Difference between revisions of "Team:Jilin China/Basic Part"

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      <h2>Editing Alert!</h2>
 
  
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      <p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
 
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      <h3>Basic Parts</h3>
 
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      <p>A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
 
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      <p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
 
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      <h3>Note</h3>
 
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      <p>This page should list all the basic parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page. Remember judges will only look at the first part in the list for the Best Basic Part award, so put your best part first!</p>
 
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      <h3>Best Basic Part Special Prize</h3>
 
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      <p> To be eligible for this award, this part must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts. If you have a part you wish to nominate your team for this <a href="https://2018.igem.org/Judging/Awards">special prize</a>, make sure you add your part number to your <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.
 
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<b>Please note:</b> Judges will only look at the first part number you list, so please only enter ONE (1) part number in the judging form for this prize. </p>
 
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       <h2>Abstract</h2>
 
       <h2>Abstract</h2>
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        <p>This year, Jilin_China added 91 basic parts to the registry, including heat-inducible RNA thermosensors, heat-repressible RNA thermosensors, cold-inducible RNA thermosensors, cold-repressible RNA thermosensors and two different sfGFP. We have characterized and measured all of these parts, calculated their melting temperatures by using mathematical modeling, and built a synRT toolkit that allows users to select the appropriate RNA thermosensors in artificial biological systems.</p>
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        <p>Our team's favorite basic part is the codon-optimized sfGFP (BBa_K2541400) and will be introduced in detail below:</p>
 
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       <h2>Parts</h2>
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       <h2>sfGFP_optimism (BBa_K2541400)</h2>
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      <table>emmm...</table>
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        <p>sfGFP (superfolder GFP), which emission and excitation wavelength are similar to GFP, but its fluorescence intensity and folding speed are higher than GFP. Because of its advantages, our measurement device used sfGFP as the reporter protein.
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However, since we use Goldengate assembly this year, the existing sfGFP (BBa_I746916) in the registry contains a BbsI endonuclease cutting site. We designed a site-directed mutation of sfGFP (BBa_K2541401), made a double-base mutation to the BbsI recognition site without changing its amino acid sequence. BBa_K2541401 is completely suitable for Goldengate assembly, so we also call it sfGFP for Goldengate.</p>
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        <p>There's still one problem that we cannot predict the effect of the sfGFP after mutation. In addition, we found a codon optimized sfGFP for prokaryote, and called it sfGFP_optimism. Then we designed a composite part, which contains J23103, B0034 and sfGFP_optimism, and did experiment to compare it with sfGFP and sfGFP for goldengate. As the result shows, the sfGFP_optimism has higher fluorescence intensity than others, so we finally chose sfGFP_optimism as our reporter gene.</p>
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        <center><a href="2018.igem.org">You can see the experiment results in the improvement page. Click Here!</a></center>
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        <p>Since sfGFP has more advantages than GFP, and Goldengate assembly will be used by more researchers as an efficient and scarless assembly method in the future, so we decided to add the sfGFP_optimism to the parts registry.</p>
 
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       <h2>Reference</h2>
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       <h2>RNA thermosensors</h2>
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        <h3>Heat-inducible RNA thermosensors</h3>
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        <h3>Heat-repressible RNA thermosensors</h3>
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        <h3>Cold-inducible RNA thermosensors</h3>
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        <h3>Cold-repressible RNA thermosensors</h3>
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      <h2>Basic parts content</h2>
  
 
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Revision as of 19:55, 8 October 2018

BASIC PART


Basic Part

  • Abstract

    This year, Jilin_China added 91 basic parts to the registry, including heat-inducible RNA thermosensors, heat-repressible RNA thermosensors, cold-inducible RNA thermosensors, cold-repressible RNA thermosensors and two different sfGFP. We have characterized and measured all of these parts, calculated their melting temperatures by using mathematical modeling, and built a synRT toolkit that allows users to select the appropriate RNA thermosensors in artificial biological systems.

    Our team's favorite basic part is the codon-optimized sfGFP (BBa_K2541400) and will be introduced in detail below:

  • sfGFP_optimism (BBa_K2541400)

    sfGFP (superfolder GFP), which emission and excitation wavelength are similar to GFP, but its fluorescence intensity and folding speed are higher than GFP. Because of its advantages, our measurement device used sfGFP as the reporter protein. However, since we use Goldengate assembly this year, the existing sfGFP (BBa_I746916) in the registry contains a BbsI endonuclease cutting site. We designed a site-directed mutation of sfGFP (BBa_K2541401), made a double-base mutation to the BbsI recognition site without changing its amino acid sequence. BBa_K2541401 is completely suitable for Goldengate assembly, so we also call it sfGFP for Goldengate.

    There's still one problem that we cannot predict the effect of the sfGFP after mutation. In addition, we found a codon optimized sfGFP for prokaryote, and called it sfGFP_optimism. Then we designed a composite part, which contains J23103, B0034 and sfGFP_optimism, and did experiment to compare it with sfGFP and sfGFP for goldengate. As the result shows, the sfGFP_optimism has higher fluorescence intensity than others, so we finally chose sfGFP_optimism as our reporter gene.

    You can see the experiment results in the improvement page. Click Here!

    Since sfGFP has more advantages than GFP, and Goldengate assembly will be used by more researchers as an efficient and scarless assembly method in the future, so we decided to add the sfGFP_optimism to the parts registry.

  • RNA thermosensors

    Heat-inducible RNA thermosensors

    Heat-repressible RNA thermosensors

    Cold-inducible RNA thermosensors

    Cold-repressible RNA thermosensors

  • Basic parts content