Team:TokyoTech/Experiment/Transcriptome Analysis
<!DOCTYPE html>
Transcriptome Analysis
Introduction
In our project, we worked on establishing an artificial cross-kingdom communication between human cells and bacteria. However, the cross-kingdom communication was not known well. Therefore, we first had to choose appropriate signaling molecules to establish it. We chose one of the AHL molecules, 3OC8HSL, as a signaling molecule from bacteria to human cells. This is because it can interact with only genetically engineered human cells (Read TraI Assay page). Next, we had to choose a signaling molecule from human cells to bacteria. Initially we had planned to use another AHL. However, we decided not to use AHLs as signal molecules from human cells to bacteria since AHLs cannot be synthesized by human cells due to lack of their materials [2]. Thus, we had to explore if there is a potential signaling molecule produced by human cells. To this end, E. coli cells were interacted with the supernatant of the medium which human cells were cultured. Then transcriptome analysis was conducted to observe if there were any differences in the gene expression in E. coli.
Summary
We checked the difference of transcription between E. coli in normal medium and E. coli in the medium which human cells were cultured. Surprisingly, there were no significant differences in almost all of the RNA expressions except for a couple of genes. The difference was only a little even for those genes.
Results
The 4318 genes were checked and malGcoding Maltose transport system permease protein MalG and malFcoding Maltose transport system permease protein MalF were transcribed about 1.7-fold. This excel file is the data of the transcriptome analysis. The value of E- FDR of the all genes was 1.
Discussion
It is said that the difference is statistically significant if the value of E-FDR is 0.5 or less. Therefore, the results showed that most of the genes were not activated or repressed by substances derived from human cells. Two genes related to maltose metabolism were transcribed about 1.7-fold higher. This fact indicates that a substance like maltose was secreted from human cells. However, it was not proper for a signaling molecule because the activation rate was very low. Considering this result, no substances derived from human could be used as our ideal signaling molecule. Therefore, we had to explore another substance which works as a signaling molecule (Read AHK4 Assay page and Project page).
Appendix: Material and Method
Reference
[1] Foundational Platform for Mammalian Synthetic Biology, 2012 Noah Davidsohn et.al
[2] Multiple reference genomes and transcriptomes for Arabidopsis thaliana, 2011 Xiangchao Gan et.al
