From 2007.igem.org

Revision as of 05:04, 27 October 2007 (view source) Katabami (Talk | contribs) (→Making Affinity Tags) ← Older edit		Latest revision as of 06:44, 27 October 2007 (view source) Maiko (Talk | contribs) (→Advanced Goal in Our Future)
(13 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|'''Fig. 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.	+	[[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|'''Fig. 2''' 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. 3''' 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
Line 82:		Line 83:
	[[Chiba/Goal| See Details]]		[[Chiba/Goal| See Details]]
-	===Advanced Goal in Our Future ===	+	===[[Chiba/Goal#In the Long Run|In the Long Run]]===
-	See below link: our brainstorming of the marimo future!	+	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

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

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

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

1. Make the affinity tag by inserting the his-tag into the flagellar fillament.
   • Sequence confirmed
   • Swarm confirmed
   • Flagella strained with anti-flagella antibody
   • Phenotype confirmed
   • Affnity confirmed

more...

Making Communication Module

1. Making Receivers
   • AHL > GFP generator (constitutive aiiA) : BBa_T729006
   • AHL > GFP & aiiA generator : BBa_I729005
   • Sensitive AHL > GFP generator : BBa_I729004
   • inverter-aiiA
2. Making Senders
   • MetK Sender : Could not deposit to registry

more...

Controlling Size

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

more...

Making Marimo

1. Moving FliC-His generator. : Not yet assembled.
2. 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