|
|
| Line 1: |
Line 1: |
| − | {{Sydney_Australia}}
| |
| − | <div style="float: right">__TOC__</div>
| |
| | | | |
| − | <h2> Model </h2>
| |
| − |
| |
| − | Harry to write
| |
| − |
| |
| − | - explain how the model works (basically how you explained it in the lab chat)
| |
| − |
| |
| − | - put some of the pictures of the translation kinetics graphs as well
| |
| − |
| |
| − | <h2> Experimental Validation</h2>
| |
| − |
| |
| − | The ''B. subtilis'' flavin-binding fluorescent protein (BsFbFP) was used as a marker to test the validity of the computational algorithm for codon harmonisation. The algorithm (Harrison Steel, unpublished data) generates a harmonised gene sequence for the expression host by considering the tRNA gene copy number (tGCN) profiles in both hosts, and by taking into account the 'wobble effect' which occurs as a result of redundant tRNA-mRNA codon and anticodon base-pairing which has been reported to slow down translation [5].
| |
| − | The particular protein (BsFbFP) used in our study to model codon harmonisation is a promising new alternative to the green fluorescent protein (GFP) family of proteins. BsFbFP is a small protein (137 amino acids), it is functional in many different cellular environments and has high tolerance to changes in pH, oxygen levels and heat, making it applicable to a wide range of experiments [6]. In contrast, GFP is much larger, matures slowly, absolutely requires oxygen for fluorescence, and is sensitive to chemical changes. Furthermore, in the context of our planned experiments, the lack of genome sequence for the GFP source organism ''Aequorea victoria'' means that no tGCN profiles are available, which is crucial for the newly-developed harmonisation algorithm.
| |
| − |
| |
| − | By measuring changes in fluorescence, the folding of the protein can be determined, and it is expected that higher fluorescence will be detected from the harmonised sequence due to better folding than other variants.
| |
| − |
| |
| − | <h2> Results & Discussions </h2>
| |
| − |
| |
| − | - sequences
| |
| − |
| |
| − | - statistics of differences in the sequences i.e. WT vs. Harr-monised
| |
| − |
| |
| − | - fluorimetric analysis
| |
| − |
| |
| − |
| |
| − |
| |
| − | <h2> Model </h2>
| |
| − |
| |
| − | Mention the literature and also how you used models for RBS initiation rate and RNA folding in conjunction with each other
| |
| − |
| |
| − | <h2> Results & Discussions </h2>
| |
| − |
| |
| − | - the movie is really good to put
| |
| − | - diagrams of RNA fold
| |