesions are classified as in an active form of disease [3]. <br />
<br />
Currently three major hypotheses of vitiligo have been proposed. The neural hypothesis implicates an accumulation of a neurochemical substance in the form of a toxin from nerve endings. This damages melanocytes and thus decreases melanin production. The biochemical hypothesis suggests an accumulation of toxic molecules from the synthesis of melanin in melanocytes, the breakdown of antioxidant molecules, and the build-up of large amounts of reactive molecules in pigment cells. Additionally, an autoimmune response in vitiligo patients has been proposed. Studies have demonstrated that vitiligo patients have developed antibodies and an activated immune system destructive against the body’s own pigment cells. Other possible causes of vitiligo have been suggested, including impaired melanocyte migration and/or development [3]. <br />
<br />
It might be that the mentioned factors act independently or together to result in the same effect, which is the disappearance of melanocytes from the skin [3]. <br />
<br />
Our research is divided up into two areas, which are long and short time effect on the skin. The long term research is focusing on both the biochemical and autoimmune hypothesis, which is to result in a repigmentation of white skin patches after a longer time period of treatment. The complementary short term research is based on repigmenting the affected patches in the similar effect of make-up while the long term treatment is under progress. This will be carried out by bacteria producing melanin on the skin, which will be absorbed and result in colored skin. <br />
<br />
'''Our aim'''<br />
<br />
Our research project uses harmless bacteria that, in fact, are already living in the human body as biological machines. These helpful bacteria are designed in our research project to become cost efficient machines to produce molecules that are deficient in vitiligo skin compared to normal skin. The goal with our project, until November 2010, is to obtain a “proof-of-concept” by having our bacteria produce and secrete molecules that we know, through previous research, are in a deficit in vitiligo skin. The lack of these specific molecules is thought to be involved in the impaired and disappeared pigment cells in vitiligo affected skin areas, leading to white spots.<br />
<br />
Currently, there are not any treatments like ours for vitiligo skin. Our idea is to develop a treatment for vitiligo skin, where an ointment with harmless bacteria is to be produced for applying on white patched skin. The bacteria will synthesize and secrete several molecules of interest, which will then target specific inner skin cells with the aim of repigmentation. <br />
<br />
One problem with this type of treatment is that the skin epidermis functions as a very efficient barrier against larger molecules. To help our potentially beneficial molecules reach their destination, we will therefore fuse them to special carrier molecules called cell-penetrating peptides (CPPs). As the name suggests, CPPs are small molecules that have the ability of penetrating into cells, but can in some cases also overcome the skin barrier. By fusing our molecules to such CPPs, we can let them hitch-hike over the skin barrier to the target area.<br />
<br />
With our research we aim to in the future develop a treatment that works faster and more efficient in achieving a repigmentation on affected skin areas compared to current medicine. <br />
</div><br />
<br />
'''References'''<br />
<br />
1. Current remedies for vitiligo Javed Ali et al. Autoimmunity Reviews, 2010 <br />
<br />
2. Vitiligo by Mauro Picardo Springer-Verlag Berlin Heidelberg, 2010<br />
<br />
3. Autoantibody responses to melanocytes in the depigmenting skin disease vitiligo Anthony P. Weetman et al. Autoimmunity Reviews, 2007<br />
<br />
----<br />
<br />
To read more about the "special carrier molecules", also known as '''cell-penetrating peptides (cpp)''':<br />
<br />
* Happy birthday cell penetrating peptides: Already 20years, Brasseur R, Divita G, Biochim Biophys Acta, 2010 (and references within)<br />
<br />
|-<br />
|colspan="3" align="right"|<br />
<html><br />
<embed <br />
src="https://static.igem.org/mediawiki/2010/3/30/SU_animation_final_version.swf" <br />
width="700"<br />
height="500"<br />
allowscriptaccess="always"<br />
allowfullscreen="true"<br />
/><br />
</html><br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-27T23:02:00Z<p>AndreasConstantinou: /* Gold */</p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|<br />[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
Characterize the new BioBrick<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team] (Team Uppsala)<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project.]<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-27T22:55:30Z<p>AndreasConstantinou: /* Silver */</p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|<br />[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
Characterize the new BioBrick<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team] (Team Uppsala)<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Team/MembersTeam:Stockholm/Team/Members2010-10-27T19:52:37Z<p>AndreasConstantinou: /* Acknowledgements */</p>
<hr />
<div>{{Stockholm/Team}}<br />
<br><br />
[[image:SU_Team_Icon.gif|400px|center]]<br />
<br />
{|<br />
|<br />
===Students===<br />
<br /><br />
<br /><br />
{|<br />
|width="200"|[[Image:Nina.jpg|100px|center]]<center><br />'''Nina Schiller'''<br />[mailto:nina@igem.se nina@igem.se]</center><br />
|width="590" border="0" align="justify"|Hi!<br />
<br />
I am one of the team-members of Team Stockholm, my name is Nina Schiller and I am a master student in molecular biology at Stockholm University. It is the endless possibilities and opportunities in the field of synthetic biology that has caught my attention to put together our iGEM team: Team Stockholm. To me, this field of research and iGEM competition drives science researchers and students to gain better insight and take advantage of the diverse and powerful characters of living organisms. This summer, I will together with my team mates work our hardest to combine biology, chemistry and engineering in order to understand, harness and imitate the complex phenomena of biological life and finally build innovative and useful biological systems.<br />
<br />
My goal with iGEM is to challenge myself to think “out of the box” and seek for ways to put together bits and pieces in science in order to design organisms that would prove useful in the obstacles in modern life. I look forward to build up my science knowledge and laboratory experience. Of course, with a great idea in our luggage, both my and the whole teams goal is to win the iGEM competition! <br />
|}<br />
<br /><br />
<br />
{|<br />
|width="200"|[[Image:2.jpg|100px|center]]<center><<br />'''Andreas Constantinou'''<br />andreas (at) igem.se</center><br />
|width="590" border="0" align="justify"|I first came in contact with synthetic biology in 2008, when I heard about attempts to create a petroleum-producing bacterium to be used as an alternative energy source. Immediately fascinated by this idea and the synthetic biology concept and methodology, my aim has been to study this interesting field ever since. This has now led to the founding of a Stockholm-based team in the 2010 iGEM competition.<br />
<br />
What fascinates me most about synthetic biology is that it links biology and engineering together. With a great interest in both, I see iGEM as a unique opportunity for me to combine my creativity and knowledge in molecular biology to design and build a biological machine that can be used in every-day life.<br />
<br />
With a revolutionary idea, dedicated and hard-working team-members and a large portion of self-confidence, Team Stockholm is ready to fight for the 2010 iGEM Gold Medal!<br />
<br />
See you at the jamboree at MIT in November!<br />
|}<br />
<br /> <br />
<br />
{|<br />
|width="200"|[[Image:J.jpg|100px|center]]<center><br />'''Johan Nordholm'''<br />[mailto:johan@igem.se johan@igem.se]</center><br />
|width="590" border="0" align="justify"|Greetings!<br />
<br />
Synthetic biology is all about putting engineering into biology. And I think there is a small engineer hidden in each and every one of us. As with the ever-increasing understanding of how the building blocks of the cell function and are put together, so is our capacity to redesign the building blocks and the way they are put together. This has immense potential, I guarantee it can change our society as much as the computer industry has the last decades. This summer, I will do my best to apply existing biological knowledge to hopefully solve a scientific problem, if even a very small one. I am currently in my third and last year in the bachelor program of molecular biology at Stockholm University. As I have not yet undergone any research traineeship or degree project, my time spent in the lab is limited. I therefore find this project as a tremendous opportunity to change that. What makes this even more fun is that my teammates are some of my best friends.<br />
|}<br />
<br /><br />
<br />
{|<br />
|width="200"|[[Image:Mim.jpg|100px|center]]<center><br />'''Emmelie Lidh'''</center><br />
|width="590" border="0" align="justify"|Hi!<br />
<br />
My name is Mimmi, right now I’m finishing my bachelor in molecular biology. <br />
<br />
I have always been fascinated by the origin of life. By how the genetic code can produce so many different life forms and make the organisms adapt to so many different niches and environments. Now, this competition is about using different traits nature invented and put them together to create new useful functions in an organism. I think this is an amazing way to study and learn more about the complex network of genes and at the same time produce a helpful organism.<br />
|}<br />
<br /><br />
<br />
{|<br />
|width="200"|[[Image:Hassan.jpg|100px|center]]<center><br />'''Hassan Foroughi Asl'''<br />hassanfa (at) kth.se</center><br />
|width="590" border="0" align="justify"|Hi,<br />
<br />
I'm a Masters student in Computational and Systems Biology at Royal Institute of Technology (KTH) and a member of the Stockholm University team for iGEM competition. My first contact with iGEM and synthetic biology wasn't so long time ago. I got introduced to iGEM competitions in 2009. Then Synthetic biology attracted my attention and it became more interesting to me when I started to study about biological circuits and how these circuits are chosen by evolution. Here I will offer all my knowledge and effort to bring our ideas and plans into reality and solve the problem with a great success.<br />
|}<br />
<br /><br />
<br />
===Mentors===<br />
<br /><br />
<br /><br />
{|<br />
|width="200"|[[Image:Eli.jpg|100px|center]]<br />
|width="590" border="0" align="justify"|<br/ >'''Prof. Elisabeth Hagg&aring;rd'''<br />Department of Genetics, Microbiology and Toxicology, Stockholm University<br />
|}<br />
{|<br />
|width="200"|[[Image:gunnar_pic1.png|100px|center]]<br />
|width="590" border="0" align="justify"|<br>'''Prof. Gunnar von Heijne'''<br />Department of Biochemistry and Biophysics, Stockholm University<br />
|}<br />
{|<br />
|width="200"|[[Image:Rob_Pick.jpg|100px|center]]<br />
|width="590" border="0" align="justify"|<br />'''Assistant Prof. Robert Daniels'''<br />Department of Biochemistry and Biophysics, Stockholm University<br />
|}<br />
<br />
<br /><br />
{|<br />
|width="200"|<br />
|width="590" border="0" align="justify"|'''Co-advisors at Stockholm University:''' Prof. Lars Wieslander, Prof. Marie &Ouml;hman, Prof. Neus Visa and Prof. Roger Karlsson.<br />
<br />
===Acknowledgements===<br />
Other than valuable help from our mentors, many more people helped us both in the lab, but also helped us shape and develop our idea for the modelling part. Among these, we would like to take this opportunity to show our gratitude to the following people:<br />
<br />
'''Sergey Surkov, Jaroslav Belotserkovsky, Sridhar Mandali and Richard Odegrip.'''<br />
<br />
Thank you for your invaluable help and support!<br />
|}<br />
<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Team/MembersTeam:Stockholm/Team/Members2010-10-27T19:47:43Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Team}}<br />
<br><br />
[[image:SU_Team_Icon.gif|400px|center]]<br />
<br />
{|<br />
|<br />
===Students===<br />
<br /><br />
<br /><br />
{|<br />
|width="200"|[[Image:Nina.jpg|100px|center]]<center><br />'''Nina Schiller'''<br />[mailto:nina@igem.se nina@igem.se]</center><br />
|width="590" border="0" align="justify"|Hi!<br />
<br />
I am one of the team-members of Team Stockholm, my name is Nina Schiller and I am a master student in molecular biology at Stockholm University. It is the endless possibilities and opportunities in the field of synthetic biology that has caught my attention to put together our iGEM team: Team Stockholm. To me, this field of research and iGEM competition drives science researchers and students to gain better insight and take advantage of the diverse and powerful characters of living organisms. This summer, I will together with my team mates work our hardest to combine biology, chemistry and engineering in order to understand, harness and imitate the complex phenomena of biological life and finally build innovative and useful biological systems.<br />
<br />
My goal with iGEM is to challenge myself to think “out of the box” and seek for ways to put together bits and pieces in science in order to design organisms that would prove useful in the obstacles in modern life. I look forward to build up my science knowledge and laboratory experience. Of course, with a great idea in our luggage, both my and the whole teams goal is to win the iGEM competition! <br />
|}<br />
<br /><br />
<br />
{|<br />
|width="200"|[[Image:2.jpg|100px|center]]<center><<br />'''Andreas Constantinou'''<br />andreas (at) igem.se</center><br />
|width="590" border="0" align="justify"|I first came in contact with synthetic biology in 2008, when I heard about attempts to create a petroleum-producing bacterium to be used as an alternative energy source. Immediately fascinated by this idea and the synthetic biology concept and methodology, my aim has been to study this interesting field ever since. This has now led to the founding of a Stockholm-based team in the 2010 iGEM competition.<br />
<br />
What fascinates me most about synthetic biology is that it links biology and engineering together. With a great interest in both, I see iGEM as a unique opportunity for me to combine my creativity and knowledge in molecular biology to design and build a biological machine that can be used in every-day life.<br />
<br />
With a revolutionary idea, dedicated and hard-working team-members and a large portion of self-confidence, Team Stockholm is ready to fight for the 2010 iGEM Gold Medal!<br />
<br />
See you at the jamboree at MIT in November!<br />
|}<br />
<br /> <br />
<br />
{|<br />
|width="200"|[[Image:J.jpg|100px|center]]<center><br />'''Johan Nordholm'''<br />[mailto:johan@igem.se johan@igem.se]</center><br />
|width="590" border="0" align="justify"|Greetings!<br />
<br />
Synthetic biology is all about putting engineering into biology. And I think there is a small engineer hidden in each and every one of us. As with the ever-increasing understanding of how the building blocks of the cell function and are put together, so is our capacity to redesign the building blocks and the way they are put together. This has immense potential, I guarantee it can change our society as much as the computer industry has the last decades. This summer, I will do my best to apply existing biological knowledge to hopefully solve a scientific problem, if even a very small one. I am currently in my third and last year in the bachelor program of molecular biology at Stockholm University. As I have not yet undergone any research traineeship or degree project, my time spent in the lab is limited. I therefore find this project as a tremendous opportunity to change that. What makes this even more fun is that my teammates are some of my best friends.<br />
|}<br />
<br /><br />
<br />
{|<br />
|width="200"|[[Image:Mim.jpg|100px|center]]<center><br />'''Emmelie Lidh'''</center><br />
|width="590" border="0" align="justify"|Hi!<br />
<br />
My name is Mimmi, right now I’m finishing my bachelor in molecular biology. <br />
<br />
I have always been fascinated by the origin of life. By how the genetic code can produce so many different life forms and make the organisms adapt to so many different niches and environments. Now, this competition is about using different traits nature invented and put them together to create new useful functions in an organism. I think this is an amazing way to study and learn more about the complex network of genes and at the same time produce a helpful organism.<br />
|}<br />
<br /><br />
<br />
{|<br />
|width="200"|[[Image:Hassan.jpg|100px|center]]<center><br />'''Hassan Foroughi Asl'''<br />hassanfa (at) kth.se</center><br />
|width="590" border="0" align="justify"|Hi,<br />
<br />
I'm a Masters student in Computational and Systems Biology at Royal Institute of Technology (KTH) and a member of the Stockholm University team for iGEM competition. My first contact with iGEM and synthetic biology wasn't so long time ago. I got introduced to iGEM competitions in 2009. Then Synthetic biology attracted my attention and it became more interesting to me when I started to study about biological circuits and how these circuits are chosen by evolution. Here I will offer all my knowledge and effort to bring our ideas and plans into reality and solve the problem with a great success.<br />
|}<br />
<br /><br />
<br />
===Mentors===<br />
<br /><br />
<br /><br />
{|<br />
|width="200"|[[Image:Eli.jpg|100px|center]]<br />
|width="590" border="0" align="justify"|<br/ >'''Prof. Elisabeth Hagg&aring;rd'''<br />Department of Genetics, Microbiology and Toxicology, Stockholm University<br />
|}<br />
{|<br />
|width="200"|[[Image:gunnar_pic1.png|100px|center]]<br />
|width="590" border="0" align="justify"|<br>'''Prof. Gunnar von Heijne'''<br />Department of Biochemistry and Biophysics, Stockholm University<br />
|}<br />
{|<br />
|width="200"|[[Image:Rob_Pick.jpg|100px|center]]<br />
|width="590" border="0" align="justify"|<br />'''Assistant Prof. Robert Daniels'''<br />Department of Biochemistry and Biophysics, Stockholm University<br />
|}<br />
<br />
<br /><br />
{|<br />
|width="200"|<br />
|width="590" border="0" align="justify"|'''Co-advisors at Stockholm University:''' Prof. Lars Wieslander, Prof. Marie &Ouml;hman, Prof. Neus Visa and Prof. Roger Karlsson.<br />
<br />
===Acknowledgements===<br />
Other than valuable help from our mentors, many more people helped us both in the lab, but also helped us understand and develop our ideas for the modelling part. Among these, we would like to take this opportunity to show our gratitude to the following people:<br />
<br />
'''Sergey Surkov, Jaroslav Belotserkovsky, Sridhar Mandali and Richard Odegrip.'''<br />
<br />
Thank you for your invaluable help and support!<br />
|}<br />
<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Lab_work/SafetyTeam:Stockholm/Lab work/Safety2010-10-27T19:16:01Z<p>AndreasConstantinou: /* Safety */</p>
<hr />
<div>{{Stockholm/Lab_work}}<br />
<div align="justify"><br />
{| <br />
|[[image:SU_Saftey_Icon.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Safety==<br />
<br />
<font size="3">'''Would any of your project ideas raise safety issues in terms of researcher safety, public safety, or environmental safety?'''</font><br /><br />
There are always safety issues to consider and precautions to take when working in a microbiological laboratory. A general safety meeting was held early this spring for the entire department and we were also asked to read through safety rules concerning laboratory work at our department.<br />
<br />
We follow good microbiological practice for all our laboratory work. All steps necessary to obtain a safe environment in the laboratory have been taken into consideration; this includes keeping lab areas clean and handling potentially hazardous reagents with appropriate safety equipment.<br />
<br />
Working with the BioBrick cloning standard we use several different antibiotic resistance markers. These types of selection markers are commonly used in our department and our group follows the handling procedures regulated by the department's safety protocols, available on the intranet. The cloning vectors carrying these selection markers are all non-conjugative and non-transferable, minimizing the risk of spread to non-laboratory environment. Furthermore, bacterial cell cultures are either iodine inactivated with Jodopax or sterilized by autoclaving.<br />
<br />
Despite these safety precautions, in the unlikely event of spread, the bacteria used in our project are all non-pathogenic, well-established laboratory ''Escherichia coli'' strains with low survival probabilities outside the laboratory environment; also, culture volumes are kept to a minimal, thereby further lowering the risk of spread.<br />
<br />
<br />
<font size="3">'''Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?'''</font><br /><br />
In addition to the selection markers mentioned above, we will also be expressing three types of cell-penetrating peptides (CPPs) that we will fuse to different proteins affecting skin cells and the immune system. At least one of these CPPs has previously been shown capable of penetrating the epidermal layer of human skin, and all three can penetrate into different types human cells. Although we do not expect the peptides to be toxic, all work involving expression of our CPPs will be performed with extra care, e.g. by always using gloves. Also, all equipment (culture tubes, pipette tips etc.) used for CPP expression will be sent for autoclaving to ensure that any potentially toxic peptides will be destroyed. To further minimize handling risks we will exclusively be working with small culture volumes (up to 10 ml).<br />
<br />
<br />
<font size="3">'''Is there a local biosafety group, committee, or review board at your institution?'''</font><br /><br />
No, but there is a general biosafety committee for Stockholm University. They are coordinating and facilitating the task for observing the regulations for contained genetically modified microorganisms and work environment issues. Unfortunately the information on their website is only in Swedish. http://www.sakerhet.su.se/pub/jsp/polopoly.jsp?d=13191 <br />
<br />
The rules and regulations are set by the Swedish Work Environment Authority. Our department (Department of Genetics, Microbiology and Toxicology) has permission to contain and handle genetically modified microorganisms (GMMs) up to containment level F activities. This is “an activity involving contained use of GMMs and entailing a negligible risk or none at all of harm to human health and environment”. The department is also following the safety measures for good microbiological practice.<br />
|}<br />
<br />
</div><br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Project_Idea/ProteinsTeam:Stockholm/Project Idea/Proteins2010-10-27T18:36:26Z<p>AndreasConstantinou: /* Cell penetrating peptides */</p>
<hr />
<div>{{Stockholm/Project_Idea}}<br />
{| <br />
|[[image:SU_Modeling_Icon_2.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
== Proteins ==<br />
<br />
=== Superoxide dismutase 1 (SOD1) ===<br />
Human soluble Superoxide dismutase 1 (SOD1) is a soluble cytoplasmic protein functional as a homodimer that binds copper and zink ions. SOD1 catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> &rarr; H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub>, protecting the cell from oxidative damage. SOD1 was first cloned and expressed in ''Escherichia coli'' by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)]. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:SOD1_dimeric.png|250px]]<br />3D structure of human SOD1 in its dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite ''et al''. (2010)]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|465 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt331 A &rarr; G<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|PfeI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|154 aa<br />
|-<br />
|'''Size'''<br />
|15,936 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].<br />
|}<br />
<br />
<br />
----<br />
<br />
=== Yeast copper chaperon (yCCS) ===<br />
Yeast copper chaperon protein (yCCS) is a helper chaperon specific for copper/zinc superoxide dismutase located to the cytoplasm. yCCS generates fully metallized, active SOD1 proteins that in turn protects the cell from oxidative damage. <br />
<br />
yCCS has been shown to successfully mediate the delivery of copper ions to human SOD1 ([http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al''. 2003]). Co-expression of SOD1 and yCCS yields proteins with higher copper contents, leading to increased activity and more stable proteins. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:YSOD+yCCS_interaction.jpg|250px]]<br />3D structure of yCCS interacting with yeast superoxide dismutase (ySOD) in it's monomeric form. Ions indicated as gray orbs. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/11524675 Lamb ''et al''. 2001]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|750 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt257 T &rarr; C<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|EcoRI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|249 aa<br />
|-<br />
|'''Size'''<br />
|27,330 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Human basic fibroblast growth factor (bFGF) ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:BFGF.jpg|250px]]<br />3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|468 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt341 C &rarr; T<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|AgeI<br />
|-<br />
|'''GenBank'''<br />
|(full mRNA) [http://www.ncbi.nlm.nih.gov/nuccore/153285460 153285460]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|155 aa<br />
|-<br />
|'''Size'''<br />
|17,353 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Protein A, z domain ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Genepart <br />
|rowspan="10" width="250"|[[Image:ProteinA_z_domain.jpg|250px]]<br />3D structure of the Z-domain of Protein A. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/9325113 Tashiro ''et al''. 2010]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|174 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
| -<br />
|-<br />
|'''Removed restr. site(s)'''<br />
| -<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/gene/2859152 2859152] (full protein)<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|58 aa <br />
(508 aa, full protein )<br />
|-<br />
|'''Size'''<br />
|55,439 Da (full protein)<br />
|-<br />
|'''Fasta'''<br />
|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== IgG protease (IdeS) ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:IdeS.jpg|250px]]<br />Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig ''et al''. 2004]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|930 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
| -<br />
|-<br />
|'''Removed restr. site(s)'''<br />
| -<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/gene/6985687 6985687]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|339 aa<br />
|-<br />
|'''Size'''<br />
|37,977 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
<br />
----<br />
<br />
== Cell penetrating peptides ==<br />
<br />
This cell-penetrating peptides, (CPPs) may be used in N- and C-terminal fusions with full-length proteins to create transduction proteins with the ability to permeate the lipid bilayer of various cell types, making it a potential gene or protein delivery vector.<br />
<br />
<br />
=== TAT cell penetrating peptide (TAT) ===<br />
Purified full-length TAT fusion proteins expressed in ''Escherichia coli'' have been shown to successfully translocate into several human cell types, including all cells found in whole blood, as well as bone marrow stem cells and osteoblasts, while still retaining the fused protein's activity ([http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). The mechanism for transduction over the bilipid membrane is still a matter of debate, but has been suggested to occur through macropinocytosis, a specialized form of endocytosis ([http://www.ncbi.nlm.nih.gov/pubmed/17913584 Gump and Dowdy, 2007]).<br />
TAT is an 11-amino acid derivative from the Human Immunodeficiency Virus 1 (HIV-1) ''trans''-activating transcriptional activator (Tat) ([http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green and Loewenstein, 1988]; [http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|33 bp<br />
|-<br />
|'''Patent PCT'''<br />
|[http://v3.espacenet.com/publicationDetails/biblio;jsessionid=646EDA06997EDDFC0CC04CCE49F87F6B.espacenet_levelx_prod_5?CC=WO&NR=2005084158A2&KC=A2&FT=D&date=20050915&DB=EPODOC&locale=se_se WO 2005/084158 A2]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|11 aa<br />
|-<br />
|'''Size'''<br />
|1,560 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])<br />
|-<br />
|colspan="2" align="center"|YGRKKRRQRRR<br />
|-<br />
|colspan="2"|First reported by <br />
[http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green ''et al''. (1988)] and [http://www.ncbi.nlm.nih.gov/pubmed/2849510 Frankel ''et al''. (1988)]<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Low molecular weight protamine (LMWP) ===<br />
Enzymatically prepared LMWP chemically conjugated to ovalbumin (OVA) and bovine serum albumin (BSA) have previously been shown to penetrate the lipid bilayer of human keratinocytes, as well as to successfully permeate mouse skin epidermis ([http://www.ncbi.nlm.nih.gov/pubmed/20232417 Huang ''et al.'', 2010]). Furthermore, LMWP/pDNA complexes can efficiently penetrate into human embryonic kidney cells ([http://www.ncbi.nlm.nih.gov/pubmed/12898639 Park ''et al.'', 2003]). As LMWP has been shown to be neither toxic nor immunogenic ([http://www.ncbi.nlm.nih.gov/pubmed/11741268 Chang ''et al.'' a, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741269 Chang ''et al.'' b, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741270 Lee ''et al.'', 2001]), it may be used as a potential vaccine, drug or gene delivery vector.<br />
LMWP is a 14-amino acid derivative from Rainbow trout (''Oncorhynchus mykiss'') protamine, an arginine-rich protein that replaces histones in chromatin during spermatogenesis ([http://www.ncbi.nlm.nih.gov/pubmed/3755398 McKay ''et al.'', 1986]; [http://www.ncbi.nlm.nih.gov/pubmed/10213181 Byun ''et al.'', 1999]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|42 bp<br />
|-<br />
|'''Patent Application'''<br />
|[http://www.freepatentsonline.com/y2007/0071677.html 20070071677]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|14 aa<br />
|-<br />
|'''Size'''<br />
|1,880 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])<br />
|-<br />
|colspan="2" align="center"|VSRRRRRRGGRRRR<br />
|-<br />
|colspan="2"|Patent application by Park et al. (2004)<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Transportan 10 (Tp10) ===<br />
Chemically synthesized Tp10 peptides conjugated to different cargo, including pDNA and protein, have been shown to efficiently penetrate the lipid bilayer of both human and mouse cells ([http://www.ncbi.nlm.nih.gov/pubmed/15763630 Kilk ''et al.'', 2005]). Membrane permeation is both energy and temperature independent ([http://www.ncbi.nlm.nih.gov/pubmed/11718666 H&auml;llbrink ''et al.'', 2001]). The exact mechanism for penetration is still unclear ([http://www.ncbi.nlm.nih.gov/pubmed/17218466 Yandek ''et al.'', 2007]).<br />
Tp10 is a 21-amino acid derivative from the parent peptide transportan (originally known as galparan), which is a peptide chimera of the neuropeptide galanin and the wasp venom peptide mastoparan ([http://www.ncbi.nlm.nih.gov/pubmed/10930519 Soomets ''et al.'', 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/8738882 Langel ''et al.'', 1996]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|rowspan="8" width="250"|[[Image:Transportan.jpg|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|63 bp<br />
|-<br />
|'''Patent Application'''<br />
|[http://www.freepatentsonline.com/y2008/0234183.html 20080234183]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|21 aa<br />
|-<br />
|'''Size'''<br />
|2,183 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])<br />
|-<br />
|colspan="2" align="center"|AGYLLGKINLKALAALAKKIL<br />
|-<br />
|colspan="2"|Patent application by Hallbrink et al. (2003)<br /><br />
|}<br />
<br />
<!--|-<br />
|rowspan="8" width="250"|[[Image:Tp10_prediction.png|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]--><br />
----<br />
<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Project_Idea/ProteinsTeam:Stockholm/Project Idea/Proteins2010-10-27T18:28:25Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Project_Idea}}<br />
{| <br />
|[[image:SU_Modeling_Icon_2.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
== Proteins ==<br />
<br />
=== Superoxide dismutase 1 (SOD1) ===<br />
Human soluble Superoxide dismutase 1 (SOD1) is a soluble cytoplasmic protein functional as a homodimer that binds copper and zink ions. SOD1 catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> &rarr; H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub>, protecting the cell from oxidative damage. SOD1 was first cloned and expressed in ''Escherichia coli'' by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)]. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:SOD1_dimeric.png|250px]]<br />3D structure of human SOD1 in its dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite ''et al''. (2010)]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|465 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt331 A &rarr; G<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|PfeI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|154 aa<br />
|-<br />
|'''Size'''<br />
|15,936 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].<br />
|}<br />
<br />
<br />
----<br />
<br />
=== Yeast copper chaperon (yCCS) ===<br />
Yeast copper chaperon protein (yCCS) is a helper chaperon specific for copper/zinc superoxide dismutase located to the cytoplasm. yCCS generates fully metallized, active SOD1 proteins that in turn protects the cell from oxidative damage. <br />
<br />
yCCS has been shown to successfully mediate the delivery of copper ions to human SOD1 ([http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al''. 2003]). Co-expression of SOD1 and yCCS yields proteins with higher copper contents, leading to increased activity and more stable proteins. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:YSOD+yCCS_interaction.jpg|250px]]<br />3D structure of yCCS interacting with yeast superoxide dismutase (ySOD) in it's monomeric form. Ions indicated as gray orbs. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/11524675 Lamb ''et al''. 2001]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|750 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt257 T &rarr; C<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|EcoRI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|249 aa<br />
|-<br />
|'''Size'''<br />
|27,330 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Human basic fibroblast growth factor (bFGF) ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:BFGF.jpg|250px]]<br />3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|468 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt341 C &rarr; T<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|AgeI<br />
|-<br />
|'''GenBank'''<br />
|(full mRNA) [http://www.ncbi.nlm.nih.gov/nuccore/153285460 153285460]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|155 aa<br />
|-<br />
|'''Size'''<br />
|17,353 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Protein A, z domain ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Genepart <br />
|rowspan="10" width="250"|[[Image:ProteinA_z_domain.jpg|250px]]<br />3D structure of the Z-domain of Protein A. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/9325113 Tashiro ''et al''. 2010]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|174 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
| -<br />
|-<br />
|'''Removed restr. site(s)'''<br />
| -<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/gene/2859152 2859152] (full protein)<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|58 aa <br />
(508 aa, full protein )<br />
|-<br />
|'''Size'''<br />
|55,439 Da (full protein)<br />
|-<br />
|'''Fasta'''<br />
|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== IgG protease (IdeS) ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:IdeS.jpg|250px]]<br />Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig ''et al''. 2004]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|930 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
| -<br />
|-<br />
|'''Removed restr. site(s)'''<br />
| -<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/gene/6985687 6985687]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|339 aa<br />
|-<br />
|'''Size'''<br />
|37,977 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
<br />
----<br />
<br />
== Cell penetrating peptides ==<br />
<br />
This cell-penetrating peptides, (CPPs) may be used in N- and C-terminal fusions with full-length proteins to create transduction proteins with the ability to permeate the lipid bilayer of various cell types, making it a potential gene or protein delivery vector.<br />
<br />
<br />
=== TAT cell penetrating peptide (TAT) ===<br />
Purified full-length TAT fusion proteins expressed in ''Escherichia coli'' have been shown to successfully translocate into several human cell types, including all cells found in whole blood, as well as bone marrow stem cells and osteoblasts, while still retaining the fused protein's activity ([http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). The mechanism for transduction over the bilipid membrane is still a matter of debate, but has been suggested to occur through macropinocytosis, a specialized form of endocytosis ([http://www.ncbi.nlm.nih.gov/pubmed/17913584 Gump and Dowdy, 2007]).<br />
TAT is an 11-amino acid derivative from the Human Immunodeficiency Virus 1 (HIV-1) ''trans''-activating transcriptional activator (Tat) ([http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green and Loewenstein, 1988]; [http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|33 bp<br />
|-<br />
|'''Patent PCT'''<br />
|[http://v3.espacenet.com/publicationDetails/biblio;jsessionid=646EDA06997EDDFC0CC04CCE49F87F6B.espacenet_levelx_prod_5?CC=WO&NR=2005084158A2&KC=A2&FT=D&date=20050915&DB=EPODOC&locale=se_se WO 2005/084158 A2]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|11 aa<br />
|-<br />
|'''Size'''<br />
|1560 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])<br />
|-<br />
|colspan="2" align="center"|YGRKKRRQRRR<br />
|-<br />
|colspan="2"|First reported by <br />
[http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green ''et al''. (1988)] and [http://www.ncbi.nlm.nih.gov/pubmed/2849510 Frankel ''et al''. (1988)]<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Low molecular weight protamine (LMWP) ===<br />
Enzymatically prepared LMWP chemically conjugated to ovalbumin (OVA) and bovine serum albumin (BSA) have previously been shown to penetrate the lipid bilayer of human keratinocytes, as well as to successfully permeate mouse skin epidermis ([http://www.ncbi.nlm.nih.gov/pubmed/20232417 Huang ''et al.'', 2010]). Furthermore, LMWP/pDNA complexes can efficiently penetrate into human embryonic kidney cells ([http://www.ncbi.nlm.nih.gov/pubmed/12898639 Park ''et al.'', 2003]). As LMWP has been shown to be neither toxic nor immunogenic ([http://www.ncbi.nlm.nih.gov/pubmed/11741268 Chang ''et al.'' a, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741269 Chang ''et al.'' b, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741270 Lee ''et al.'', 2001]), it may be used as a potential vaccine, drug or gene delivery vector.<br />
LMWP is a 14-amino acid derivative from Rainbow trout (''Oncorhynchus mykiss'') protamine, an arginine-rich protein that replaces histones in chromatin during spermatogenesis ([http://www.ncbi.nlm.nih.gov/pubmed/3755398 McKay ''et al.'', 1986]; [http://www.ncbi.nlm.nih.gov/pubmed/10213181 Byun ''et al.'', 1999]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|42 bp<br />
|-<br />
|'''Patent Application'''<br />
|[http://www.freepatentsonline.com/y2007/0071677.html 20070071677]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|14 aa<br />
|-<br />
|'''Size'''<br />
|1880 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])<br />
|-<br />
|colspan="2" align="center"|VSRRRRRRGGRRRR<br />
|-<br />
|colspan="2"|Patent application by Park et al. (2004)<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Transportan 10 (Tp10) ===<br />
Chemically synthesized Tp10 peptides conjugated to different cargo, including pDNA and protein, have been shown to efficiently penetrate the lipid bilayer of both human and mouse cells ([http://www.ncbi.nlm.nih.gov/pubmed/15763630 Kilk ''et al.'', 2005]). Membrane permeation is both energy and temperature independent ([http://www.ncbi.nlm.nih.gov/pubmed/11718666 H&auml;llbrink ''et al.'', 2001]). The exact mechanism for penetration is still unclear ([http://www.ncbi.nlm.nih.gov/pubmed/17218466 Yandek ''et al.'', 2007]).<br />
Tp10 is a 21-amino acid derivative from the parent peptide transportan (originally known as galparan), which is a peptide chimera of the neuropeptide galanin and the wasp venom peptide mastoparan ([http://www.ncbi.nlm.nih.gov/pubmed/10930519 Soomets ''et al.'', 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/8738882 Langel ''et al.'', 1996]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|rowspan="8" width="250"|[[Image:Transportan.jpg|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|63 bp<br />
|-<br />
|'''Patent Application'''<br />
|[http://www.freepatentsonline.com/y2008/0234183.html 20080234183]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|21 aa<br />
|-<br />
|'''Size'''<br />
|2183 Da ([http://www.scripps.edu/~cdputnam/protcalc.html calculated])<br />
|-<br />
|colspan="2" align="center"|AGYLLGKINLKALAALAKKIL<br />
|-<br />
|colspan="2"|Patent application by Hallbrink et al. (2003)<br /><br />
|}<br />
<br />
<!--|-<br />
|rowspan="8" width="250"|[[Image:Tp10_prediction.png|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]--><br />
----<br />
<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Project_Idea/ProteinsTeam:Stockholm/Project Idea/Proteins2010-10-27T18:26:47Z<p>AndreasConstantinou: /* TAT cell penetrating peptide (TAT) */</p>
<hr />
<div>{{Stockholm/Project_Idea}}<br />
{| <br />
|[[image:SU_Modeling_Icon_2.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
== Proteins ==<br />
<br />
=== Superoxide dismutase 1 (SOD1) ===<br />
Human soluble Superoxide dismutase 1 (SOD1) is a soluble cytoplasmic protein functional as a homodimer that binds copper and zink ions. SOD1 catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> &rarr; H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub>, protecting the cell from oxidative damage. SOD1 was first cloned and expressed in ''Escherichia coli'' by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)]. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:SOD1_dimeric.png|250px]]<br />3D structure of human SOD1 in its dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite ''et al''. (2010)]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|465 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt331 A &rarr; G<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|PfeI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|154 aa<br />
|-<br />
|'''Size'''<br />
|15,936 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].<br />
|}<br />
<br />
<br />
----<br />
<br />
=== Yeast copper chaperon (yCCS) ===<br />
Yeast copper chaperon protein (yCCS) is a helper chaperon specific for copper/zinc superoxide dismutase located to the cytoplasm. yCCS generates fully metallized, active SOD1 proteins that in turn protects the cell from oxidative damage. <br />
<br />
yCCS has been shown to successfully mediate the delivery of copper ions to human SOD1 ([http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al''. 2003]). Co-expression of SOD1 and yCCS yields proteins with higher copper contents, leading to increased activity and more stable proteins. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:YSOD+yCCS_interaction.jpg|250px]]<br />3D structure of yCCS interacting with yeast superoxide dismutase (ySOD) in it's monomeric form. Ions indicated as gray orbs. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/11524675 Lamb ''et al''. 2001]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|750 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt257 T &rarr; C<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|EcoRI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|249 aa<br />
|-<br />
|'''Size'''<br />
|27,330 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Human basic fibroblast growth factor (bFGF) ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:BFGF.jpg|250px]]<br />3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|468 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt341 C &rarr; T<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|AgeI<br />
|-<br />
|'''GenBank'''<br />
|(full mRNA) [http://www.ncbi.nlm.nih.gov/nuccore/153285460 153285460]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|155 aa<br />
|-<br />
|'''Size'''<br />
|17,353 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Protein A, z domain ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Genepart <br />
|rowspan="10" width="250"|[[Image:ProteinA_z_domain.jpg|250px]]<br />3D structure of the Z-domain of Protein A. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/9325113 Tashiro ''et al''. 2010]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|174 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
| -<br />
|-<br />
|'''Removed restr. site(s)'''<br />
| -<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/gene/2859152 2859152] (full protein)<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|58 aa <br />
(508 aa, full protein )<br />
|-<br />
|'''Size'''<br />
|55,439 Da (full protein)<br />
|-<br />
|'''Fasta'''<br />
|[http://www.uniprot.org/uniprot/P38507.fasta Protein A] (full protein)<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== IgG protease (IdeS) ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:IdeS.jpg|250px]]<br />Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig ''et al''. 2004]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|930 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
| -<br />
|-<br />
|'''Removed restr. site(s)'''<br />
| -<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/gene/6985687 6985687]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|339 aa<br />
|-<br />
|'''Size'''<br />
|37,977 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
<br />
----<br />
<br />
== Cell penetrating peptides ==<br />
<br />
This cell-penetrating peptides, (CPPs) may be used in N- and C-terminal fusions with full-length proteins to create transduction proteins with the ability to permeate the lipid bilayer of various cell types, making it a potential gene or protein delivery vector.<br />
<br />
<br />
=== TAT cell penetrating peptide (TAT) ===<br />
Purified full-length TAT fusion proteins expressed in ''Escherichia coli'' have been shown to successfully translocate into several human cell types, including all cells found in whole blood, as well as bone marrow stem cells and osteoblasts, while still retaining the fused protein's activity ([http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). The mechanism for transduction over the bilipid membrane is still a matter of debate, but has been suggested to occur through macropinocytosis, a specialized form of endocytosis ([http://www.ncbi.nlm.nih.gov/pubmed/17913584 Gump and Dowdy, 2007]).<br />
TAT is an 11-amino acid derivative from the Human Immunodeficiency Virus 1 (HIV-1) ''trans''-activating transcriptional activator (Tat) ([http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green and Loewenstein, 1988]; [http://www.ncbi.nlm.nih.gov/pubmed/9846587 Nagahara ''et al.'' 1998]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|33 bp<br />
|-<br />
|'''Patent PCT'''<br />
|[http://v3.espacenet.com/publicationDetails/biblio;jsessionid=646EDA06997EDDFC0CC04CCE49F87F6B.espacenet_levelx_prod_5?CC=WO&NR=2005084158A2&KC=A2&FT=D&date=20050915&DB=EPODOC&locale=se_se WO 2005/084158 A2]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|11 aa<br />
|-<br />
|'''Size'''<br />
|1560 Da ([http://www.scripps.edu/~cdputnam/protcalc.html Calculated])<br />
|-<br />
|colspan="2" align="center"|YGRKKRRQRRR<br />
|-<br />
|colspan="2"|First reported by <br />
[http://www.ncbi.nlm.nih.gov/pubmed/2849509 Green ''et al''. (1988)] and [http://www.ncbi.nlm.nih.gov/pubmed/2849510 Frankel ''et al''. (1988)]<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Low molecular weight protamine (LMWP) ===<br />
Enzymatically prepared LMWP chemically conjugated to ovalbumin (OVA) and bovine serum albumin (BSA) have previously been shown to penetrate the lipid bilayer of human keratinocytes, as well as to successfully permeate mouse skin epidermis ([http://www.ncbi.nlm.nih.gov/pubmed/20232417 Huang ''et al.'', 2010]). Furthermore, LMWP/pDNA complexes can efficiently penetrate into human embryonic kidney cells ([http://www.ncbi.nlm.nih.gov/pubmed/12898639 Park ''et al.'', 2003]). As LMWP has been shown to be neither toxic nor immunogenic ([http://www.ncbi.nlm.nih.gov/pubmed/11741268 Chang ''et al.'' a, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741269 Chang ''et al.'' b, 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11741270 Lee ''et al.'', 2001]), it may be used as a potential vaccine, drug or gene delivery vector.<br />
LMWP is a 14-amino acid derivative from Rainbow trout (''Oncorhynchus mykiss'') protamine, an arginine-rich protein that replaces histones in chromatin during spermatogenesis ([http://www.ncbi.nlm.nih.gov/pubmed/3755398 McKay ''et al.'', 1986]; [http://www.ncbi.nlm.nih.gov/pubmed/10213181 Byun ''et al.'', 1999]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|42 bp<br />
|-<br />
|'''Patent Application'''<br />
|[http://www.freepatentsonline.com/y2007/0071677.html 20070071677]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|14 aa<br />
|-<br />
|'''Size'''<br />
|<br />
|-<br />
|colspan="2" align="center"|VSRRRRRRGGRRRR<br />
|-<br />
|colspan="2"|Patent application by Park et al. (2004)<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
=== Transportan 10 (Tp10) ===<br />
Chemically synthesized Tp10 peptides conjugated to different cargo, including pDNA and protein, have been shown to efficiently penetrate the lipid bilayer of both human and mouse cells ([http://www.ncbi.nlm.nih.gov/pubmed/15763630 Kilk ''et al.'', 2005]). Membrane permeation is both energy and temperature independent ([http://www.ncbi.nlm.nih.gov/pubmed/11718666 H&auml;llbrink ''et al.'', 2001]). The exact mechanism for penetration is still unclear ([http://www.ncbi.nlm.nih.gov/pubmed/17218466 Yandek ''et al.'', 2007]).<br />
Tp10 is a 21-amino acid derivative from the parent peptide transportan (originally known as galparan), which is a peptide chimera of the neuropeptide galanin and the wasp venom peptide mastoparan ([http://www.ncbi.nlm.nih.gov/pubmed/10930519 Soomets ''et al.'', 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/8738882 Langel ''et al.'', 1996]). This part was back translated from the corresponding amino acid sequence and optimized for expression in ''Escherichia coli''. Codon usage has been varied for repetitive amino acids to enable DNA synthesis.<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Sequence <br />
|rowspan="8" width="250"|[[Image:Transportan.jpg|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|63 bp<br />
|-<br />
|'''Patent Application'''<br />
|[http://www.freepatentsonline.com/y2008/0234183.html 20080234183]<br /><br />
|-<br />
!colspan="2"|Peptide<br />
|-<br />
|'''Length'''<br />
|21 aa<br />
|-<br />
|'''Size'''<br />
|<br />
|-<br />
|colspan="2" align="center"|AGYLLGKINLKALAALAKKIL<br />
|-<br />
|colspan="2"|Patent application by Hallbrink et al. (2003)<br /><br />
|}<br />
<br />
<!--|-<br />
|rowspan="8" width="250"|[[Image:Tp10_prediction.png|250px]]<br />3D structure of transportan<br /> [http://www.dbb.su.se/Faculty/Lena_M%C3%A4ler/Structural_basis_for_peptide-membrane_interactions www.dbb.su.se]--><br />
----<br />
<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Project_Idea/Future_applicationsTeam:Stockholm/Project Idea/Future applications2010-10-27T18:09:49Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Project_Idea}}<br />
{| <br />
|[[Image:SU_2010_futurework.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<div align="justify"><br />
==Future applications==<br />
<br />
We believe that this project has great potential. In our point of view it is a new and innovative method when dealing with many skin disorders. It would have been great if we had more time to test the skin penetrating capabilities of our proteins bound to cell penetrating peptides (CPPs) derived from E.coli. However there was a shortage of experimental time. We still hope that this project will open up doors and possibly new methods in the field of bacteria theraphy and synthetic biology. In addition we wish that more research focus would highlight skin disorders such as Vitiligo in combination with the vast capacity of synthetic biology. <br />
<br />
Future work would have been for us to succesfully purify our fusion proteins. These are made up of proteins of interest when targeting Vitiligo and the three different types of CPPs that have caught our eyes. The purified fusion proteins is supposed to be applied both on skin cells, such as keratinocytes and melanocytes on a dish, and also on artificial skin. This would allow us to investigate the penetrating capability of the fusion proteins on both cell and skin level. This is a crucial moment to understand since it opens up for further experiments to take place. The approach for the penetrating experiments is by immunohistochemistry on cells and skin layers. An interesting follow up on this would be to have the bacteria produce and secrete the proteins with CPPs out of the bacteria by skipping the extra step in protein purifications. This would be a very optimal set up since we would not need laborative costs related to protein purification.<br />
<br />
We would need a success in either protein purification or secretion of the proteins with CPP. This should be followed by a fortunate cell and skin penetratration experiment. Then we could have experiments focusing on protein activity. It would be interesting to analyze how well the proteins activity is preserved during the penetration of the skin barrier and into the different skin layers. <br />
<br />
It is unfortunate that we did not have more experimental time to spend on our research project. However it is also important for us to emphasize all the experience we all have learned from this journey. <br />
<br />
Thank you for this opportunity iGEM, supervisors and the the Faculty of Science at Stockholm University! <br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T18:04:02Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<div align="justify"><br />
{|align="right"<br />
| width="265"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===IdeS&middot;PtA-Z fusion protein===<br />
One of our approaches for protecting affected Vitiligo skin from autoantibodies was to locally digest IgG immunoglobulins using the IgG degrading bacterial protease IdeS. In an attempt to increase the efficiency of IdeS in the skin we suggested that IdeS be fused to the Z-domain of Protein A, which possesses the ability of binding to the Fc (constant) region of immunoglobulins. By combining the features of these two proteins, we could possibly create a protein chimera which binds with a high(er) affinity to IgG, thus increasing the protease's access to antibodies, resulting in a higher antibody degradation than native IdeS.<br />
<br />
The PtA-Z&middot;IdeS fusion protein was constructed as shown in the figure below:<br /><br />
[[Image:PtA-Z IdeS fusion BioBrick.png|800px]]<br />
<br />
===CPP fusions===<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|C-terminal CPP fusions<br />
|-<br />
!align="center"|Purification tag<br />
!align="center"|Protein<br />
!align="center"|CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|N-terminal CPP fusions<br />
|-<br />
!align="center"|N-part CPP<br />
!align="center"|Protein<br />
!align="center"|Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
<br />
===Construction of a ''sod1''-''yccs'' operon===<br />
[[Image:Sod yccs operon.png|200px|thumb|right|'''Cloning strategy for ''sod-yccs'' operon for co-expression in pEX.''']]<br />
For SOD1 to be fully active it needs to be co-expressed with its helper copper chaperone, which provides SOD1 with necessary copper ions prior to folding. We are using a yeast copper chaperone (yCCS) for this.<br />
<br />
Since we were (for several reasons) restricted to the pEX vector for protein expression, we wanted construct a ''sod1''-''yccs'' operon allowing us to co-express the two genes from the same P<sub>tac</sub> promoter, which comes pre-installed in pEX. Previous studies (e.g. by [http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al.'' (2004)]) show that high copper content SOD1 is obtained with the protein is expressed in levels equal to yCCS. As we wanted to copy this behavior, transcription from the same promoter is an advantage. We then set out to look for a Shine-Dalgarno (SD) sequence with the same strength as the one found in pEX. Since no experimental comparison data with the pEX SD was available we chose the most similar with respect to (1) the ribosome-binding nucleotides and (2) distance to the start codon; thus we selected [http://partsregistry.org/Part:BBa_B0034 BBa_B0034].<br />
<br />
The operon was then assembled into pEX as illustrated. The same principle was used for constructing operons expressing CPP-SOD1 fusions.<br />
<br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T18:03:33Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<div align="justify"><br />
{|align="right"<br />
| width="280"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===IdeS&middot;PtA-Z fusion protein===<br />
One of our approaches for protecting affected Vitiligo skin from autoantibodies was to locally digest IgG immunoglobulins using the IgG degrading bacterial protease IdeS. In an attempt to increase the efficiency of IdeS in the skin we suggested that IdeS be fused to the Z-domain of Protein A, which possesses the ability of binding to the Fc (constant) region of immunoglobulins. By combining the features of these two proteins, we could possibly create a protein chimera which binds with a high(er) affinity to IgG, thus increasing the protease's access to antibodies, resulting in a higher antibody degradation than native IdeS.<br />
<br />
The PtA-Z&middot;IdeS fusion protein was constructed as shown in the figure below:<br /><br />
[[Image:PtA-Z IdeS fusion BioBrick.png|800px]]<br />
<br />
===CPP fusions===<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|C-terminal CPP fusions<br />
|-<br />
!align="center"|Purification tag<br />
!align="center"|Protein<br />
!align="center"|CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|N-terminal CPP fusions<br />
|-<br />
!align="center"|N-part CPP<br />
!align="center"|Protein<br />
!align="center"|Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
<br />
===Construction of a ''sod1''-''yccs'' operon===<br />
[[Image:Sod yccs operon.png|200px|thumb|right|'''Cloning strategy for ''sod-yccs'' operon for co-expression in pEX.''']]<br />
For SOD1 to be fully active it needs to be co-expressed with its helper copper chaperone, which provides SOD1 with necessary copper ions prior to folding. We are using a yeast copper chaperone (yCCS) for this.<br />
<br />
Since we were (for several reasons) restricted to the pEX vector for protein expression, we wanted construct a ''sod1''-''yccs'' operon allowing us to co-express the two genes from the same P<sub>tac</sub> promoter, which comes pre-installed in pEX. Previous studies (e.g. by [http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al.'' (2004)]) show that high copper content SOD1 is obtained with the protein is expressed in levels equal to yCCS. As we wanted to copy this behavior, transcription from the same promoter is an advantage. We then set out to look for a Shine-Dalgarno (SD) sequence with the same strength as the one found in pEX. Since no experimental comparison data with the pEX SD was available we chose the most similar with respect to (1) the ribosome-binding nucleotides and (2) distance to the start codon; thus we selected [http://partsregistry.org/Part:BBa_B0034 BBa_B0034].<br />
<br />
The operon was then assembled into pEX as illustrated. The same principle was used for constructing operons expressing CPP-SOD1 fusions.<br />
<br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T18:02:51Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<div align="justify"><br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===IdeS&middot;PtA-Z fusion protein===<br />
One of our approaches for protecting affected Vitiligo skin from autoantibodies was to locally digest IgG immunoglobulins using the IgG degrading bacterial protease IdeS. In an attempt to increase the efficiency of IdeS in the skin we suggested that IdeS be fused to the Z-domain of Protein A, which possesses the ability of binding to the Fc (constant) region of immunoglobulins. By combining the features of these two proteins, we could possibly create a protein chimera which binds with a high(er) affinity to IgG, thus increasing the protease's access to antibodies, resulting in a higher antibody degradation than native IdeS.<br />
<br />
The PtA-Z&middot;IdeS fusion protein was constructed as shown in the figure below:<br /><br />
[[Image:PtA-Z IdeS fusion BioBrick.png|800px]]<br />
<br />
===CPP fusions===<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|C-terminal CPP fusions<br />
|-<br />
!align="center"|Purification tag<br />
!align="center"|Protein<br />
!align="center"|CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|N-terminal CPP fusions<br />
|-<br />
!align="center"|N-part CPP<br />
!align="center"|Protein<br />
!align="center"|Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
<br />
===Construction of a ''sod1''-''yccs'' operon===<br />
[[Image:Sod yccs operon.png|200px|thumb|right|'''Cloning strategy for ''sod-yccs'' operon for co-expression in pEX.''']]<br />
For SOD1 to be fully active it needs to be co-expressed with its helper copper chaperone, which provides SOD1 with necessary copper ions prior to folding. We are using a yeast copper chaperone (yCCS) for this.<br />
<br />
Since we were (for several reasons) restricted to the pEX vector for protein expression, we wanted construct a ''sod1''-''yccs'' operon allowing us to co-express the two genes from the same P<sub>tac</sub> promoter, which comes pre-installed in pEX. Previous studies (e.g. by [http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al.'' (2004)]) show that high copper content SOD1 is obtained with the protein is expressed in levels equal to yCCS. As we wanted to copy this behavior, transcription from the same promoter is an advantage. We then set out to look for a Shine-Dalgarno (SD) sequence with the same strength as the one found in pEX. Since no experimental comparison data with the pEX SD was available we chose the most similar with respect to (1) the ribosome-binding nucleotides and (2) distance to the start codon; thus we selected [http://partsregistry.org/Part:BBa_B0034 BBa_B0034].<br />
<br />
The operon was then assembled into pEX as illustrated. The same principle was used for constructing operons expressing CPP-SOD1 fusions.<br />
<br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/File:Sod_yccs_operon.pngFile:Sod yccs operon.png2010-10-27T18:00:22Z<p>AndreasConstantinou: </p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T16:10:41Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<div align="justify"><br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===IdeS&middot;PtA-Z fusion protein===<br />
One of our approaches for protecting affected Vitiligo skin from autoantibodies was to locally digest IgG immunoglobulins using the IgG degrading bacterial protease IdeS. In an attempt to increase the efficiency of IdeS in the skin we suggested that IdeS be fused to the Z-domain of Protein A, which possesses the ability of binding to the Fc (constant) region of immunoglobulins. By combining the features of these two proteins, we could possibly create a protein chimera which binds with a high(er) affinity to IgG, thus increasing the protease's access to antibodies, resulting in a higher antibody degradation than native IdeS.<br />
<br />
The PtA-Z&middot;IdeS fusion protein was constructed as shown in the figure below:<br /><br />
[[Image:PtA-Z IdeS fusion BioBrick.png|800px]]<br />
<br />
===CPP fusions===<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|C-terminal CPP fusions<br />
|-<br />
!align="center"|Purification tag<br />
!align="center"|Protein<br />
!align="center"|CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|N-terminal CPP fusions<br />
|-<br />
!align="center"|N-part CPP<br />
!align="center"|Protein<br />
!align="center"|Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
<br />
===Construction of a ''sod1''-''yccs'' operon===<br />
For SOD1 to be fully active it needs to be co-expressed with its helper copper chaperone, which provides SOD1 with necessary copper ions prior to folding. We are using a yeast copper chaperone (yCCS) for this.<br />
<br />
Since we were (for several reasons) restricted to the pEX vector for protein expression, we wanted construct a ''sod1''-''yccs'' operon allowing us to co-express the two genes from the same P<sub>tac</sub> promoter, which comes pre-installed in pEX. Previous studies (e.g. by [http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al.'' (2004)]) show that high copper content SOD1 is obtained with the protein is expressed in levels equal to yCCS. As we wanted to copy this behavior, transcription from the same promoter is an advantage. We then set out to look for a Shine-Dalgarno (SD) sequence with the same strength as the one found in pEX. Since no experimental comparison data with the pEX SD was available we chose the most similar with respect to (1) the ribosome-binding nucleotides and (2) distance to the start codon; thus we selected [http://partsregistry.org/Part:BBa_B0034 BBa_B0034].<br />
<br />
The operon was then assembled into pEX as illustrated. The same principle was used for constructing operons expressing CPP-SOD1 fusions.<br />
<br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T15:36:01Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<div align="justify"><br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
====IdeS&middot;PtA-Z fusion protein====<br />
One of our approaches for protecting affected Vitiligo skin from autoantibodies was to locally digest IgG immunoglobulins using the IgG degrading bacterial protease IdeS. In an attempt to increase the efficiency of IdeS in the skin we suggested that IdeS be fused to the Z-domain of Protein A, which possesses the ability of binding to the Fc (constant) region of immunoglobulins. By combining the features of these two proteins, we could possibly create a protein chimera which binds with a high(er) affinity to IgG, thus increasing the protease's access to antibodies, resulting in a higher antibody degradation than native IdeS.<br />
<br />
The PtA-Z&middot;IdeS fusion protein was constructed as shown in the figure below:<br /><br />
[[Image:PtA-Z IdeS fusion BioBrick.png|800px]]<br />
<br />
====CPP fusions====<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|C-terminal CPP fusions<br />
|-<br />
!align="center"|Purification tag<br />
!align="center"|Protein<br />
!align="center"|CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|N-terminal CPP fusions<br />
|-<br />
!align="center"|N-part CPP<br />
!align="center"|Protein<br />
!align="center"|Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T15:31:34Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<div align="justify"><br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===Cloning strategies===<br />
<br />
====IdeS&middot;PtA-Z fusion protein====<br />
One of our approaches for protecting affected Vitiligo skin from autoantibodies was to locally digest IgG immunoglobulins using the IgG degrading bacterial protease IdeS. In an attempt to increase the efficiency of IdeS in the skin we suggested that IdeS be fused to the Z-domain of Protein A, which possesses the ability of binding to the Fc (constant) region of immunoglobulins. By combining the features of these two proteins, we could possibly create a protein chimera which binds with a high(er) affinity to IgG, thus increasing the protease's access to antibodies, resulting in a higher antibody degradation than native IdeS.<br />
<br />
The PtA-Z&middot;IdeS fusion protein was constructed as shown in the figure below:<br /><br />
[[Image:PtA-Z IdeS fusion BioBrick.png|800px]]<br />
<br />
====CPP fusions====<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|C-terminal CPP fusions<br />
|-<br />
!align="center"|Purification tag<br />
!align="center"|Protein<br />
!align="center"|CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!align="center" colspan="3"|N-terminal CPP fusions<br />
|-<br />
!align="center"|N-part CPP<br />
!align="center"|Protein<br />
!align="center"|Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T15:02:31Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<div align="justify"><br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===Cloning strategies===<br />
<br />
====IdeS&middot;PtA-Z fusion protein====<br />
Information here.<br />
<br />
====CPP fusions====<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!colspan="3"|C-terminal CPP fusions<br />
|-<br />
!Purification tag<br />
!Protein<br />
!CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!colspan="3"|N-terminal CPP fusions<br />
|-<br />
!N-part CPP<br />
!Protein<br />
!Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="400" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
[[Image:PtA-Z_IdeS_fusion_BioBrick.png|400px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
</div><br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/File:PtA-Z_IdeS_fusion_BioBrick.pngFile:PtA-Z IdeS fusion BioBrick.png2010-10-27T15:01:17Z<p>AndreasConstantinou: uploaded a new version of "Image:PtA-Z IdeS fusion BioBrick.png"</p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:PtA-Z_IdeS_fusion_BioBrick.pngFile:PtA-Z IdeS fusion BioBrick.png2010-10-27T14:48:10Z<p>AndreasConstantinou: </p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T13:23:25Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===Cloning strategies===<br />
<br />
====IdeS&middot;PtA-Z fusion protein====<br />
Information here.<br />
<br />
====CPP fusions====<br />
As described in our project introduction, one of our aims was to target proteins to keratinocytes and melanocytes in human skin using cell-penetrating peptides. As we didn't know which of (or if) our CPPs would be most efficient in protein delivery, we set out to test all three in parallel.<br />
<br />
At least two of our CPPs (LMWP and Tp10) have not previously been tested using recombinant technique, i.e. in protein fusions. Although these have been shown to successfully deliver protein cargo into cells and/or skin, these proteins have been chemically conjugated to the CPPs, [[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]usually to amino acid side chains. We were therefore unsure as to whether membrane and skin penetration would be most effective when fusing the CPPs to our proteins' N- or C-termini; we also discussed that this may possibly vary for different proteins, as different cargo properties may interact and possibly disturb our CPPs. In relation to this, we also discussed the probability of the CPPs disturbing the enzymatic activity of our fused cargo proteins, and whether this risk would differ depending on to which side of the protein (N- or C-terminus) the CPP is fused.<br />
<br />
As time is very limited in the iGEM competition, and as we would not be able to test fusion to one side at the time, we decided to fuse the CPPs to both sides of our proteins, and draw our own conclusions by investigating both CPP and protein activity.<br />
<br />
Another factor we took into consideration was the additional amino acids added to parts adapted to the [[http://partsregistry.org/Assembly_standard_25 Freiburg assembly standard]]. Due to the small size of our CPPs (11-21 a.a.) we thought that even a very small variation to the amino acid sequence could affect their function. For our N-terminal protein fusions we therefore designed N-part versions of our CPPs, which prevents the addition of the two extra amino acids in the CPP N-terminal (Ala & Gly) by removing the standard-specific NgoMIV restriction site.<br />
<br />
Finally, we also attached a 6x His tag to each one of our protein fusions to enable antibody detection and protein purification.<br />
<br />
The figures to the right illustrate the cloning strategy for our CPP&middot;protein fusions, and insertion into the IPTG-inducible protein expression pEX ([http://partsregistry.org/Part:BBa_K243033 BBa_K243033]). Tables below show an overview of our many CPP&middot;protein fusion combinations.<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!colspan="3"|C-terminal CPP fusions<br />
|-<br />
!Purification tag<br />
!Protein<br />
!CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|}<br />
<br /><br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!colspan="3"|N-terminal CPP fusions<br />
|-<br />
!N-part CPP<br />
!Protein<br />
!Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="400" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-27T11:59:43Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
<br />
===Cloning strategies===<br />
<br />
====CPPs====<br />
<br />
{|border="1" cellpadding="0" cellspacing="0"<br />
!colspan="3"|C-terminal CPP fusions<br />
|-<br />
!Purification tag<br />
!Protein<br />
!CPP<br />
|-<br />
|width="170" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|width="410" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
|width="220" align="center"|[[Image:TAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:LMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:Tp10_BioBrick.png|180px]]<br />
|-<br />
!colspan="3"|N-terminal CPP fusions<br />
|-<br />
!N-part CPP<br />
!Protein<br />
!Purification tag<br />
|-<br />
|width="220" align="center"|[[Image:nTAT_BioBrick.png|170px]]<br /><br /><br />
[[Image:nLMWP_BioBrick.png|175px]]<br /><br /><br />
[[Image:nTp10_BioBrick.png|180px]]<br />
|width="400" align="center"|[[Image:BFGF_BioBrick.png|245px]]<br /><br />
[[Image:SOD1_BioBrick.png|245px]]<br /><br />
[[Image:IdeS_BioBrick.png|380px]]<br /><br />
[[Image:ProteinA_BioBrick.png|215px]]<br /><br />
|width="160" align="center"|<br /><br /><br />[[Image:His-tag_BioBrick.png|145px]]<br />
|}<br />
<br />
<br />
[[Image:PEX.his protein CPP.png|200px|thumb|right|'''Cloning strategy for proteins fused to CPPs''']]<br />
<br />
[[Image:PEX.nCPP_protein_his.png|200px|thumb|right|'''Cloning strategy for proteins fused to N-part CPPs''']]<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/File:His-tag_BioBrick.pngFile:His-tag BioBrick.png2010-10-27T11:33:29Z<p>AndreasConstantinou: </p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:PEX.nCPP_protein_his.pngFile:PEX.nCPP protein his.png2010-10-27T11:07:58Z<p>AndreasConstantinou: </p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:PEX.his_protein_CPP.pngFile:PEX.his protein CPP.png2010-10-27T11:06:44Z<p>AndreasConstantinou: uploaded a new version of "Image:PEX.his protein CPP.png"</p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:PEX.his_protein_CPP.pngFile:PEX.his protein CPP.png2010-10-27T11:02:28Z<p>AndreasConstantinou: </p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:BFGF.jpgFile:BFGF.jpg2010-10-27T07:48:02Z<p>AndreasConstantinou: uploaded a new version of "Image:BFGF.jpg"</p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Project_Idea/ProteinsTeam:Stockholm/Project Idea/Proteins2010-10-27T07:39:52Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Project_Idea}}<br />
{| <br />
|[[image:SU_Modeling_Icon_2.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
== Proteins ==<br />
<br />
=== Superoxide dismutase 1 (SOD1) ===<br />
Human soluble Superoxide dismutase 1 (SOD1) is a soluble cytoplasmic protein functional as a homodimer that binds copper and zink ions. SOD1 catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> &rarr; H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub>, protecting the cell from oxidative damage. SOD1 was first cloned and expressed in ''Escherichia coli'' by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)]. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:SOD1_dimeric.png|250px]]<br />3D structure of human SOD1 in its dimeric form. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20822138 Leinartaite ''et al''. (2010)]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|465 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt331 A &rarr; G<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|PfeI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nucleotide/38489879?report=genbank&log$=nucltop&blast_rank=22&RID=CAM83NYN01S AY450286.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|154 aa<br />
|-<br />
|'''Size'''<br />
|15,936 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/49456443?report=fasta SOD1]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/3889846 Hallewell ''et al''., (1985)].<br />
|}<br />
<br />
<br />
----<br />
<br />
<br />
=== Yeast copper chaperon (yCCS) ===<br />
Yeast copper chaperon protein (yCCS) is a helper chaperon specific for copper/zinc superoxide dismutase located to the cytoplasm. yCCS generates fully metallized, active SOD1 proteins that in turn protects the cell from oxidative damage. <br />
<br />
yCCS has been shown to successfully mediate the delivery of copper ions to human SOD1 ([http://www.ncbi.nlm.nih.gov/pubmed/15358352 Ahl ''et al''. 2003]). Co-expression of SOD1 and yCCS yields proteins with higher copper contents, leading to increased activity and more stable proteins. <br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:YSOD+yCCS_interaction.jpg|250px]]<br />3D structure of yCCS interacting with yeast superoxide dismutase (ySOD) in it's monomeric form. Ions indicated as gray orbs. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/11524675 Lamb ''et al''. 2001]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|750 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt257 T &rarr; C<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|EcoRI<br />
|-<br />
|'''GenBank'''<br />
|[http://www.ncbi.nlm.nih.gov/nuccore/NM_001182535.1?report=genbank&log$=seqview NM_001182535.1]<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|249 aa<br />
|-<br />
|'''Size'''<br />
|27,330 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/596088?report=fasta yCCS]<br /><br />
|-<br />
|colspan="2"|First reported by [http://www.ncbi.nlm.nih.gov/pubmed/9295278 Culotta ''et al''. (1997)].<br /><br />
|}<br />
<br />
<br />
----<br />
<br />
<br />
=== Human basic fibroblast growth factor (bFGF) ===<br />
<br />
{|border="1" align="center" cellpadding="3" cellspacing="0"<br />
!colspan="2"|Gene (cDNA) <br />
|rowspan="10" width="250"|[[Image:BFGF.jpg|250px]]<br />3D structure of bFGF. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/20133753 Bae ''et al''. 2010]<br />
|-<br />
|width="130"|'''Length'''<br />
|width="130"|468 bp<br />
|-<br />
|'''Edited nucleotide(s)'''<br />
|nt341 C &rarr; T<br />
|-<br />
|'''Removed restr. site(s)'''<br />
|AgeI<br />
|-<br />
|'''GenBank'''<br />
|&nbsp;<br /><br />
|-<br />
!colspan="2"|Protein<br />
|-<br />
|'''Length'''<br />
|155 aa<br />
|-<br />
|'''Size'''<br />
|17,353 Da<br />
|-<br />
|'''Fasta'''<br />
|[http://www.ncbi.nlm.nih.gov/protein/153285461?report=fasta bFGF]<br /><br />
|-<br />
|colspan="2"|First reported by <unknown><br /><br />
|}<br />
<br />
<br />
----<br />
<br />
<br />
=== Protein A, z domain ===<br />
[http://partsregistry.org/Part:BBa_K380009 Part:BBa_K380009]<br />
<br />
<br />
<br />
[[Image:|300px|thumb|right|]]<br />
<br />
<br />
<br />
{| <br />
| '''Genepart''' <br />
| <br />
|-<br />
| length<br />
| 174 bp<br />
|-<br />
| removed restriction sites<br />
| -<br />
|-<br />
| exchanged nt<br />
| -<br />
|-<br />
| '''Protein'''<br />
| <br />
|-<br />
| length<br />
| 58 aa<br />
|-<br />
| size<br />
| <br />
|-<br />
| Fasta<br />
| <br />
|}<br />
<br />
<br />
GenBank:<br />
<br />
First reported by:<br />
<br />
<br />
<br />
<br />
<br />
<br />
----<br />
<br />
<br />
=== IgG protease, IdeS ===<br />
[http://partsregistry.org/Part:BBa_K380010 Part:BBa_K380010]<br />
<br />
<br />
<br />
[[Image:IdeS.jpg|200px|thumb|right|3D structure of IdeS. Primary citation [http://www.ncbi.nlm.nih.gov/pubmed/15574492 Wenig ''et al''. 2004] ]]<br />
<br />
<br />
<br />
{| <br />
| '''Gene''' (cDNA)<br />
| <br />
|-<br />
| length<br />
| 930 bp<br />
|-<br />
| removed restriction sites<br />
| -<br />
|-<br />
| exchanged nt<br />
| -<br />
|-<br />
| '''Protein'''<br />
| <br />
|-<br />
| length<br />
| 339 aa<br />
|-<br />
| size<br />
| 37,977 Da<br />
|-<br />
| Fasta<br />
| [http://www.ncbi.nlm.nih.gov/protein/209559219?report=fasta IdeS]<br />
|}<br />
<br />
<br />
GenBank:<br />
<br />
First reported by:<br />
<br />
<br />
<br />
<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/File:250px-BFGF.jpgFile:250px-BFGF.jpg2010-10-27T07:38:51Z<p>AndreasConstantinou: </p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:YSOD%2ByCCS_interaction.jpgFile:YSOD+yCCS interaction.jpg2010-10-27T07:26:10Z<p>AndreasConstantinou: uploaded a new version of "Image:YSOD+yCCS interaction.jpg"</p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-26T22:18:20Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|<br />[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Proteins Characterize the new BioBrick]<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team] (Team Uppsala)<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-26T22:17:57Z<p>AndreasConstantinou: /* Medals criteria */</p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Proteins Characterize the new BioBrick]<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team] (Team Uppsala)<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-26T22:17:43Z<p>AndreasConstantinou: /* Assemblies */</p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
Assemblies go here.<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-26T22:17:20Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
=Assemblies=<br />
Assemblies go here.<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-26T22:17:03Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
=Medals criteria=<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Proteins Characterize the new BioBrick]<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team] (Team Uppsala)<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/AssembliesTeam:Stockholm/Results/Assemblies2010-10-26T22:16:03Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==Assemblies==<br />
Assemblies go here.<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Results/BioBricksTeam:Stockholm/Results/BioBricks2010-10-26T22:15:04Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
{|width="800px"<br />
|<br />
{|align="right"<br />
| width="300"| __TOC__ <br />
|}<br />
==BioBricks==<br />
===''Trans''-Activating Transcriptional Activator (TAT)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380000 BBa_K380000]: Standard part====<br />
[[image:TAT_BioBrick.png]]<br />
<br />
:'''Part name:''' TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> (fasta)<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380001 BBa_K380001]: N-part====<br />
[[image:NTAT_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part TAT cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_12_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Low Molecular Weight Protamine (LMWP)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380002 BBa_K380002]: Standard part)====<br />
[[image:LMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> (fasta)<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380003 BBa_K380003]: N-part====<br />
[[image:nLMWP_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part LMWP cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_11_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===Transportan 10 (Tp10)===<br />
<br />
====[http://partsregistry.org/Part:BBa_K380004 BBa_K380004]: Standard part====<br />
[[image:Tp10_BioBrick.png]]<br />
<br />
:'''Part name:''' Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> (fasta)<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br /><br />
<br />
====[http://partsregistry.org/Part:BBa_K380005 BBa_K380005]: N-part====<br />
[[image:nTp10_BioBrick.png]]<br />
<br />
:'''Part name:''' N-part Tp10 cell-penetrating peptide<br /><br />
:'''Property:''' Cell-penetrating peptide ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.nCCP_5_premix.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380006 BBa_K380006]: Human Basic Fibroblast Growth Factor (bFGF)===<br />
[[image:BFGF_BioBrick.png]]<br />
<br />
:'''Part name:''' Human basic fibroblast growth factor, bFGF<br /><br />
:'''Property:''' Growth factor ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.bFGF_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380007 BBa_K380007]: Superoxide dismutase 1 (SOD1)===<br />
[[image:SOD1_BioBrick.png]]<br />
<br />
:'''Part name:''' Superoxide dismutase 1 protein<br /><br />
:'''Property:''' Catalyzes the reaction O<sup>-</sup><sub>2</sub> + O<sup>-</sup><sub>2</sub> + 2H<sup>+</sup> → H<sub>2</sub>O<sub>2</sub> + O<sub>2</sub> ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.SOD_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380008 BBa_K380008]: Yeast Copper Chaperone (yCCS)===<br />
[[image:YCCS_BioBrick.png]]<br />
<br />
:'''Part name:''' Yeast copper chaperone protein<br /><br />
:'''Property:''' Mediates the delivery of copper ions to SOD1 ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.yCCS_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380009 BBa_K380009]: Protein A Z-domain (PtA-Z)===<br />
[[image:ProteinA_BioBrick.png]]<br />
<br />
:'''Part name:''' protein A<br /><br />
:'''Property:''' - ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.ProtA VR premix fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
<br />
<br /><br />
----<br />
<br /><br />
<br />
===[http://partsregistry.org/Part:BBa_K380010 BBa_K380010]: Immunoglobulin G protease (IdeS)===<br />
[[image:IdeS_BioBrick.png]]<br />
<br />
:'''Part name:''' igg protease<br /><br />
:'''Property:''' - ([[Team:Stockholm/Project Idea/Proteins|more]])<br /><br />
:'''Sequenced:''' <span style="color:green;">Yes</span> ([[Media:PSB1C3.IgGp_VR_premix_fasta.txt|fasta]])<br /><br />
:'''Works:''' <span style="color:red;">Not known</span><br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-26T21:59:06Z<p>AndreasConstantinou: /* Gold */</p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Proteins Characterize the new BioBrick]<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team] (Team Uppsala)<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-26T21:58:28Z<p>AndreasConstantinou: /* Gold */</p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Proteins Characterize the new BioBrick]<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team] (Team Uppsala)]<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/File:SUResults2_wiki.pngFile:SUResults2 wiki.png2010-10-26T21:57:13Z<p>AndreasConstantinou: uploaded a new version of "Image:SUResults2 wiki.png"</p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:SUResults2_wiki.pngFile:SUResults2 wiki.png2010-10-26T21:48:56Z<p>AndreasConstantinou: uploaded a new version of "Image:SUResults2 wiki.png"</p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-26T21:36:59Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|[[image:SUResults2_wiki.png|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Proteins Characterize the new BioBrick]<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team (Team Uppsala)]<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/File:SUResults2_wiki.pngFile:SUResults2 wiki.png2010-10-26T21:36:46Z<p>AndreasConstantinou: uploaded a new version of "Image:SUResults2 wiki.png"</p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/File:SUResults2_wiki.pngFile:SUResults2 wiki.png2010-10-26T21:32:17Z<p>AndreasConstantinou: </p>
<hr />
<div></div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Medals_criteriaTeam:Stockholm/Medals criteria2010-10-26T21:31:29Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Results}}<br />
__NOTOC__<br />
{| <br />
|[[image:SU_Modeling_Icon_2.gif|200px]]<br />
|width="10px"|&nbsp;<br />
|width="590px"|<br />
==Medals criteria==<br />
<br />
===Bronze===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://igem.org/Team.cgi Register the team]<br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Jamboree/Project_Abstract/Team_Abstracts Submit project summary] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Introduction Description of project] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Plan to present a poster and talk <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Results/BioBricks Information on a new BioBrick] <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] Submit DNA for a new BioBrick<br />
<br />
===Silver===<br />
<br />
BioBrick work as expected <br />
<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/Project_Idea/Proteins Characterize the new BioBrick]<br />
<br />
===Gold===<br />
<br />
[[Image:Aq30.jpg|25px]] [https://2010.igem.org/Team:Stockholm/18_October_2010#PCR_verification_for_Uppsala-Sweden_team Help another iGEM team (Team Uppsala)]<br />
<br />
[[Image:Aq30.jpg|25px]] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K193600 Improve an existing BioBrick Part and enter this information back on the Registry.] We informed iGEM09_Tokyo_Tech that the melA gene DNA sequence was incorrect and they changed it to the correct one.<br />
|}<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Team/MembersTeam:Stockholm/Team/Members2010-10-26T21:26:29Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Team}}<br />
==Team members==<br />
[[image:SU_Team_Icon.gif|400px|center]]<br />
===Students===<br />
{|width="800" border="0"<br />
|width="130"|[[Image:Nina.jpg|100px]]<br />'''Nina Schiller'''<br />[mailto:nina@igem.se nina@igem.se]<br />
|width="5"|&nbsp;<br />
|align="justify"|Hi!<br />
<br />
I am one of the team-members of Team Stockholm, my name is Nina Schiller and I am a master student in molecular biology at Stockholm University. It is the endless possibilities and opportunities in the field of synthetic biology that has caught my attention to put together our iGEM team: Team Stockholm. To me, this field of research and iGEM competition drives science researchers and students to gain better insight and take advantage of the diverse and powerful characters of living organisms. This summer, I will together with my team mates work our hardest to combine biology, chemistry and engineering in order to understand, harness and imitate the complex phenomena of biological life and finally build innovative and useful biological systems.<br />
<br />
My goal with iGEM is to challenge myself to think “out of the box” and seek for ways to put together bits and pieces in science in order to design organisms that would prove useful in the obstacles in modern life. I look forward to build up my science knowledge and laboratory experience. Of course, with a great idea in our luggage, both my and the whole teams goal is to win the iGEM competition! <br />
|}<br />
<br /><br />
<br />
{|width="800" border="0"<br />
|width="130"|[[Image:2.jpg|100px]]<br />'''Andreas Constantinou'''<br />andreas (at) igem.se<br />
|width="5"|&nbsp;<br />
|align="justify"|I first came in contact with synthetic biology in 2008, when I heard about attempts to create a petroleum-producing bacterium to be used as an alternative energy source. Immediately fascinated by this idea and the synthetic biology concept and methodology, my aim has been to study this interesting field ever since. This has now led to the founding of a Stockholm-based team in the 2010 iGEM competition.<br />
<br />
What fascinates me most about synthetic biology is that it links biology and engineering together. With a great interest in both, I see iGEM as a unique opportunity for me to combine my creativity and knowledge in molecular biology to design and build a biological machine that can be used in every-day life.<br />
<br />
With a revolutionary idea, dedicated and hard-working team-members and a large portion of self-confidence, Team Stockholm is ready to fight for the 2010 iGEM Gold Medal!<br />
<br />
See you at the jamboree at MIT in November!<br />
|}<br />
<br /> <br />
<br />
{|width="800" border="0"<br />
|width="130"|[[Image:J.jpg|100px]]<br />'''Johan Nordholm'''<br />[mailto:johan@igem.se johan@igem.se] <br />
|width="5"|&nbsp;<br />
|align="justify"|Greetings!<br />
<br />
Synthetic biology is all about putting engineering into biology. And I think there is a small engineer hidden in each and every one of us. As with the ever-increasing understanding of how the building blocks of the cell function and are put together, so is our capacity to redesign the building blocks and the way they are put together. This has immense potential, I guarantee it can change our society as much as the computer industry has the last decades. This summer, I will do my best to apply existing biological knowledge to hopefully solve a scientific problem, if even a very small one. I am currently in my third and last year in the bachelor program of molecular biology at Stockholm University. As I have not yet undergone any research traineeship or degree project, my time spent in the lab is limited. I therefore find this project as a tremendous opportunity to change that. What makes this even more fun is that my teammates are some of my best friends.<br />
|}<br />
<br /><br />
<br />
{|width="800" border="0"<br />
|width="130"|[[Image:Mim.jpg|100px]]<br />'''Emmelie Lidh''' <br />
|width="5"|&nbsp;<br />
|align="justify"|Hi!<br />
<br />
My name is Mimmi, right now I’m finishing my bachelor in molecular biology. <br />
<br />
I have always been fascinated by the origin of life. By how the genetic code can produce so many different life forms and make the organisms adapt to so many different niches and environments. Now, this competition is about using different traits nature invented and put them together to create new useful functions in an organism. I think this is an amazing way to study and learn more about the complex network of genes and at the same time produce a helpful organism.<br />
|}<br />
<br /><br />
<br />
{|width="800" border="0"<br />
|width="130"|[[Image:Hassan.jpg|100px]]<br />'''Hassan Foroughi Asl'''<br />hassanfa (at) kth.se<br />
|width="5"|&nbsp;<br />
|align="justify"|Hi,<br />
<br />
I'm a Masters student in Computational and Systems Biology at Royal Institute of Technology (KTH) and a member of the Stockholm University team for iGEM competition. My first contact with iGEM and synthetic biology wasn't so long time ago. I got introduced to iGEM competitions in 2009. Then Synthetic biology attracted my attention and it became more interesting to me when I started to study about biological circuits and how these circuits are chosen by evolution. Here I will offer all my knowledge and effort to bring our ideas and plans into reality and solve the problem with a great success.<br />
|}<br />
<br /><br />
<br />
===Mentors===<br />
[[Image:Eli.jpg|100px]]<br/ ><br />
'''Prof. Elisabeth Hagg&aring;rd'''<br /><br />
Department of Genetics, Microbiology and Toxicology, Stockholm University<br />
<br />
<br /><br />
<br />
[[Image:gunnar_pic1.png|100px]]<br><br />
'''Prof. Gunnar von Heijne'''<br /><br />
Department of Biochemistry and Biophysics, Stockholm University<br />
<br />
<br /><br />
<br />
[[Image:Rob_Pick.jpg|100px]]<br /><br />
'''Assistant Prof. Robert Daniels'''<br /><br />
Department of Biochemistry and Biophysics, Stockholm University<br />
<br />
<br />
----<br />
<br />
<br />
'''Co-advisors at Stockholm University:''' Prof. Lars Wieslander, Prof. Marie &Ouml;hman, Prof. Neus Visa and Prof. Roger Karlsson.<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinouhttp://2010.igem.org/Team:Stockholm/Project_Idea/Future_applicationsTeam:Stockholm/Project Idea/Future applications2010-10-26T20:51:45Z<p>AndreasConstantinou: </p>
<hr />
<div>{{Stockholm/Project_Idea}}<br />
{|<br />
|width="195"|200px image goes here<br />
|width="10"|&nbsp;<br />
|width="590"|<br />
==Future applications==<br />
Text goes here.<br />
|}<br />
<br />
{{Stockholm/Footer}}</div>AndreasConstantinou