"

From 2012hs.igem.org

Revision as of 05:36, 3 March 2012 (view source) Micomaris (Talk | contribs) ← Older edit		Latest revision as of 11:12, 17 June 2012 (view source) Eugeniestar (Talk | contribs) (→Simulation of the display)
(170 intermediate revisions not shown)
Line 1:		Line 1:
-	{|align="justify"	+	[[Image:CSIA_SouthKorea_team.png|right|frame|OUR FANTASTIC TEAM LOGO by Aileen Shin]]
-	|Our team is consisted of four students who are fond of thinking creatively, sharing our knowledge with others and making contributions to the society. We hope that iGEM 2012 could be a great opportunity for us to get our feet wet in the field of synthetic biology and interact with many other students around the world who are also interested in this field!	+
-	|[[Image:CSIA_SouthKorea_logo.png|200px|right|frame]]	+
-	|-	+
-	|	+
-	''Tell us more about your project.  Give us background.  Use this as the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''	+
-	|[[Image:CSIA_SouthKorea_team.png|right|frame|Your team picture]]	+
-	|-	+
-	|	+
-	|align="center"|[[Team:CSIA_SouthKorea | Team CSIA_SouthKorea]]	+
-	|}	+
-	<!--- Team Information Link --->	+	Our team is consisted of four students who are fond of thinking creatively, sharing our knowledge with others and making contributions to the society. We hope that iGEM 2012 could be a great opportunity for us to get our feet wet in the field of synthetic biology and interact with many other students around the world who are also interested in this field! Since our school does not have facilities for wet lab, team CSIA_SouthKorea asked professor In-Geol Choi in Korea University for guide. Professor Choi, Instructor Hyeok-Jin Ko and Hongjae Park let us to be familiar with synthetic biology, taught us how to use basic lab facilities and helped every part in our projects :)
-	{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"	+	[[Image:CSIA_SouthKorea.png|left|frame|TEAM LOGO♥]]
-	!align="center"|[https://igem.org/Team.cgi?year=2012&division=high_school&team_name=CSIA_SouthKorea Official Team Profile]	+
-	|}	+
-	=Team=	+	[[Image:CSIA_SouthKorea2.png|left|frame|TEAM LOGO]]
-	=Brainstorming=
-	==Ideas from imagination==
-	===Lactose intolerance curing E. coli===
-	We thought about the mechanism of making E. Coli to do apoptosis when there is excessive nutrient in human colon (e.g. when a lactose intolerant individual intakes dairy product) so that it prevents excessive growth of E. Coli culture and reduces lactose-intolerant symptoms, such as diarrhea.
-	* Mechanism step (hypothetical) 1. Sensing lactose
-	: We could not find an adaptable lactose-sensing gene. Therefore, it would be better to adopt the glucose sensing mechanism of Baker's yeast.
-	# Put in lactase making gene inside the E. Coli's DNA. Put in the spliced mRNA version (of course it would be transferred into DNA by using reverse transcriptase before putting the mRNA strand into the E. Coli's gene) of Baker's yeast's glucose-sensing gene.
-	# When there is lactase inside human colon, the lactase-producing gene will express and E.Coli will produce lactase.
-	# Lactase will decompose lactose into galactose and glucose.
-	# The glucose sensing gene will detect glucose.
-	* Mechanism step 2. Apoptosis signal
-	: In ‘Baker's yeast’, the gene HXT is expressed when glucose is detected. Instead of HXT, if we put the gene that induces cell death in parts registry, we predicted that the cell will apoptosis when the glucose is detected.
-	* Things to consider :
-	: Since the cell should not die from the signal it sent to itself, the genetically modified E.Coli should be resistant to the apoptosis signal sent from itself. Further, the power of the signal should be controlled in its time and magnitude.
-	==Ideas based on previous iGEM teams==	+
		+
		+
		+
		+
		+
		+
		+
		+
		+
		+
		+	=Team=
		+
		+	: Our [[Team:CSIA_SouthKorea/team | team]] and school is introduced in this page! :)
	=Project=		=Project=
-
-	=Diary=
-	* 2012.02.16: meeting with professor
-	* Our team had a meeting with professor In-Geol Choi in order to discuss our topic for the igem project. We had some creative ideas of our own, but we weren’t sure if they were appropriate topics for this project. As our discussion went on, professor Choi gave us some advices in selecting the topic:
-	* First, the project should have some kind of purpose – something like ‘saving environment’. We need to synthesize and create biological machine of certain function that can fulfill the fundamental purpose of our own.
-	* Second, considering that we don’t have much time nor the professional knowledge for the research and experiments, as high school students, it might be more appropriate to work with relatively easy project. He recommended us to do some research on websites such as biobuilders, and read about some labs that students can conduct.
-	* Third, note the parts registry that we can use. In parts registry site ( http://partsregistry.org/Catalog) we can find out which devices and functions we are able to use, and that will help us with selecting our topic. We decided to consider these points and brainstorm more about the topics. We are to determine our topic by the end of this February.
		+	==Abstract==
		+	: Based on the design of ''V.fischeri'', we placed luxR gene under luxpL promotor and placed luxI, Aiia, and GFP gene under luxpR promotor. In this V.fischeri quorum sensing system<sup>1</sup>, LuxI synthase produces an acyl-homoserine lactone (AHL), which is a small molecule diffuses extracellularly and triggers quorum sensing. When AHL binds to LuxR, it produces LuxR–AHL complex that activates luxI promoter. This also activate GFP genes, so fluorescence can be detected. AiiA 'represses'<sup>2</sup> continuing activation of luxI promotor by degrading of AHL. Therefore, fluorescence may have the cycle under right conditions.
		+	: This network which an activator triggers its own repressor illustrates a concept of synthetic oscillator design. Further, theoretical work shows how an autoinducer leads  synchronized oscillations in a single cell and a population of cells<sup>3</sup>.
-	=Results/Conclusions=	+	: The team got interested in synchronized oscillator while reading Team Wageningen's 2011 project. However, we modified their model a little to increase the probability of success in experiment by using each luxpL and luxpR promoter for only one time.
-	What did you achieve over the course of your semester?	+
		+	: Our research goal is to build the circuit for synchronized oscillator and use them for display. Based on the idea that oscillatory period differs for different cell population, we plan to have a 3 x 3 array, each well consisted of different colonies. The difference in period of GFP expression will allow to display certain figure at certain time. For instance, the display could be like this:
-	=Safety=	+	: [[File:gfp.jpg]]
-		+
		+	: In the world where people suffer from energy deficiency, we expect that this technology could be applied to many different areas. Among them, we think the most successful adaptation would be as an alternative for signs, secret messages and night stand.
-	=Attributions=
		+	==Introduction of E.Coli display using repressilator==
		+	: Our [[Team:CSIA_SouthKorea/introduction | introduction]] further explains the system and goals.
-	=Human Practices=
		+	==Mechanism of the circuit==
		+
		+	: This is further explanation about [[Team:CSIA_SouthKorea/mechanism | mechanism]] of the circuit and explanation about the parts we used.
		+
		+
		+	==Design of the circuit==
		+
		+	: This is the ultimate [[Team:CSIA_SouthKorea/design | design]] of the circuit and how we cloned different parts together.
		+
		+
		+	==Variables that determine period of the circuit==
		+
		+	: Since we assumed that difference of the period in each array leads to different patterns, it is important to find the [[Team:CSIA_SouthKorea/variables | variables]] which affect the period.
		+
		+
		+	==Simulation of the display==
		+
		+	: Before doing the wet lab, in order to predict the results of our experiment, we did computer [[Team:CSIA_SouthKorea/simulation | simulation]]  of the light bulbs of the night stand that we are trying to make with colonies of ''E. coli''.
		+
		+	==Protocols==
		+
		+	: You will see us conducting the experiments according to the [[Team:CSIA_SouthKorea/protocols | protocols]].
		+
		+
		+	==Applications==
		+
		+	: The page introduces possible [[Team:CSIA_SouthKorea/applications | application]] of our unique use of synthetic oscillator.
		+
		+
		+	==Results & Conclusions==
		+
		+	: This [[Team:CSIA_SouthKorea/results | page]] shows the results and conclusions of our project so far!
		+
		+
		+	=Outreach & Human Practice=
		+
		+	: [[Team:CSIA_SouthKorea/outreach | Outreach]] will lead you to a page about our introducing brochure about synthetic biology, and Synbio class in Suri Nature School.
		+
		+
		+
		+
		+	=Brainstorming=
		+
		+	: Please see our [[Team:CSIA_SouthKorea/brainstorming | Brainstorming]] section. We have more than ten ideas explained!
		+
		+
		+
		+
		+	=Notebook=
		+
		+	: Please see our [[Team:CSIA_SouthKorea/Diary | Notebook]]. We have an extensive log from September 2011 on our experiments! :)
		+
		+
		+
		+
		+	=Safety=
		+
		+	: In this page, [[Team:CSIA_SouthKorea/safety | Safety]] , you will see our team CSIA_SouthKorea's lab safety practice and learnings.
-	=Fun!=
		+	=References=
		+	# Danino et al, A synchronized quorum of genetic clocks”, Nature vol. 463, 326-330 (2010)
		+	# Liu, D. et al. Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures. Biochemistry 47, 7706–7714 (2008).
		+	# Garcia-Ojalvo, J., Elowitz, M. & Strogatz, S. Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc. Natl Acad. Sci. USA 101, 10955–10960 (2004).
		+	# http://avena.pw.usda.gov
	<forum_subtle />		<forum_subtle />

---

Latest revision as of 11:12, 17 June 2012

Our team is consisted of four students who are fond of thinking creatively, sharing our knowledge with others and making contributions to the society. We hope that iGEM 2012 could be a great opportunity for us to get our feet wet in the field of synthetic biology and interact with many other students around the world who are also interested in this field! Since our school does not have facilities for wet lab, team CSIA_SouthKorea asked professor In-Geol Choi in Korea University for guide. Professor Choi, Instructor Hyeok-Jin Ko and Hongjae Park let us to be familiar with synthetic biology, taught us how to use basic lab facilities and helped every part in our projects :)

Contents 1 Team 2 Project 2.1 Abstract 2.2 Introduction of E.Coli display using repressilator 2.3 Mechanism of the circuit 2.4 Design of the circuit 2.5 Variables that determine period of the circuit 2.6 Simulation of the display 2.7 Protocols 2.8 Applications 2.9 Results & Conclusions 3 Outreach & Human Practice 4 Brainstorming 5 Notebook 6 Safety 7 References

Team

Our team and school is introduced in this page! :)

Project

Abstract

Based on the design of V.fischeri, we placed luxR gene under luxpL promotor and placed luxI, Aiia, and GFP gene under luxpR promotor. In this V.fischeri quorum sensing system¹, LuxI synthase produces an acyl-homoserine lactone (AHL), which is a small molecule diffuses extracellularly and triggers quorum sensing. When AHL binds to LuxR, it produces LuxR–AHL complex that activates luxI promoter. This also activate GFP genes, so fluorescence can be detected. AiiA 'represses'² continuing activation of luxI promotor by degrading of AHL. Therefore, fluorescence may have the cycle under right conditions.

This network which an activator triggers its own repressor illustrates a concept of synthetic oscillator design. Further, theoretical work shows how an autoinducer leads synchronized oscillations in a single cell and a population of cells³.

The team got interested in synchronized oscillator while reading Team Wageningen's 2011 project. However, we modified their model a little to increase the probability of success in experiment by using each luxpL and luxpR promoter for only one time.

Our research goal is to build the circuit for synchronized oscillator and use them for display. Based on the idea that oscillatory period differs for different cell population, we plan to have a 3 x 3 array, each well consisted of different colonies. The difference in period of GFP expression will allow to display certain figure at certain time. For instance, the display could be like this:

In the world where people suffer from energy deficiency, we expect that this technology could be applied to many different areas. Among them, we think the most successful adaptation would be as an alternative for signs, secret messages and night stand.

Introduction of E.Coli display using repressilator

Our introduction further explains the system and goals.

Mechanism of the circuit

This is further explanation about mechanism of the circuit and explanation about the parts we used.

Design of the circuit

This is the ultimate design of the circuit and how we cloned different parts together.

Variables that determine period of the circuit

Since we assumed that difference of the period in each array leads to different patterns, it is important to find the variables which affect the period.

Simulation of the display

Before doing the wet lab, in order to predict the results of our experiment, we did computer simulation of the light bulbs of the night stand that we are trying to make with colonies of E. coli.

Protocols

You will see us conducting the experiments according to the protocols.

Applications

The page introduces possible application of our unique use of synthetic oscillator.

Results & Conclusions

This page shows the results and conclusions of our project so far!

Outreach & Human Practice

Outreach will lead you to a page about our introducing brochure about synthetic biology, and Synbio class in Suri Nature School.

Brainstorming

Please see our Brainstorming section. We have more than ten ideas explained!

Notebook

Please see our Notebook. We have an extensive log from September 2011 on our experiments! :)

Safety

In this page, Safety , you will see our team CSIA_SouthKorea's lab safety practice and learnings.

References

1. Danino et al, A synchronized quorum of genetic clocks”, Nature vol. 463, 326-330 (2010)
2. Liu, D. et al. Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures. Biochemistry 47, 7706–7714 (2008).
3. Garcia-Ojalvo, J., Elowitz, M. & Strogatz, S. Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc. Natl Acad. Sci. USA 101, 10955–10960 (2004).
4. http://avena.pw.usda.gov

<forum_subtle />