Difference between revisions of "Team:IIT-Madras/Description"
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| − | <span style="padding-right: | + | <span style="padding-right: 77%;"><strong>Motivation:</strong></span> |
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When we approached companies for codon-optimized reporter proteins they did not have a codon bias table available for <em>A. baylyi</em>.Thus we made a freely available online tool called CUTE (Codon Usage Table Enumerator) that can generate a codon usage table by taking the protein coding annotation into consideration. This tool can be used for all organisms whose genome has been sequenced and whose protein coding regions are annotated. CUTE can be found on the <a href="https://cute.chassidex.org" target="_blank">CUTE ChassiDex website.</a> <br> | When we approached companies for codon-optimized reporter proteins they did not have a codon bias table available for <em>A. baylyi</em>.Thus we made a freely available online tool called CUTE (Codon Usage Table Enumerator) that can generate a codon usage table by taking the protein coding annotation into consideration. This tool can be used for all organisms whose genome has been sequenced and whose protein coding regions are annotated. CUTE can be found on the <a href="https://cute.chassidex.org" target="_blank">CUTE ChassiDex website.</a> <br> | ||
| − | </br> We generated the codon usage table from the protein annotation of <em>A. baylyi</em> available on the <a href="https://ncbi.nlm.nih.gov" target="_blank">NCBI</a>website. Using this codon table, we codon optimized reporter proteins and the characterization can be found here. | + | </br> We generated the codon usage table from the protein annotation of <em>A. baylyi</em> available on the <a href="https://ncbi.nlm.nih.gov" target="_blank">NCBI</a>website. Using this codon table, we codon optimized reporter proteins and the characterization can be found here. <br> |
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Following this we conceptualised our next tool - a synthetic promoter library for <em>Acinetobacter baylyi</em> ADP1. We designed a T5 promoter-based library which can exhibit varying expression strengths. Our aim was to make this library as generic as possible so as it maximise its use in synthetic biology. | Following this we conceptualised our next tool - a synthetic promoter library for <em>Acinetobacter baylyi</em> ADP1. We designed a T5 promoter-based library which can exhibit varying expression strengths. Our aim was to make this library as generic as possible so as it maximise its use in synthetic biology. | ||
Revision as of 15:45, 17 October 2018
Description
ADaPtat1on
Ideation:
- The original idea was to study the degradation of lignin to produce vanillin which has higher economic value. We conducted a literature survey regarding the degradation of the aromatic rings of lignin and organisms capable of degrading such aromatics.
- For popular organisms like E. coli and L. lactis. competent cells are required for transformation. From a brief literature survey we found several ‘naturally competent’ microorganisms. However, most of them were pathogenic and are known to harm humans. Hence, we cannot work with them in a biosafety level 1 laboratory.
An organism that best fits both these requirements is Acinetobacter baylyi. The ADP1 strain of this organism is naturally competent, non-pathogenic, and has the property of degrading aromatics. This strain can be purchased from DSMZ.
Motivation:While perusing literature for Acinetobacter baylyi ADP1 we couldn't find substantial material, as information was sparse and not many tools were available to undertake synthetic biology experiments with this organism. This motivated us to build a toolbox for Acinetobacter baylyi that was generic and hence could effectively be used by research groups working with other organisms as well.
Project:A primary requirement for experimentation in synthetic biology is a fluorescent reporter protein. Hence we planned to codon-optimize two reporter proteins, GFP and mCherry, for A. baylyi.
When we approached companies for codon-optimized reporter proteins they did not have a codon bias table available for A. baylyi.Thus we made a freely available online tool called CUTE (Codon Usage Table Enumerator) that can generate a codon usage table by taking the protein coding annotation into consideration. This tool can be used for all organisms whose genome has been sequenced and whose protein coding regions are annotated. CUTE can be found on the CUTE ChassiDex website.
We generated the codon usage table from the protein annotation of A. baylyi available on the NCBIwebsite. Using this codon table, we codon optimized reporter proteins and the characterization can be found here.
Following this we conceptualised our next tool - a synthetic promoter library for Acinetobacter baylyi ADP1. We designed a T5 promoter-based library which can exhibit varying expression strengths. Our aim was to make this library as generic as possible so as it maximise its use in synthetic biology.