From 2012hs.igem.org

(Difference between revisions)

Latest revision as of 11:12, 17 June 2012

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! 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 :)

TEAM LOGO♥

TEAM LOGO

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

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 />

@@ Line 1: / Line 1: @@
 [[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!
+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 :)
 [[Image:CSIA_SouthKorea.png|left|frame|TEAM LOGO♥]]
@@ Line 26: / Line 26: @@
-=Team Members=
+=Team=
-[https://2012hs.igem.org/Team:CSIA_SouthKorea/_Juyeon_Han Juyeon Han ]
+: Our [[Team:CSIA_SouthKorea/team | team]] and school is introduced in this page! :)
-[https://2012hs.igem.org/Team:CSIA_SouthKorea/_Minji_Kim Minji Kim ]
+=Project=
-[https://2012hs.igem.org/Team:CSIA_SouthKorea/_DaYeon_Lee DaYeon Lee ]
-[https://2012hs.igem.org/Team:CSIA_SouthKorea/_Eugenie_Choe Eugenie Choe]
-=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 system, 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<sup>1</sup>. This also activate GFP genes, so fluorescence can be detected. AiiA 'represses' continuing activation of luxI promotor by degrading of AHL. Therefore, fluorescence may have the cycle under right conditions.
+: 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.
-: 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 light bulbs such as those in night stand.
+: 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>.
-: We 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 only one promoter.
+: 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.
-==Introduction of E.Coli display using repressilator==
+: 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:
-: The main mechanism that we are planning to use is the repressilator. Repressilator is a synthetic genetic regulatory network. It was reported by Michael Elowitz and Stanislas Leibler in 2000. This network is composed of 3 genes connected in a feedback loop, and each of the genes is repressed by the previous gene. This system is designed to exhibit a stable oscillation in the expression of each gene with fixed time period. In each of the wells in the 96 well plate, a colony of Escherichia Coli that expresses fluorescent protein with repressilator system will be put in. Then, by putting in different inducers in each of the wells, we are planning to control the time period and the gene expression of the E. Coli colonies and therefore express the specific shape that we are trying to express withe E. Coli display.
+: [[File:gfp.jpg]]
-:[[File:123.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.
-: Using this mechanism of repressilator to make <font color="#FF9800">time difference</font> in expressing GFP, we would be able to make a certain figure on a 96 well plate. However, the periods of GFP expression in each cell will be slightly different, so we thought of applying quorum sensing to <font color="#CA19C7">synchronize</font> the periods of bacterias.
-: [[File:abcd.jpg]]
+==Introduction of E.Coli display using repressilator==
-: picture of a 96 well plate (http://avena.pw.usda.gov)
+: Our [[Team:CSIA_SouthKorea/introduction | introduction]] further explains the system and goals.
-: Our project has several steps, including cloning the repressilator, determining the variable that controls the period of oscillation, and cultivating E.Coli in a batch culture.
 ==Mechanism of the circuit==
-: Our construction of genetic circuit is based on "A synthetic oscillatory network of transcriptional regulators" by Michael B. Elowitz & Stanislas Leibler, and the article “A synchronized quorum of genetic clocks” by Danino et al.
+: This is further explanation about [[Team:CSIA_SouthKorea/mechanism | mechanism]] of the circuit and explanation about the parts we used.
-: In the diagram above, luxpL is a constitutive promoter and continuously expresses luxR.
-: luxpR is an inducible promotor that is activated by luxR-AHL complex. AHL is the auto-inducer molecule N-(3-oxohexanoyl)-homoserine lactone that can diffuse across other cell membranes, gives many cells identical AHL levels, and creates quorum sensing by synchronizing AHL dependent gene expression. Under luxpR, there are both luxI, which produces AHL, and aiia, which degrades AHL, which generates feedback loops that controls the amount of luxR-AHL complex. (LuxI only increases level of AHL, which makes positive feedback loop, and aiia degenerates AHL, which builds negative feedback loop)
-: Green Fluorescent protein is also under luxpR and demonstrates AHL concentration through its brightness at certain time point. Because rate of synthesis in luxI and rate of degradation in aiia differs, there exists a certain condition that enables periodic oscillation in AHL concentration.
-: The parts we used in the assembly are as follows: BBa_R0062 for luxpR, BBa_R0063 for luxpL, BBa_C0060 for aiia, BBa_C0061 for luxI, and BBa_K082006 for luxR. We changed the part for luxR because we found that this part, although previously used by Wageningen_UR in 2011, is inconsistent and is not confirmed.
 ==Design of the circuit==
-: [[File:system.jpg]]
+: This is the ultimate [[Team:CSIA_SouthKorea/design | design]] of the circuit and how we cloned different parts together.
-: Since gene parts were already on the partsregistry, we linked them using Gibson assembly. However, our model is different from original plasmids used by Danino et al. We used luxpR only once to bring aiia, GFP, and luxI protein under the promoter. And we used luxpL promoter only once, placing luxR under it.
-: [[File:fourparts.jpg]]
-: Since RBS sequence was short, we used gibson assembly to synthesize those four parts.
-: Then, by connecting those four parts and restriction enzymes, we made luxpR-aiia part to be cutted by EcoRI and SpeI, luxpL-luxR part by PstI and SpeI, and GFP-luxI by XbaI and PstI(illustrate below!).
-: [[File:plasmid1.jpg]]   [[File:plasmid2.jpg]]   [[File:plasmid3.jpg]]
-: Then, by using iGEM standard protocol, in two different types of vectors, PSB1A2 and PSB1K3, we ligated the parts with vectors as shown below.
-: [[File:ligation1.jpg]]                                     [[File:ligation2.jpg]]
 ==Variables that determine period of the circuit==
-: According to the thesis 'A synthetic oscillatory network of transcriptional regulators' by Michael B. Elowitz & Stanislas Leibler, he period of oscillations in such networks is determined mainly by the <font color="#FF9800">stability of the protein</font> that is expressed by the synchronized oscillators.
+: 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.
-: Further, 'A synchronized quorum of genetic clocks' by Danino et al. suggests that effective AHL dissipation rate affects the period of the oscillations. In other words, this means that <font color="#FF9800">flow rate</font> significantly affects period. According to their experiment, at high flow rate, the stabilized oscillations exhibit period of 90+-6 min and mean amplitude of 54+-6 GFP arbitrary units. At low flow rate, they observed a period of 55 +-6min and amplitude of 30 +-9GFP arbitrary units. Overall, when they changed the flow rate from 180 to 296 micrometer per minute, the team observed an increasing oscillatory period from 52 to 90 min.
-: Both factors are beyond our control as we do not have proper equipments to control both factors.
 ==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 Escherichia coli.
+: 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''.
-: We simplified the oscillations of GFP expression in each E. coli colonies into sine function on time. Therefore, when the periods of the oscillation of the E. coli colonies are entered as input, in each cell of the 3*3 array, which represents the 9-well-plate, the sine function with each of the entered period is corresponded. We set -1 as the value of the sine function when the GFP expression is the lowest and 1 as the value of the sine function when the GFP expression is the highest. We assumed that the GFP expression of all the colonies started from the sine function value of 0.
-: Then, when the step size of time, tolerance of error, the picture that we are trying to express with the night stand are entered as the input, the program calculates the sine function value of each cell at certain time and seeks for the point where only the colonies of certain cells have the sine function value close to 1 inside the tolerance of error that was entered as input. Until the point is reached, the program keeps on calculating the sine function value of each colony by increasing the elapsed time by the step size of time that was entered as input.
-: The program continuously shows the process; we can actually see the numerical value of sine function of each cell at each moment. The program stops running at the time when the picture that we want to obtain (when the certain cells that make the picture have sine function values very close to 1) is expressed, and the program prints the elapsed time as output.
-: As a result, we are able to calculate the time needed to express the picture that we want to obtain using the light bulbs (colonies of E. coli in each cell) of the night stand (9-well-plate).
-: [[File:algorithm.jpg]]
-: [[Team:CSIA_SouthKorea/Source | This]] is the instruction of how the values are put into the program.
 ==Protocols==
-: Our protocols have changed several times. First, we have been strictly following standard assembly, according to Biobrick Assembly
+: You will see us conducting the experiments according to the [[Team:CSIA_SouthKorea/protocols | protocols]].
-: http://ginkgobioworks.com/support/
-: [[File:exp3.jpg]]
+==Applications==
-: [[File:exp4.jpg]]
-: [[File:exp5.jpg]]
-: [[File:exp6.jpg]]
+: 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=
-==Applications==
+: [[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.
-: 1.	Electronic display
-: While working on the project, we wondered if we could synchronize the period of each cell in the well plate and let them have the same period of oscillation. If this is possible, then we would be able to let the bacteria glow and turn off the light in the same period, and therefore use it to make certain signals that we want on the well plate. It can be some shapes such as square, circle, cross, or star; it can be some letters such as a, b, or c; and if the technique can be applied to larger plate, then we would even be able to display a phrase or a short sentence on the plate. This might as well work as electronic displays that are widely used nowadays for advertising the stores.
-: If the glowing bacteria-project that we are working on can be produced with enough light intensity and possible to program the cells of the plate, then it will be truly beneficial both for people and the environment. Currently the electricity deficiency is a huge problem all over the world. Great dark-outs occur because of excessive usage of electricity, and people are paying a great amount of money for using the electricity. If we can replace these electronic displays with glowing bacteria-display, then we will be able to save quite amount of electricity usage and thus contribute to the saving of electricity.
-: 2.	Light source
-: Second possible application is the usage of glowing bacteria as the light sources, such as reading lamps or small-sized flashlights. It is true that certain level of light intensity is necessary in order to be used in the way proposed. However, we do believe that after some extensive research and laboratory, enough level of light intensity will be reached.
-: If the light source using biological method (glowing bacteria) is developed, it will have positive impact on the society. First, since it glows with no need of external power source, battery and electricity will be saved for other usages. Second, the biological-light source will be able to be used by people in the regions where electricity supply isn’t enough or easy. Even now, there are regions where people can’t easily get access to electricity, and thus have to live in dark when the sun sets. If our project can be developed and applied to making a self-glowing light source, then it will surely bring some benefits.
+=Brainstorming=
-=Outreach & contribution=
+: Please see our [[Team:CSIA_SouthKorea/brainstorming | Brainstorming]] section. We have more than ten ideas explained!
-: [[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!
@@ Line 162: / Line 104: @@
 : Please see our [[Team:CSIA_SouthKorea/Diary | Notebook]]. We have an extensive log from September 2011 on our experiments! :)
@@ Line 171: / Line 115: @@
 =References=
-# ere
+# 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 />

Team:CSIA SouthKorea