Chiba

From 2007.igem.org

(Difference between revisions)
(→How To Make Our Marimo)
 
(18 intermediate revisions not shown)
Line 2: Line 2:
[[Image:chiba_logo.png|center]]
[[Image:chiba_logo.png|center]]
__NOTOC__
__NOTOC__
-
{| style="border:0;width:100%;" cellpadding="20px" cellspacing="0"
+
{| style="border:0;width:100%;font-family:'Trebuchet MS'" cellpadding="20px" cellspacing="0"
| align="center" |
| align="center" |
-
[[Chiba/Introduction|Introduction]] | [[Chiba/Project_Design|Project Design]] ( [[Chiba/Engeneering_Flagella|1.Affinity Tag]] | [[Chiba/Communication|2.Communication Module]] | [[Chiba/Quorum_Sensing|3.Size Control]] ) |  [[Chiba/Making Marimo|Making Marimos]] |  [[Chiba/Goal|Our Goal]]<br>
+
[[Chiba|Home]]<br>
 +
<span style="font-size:120%;font-weight:bold;">[[Chiba/Introduction|Introduction]] | [[Chiba/Project_Design|Project Design]] ( [[Chiba/Engeneering_Flagella|1.Affinity Tag]] | [[Chiba/Communication|2.Communication Module]] | [[Chiba/Quorum_Sensing|3.Size Control]] ) |  [[Chiba/Making Marimo|Making Marimos]] |  [[Chiba/Goal|Our Goal]]</span><br>
[[Chiba/Acknowledgements|Acknowledgements]] | [[Chiba/Team_Members|Team Members]] | [http://chem.tf.chiba-u.jp/igem/ iGEM Chiba Website] | [[Chiba/Members_Only|メンバ連絡簿]]  
[[Chiba/Acknowledgements|Acknowledgements]] | [[Chiba/Team_Members|Team Members]] | [http://chem.tf.chiba-u.jp/igem/ iGEM Chiba Website] | [[Chiba/Members_Only|メンバ連絡簿]]  
|}
|}
==Project Overview==
==Project Overview==
-
[[Image:Chiba_marimobig.jpg|frame|''Fig1.''Marimo in the lake]]Our iGEM project is to make a '''Marimo-ish gathering of bacteria'''. Marimo is a green spherical shaped algae (shown in Fig.1), which is a popular living organism in Japan as a National Treasure because of its beautiful shape and its smoothness.
+
[[Image:Chiba_marimobig.jpg|frame|'''photo. 1''' Marimo in the lake]]Our iGEM project is to make a '''Marimo-ish gathering of bacteria'''. Marimo is a green spherical shaped algae (shown in Fig.1), which is a popular living organism in Japan as a National Treasure because of its beautiful shape and its smoothness.
-
===[[Chiba/Introduction|Why We Make a Marimo : Spherical Multicellular Organism!?]]===
+
===[[Chiba/Introduction|Introduction: Why We Make a Marimo]]===
 +
====Spherical Multicellular Organism!?====
When you see a shape in Nature, you will notice whether a sphere, which is absolutely symmetric in 3D, is really stable or not in Nature.
When you see a shape in Nature, you will notice whether a sphere, which is absolutely symmetric in 3D, is really stable or not in Nature.
In fact, an oil droplet is a sphere in water. Red blood cell in a hypotonic solution shows its shape change to a spherical balloon.  
In fact, an oil droplet is a sphere in water. Red blood cell in a hypotonic solution shows its shape change to a spherical balloon.  
Line 19: Line 21:
[[Chiba/Introduction|more...]]
[[Chiba/Introduction|more...]]
-
===[[Chiba/Project Design|How To Make Our Marimo]]===
+
===[[Chiba/Project Design|Project Design: How To Make Our Marimo]]===
-
[[Image:Chiba_marimosystem.png|frame|'''Fig2.''' Our marimo system.]]What we require to our system is as follows:
+
[[Image:Chiba_marimosystem.png|frame|'''scheme. 1''' Our marimo system.]]What we require to our system is as follows:
#Affinity Tag.
#Affinity Tag.
#Communication Module.
#Communication Module.
Line 35: Line 37:
===[[Chiba/Engeneering_Flagella|Making Affinity Tags]]===
===[[Chiba/Engeneering_Flagella|Making Affinity Tags]]===
-
[[Image:Chiba_flichisgene.png|frame|'''Fig.''' The short peptide with six histidine (“His-Tag”) was inserted into the fliC D3 domain.]]
+
[[Image:Chiba_flichisgene.png|frame|'''scheme. 2''' The short peptide with six histidine (“His-Tag”) was inserted into the fliC D3 domain.]]
#Make the affinity tag by inserting the his-tag into the flagellar fillament.
#Make the affinity tag by inserting the his-tag into the flagellar fillament.
#*[[Image:Chiba_check.png]] Sequence confirmed
#*[[Image:Chiba_check.png]] Sequence confirmed
Line 46: Line 48:
===[[Chiba/Communication|Making Communication Module]]===
===[[Chiba/Communication|Making Communication Module]]===
 +
[[Image:BBa I729005 circuit.jpg|frame|'''scheme.3''' New parts BBa_I729005.]]
#Making Receivers
#Making Receivers
#*[[Image:Chiba_check.png]] AHL > GFP generator (constitutive aiiA) : BBa_T729006
#*[[Image:Chiba_check.png]] AHL > GFP generator (constitutive aiiA) : BBa_T729006
Line 56: Line 59:
===[[Chiba/Quorum_Sensing|Controlling Size]]===
===[[Chiba/Quorum_Sensing|Controlling Size]]===
-
[[Image:MLuxR-test.gif|frame|'''Fig.''' Improved Receiver.]]
+
[[Image:MLuxR-test.gif|frame|'''photo. 2''' Improved Receiver.]]
#Improve Sender
#Improve Sender
#*[[Image:Chiba_check.png]] Overexpressed the metK (the AHL precursur synthesis enzyme) in the hope to increase AHL synthesis. : Turned out not to work
#*[[Image:Chiba_check.png]] Overexpressed the metK (the AHL precursur synthesis enzyme) in the hope to increase AHL synthesis. : Turned out not to work
Line 71: Line 74:
#[[Image:Chiba_nocheck.png]] FliC-his biobrick : Not yet assembled.
#[[Image:Chiba_nocheck.png]] FliC-his biobrick : Not yet assembled.
[[Chiba/Making Marimo|more...]]
[[Chiba/Making Marimo|more...]]
-
 
-
 
==[[Chiba/Goal|Our Goal]]==
==[[Chiba/Goal|Our Goal]]==
-
Below we describe the goal to make a marimo bacteria.
+
Although we could not reach them, below we describe the goal that we set to make a marimo bacteria.
*A test of adsorption between flagella
*A test of adsorption between flagella
*A test to confirm a limit of size
*A test to confirm a limit of size
*A test to form Marimo
*A test to form Marimo
*A test of size control
*A test of size control
-
===Advanced Goal in Our Future ===
+
[[Chiba/Goal| See Details]]
-
See below link: our brainstorming of the marimo future!
+
 
 +
===[[Chiba/Goal#In the Long Run|In the Long Run]]===
 +
See [[Chiba/Goal#In the Long Run|here]] : our brainstorming of the marimo future!
[[Chiba/Goal|more...]]
[[Chiba/Goal|more...]]
 +
 +
==Sponsers==
 +
<center>
 +
[[Image:Chiba_Knowledge.jpg]]　
 +
[[Image:Chiba_yakukensha.gif]]　
 +
[[Image:Chiba_Stratagene.gif]]　
 +
[[Image:Chiba_Greiner.gif]]<br><br>
 +
[[Image:Chiba-u.gif]]
 +
</center>

Latest revision as of 06:44, 27 October 2007

Chiba logo.png

Home
Introduction | Project Design ( 1.Affinity Tag | 2.Communication Module | 3.Size Control ) | Making Marimos | Our Goal
Acknowledgements | Team Members | [http://chem.tf.chiba-u.jp/igem/ iGEM Chiba Website] | メンバ連絡簿

Project Overview

photo. 1 Marimo in the lake
Our iGEM project is to make a Marimo-ish gathering of bacteria. Marimo is a green spherical shaped algae (shown in Fig.1), which is a popular living organism in Japan as a National Treasure because of its beautiful shape and its smoothness.

Introduction: Why We Make a Marimo

Spherical Multicellular Organism!?

When you see a shape in Nature, you will notice whether a sphere, which is absolutely symmetric in 3D, is really stable or not in Nature. In fact, an oil droplet is a sphere in water. Red blood cell in a hypotonic solution shows its shape change to a spherical balloon. However multicellular organisms have their shape different from a sphere except Marimo. Of course, other algae do not show spherical shape, they live on a surface of stone. It is quite intriguing how Marimo remains its spherical shape in a lake!

Our team focuses understanding how such spherical structure can be sustained even when it Is multicellular organisms.
more...

Project Design: How To Make Our Marimo

scheme. 1 Our marimo system.
What we require to our system is as follows:
  1. Affinity Tag.
  2. Communication Module.
  3. Size Control.

Two cells are used in our system: AHL senders and receivers. Senders generates the affinity tags constitutively, while receivers generates them only when they are induced by AHL. The marimo-forming goes like this:

  • Make the sender core by sticking with the affinity tag.
  • Insert the sender core into the receiver culture.
  • The sender core produces AHL, which make the near receivers to generate the affinity tags and GFPs.
  • The affinity tagged receiver sticks with the central sender core. This will continue until the AHL cannnot reach the marimo boundary,
  • When the AHL reached the marimo boundary, the adsorping stops, which makes a finite-sized marimo bacteria.

more...

Experiments Overview

Making Affinity Tags

scheme. 2 The short peptide with six histidine (“His-Tag”) was inserted into the fliC D3 domain.
  1. Make the affinity tag by inserting the his-tag into the flagellar fillament.
    • Chiba check.png Sequence confirmed
    • Chiba check.png Swarm confirmed
    • Chiba check.png Flagella strained with anti-flagella antibody
    • Chiba check.png Phenotype confirmed
    • Chiba check.png Affnity confirmed

more...

Making Communication Module

scheme.3 New parts BBa_I729005.
  1. Making Receivers
    • Chiba check.png AHL > GFP generator (constitutive aiiA) : BBa_T729006
    • Chiba check.png AHL > GFP & aiiA generator : BBa_I729005
    • Chiba check.png Sensitive AHL > GFP generator : BBa_I729004
    • Chiba nocheck.png inverter-aiiA
  2. Making Senders
    • Chiba nocheck.png MetK Sender : Could not deposit to registry

more...

Controlling Size

photo. 2 Improved Receiver.
  1. Improve Sender
    • Chiba check.png Overexpressed the metK (the AHL precursur synthesis enzyme) in the hope to increase AHL synthesis. : Turned out not to work
  2. Improve Receiver
    • Chiba check.png Inserted 2 mutations in LuxR which is known from the paper to increase activity.
  3. Localize AHL
    • Chiba check.png Tested the GFP expression in constitutive aiiA generator receiver : Went too much.
    • Chiba check.png Tested the GFP expression in AHL-induced aiiA generator receiver : Needed to twist the circuit more.
    • Chiba nocheck.png AHL-induced inverter aiiA receiver. Not yet assembled.

more...

Making Marimo

  1. Chiba nocheck.png Moving FliC-His generator. : Not yet assembled.
  2. Chiba nocheck.png FliC-his biobrick : Not yet assembled.

more...

Our Goal

Although we could not reach them, below we describe the goal that we set to make a marimo bacteria.

  • A test of adsorption between flagella
  • A test to confirm a limit of size
  • A test to form Marimo
  • A test of size control

See Details

In the Long Run

See here : our brainstorming of the marimo future!

more...

Sponsers

Chiba Knowledge.jpg　 Chiba yakukensha.gif　 Chiba Stratagene.gif　 Chiba Greiner.gif

Chiba-u.gif

Retrieved from "http://2007.igem.org/wiki/index.php/Chiba"