Difference between revisions of "Team:IIT-Madras/Description"
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The first thing that is required for any synthetic biology experiments are fluorescent reporter proteins. We wished to codon optimize GFP and mCherry for A. baylyi. However, when we asked the companies to codon optimize the fluoroscent proteins, the problem with companies was they did not have the codon bias table for <em>A. baylyi</em>.<br><br> | The first thing that is required for any synthetic biology experiments are fluorescent reporter proteins. We wished to codon optimize GFP and mCherry for A. baylyi. However, when we asked the companies to codon optimize the fluoroscent proteins, the problem with companies was they did not have the codon bias table for <em>A. baylyi</em>.<br><br> | ||
| − | <strong>Solution 1:</strong> We made a free use online tool called CUTE (codon usage table enumerator) that can generate Codon usage table by taking into consideration the protein coding annotation. This tool can be used for any other organism whose Genome has been sequences and protein coding regions are annotated. Cute can be found on the <a href="https://cute.chassidex.org" target="_blank">CUTE ChassiDex.</a><br>We generated the codon usage table as the protein annotation of <em>A. baylyi</em> is available on <a href="https://ncbi.nlm.nih.gov" target="_blank">NCBI</a>website. Using this table, we generated the codon usage table for <em>A. baylyi</em> which can be found on.<br>Using this codon table, we codon optimized reporter proteins and its characterization can be found here. <br><br> | + | <strong>Solution 1:</strong> We made a free use online tool called CUTE (codon usage table enumerator) that can generate Codon usage table by taking into consideration the protein coding annotation. This tool can be used for any other organism whose Genome has been sequences and protein coding regions are annotated. Cute can be found on the <a href="https://cute.chassidex.org" target="_blank">CUTE ChassiDex.</a><br>We generated the codon usage table as the protein annotation of <em>A. baylyi</em> is available on the <a href="https://ncbi.nlm.nih.gov" target="_blank">NCBI</a>website. Using this table, we generated the codon usage table for <em>A. baylyi</em> which can be found on.<br>Using this codon table, we codon optimized reporter proteins and its characterization can be found here. <br><br> |
<strong>Solution 2:</strong> Next we move on to building a Synthetic promoter library for <em>Acinetobacter baylyi</em> ADP1 but we wanted to make the promoter library as generic as possible. So we made a T5 promoter based library which can have varying strengths. This library can be extremely useful for metabolic engineering and synthetic biology experiments.<br> | <strong>Solution 2:</strong> Next we move on to building a Synthetic promoter library for <em>Acinetobacter baylyi</em> ADP1 but we wanted to make the promoter library as generic as possible. So we made a T5 promoter based library which can have varying strengths. This library can be extremely useful for metabolic engineering and synthetic biology experiments.<br> | ||
Revision as of 17:58, 14 October 2018
Description
ADaPtat1on
Motivations:
- Initial Idea of lignin degradation to produce higher valued vanillin. We look up the literature and we look at nature that can degrade the aromatic rings of Lignin. We needed an organism that could degrade aromatics.
- For popular organism like E.coli and L. lactis., we need to make competent cells for transformation. We looked up into literature and nature and found many ‘Naturally Competent’ microorganisms. However, most of them are pathogenic and known to cause harm to humans. Hence, you cannot work with it in Biosafety level 1 lab. For example: Streptococcus pneumoniae (Griffith's "pneumococcus"), Neisseria gonorrhoeae, Bacillus subtilis and Haemophilus influenzae.
The organism that best fits into both requirements was Acinetobacter baylyi ADP1 strain. This organism is naturally competent, nonpathogenic, has amazing property of degrading aromatics. (the strain can be purchased from DSMZ.)
Motivations:We looked up the literature for Acinetobacter baylyi ADP1 but could not find substantial literature backing. The literature was too less and not many tools were available to do synthetic biology experiments with this organism. So, This was the motivation to generate a toolbox for Acinetobacter baylyi and try to make it as generic as possible so that if any other team or research groups wish to work with other organism then they can used these tools.
Project:
The first thing that is required for any synthetic biology experiments are fluorescent reporter proteins. We wished to codon optimize GFP and mCherry for A. baylyi. However, when we asked the companies to codon optimize the fluoroscent proteins, the problem with companies was they did not have the codon bias table for A. baylyi.
Solution 1: We made a free use online tool called CUTE (codon usage table enumerator) that can generate Codon usage table by taking into consideration the protein coding annotation. This tool can be used for any other organism whose Genome has been sequences and protein coding regions are annotated. Cute can be found on the CUTE ChassiDex.
We generated the codon usage table as the protein annotation of A. baylyi is available on the NCBIwebsite. Using this table, we generated the codon usage table for A. baylyi which can be found on.
Using this codon table, we codon optimized reporter proteins and its characterization can be found here.
Solution 2: Next we move on to building a Synthetic promoter library for Acinetobacter baylyi ADP1 but we wanted to make the promoter library as generic as possible. So we made a T5 promoter based library which can have varying strengths. This library can be extremely useful for metabolic engineering and synthetic biology experiments.