Difference between revisions of "Team:Marburg/Improve"

Line 93: Line 93:
 
     <section class="section">
 
     <section class="section">
 
       <article>
 
       <article>
         <p style="text-align: justify; margin-bottom: 1em;">
+
         <div>
           Every Synbio Experiment is more or less based on the same principle: You change a system in some way and you
+
           <figure style="float:right; margin-left: 25px;">
          look at the outcome. This readout is one of the most important things in all natural science, a wrong readout
+
            <img style="height: 500px; width: 750px;"
          can easily flaw your whole experiment or can lead to serious misconclusion.
+
              src="https://static.igem.org/mediawiki/2019/4/4f/T--Marburg--Measurement-TeLUC%2BNanoluc.png"
        </p>
+
              alt="Comparison of Nanoluc, TeLuc luminescence spectra">
        <p style="text-align: justify; margin-bottom: 1em;">
+
            <figcaption style="max-width: 550px; text-align: center">
          The most common way to measure localisation, interaction or even the intensity of genetic elements is via
+
              Fig.1 - Comparison of NanoLuc and teLuc Luminescence Spectra in comparison with Synechococcus elongatus
          Fluorescence as readout. Fluorescence Proteins (FP), started with the green fluorescent protein, are based on
+
              UTEX
          the ability of a chromophore to absorb photons of specific wavelength and emit this photon at another. Even on
+
              2973 Absorption spectra.
          the iGEM registry, the characterization via FPs is the suggested way to characterise a part. This Method is
+
            </figcaption>
          prone to Background noise, depends on the folding of the Protein at the specific cell conditions and
+
          </figure>
          furthermore the chromophore can even bleach after to much exposure, so the drawbacks are obvious.
+
        </p>
+
        <p style="text-align: justify; margin-bottom: 1em;">
+
          Bioluminescence could make the desired difference, but the original Luciferase Assays either consistent of an
+
          whole Operon systems, or put an unnecessary high metabolic burden through ATP dependency and/or trough its
+
          relatively large size (Firefly-Luciferase 61,5 kDa). Together with the low quantity, which can be several
+
          orders of magnitude lower than a fluorescence based system, the common breakthrough of Lumincese in Synthetic
+
          biology is still missing.
+
        </p>
+
        <p style="text-align: justify; margin-bottom: 1em;">
+
          Newly developed small ATP independent Lucferase Proteins, are interesting candidates to bypass these Problems.
+
          Nanoluc, with its 19 kDa and up to 150 fold increase in brightness compared to the Firefly-Luciferase is
+
          handled as an suitable alternative. This Protein use the patented Substrate Furimazine, and emits Photons at
+
          460 nm. Nanoluc has been successfully implemented in Promoter testing and as an alternative in Interaction
+
          messurement via Bilumiecnce Resonace energy transfer, but sadly only few team ever used this system.
+
        </p>
+
        <figure style="float:right; margin-left: 25px;">
+
          <img style="height: 500px; width: 700px;"
+
            src="https://static.igem.org/mediawiki/2019/4/4f/T--Marburg--Measurement-TeLUC%2BNanoluc.png"
+
            alt="Comparison of Nanoluc, TeLuc luminescence spectra">
+
          <figcaption style="max-width: 550px; text-align: center">
+
            Fig.1 - Comparison of NanoLuc and teLuc Luminescence Spectra in comparison with Synechococcus elongatus UTEX
+
            2973 Absorption spectra.
+
          </figcaption>
+
        </figure>
+
        <p style="text-align: justify; margin-bottom: 1em;">
+
          One scratch on the surface of Nanoluc is for sure the restriction of the wavelength. While for Measurements
+
          in
+
          many organisms and Tissues, this looming Problem did not occur, it's becoming obvious, when looking into
+
          phototrophic Organisms and deep-tissue mammalian cells. As the keen reader might guess, cells absorb Light
+
          of
+
          the wavelength under 600 nm to a great extent and even more if they have a photosystem. Chlorophyll a have
+
          one
+
          their two peaks at 440 nm [fig.1]. If one would compare that with the nanoluc spectra, a devastating
+
          conclusion could be made: The Photosystem will absorb photons from the Signal, leading to weaker peaks, and
+
          maybe more grave/frightening/alarming, a dependency of Signal on the chlorophyll content. Althroug
+
          localisation experiments should´t be affected that much, Measurement and characterisation, the foundation of
+
          which synthetic Biology is build on, could be shaken.
+
        </p>
+
        <p style="text-align: justify; margin-bottom: 1em;">
+
          Driven by this problem, we dig ourselves in <a style="padding: 0"
+
            href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678970/">literature</a> and found a solution: A
+
          mutated
+
          Version of nanoLuc, so called <a style="padding: 0" href="http://parts.igem.org/Part:BBa_K3228042">teLuc</a>
+
          which has a
+
          severe red shifted pattern with a peak at 502 nm (Figure 2). What is even more serviere is the astonishing
+
          brightness, wich even surpass nanoluc by several folds (5,7) in vitro. In vivo this effect is even more
+
          dramatic, through its ability to bypass the absorption of Light. We expect this ability of teLuc to surpass
+
          the limits of Luminescence in plants to an amazing extent, and allow the plant synthetic biology community
+
          to
+
          accelerate their research.
+
  
           TeLuc differs from its deep-sea origin ortholog only in 3 Amino Acid changes in Substrate Binding pocket
+
           <p style="text-align: justify; margin-bottom: 1em;">
           (D19S/D85N/C164H), which basically allows Diphenylterazine (DTZ) to prominently bind. This improved and
+
            Every Synbio Experiment is more or less based on the same principle: You change a system in some way and you
           better part could catalyse a whole new and bright era of characterisation of Synthetic biology.
+
            look at the outcome. This readout is one of the most important things in all natural science, a wrong
        </p>
+
            readout
        <p style="text-align: justify; margin-bottom: 1em;">
+
            can easily flaw your whole experiment or can lead to serious misconclusion.
          To demonstrate the redshift, transformed both <a style="padding: 0"
+
           </p>
             href="http://parts.igem.org/Part:BBa_K1159001">NanoLuc</a>and TeLuc under the Promoter 2_05 in e.coli.
+
          <p style="text-align: justify; margin-bottom: 1em;">
          This rather weak Promoter were chosen to showcase the ability of Luminescence to measure weak genetic
+
            The most common way to measure localisation, interaction or even the intensity of genetic elements is via
          elements. Both cells were grown to an OD600 of 0,8. After that a 1:100 dilution were used for the
+
            Fluorescence as readout. Fluorescence Proteins (FP), started with the green fluorescent protein, are based
          Measurements of the Luminescence spectra. The Results are summarized in Figure 2.
+
            on
        </p>
+
            the ability of a chromophore to absorb photons of specific wavelength and emit this photon at another. Even
        <figure style="float:right; margin-left: 25px;">
+
            on
          <img style="height: 500px; width: 700px;"
+
            the iGEM registry, the characterization via FPs is the suggested way to characterise a part. This Method is
            src="https://static.igem.org/mediawiki/2019/8/82/T--Marburg--TeLucandNanoLuc%2BUTEXSpectra.png"
+
            prone to Background noise, depends on the folding of the Protein at the specific cell conditions and
            alt="TeLuc and NanoLuc measurement in E.coli">
+
            furthermore the chromophore can even bleach after to much exposure, so the drawbacks are obvious.
          <figcaption style="max-width: 550px; text-align: center">
+
           </p>
            Fig.2 - Normalized Luminescence measurements of TeLuc and NanoLuc over their full spectra in e.coli.
+
          <p style="text-align: justify; margin-bottom: 1em;">
          </figcaption>
+
            Bioluminescence could make the desired difference, but the original Luciferase Assays either consistent of
        </figure>
+
            an
        <p style="text-align: justify; margin-bottom: 1em;">
+
            whole Operon systems, or put an unnecessary high metabolic burden through ATP dependency and/or trough its
           We successfully showed the redshift of teluc in comparison to nanoLuc. This could will lead to a further
+
            relatively large size (Firefly-Luciferase 61,5 kDa). Together with the low quantity, which can be several
          ~7 fold increase of Lumience in Cyanobacteria or plants.
+
            orders of magnitude lower than a fluorescence based system, the common breakthrough of Lumincese in
          Buy using our improve BioBrick for Luminescence Measurement, accurate and precise data can be obtained in
+
            Synthetic
          phototrophic Organism.
+
            biology is still missing.
        </p>
+
          </p>
 +
          <p style="text-align: justify; margin-bottom: 1em;">
 +
            Newly developed small ATP independent Lucferase Proteins, are interesting candidates to bypass these
 +
            Problems.
 +
            Nanoluc, with its 19 kDa and up to 150 fold increase in brightness compared to the Firefly-Luciferase is
 +
            handled as an suitable alternative. This Protein use the patented Substrate Furimazine, and emits Photons at
 +
             460 nm. Nanoluc has been successfully implemented in Promoter testing and as an alternative in Interaction
 +
            messurement via Bilumiecnce Resonace energy transfer, but sadly only few team ever used this system.
 +
          </p>
 +
 
 +
          <p style="text-align: justify; margin-bottom: 1em;">
 +
            One scratch on the surface of Nanoluc is for sure the restriction of the wavelength. While for Measurements
 +
            in
 +
            many organisms and Tissues, this looming Problem did not occur, it's becoming obvious, when looking into
 +
            phototrophic Organisms and deep-tissue mammalian cells. As the keen reader might guess, cells absorb Light
 +
            of
 +
            the wavelength under 600 nm to a great extent and even more if they have a photosystem. Chlorophyll a have
 +
            one
 +
            their two peaks at 440 nm [fig.1]. If one would compare that with the nanoluc spectra, a devastating
 +
            conclusion could be made: The Photosystem will absorb photons from the Signal, leading to weaker peaks, and
 +
            maybe more grave/frightening/alarming, a dependency of Signal on the chlorophyll content. Althroug
 +
            localisation experiments should´t be affected that much, Measurement and characterisation, the foundation of
 +
            which synthetic Biology is build on, could be shaken.
 +
          </p>
 +
          <figure style="float:right; margin-left: 25px;">
 +
            <img style="height: 500px; width: 750px;"
 +
              src="https://static.igem.org/mediawiki/2019/8/82/T--Marburg--TeLucandNanoLuc%2BUTEXSpectra.png"
 +
              alt="TeLuc and NanoLuc measurement in E.coli">
 +
            <figcaption style="max-width: 550px; text-align: center">
 +
              Fig.2 - Normalized Luminescence measurements of TeLuc and NanoLuc over their full spectra in e.coli.
 +
            </figcaption>
 +
          </figure>
 +
          <p style="text-align: justify; margin-bottom: 1em;">
 +
            Driven by this problem, we dig ourselves in <a style="padding: 0"
 +
              href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678970/">literature</a> and found a solution: A
 +
            mutated
 +
            Version of nanoLuc, so called <a style="padding: 0" href="http://parts.igem.org/Part:BBa_K3228042">teLuc</a>
 +
            which has a
 +
            severe red shifted pattern with a peak at 502 nm (Figure 2). What is even more serviere is the astonishing
 +
            brightness, wich even surpass nanoluc by several folds (5,7) in vitro. In vivo this effect is even more
 +
            dramatic, through its ability to bypass the absorption of Light. We expect this ability of teLuc to surpass
 +
            the limits of Luminescence in plants to an amazing extent, and allow the plant synthetic biology community
 +
            to
 +
            accelerate their research.
 +
 
 +
            TeLuc differs from its deep-sea origin ortholog only in 3 Amino Acid changes in Substrate Binding pocket
 +
            (D19S/D85N/C164H), which basically allows Diphenylterazine (DTZ) to prominently bind. This improved and
 +
            better part could catalyse a whole new and bright era of characterisation of Synthetic biology.
 +
           </p>
 +
          <p style="text-align: justify; margin-bottom: 1em;">
 +
            To demonstrate the redshift, transformed both <a style="padding: 0"
 +
              href="http://parts.igem.org/Part:BBa_K1159001">NanoLuc</a>and TeLuc under the Promoter 2_05 in e.coli.
 +
            This rather weak Promoter were chosen to showcase the ability of Luminescence to measure weak genetic
 +
            elements. Both cells were grown to an OD600 of 0,8. After that a 1:100 dilution were used for the
 +
            Measurements of the Luminescence spectra. The Results are summarized in Figure 2.
 +
          </p>
 +
 
 +
          <p style="text-align: justify; margin-bottom: 1em;">
 +
            We successfully showed the redshift of teluc in comparison to nanoLuc. This could will lead to a further
 +
            ~7 fold increase of Lumience in Cyanobacteria or plants.
 +
            Buy using our improve BioBrick for Luminescence Measurement, accurate and precise data can be obtained in
 +
            phototrophic Organism.
 +
          </p>
 +
        </div>
 
       </article>
 
       </article>
 
     </section>
 
     </section>

Revision as of 02:10, 22 October 2019

P A R T S


Improve

Comparison of Nanoluc, TeLuc luminescence spectra
Fig.1 - Comparison of NanoLuc and teLuc Luminescence Spectra in comparison with Synechococcus elongatus UTEX 2973 Absorption spectra.

Every Synbio Experiment is more or less based on the same principle: You change a system in some way and you look at the outcome. This readout is one of the most important things in all natural science, a wrong readout can easily flaw your whole experiment or can lead to serious misconclusion.

The most common way to measure localisation, interaction or even the intensity of genetic elements is via Fluorescence as readout. Fluorescence Proteins (FP), started with the green fluorescent protein, are based on the ability of a chromophore to absorb photons of specific wavelength and emit this photon at another. Even on the iGEM registry, the characterization via FPs is the suggested way to characterise a part. This Method is prone to Background noise, depends on the folding of the Protein at the specific cell conditions and furthermore the chromophore can even bleach after to much exposure, so the drawbacks are obvious.

Bioluminescence could make the desired difference, but the original Luciferase Assays either consistent of an whole Operon systems, or put an unnecessary high metabolic burden through ATP dependency and/or trough its relatively large size (Firefly-Luciferase 61,5 kDa). Together with the low quantity, which can be several orders of magnitude lower than a fluorescence based system, the common breakthrough of Lumincese in Synthetic biology is still missing.

Newly developed small ATP independent Lucferase Proteins, are interesting candidates to bypass these Problems. Nanoluc, with its 19 kDa and up to 150 fold increase in brightness compared to the Firefly-Luciferase is handled as an suitable alternative. This Protein use the patented Substrate Furimazine, and emits Photons at 460 nm. Nanoluc has been successfully implemented in Promoter testing and as an alternative in Interaction messurement via Bilumiecnce Resonace energy transfer, but sadly only few team ever used this system.

One scratch on the surface of Nanoluc is for sure the restriction of the wavelength. While for Measurements in many organisms and Tissues, this looming Problem did not occur, it's becoming obvious, when looking into phototrophic Organisms and deep-tissue mammalian cells. As the keen reader might guess, cells absorb Light of the wavelength under 600 nm to a great extent and even more if they have a photosystem. Chlorophyll a have one their two peaks at 440 nm [fig.1]. If one would compare that with the nanoluc spectra, a devastating conclusion could be made: The Photosystem will absorb photons from the Signal, leading to weaker peaks, and maybe more grave/frightening/alarming, a dependency of Signal on the chlorophyll content. Althroug localisation experiments should´t be affected that much, Measurement and characterisation, the foundation of which synthetic Biology is build on, could be shaken.

TeLuc and NanoLuc measurement in E.coli
Fig.2 - Normalized Luminescence measurements of TeLuc and NanoLuc over their full spectra in e.coli.

Driven by this problem, we dig ourselves in literature and found a solution: A mutated Version of nanoLuc, so called teLuc which has a severe red shifted pattern with a peak at 502 nm (Figure 2). What is even more serviere is the astonishing brightness, wich even surpass nanoluc by several folds (5,7) in vitro. In vivo this effect is even more dramatic, through its ability to bypass the absorption of Light. We expect this ability of teLuc to surpass the limits of Luminescence in plants to an amazing extent, and allow the plant synthetic biology community to accelerate their research. TeLuc differs from its deep-sea origin ortholog only in 3 Amino Acid changes in Substrate Binding pocket (D19S/D85N/C164H), which basically allows Diphenylterazine (DTZ) to prominently bind. This improved and better part could catalyse a whole new and bright era of characterisation of Synthetic biology.

To demonstrate the redshift, transformed both NanoLucand TeLuc under the Promoter 2_05 in e.coli. This rather weak Promoter were chosen to showcase the ability of Luminescence to measure weak genetic elements. Both cells were grown to an OD600 of 0,8. After that a 1:100 dilution were used for the Measurements of the Luminescence spectra. The Results are summarized in Figure 2.

We successfully showed the redshift of teluc in comparison to nanoLuc. This could will lead to a further ~7 fold increase of Lumience in Cyanobacteria or plants. Buy using our improve BioBrick for Luminescence Measurement, accurate and precise data can be obtained in phototrophic Organism.