Revision as of 13:21, 29 October 2017

<!DOCTYPE html> Coli Sapiens

iGEM Tokyo Tech

Transcriptome Analysis

Introduction

In our project, we worked on establishing an artificial inter-kingdom communication between human cells and bacteria. However, the inter-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, 3-oxo-C8 HSL, as a signaling molecule from bacteria to human cells. This is because it can interact with only genetically engineered human cells [1, 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

This excel file is the data of the transcriptome analysis. The value of E- FDR of the all genes was 1. https://static.igem.org/mediawiki/2017/a/a7/T--TokyoTech--Transcriptome_Analysis.xlsx

Discussion

It said that the difference is statistically significant if the value of E-FDR is 0.5 or less. Therefore, the results show 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 is secreted from human cells. However, it is not proper for a signaling molecule because the activation rate is very low. Considering this result, no substances derived from human can be used as our ideal signaling molecule. Therefore, we have to explore another substance which works as a signaling molecule (Read AHK4 Assay page and Project page).

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      <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Introduction</b></h1><!-- 小見出し -->
      <hr style="width:50px;border:5px solid red" class="w3-round">
-     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em"> In our project, we worked on establishing an artificial inter-kingdom communication between human cells and bacteria. However, the inter-kingdom communication was not known well, so we had to choose appropriate signaling molecules to establish it. We chose one of AHLs, 3-oxo-C8 HSL as a signaling molecule from bacteria to human cells because it could be worked to specific genetically engineered human cells [1, read TraI Assay page]. However, AHLs cannot be synthesized by human cells because of their material[2]. Thus, we conducted transcriptome analysis to explore an appropriate substance derived from human as a signaling molecule from human cells to bacteria.</p>
+     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em"> In our project, we worked on establishing an artificial inter-kingdom communication between human cells and bacteria. However, the inter-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, 3-oxo-C8 HSL, as a signaling molecule from bacteria to human cells. This is because it can interact with only genetically engineered human cells [1, 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, <span style="font-style: italic">E. coli</span> 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 <span style="font-style: italic">E. coli</span>.</p>
      </p>
@@ Line 71: / Line 71: @@
      <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Summary</b></h1><!-- 小見出し -->
      <hr style="width:50px;border:5px solid red" class="w3-round">
-     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">We checked the difference of transcription level between <span style="font-style: italic">E. coli</span> in normal medium and <span style="font-style: italic">E. coli</span> in the medium cultured human cells. Surprisingly, there were no significant differences as for the transcription of all genes though transcription of only a couple of genes were slightly different.  </p>
+     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">We checked the difference of transcription between <span style="font-style: italic">E. coli</span> in normal medium and <span style="font-style: italic">E. coli</span> 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. </p>
 <div style="margin-top:16px">
 <p style="text-indent:1em"> </p>
@@ Line 88: / Line 88: @@
-     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">This excel file is the data of the transcriptome analysis. The values of E- FDR of the all genes were 1. https://static.igem.org/mediawiki/2017/a/a7/T--TokyoTech--Transcriptome_Analysis.xlsx</p>
+     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">This excel file is the data of the transcriptome analysis. The value of E- FDR of the all genes was 1.
+https://static.igem.org/mediawiki/2017/a/a7/T--TokyoTech--Transcriptome_Analysis.xlsx</p>
      	<div class="w3-xxxlarge" style="padding-bottom: 10px;padding-top: 10px;text-align: center">
@@ Line 102: / Line 103: @@
      <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Discussion</b></h1>
      <hr style="width:50px;border:5px solid red" class="w3-round">
-     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">In general, the difference is said to be statistically significant if the value of E-FDR is 0.5 and less. The above results indicated that no genes were activated or repressed by substances derived from human cells. Two genes related to maltose metabolism were transcribed about 1.7-fold higher in medium cultured human cells. This is considered that a substance like maltose is secreted from human cells. However, it is not an appropriate signaling molecule because the activation rate is very low. From this result, no substances derived from human are supposed to be used as a signaling molecule. Therefore, we have to explore another substance which works as a signaling molecule (Read AHK4 Assay page and Project page).
+     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">It said that the difference is statistically significant if the value of E-FDR is 0.5 or less.  Therefore, the results show 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 is secreted from human cells. However, it is not proper for a signaling molecule because the activation rate is very low. Considering this result, no substances derived from human can be used as our ideal signaling molecule. Therefore, we have to explore another substance which works as a signaling molecule (Read AHK4 Assay page and Project page).