Team:iHKU/Project

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Latest revision as of 08:21, 3 August 2008

Home	The Team	The Project	Parts Submitted to the Registry	Modeling	Notebook

Overview

Pattern formation is one of the most common yet fascinating biological phenomena happening in our daily lives, though for centuries, biologists, physicists and mathematicians have struggled to understand its nature. How do highly ordered patterns arise from a few living cells? How can our hands, our eyes, our bones form their shape with such an extremely low mistake rate? This question is fascinating but crucial. There are many possible way to form highly complicated patterns. Controlled cell movement is one possible way. Our group is now focusing on pattern formation through cell motility control. The aim of our project is to generate a simple pattern, a set of concentric circles based on a strain of E. coli that we created. We also aim to model the pattern formation by controlled cell movement.

Bacteria use their flagella to move around. To generate a recognizable and stable pattern, bacterial movement must be controlled and coordinated. This can be accomplished by designing a genetic circuits coupling bacterial quorum sensing system and genes controlling mobility. There are several key genes responsible for the movement of flagella, two of them are cheY and cheZ. CheY protein has two forms: its phosphorylated form makes flagella rotate clockwise and the cell will tumble; its dephosphorylated form makes flagella rotate counterclockwise and the cell will be driven straight in one direction (run). CheZ protein can help the progress of dephosphorylation of protein cheY. By controlling the expression of cheZ we can control the cell movement. We have generated MG3, a strain in which gene cheZ is knocked out from its genome. Plasmids containing gene cheZ with engineered promoters will response to the quorum sensing signals according to local cell density, and gene cheZ is either activated or inhibited consequently. The cell will “run” away from or stay in one place using cell density as a cue. Thus by controlling the initial cell density and growth conditions, andthe quorum sensing between cells, we canl lead them to form different patterns.

Project Details

In the beginning we managed control the motility of the cell by knocking out the cheZ, a gene responsible for the regulation of cell motility, we generated a cell strain liable for motility regulation--MG3.
In order to generate coordinated cell movement according to the location of cells, we design a genetic circuit to place the cheZ at the downstream of an artificial quorum sensing system.
We have synthesized the circuit part by part. Firstly the quorum sensing part of luxR, luxRI2 and plux, then the motility part of cheZ. After testing and calibrating the two part separately by reporter gene assay and migration test, we coupled the two parts in MG3.
The engineered MG3 cells were inoculated onto Agar plates to observe the pattern formed. So far we are able to generate different forms of concentric cycles on the Agar plate by varying the initial inoculation condition. We are now trying to generate different patterns such as Olympic rings by fine tuning the genetic circuits and and environmental factors. At the same time, we are building a math model and trying to understand the patterns formed.

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-|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
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-|-
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-''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
-|[[Image:Team.png|right|frame|Your team picture]]
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-|align="center"|[[Team:iHKU | Team Example 2]]
-|}
-<!--- The Mission, Experiments --->
 {| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
 !align="center"|[[Team:iHKU|Home]]
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 !align="center"|[[Team:iHKU/Notebook|Notebook]]
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-(''Or you can choose different headings.  But you must have a team page, a project page, and a notebook page.'')
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 == '''Overview''' ==
-Pattern formation is one of the most common yet fascinating biological phenomena happening in our daily lives, though for centuries, biologists, physicists and mathematicians have struggled to understand its nature. How do living cells form highly ordered patterns, without a leader or a exotic command? How can our hands, our eyes, our bones form their shape with such an extremely low mistake rate? This question is fascinating but crucial. Our group is now focusing on this issue.
+Pattern formation is one of the most common yet fascinating biological phenomena happening in our daily lives, though for centuries, biologists, physicists and mathematicians have struggled to understand its nature. How do highly ordered patterns arise from a few living cells? How can our hands, our eyes, our bones form their shape with such an extremely low mistake rate? This question is fascinating but crucial. There are many possible way to form highly complicated patterns. Controlled cell movement is one possible way. Our group is now focusing on pattern formation through cell motility control. The aim of our project is to generate a simple pattern, a set of concentric circles based on a strain of ''E. coli'' that we created.  We also aim to model the pattern formation by controlled cell movement.
-The aim of our project is to control a simple pattern formation → ring formation based on a strain of E. Coli that we created, meanwhile by the conditions used in controlling the patterns, to find out an elucidation of the pathways in pattern formation.
-As we know, bacteria use their flagella to move around. To reach a recognizable and stable pattern, we must control this random movement. This can be accomplished by quorum sensing and modification of the related genes. There are several key genes responsible for the movement of flagella, two of them are cheY and cheZ. cheY protein has two forms: its phosphorylated form makes flagella rotate clockwise and the cell will tumble; its dephosphorylated form makes flagella rotate counterclockwise and the cell will be driven straight in a direction (run). cheZ protein can help the progress of dephosphorylation of protein cheY. So by controlling the expression of cheZ we can control the cell movement.
+Bacteria use their flagella to move around. To generate a recognizable and stable pattern, bacterial movement must be controlled and coordinated. This can be accomplished by designing a genetic circuits coupling bacterial quorum sensing system and genes controlling mobility. There are several key genes responsible for the movement of flagella, two of them are ''cheY'' and ''cheZ''. CheY protein has two forms: its phosphorylated form makes flagella rotate clockwise and the cell will tumble; its dephosphorylated form makes flagella rotate counterclockwise and the cell will be driven straight in one direction (run). CheZ protein can help the progress of dephosphorylation of protein cheY. By controlling the expression of cheZ we can control the cell movement. We have generated MG3, a strain in which gene cheZ is knocked out from its genome. Plasmids containing gene cheZ with engineered promoters will response to the quorum sensing signals according to local cell density, and gene cheZ is either activated or inhibited consequently. The cell will “run” away from or stay in one place using cell density as a cue. Thus by controlling the initial cell density and growth conditions, andthe quorum sensing between cells, we canl lead them to form different patterns.
-MG3 is a strain in which gene cheZ is knocked out from its genome. Plasmids containing gene cheZ with selected promoters will response to the quorum sensing signals, and gene cheZ is expressed or inhibited consequently, and the cell will “run” or stay in one place. Thus by controlling the initial conditions, quorum sensing between cells will lead them to form different patterns.
 == Project Details==
-*In the beginning we managed to hold control on the motility of the cell. By knocking out the cheZ, a gene responsible for the regulation of cell motility, we generated a cell strain liable for motility regulation—MG3.
+*In the beginning we managed control the motility of the cell by knocking out the cheZ, a gene responsible for the regulation of cell motility, we generated a cell strain liable for motility regulation--MG3.
+*In order to generate coordinated cell movement according to the location of cells, we design a genetic circuit to place the cheZ at the downstream of an artificial quorum sensing system.
-*In order to hold a control on the motility of the uniform cells according to the location of the cell, we design the genetic circuit with the cheZ at the downstream of the quorum sensing system.
+*We have synthesized the circuit part by part. Firstly the quorum sensing part of luxR, luxRI2 and plux, then the motility part of cheZ. After testing and calibrating the two part separately by reporter gene assay and migration test, we coupled the two parts in MG3.
+*The engineered MG3 cells were inoculated onto Agar plates to observe the pattern formed. So far we are able to generate different forms of concentric cycles on the Agar plate by varying the initial inoculation condition. We are now trying to generate different patterns such as Olympic rings by fine tuning the genetic circuits and and environmental factors. At the same time, we are building a math model and trying to understand the patterns formed.
-*We have been synthesized the circuit part by part. Firstly the quorum sensing part of luxR, luxRI2 and plux,then the cheZ part. After testing and calibrating the two part seperately by reporter gene assay and migration test, we combine the two parts in MG3.
-*The transformed MG3 was applied to the LB Agar medium to observe the pattern formed. So far we have already achieved different forms of concentric cycles on the Agar plate. And we are now to have finer regulation on the pattern formed by varifying the level of gene expression and the enviromental factors. And in the end we will come to a math model and hold complete control on the pattern by varifying the parameters.