<p>For more information on this part, please consult the 2021 TAU Israel wiki results page found <a href = "https://2021.igem.org/Team:TAU_Israel/Results" style="padding-right: 0px;">here.</a> Information about experimental procedures can be found <a href = "https://2021.igem.org/Team:TAU_Israel/Notebook" style="padding-right: 0px;">here</a> and <a href = "https://2021.igem.org/Team:TAU_Israel/Proof_Of_Concept" style="padding-right: 0px;">here.</a></p>
<p>For more information on this part, please consult the 2021 TAU Israel wiki results page found <a href = "https://2021.igem.org/Team:TAU_Israel/Results" style="padding-right: 0px;">here.</a> Information about experimental procedures can be found <a href = "https://2021.igem.org/Team:TAU_Israel/Notebook" style="padding-right: 0px;">here</a> and <a href = "https://2021.igem.org/Team:TAU_Israel/Proof_Of_Concept" style="padding-right: 0px;">here.</a></p>
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<h3>Typical Decoding Rate (TDR) [8]:</h3>
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<center><img src="https://2021.igem.org/wiki/images/6/60/T--TAU_Israel--fig37_model.jpeg" style="max-width: 105%;"><br><span><b>Figure 3.7:</b> TDR scores of E. Coli genes vs. their expression levels</span></center><br>
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</div><p>This measurement is based on ribosome profiling data (Ribo-Seq), which provides a snapshot of a mid-translation ribosomal position on the mRNA molecules in a cell during certain conditions. </p>
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<p>*This index is relatively complicated because the Ribo-Seq data is hard to produce and very noisy. Additionally, the sequences optimized according to this index underperformed in the POC experiment, thus we decided not to add this optimization to our final software.</p>
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<p id="read_more_4">Read more about TDR <b>here.</b></p>
<li> The Ribo-Seq reads are mapped to the CDS of the proteome</li>
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<li><span style="text-decoration: underline;">Normalization </span>- The amount of reads per gene is normalized in order to neutralize bias originated in one codon being present in more highly expressed genes. The normalization is given by:<br>
<p>Where <em>NFC<sub>i</sub></em> is the normalized read count of the i-th codon, <em>RC<sub>i</sub></em> is the read count of the i-th codon, and L is the number of codons that compose the gene . </p></li>
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<li><span style="text-decoration: underline;">Merging read information</span> - The normalized number of reads mapped to each codon is collected from all mRNAs mapped, and a histogram is constructed from them.</li>
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<li><span style="text-decoration: underline;">Estimation of the distribution for each codon</span> - An exponentially modified gaussian distribution (EMG) [9] is fit to the constructed curve, and the gaussian mean is extracted as the score of that codon.</li>
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<li><span style="text-decoration: underline;">Calculating the MTDR score of the gene</span> - calculate geometric mean of the typical decoding time of each codon of the gene:<br>
<p>Where <em>MTDR<sub>seq</sub></em> is the mean translation time of the gene, iis the typical decoding time of the i-th codon, and <em>L</em> is the number of codons that compose the gene. </p></li>
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Latest revision as of 02:19, 22 October 2021
Description
mCherry is a red fluorescent protein used as a reporter derived from the
fluorophore DsRed, which was originally isolated from
Discosoma sea anemones. It is commonly used due to its colour and
photostability compared to other monomeric fluorophores.
This part is a variant of mCherry, the sequence of which was modified to
optimize its expression in Bacillus subtilis against E. coli using the
Communique tool developed
by the 2021 TAU Israel team. This specific variant was optimized based on
codon usage bias in highly expressed genes in B. subtilis. You may
read more about the optimization model
here.
For more information on this part, please consult the 2021 TAU Israel wiki results page found here. Information about experimental procedures can be found here and here.
