Team:NCTU Formosa/Improve
Improvement - Finding more pest-resistant candidates for former NCTU_Formosa
- Using the same method SCM to build pest-resistant peptide prediction system
To improve the project of NCTU_Formosa 2016, we applied SCM to make an insecticidal peptide prediction system, using a quicker way to search for their target peptides and leaving them a group of potential target peptides.
Content:
- Datasets
- Results and the candidates we suggested
The way we use SCM to cure fungal diseases is just a part for its ability. In fact, the peptide prediction system based on the SCM can be specialized in different cases of evaluating sequences.
We decided to apply the method to NCTU_Formosa 2016, which utilized spider toxin to kill the pests. We introduced the scoring card to the insecticidal protein to see whether we could also predict invertebrate proteins from ion channel impairing toxins, improving their searching tool while finding more candidates for the project last year.
First, we collected the insecticidal and ion channel impairing toxins by 2016 selection database. After deleting peptides which contained non-standard amino acids, we randomly chose positive and negative data to our datasets and divided them into two datasets, training datasets and testing datasets.
For training parts, after initializing the first scorecard, we used IGA to optimize the scorecard for ten generations.
Results
FullTrain_acc=91.70454568181819
CV acc(train)=93.8636343698348
CV auc(train)=95.44599143143164
Best
theshold=498.75
Best_acc(test)=88.86363681818182
Sensitivity(test)=0.7031249936523439
Specitivity(test)=0.9202127637222726
Discussion
To improve the project of NCTU_Formosa 2016, we introduced the scoring card method to the insecticidal proteins. By using the method, we can predict more new insecticidal proteins.
We collected about three thousands of ion channel impairing toxins.
Below is the excerpt of the peptide list.
一個表格
NEW PART:
- fMT with a constitutive promoter
Introduction
This sequence is designed for constitutively chelating arsenic ions.
We ligated a constitutive promoter(BBa_J23119) with metallothionein (fMT, BBa_K190019) to produce arsenic-binding protein. This metallothionein (fMT) is a kind of chelating protein from Fucus vesiculosus. It can bind both Arsenite (III) and Arsenate(V). This part was first designed by Groningen of iGEM 2009. The part of K190019 consists of fMT and RBS
Modifying and Improving the Existing Biobrick
1. Previous biobrick: BBa_K190031 of 2009 iGEM Groningen
This is the electrophoresis of BBa_K190019
This is the electrophoresis of BBa_J23119 (left) and BBa_J23109(right)
Results
We first examined the growth curve of E. coli DH5α in arsenic solution. We compared the growth curve of E. coli DH5α in arsenic solution with that curve in solution without arsenic ions.
In this experiment, we find that E. coli DH5α won’t be affected by arsenic concentration below 100ppm. The doubling time is about 60 minutes.
Doubling time≒60min.
The results of this experiment indicate that E. coli DH5 containing the transformed plasmid can survive in arsenic concentrations from 1 ppm to 100 ppm
Figure. The growth curve of fMT- E. coli in different concentration of arsenate in SOC (595nm)
In conclusion, we modified the part of BBa_K190031 by replacing the promoter BBa_J23109 by BBa_J23119. The growth of E. coli with this new plasmid does not affected the arsenic concentration.
