Difference between revisions of "Team:Bielefeld-CeBiTec/Composite Part"

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                 <div class="title">Composite Parts</div>
 
                 <div class="title">Composite Parts</div>
  
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  <article>For our metal resource recovery system we build lots of new basic biobricks for accumulation and storage of metal ions, toxicity counteractions and nanoparticle formation. In order to find the best expression ratios, we tried different regulator elements, such as promoters, ribosome binding sites and terminators in combination with our genes. Some of our proteins were also fused to other proteins with flexible or rigid linkers connecting them. On this page we list all these composite parts and their components. The siRNA expression and detection system to regulate gene expression consists mainly of composite parts too, as our promoter testing device does.
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  <article>For our metal resource recovery system we build lots of new basic biobricks for accumulation and storage of metal ions, toxicity counteractions and nanoparticle formation. In order to find the best expression ratios, we tried different regulator elements, such as promoters, ribosome binding sites and terminators in combination with our genes. Some of our proteins were also fused to other proteins with flexible or rigid linkers connecting them. On this page we list all these composite parts and their components.Not only our promotor testing device, but also our (LINK) TACE siRNA testing system consists mainly of composite parts. An important part are the target vectors, which transcribe a target mRNA and express a reporter Protein to allow the user to measure and quantify the silencing efficiency of siRNAs. So we constructed two generations of target vectors, with a member of the second generation being our best composite part:<br>
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<b< Best Composite Part – pTale2_B_GS </b><br>
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This Composite Part Our new TACE system consists of an expression vector which transcribes siRNAs, and a target vector which transcribes a target mRNA as well as a reporter protein which enables the user to quantify the silencing ability of a tested siRNA.<br>
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The first generation of target vectors featured a direct fusion of a target sequence to a Reporter Protein (Blue fluorescent Protein BFP or AmilCP). This assures the shortest reaction time possible to the degradation of the target mRNA, as the destruction of the target mRNA also leads to the degradation of the marker proteins mRNA. However this has a problem, as a non-functional reporter protein can lead to false positives. This led to the development of the second generation of vectors. This Generation also features an inverter as well as additional control mechanisms. The vector is shown in Figure 1:<br>
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<figure role="group">
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                      <img class="figure hundred" src="https://static.igem.org/mediawiki/2018/1/10/T--Bielefeld-CeBiTec--ALE-pTale2_B_GS_V1_for_Best_composite_Part.png">
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                      <figcaption>
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                          <b>Figure 2:</b> Illustration of Biobrick <a href="http://parts.igem.org/Part:BBa_K2638702">BBa_K2638702</a>, an expression Vector for siRNAs. The Biobrick includes a Golden Gate cassette which can be cut out using the BbsI restriction enzyme to seamlessly fuse an siRNA to the Hfq binding Sequence inside the expression Vector.
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                      </figcaption>
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                  </figure>
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                   </article>
 
                   </article>
  

Revision as of 03:11, 18 October 2018

Composite Parts
For our metal resource recovery system we build lots of new basic biobricks for accumulation and storage of metal ions, toxicity counteractions and nanoparticle formation. In order to find the best expression ratios, we tried different regulator elements, such as promoters, ribosome binding sites and terminators in combination with our genes. Some of our proteins were also fused to other proteins with flexible or rigid linkers connecting them. On this page we list all these composite parts and their components.Not only our promotor testing device, but also our (LINK) TACE siRNA testing system consists mainly of composite parts. An important part are the target vectors, which transcribe a target mRNA and express a reporter Protein to allow the user to measure and quantify the silencing efficiency of siRNAs. So we constructed two generations of target vectors, with a member of the second generation being our best composite part:

This Composite Part Our new TACE system consists of an expression vector which transcribes siRNAs, and a target vector which transcribes a target mRNA as well as a reporter protein which enables the user to quantify the silencing ability of a tested siRNA.
The first generation of target vectors featured a direct fusion of a target sequence to a Reporter Protein (Blue fluorescent Protein BFP or AmilCP). This assures the shortest reaction time possible to the degradation of the target mRNA, as the destruction of the target mRNA also leads to the degradation of the marker proteins mRNA. However this has a problem, as a non-functional reporter protein can lead to false positives. This led to the development of the second generation of vectors. This Generation also features an inverter as well as additional control mechanisms. The vector is shown in Figure 1:
Figure 2: Illustration of Biobrick BBa_K2638702, an expression Vector for siRNAs. The Biobrick includes a Golden Gate cassette which can be cut out using the BbsI restriction enzyme to seamlessly fuse an siRNA to the Hfq binding Sequence inside the expression Vector.
Table 1: All composite Parts submitted by iGEM Bielefeld 2018.
Identifier Components Description Designer Length
BBa_K2638003 BBa_K525998, BBa_K2638001 T7 + RBS + CopC Erika Schneider 425
BBa_K2638004 BBa_K525998, BBa_K2638002 T7 + RBS + CopD Erika Schneider 950
BBa_K2638005 BBa_I0500, BBa_B0030, BBa_K2638001 T7 + RBS + CopC Erika Schneider XXX
BBa_K2638006 BBa_I0500, BBa_B0030, BBa_K2638002 T7 + RBS + CopD Erika Schneider XXX
BBa_K2638109 BBa_R0040, BBa_K1460002 PTetR + CRS5 Johannes Ruhnau 1032
BBa_K2638110 BBa_J61101, BBa_K2638103, BBa_J61101, BBa_K2638150 PTetR + gshA + gshB + Phyto Johannes Ruhnau 2450
BBa_K2638112 BBa_I0500, BBa_B0034, BBa_K2638121, BBa_B0034, BBa_K2638103, BBa_B0034, BBa_K2638120 PTetR + gshA + gshB + GSR Johannes Ruhnau 4144
BBa_K2638113 BBa_I0500, BBa_B0034, BBa_K2638100 PTetR + ahpC + ahpF Vanessa Krämer 1800
BBa_K2638114 BBa_R0040, BBa_K554003, BBa_K1104200 PTetR + SoxR + RBS + OxyR Johannes Ruhnau 1489
BBa_K2638117 BBa_R0040, BBa_J61101, BBa_K2638106 PTetR + RBS + sodA + KatE Johannes Ruhnau 701
BBa_K2638118 BBa_R0040, BBa_J61101, BBa_K2638106, BBa_J61101, BBa_K2638105 PTetR + RBS + sodA + KatG Johannes Ruhnau 2989
BBa_K2638201 BBa_K525998, BBa_K2638200 OprC (TonB dependent copper transport porin, BBa_K2638200) with T7 promotor and RBS (BBa_K525998) Jakob Zubek 2165
BBa_K2638204 BBa_I0500, BBa_B0030, BBa_K2638200 OprC (TonB dependent copper transport porin, BBa_K2638200) with T7 promotor and RBS (BBa_K525998) Jakob Zubek 2165
BBa_K2638400 BBa_K2638500 Combination of BBa_K2638500 + BBa_K2638560 Levin Joe Klages 889
BBa_K2638401 BBa_K2638502, BBa_K2638426 13 Levin Joe Klages 889
BBa_K2638402 BBa_K2638503, BBa_K2638426 14 Levin Joe Klages 889
BBa_K2638403 BBa_K2638504, BBa_K2638426 15 Levin Joe Klages 889
BBa_K2638404 BBa_K2638506, BBa_K2638426 17 Levin Joe Klages 889
BBa_K2638405 BBa_K2638507, BBa_K2638426 18 Levin Joe Klages 889
BBa_K2638406 BBa_K2638509, BBa_K2638426 110 Levin Joe Klages 889
BBa_K2638407 BBa_K2638510, BBa_K2638426 111 Levin Joe Klages 889
BBa_K2638408 BBa_K2638511, BBa_K2638426 112 Levin Joe Klages 889
BBa_K2638409 BBa_K2638517, BBa_K2638426 118 Levin Joe Klages 903
BBa_K2638410 BBa_K2638520, BBa_K2638426 21 Levin Joe Klages 890
BBa_K2638411 BBa_K26358522, BBa_K2638426 23 Levin Joe Klages 890
BBa_K2638412 BBa_K2638525, BBa_K2638426 26 Levin Joe Klages 890
BBa_K2638413 BBa_K2638526, BBa_K2638426 27 Levin Joe Klages 890
BBa_K2638414 BBa_K2638528, BBa_K2638426 29 Levin Joe Klages 890
BBa_K2638415 BBa_K2638531, BBa_K2638426 212 Levin Joe Klages 890
BBa_K2638416 BBa_K2638532, BBa_K2638426 213 Levin Joe Klages 889
BBa_K2638417 BBa_K2638534, BBa_K2638426 215 Levin Joe Klages 900
BBa_K2638418 BBa_K2638537, BBa_K2638426 218 Levin Joe Klages 904
BBa_K2638419 BBa_K2638542, BBa_K2638426 33 Levin Joe Klages 889
BBa_K2638420 BBa_K2638545, BBa_K2638426 36 Levin Joe Klages 889
BBa_K2638421 BBa_K2638548, BBa_K2638426 39 Levin Joe Klages 889
BBa_K2638422 BBa_K2638551, BBa2638426 312 Levin Joe Klages 889
BBa_K2638423 BBa_K2638554, BBa_K2638426 315 Levin Joe Klages 899
BBa_K2638424 BBa_K26358556, BBa_2638426 317 Levin Joe Klages 909
BBa_K2638425 BBa_K2638557, BBa_K2638426 318 Levin Joe Klages 903
BBa_K2638703 BBa_K2638716, BBa_B0010, BBa_B0012, BBa_R0010, BBa_B0032, BBa_K592100 siRNA Target Vector 2 with BFP and GGGGS Linker Antonin Lenzen 2787
BBa_K2638704 BBa_K2638717, BBa_B0010, BBa_B0012, BBa_R0010, BBa_B0032, BBa_K592100 siRNA Target Vector 2 with BFP and GGGGS Linker Antonin Lenzen 2787
BBa_K2638705 BBa_K2638718, BBa_B0010, BBa_B0012, BBa_R0010, BBa_B0032, BBa_K592100 siRNA Target Vector 2 with BFP and cMyc Linker Antonin Lenzen 2787
BBa_K2638706 BBa_K2638719, BBa_B0010, BBa_B0012, BBa_R0010, BBa_B0032, BBa_K592100 siRNA Target Vector 2 with BFP and XP Linker Antonin Lenzen 2787
BBa_K2638991 araBAD and RBS and Mutated Human Ferritin Heavy Chain (without Stop) Vanessa Krämer 1210
BBa_K2638997 araBAD and RBS and Human Ferritin Heavy Chain Vanessa Krämer 552
BBa_K2638998 araBAD and RBS and Mutated Human Ferritin Heavy Chain Vanessa Krämer