Chiba/Sandbox/Home2

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[[Image:chiba_logo.png|center]]
__NOTOC__
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{| style="border:0;width:100%;" cellpadding="20px" cellspacing="0"
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| align="center" |
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[[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>
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[[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]]
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{| style="border:0;width:100%;height:100%;" cellpadding="20px" cellspacing="0"
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==Project Overview==
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[[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.
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==MENU==
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===Why We Make a Marimo : Spherical Multicellular Organism!? ===
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#Concepts
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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.
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#*About marimo
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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.
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#*Why make a marimo bacteira?
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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.
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#Projects
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It is quite intriguing how Marimo remains its spherical shape in a lake!
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#*Model
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#*Genetic Circuit
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Our team focuses understanding how such spherical structure can be sustained even when it Is multicellular organisms.<br>
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[[Chiba/Introduction|more...]]
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===How To Make Our Marimo===
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[[Image:Chiba_marimosystem.png|frame|'''Fig2.''' Our marimo system.]]What we require to our system is as follows:
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#Affinity Tag.
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#Communication Module.
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#Size Control.
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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:
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*Make the sender core by sticking with the affinity tag.
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*Insert the sender core into the receiver culture.
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*The sender core produces AHL, which make the near receivers to generate the affinity tags and GFPs.
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*The affinity tagged receiver sticks with the central sender core. This will continue until the AHL cannnot reach the marimo boundary,
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*When the AHL reached the marimo boundary, the adsorping stops, which makes a finite-sized marimo bacteria.
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| width="80%" valign="top" |
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==Experiments Overview==
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==Concepts==
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===[[Chiba/Engeneering_Flagella|Making Affinity Tags]]===
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[[Image:chiba_marimobig.jpg|frame|Marimo in the lake]]
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[[Image:Chiba_flichisgene.png|frame|'''Fig.''' The short peptide with six histidine (“His-Tag”) was inserted into the fliC D3 domain.]]
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Chiba University iGEM07 team's project is to make a '''''Marimo-ish bacteria'''''. ''Marimo'' is a green spherical shaped algae, which is a popular living organism in Japan as a National Monument. When you come to Japan, you absolutely come across to Marimo in Aquarisms, TV programs or Mangas :)
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#Make the affinity tag by inserting the his-tag into the flagellar fillament.
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#*[[Image:Chiba_check.png]] Sequence confirmed
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#*[[Image:Chiba_check.png]] Swarm confirmed
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#*[[Image:Chiba_check.png]] Flagella strained with anti-flagella antibody
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#*[[Image:Chiba_check.png]] Phenotype confirmed
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#*[[Image:Chiba_check.png]] Affnity confirmed
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[[Chiba/Engeneering_Flagella|more...]]
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<br clear="all">
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===[[Chiba/Communication|Making Communication Module]]===
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#Making Receivers
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#*[[Image:Chiba_check.png]] AHL > GFP generator (constitutive aiiA) : BBa_T729006
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#*[[Image:Chiba_check.png]] AHL > GFP & aiiA generator : BBa_I729005
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#*[[Image:Chiba_check.png]] Sensitive AHL > GFP generator : BBa_I729004
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#*[[Image:Chiba_nocheck.png]] inverter-aiiA
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#Making Senders
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#*[[Image:Chiba_nocheck.png]] MetK Sender : Could not deposit to registry
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[[Chiba/Communication|more...]]
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===About Marimo===
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===[[Chiba/Quorum_Sensing|Controlling Size]]===
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Actually, the name "marimo" indicates the algae filament, not the sphere.  The sphere shape is one of the three growth forms of the aggregated marimos. (For further information, see [[Chiba/Marimo|here]].)  The spherical marimo is known to be constructed in following mechanisms:
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[[Image:MLuxR-test.gif|frame|'''Fig.''' Improved Receiver.]]
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#The filaments forms a sphere shape around the 土，砂などのcore.
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#Improve Sender
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#As the sphere become big, the inside of the sphere dies because of the innability of photosynthesis which leads to a hollow in the sphere.
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#*[[Image:Chiba_check.png]] Overexpressed the metK (the AHL precursur synthesis enzyme) in the hope to increase AHL synthesis. : Turned out not to work
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#The sphere is smashed up because of the inner hole. A several segmentalized marimo filaments group will be born.
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#Improve Receiver
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#Those segments became the next generation marimo's core, which resluts in '''non-core spherical marimo'''.
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#*[[Image:Chiba_check.png]] Inserted 2 mutations in LuxR which is known from the paper to increase activity.  
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#Go back to no.2.
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#Localize AHL
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#*[[Image:Chiba_check.png]] Tested the GFP expression in constitutive aiiA generator receiver : Went too much.  
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#*[[Image:Chiba_check.png]] Tested the GFP expression in AHL-induced aiiA generator receiver : Needed to twist the circuit more.
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#*[[Image:Chiba_nocheck.png]] AHL-induced inverter aiiA receiver. Not yet assembled.
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[[Chiba/Quorum_Sensing|more...]]
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（わかりにくいので後ほど絵をつけようと思っています）（英語も酷いので直してほしいです…）
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===[[Chiba/Making Marimo|Making Marimo]]===
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#[[Image:Chiba_nocheck.png]] Moving FliC-His generator. : Not yet assembled.
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#[[Image:Chiba_nocheck.png]] FliC-his biobrick : Not yet assembled.
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[[Chiba/Making Marimo|more...]]
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[[Chiba/Marimo|more...]]
 
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References:
 
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*Yoshio Sakai, Marimo no Kagaku, 北海道大学図書刊行会, 1991
 
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==[[Chiba/Goal|Our Goal]]==
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Below we describe the goal to make a marimo bacteria.
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*A test of adsorption between flagella
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*A test to confirm a limit of size
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*A test to form Marimo
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*A test of size control
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===Advanced Goal in Our Future ===
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See below link: our brainstorming of the marimo future!
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===Why Make a Marimo Bacteria?===
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[[Chiba/Goal|more...]]
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どうき
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==Project==
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===Model===
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*Gather bacteria: Quorum Sensing
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*Stick bacteria together: flagella & his-tag
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*Control Size: Quorum Sensing
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（絵）
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===Genetic Circuit===
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[[Image:Chiba_marimosystem.png]]
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====Sender====
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====Reciever====
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Latest revision as of 04:58, 27 October 2007

Chiba logo.png

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

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.

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...

How To Make Our Marimo

Fig2. 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.

Experiments Overview

Making Affinity Tags

Fig. 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

  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

Fig. 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

Below we describe the goal 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

Advanced Goal in Our Future

See below link: our brainstorming of the marimo future!

more...

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