Chiba

From 2007.igem.org

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{| style="border:0;width:100%;font-family:'Trebuchet MS'" cellpadding="20px" cellspacing="0"
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! style="border:2px solid #000000;" | People
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[[Chiba|Home]]<br>
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! style="border:solid #000000;border-width:2px 2px 2px 0;" | Project
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<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>
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! style="border:solid #000000;border-width:2px 2px 2px 0;" | Lab Notes
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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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<!-- 左側 -->
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===Members===
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*[[User:Hiroki|Hiroki Fukutomi]]
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*[[User:Mutsuko|Mutsuko Kazama]]
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*[[User:Risa|Risa Kajiwara]]
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*[[User:Mrina|Marina Gushiken]]
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*[[User:Yukihiro|Yukihiro Takami]]
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*[[User:Masahiro|Masahiro Tominaga]]
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===Supporters===
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==Project Overview==
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*Akinori Katabami
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[[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.
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*[[User:Maiko|Maiko Furubayashi]]
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===[[Chiba/Introduction|Introduction: Why We Make a Marimo]]===
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*Yohei Tashiro
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====Spherical Multicellular Organism!?====
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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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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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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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It is quite intriguing how Marimo remains its spherical shape in a lake!
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===Facluty Advisors===
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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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*Daisuke Umeno
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[[Chiba/Introduction|more...]]
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*Taro Toyota
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<!-- 真ん中 -->
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===[[Chiba/Project Design|Project Design: How To Make Our Marimo]]===
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[[Image:Chiba_marimosystem.png|frame|'''scheme. 1''' Our marimo system.]]What we require to our system is as follows:
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*[[Chiba/Project Description|Project Description]]
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#Affinity Tag.
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*[[Chiba/Assembly process|Assembly Process]]
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#Communication Module.
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*[[Chiba/Brainstorming|Brainstorming]]
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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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[[Chiba/Project Design|more...]]
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==Experiments Overview==
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<!-- 右側 -->
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===[[Chiba/Engeneering_Flagella|Making Affinity Tags]]===
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[[Image:Chiba_flichisgene.png|frame|'''scheme. 2''' The short peptide with six histidine (“His-Tag”) was inserted into the fliC D3 domain.]]
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===Experiments===
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#Make the affinity tag by inserting the his-tag into the flagellar fillament.
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*[[Chiba/Schedule|Schedule]]
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#*[[Image:Chiba_check.png]] Sequence confirmed
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*[[Chiba/Week1|Week1(8/14~8/20)]]
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#*[[Image:Chiba_check.png]] Swarm confirmed
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*[[Chiba/Week2|Week2(8/21~8/27)]]
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#*[[Image:Chiba_check.png]] Flagella strained with anti-flagella antibody
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*[[Chiba/Week3|Week3(8/28~9/3)]]
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#*[[Image:Chiba_check.png]] Phenotype confirmed
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*[[Chiba/Week4|Week4(9/4~9/10)]]
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#*[[Image:Chiba_check.png]] Affnity confirmed
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*[[Chiba/Week5|Week5(9/11~9/17)]]
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[[Chiba/Engeneering_Flagella|more...]]
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*[[Chiba/Week6|Week6(9/18~9/24)]]
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<br clear="all">
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*[[Chiba/Week7|Week7(9/25~10/1)]]
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*[[Chiba/Week8|Week8(10/2~10/8)]]
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*[[Chiba/Week9|Week9(10/9~10/15)]]
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*[[Chiba/Week10|Week10(10/16~10/22)]]
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*[[Chiba/Week11|Week11(10/23~10/29)]]
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*[[Chiba/Week12|Week12(10/30~11/1)]]
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===Meetings===
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===[[Chiba/Communication|Making Communication Module]]===
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[[Image:BBa I729005 circuit.jpg|frame|'''scheme.3''' New parts BBa_I729005.]]
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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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===連絡簿===
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===[[Chiba/Quorum_Sensing|Controlling Size]]===
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*[http://ja.wikipedia.org/wiki/Wikipedia:%E7%B7%A8%E9%9B%86%E3%81%AE%E4%BB%95%E6%96%B9 Wikipedia:編集の仕方]　wiki編集の参考にしてください。
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[[Image:MLuxR-test.gif|frame|'''photo. 2''' Improved Receiver.]]
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*[[Chiba/hotel|Hotel]]
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#Improve Sender
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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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#Improve Receiver
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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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#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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|}
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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/Goal|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
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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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[[Chiba/Goal| See Details]]
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===[[Chiba/Goal#In the Long Run|In the Long Run]]===
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See [[Chiba/Goal#In the Long Run|here]] : our brainstorming of the marimo future!
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[[Chiba/Goal|more...]]
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==Sponsers==
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<center>
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[[Image:Chiba_Knowledge.jpg]]　
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[[Image:Chiba_yakukensha.gif]]　
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[[Image:Chiba_Stratagene.gif]]　
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[[Image:Chiba_Greiner.gif]]<br><br>
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[[Image:Chiba-u.gif]]
</center>
</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

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