Team:Tsinghua/Introduction-Our-Idea

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<h1>Our Idea</h1>
<h1>Our Idea</h1>
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<p>To meet the foregoing challenge, a potable pathogen detector which is able to be reached anytime at hand is required. Our ¬detector is designed as the test paper, which emerges color change when pathogen is detected. The test paper possesses the advantage of low cost, quick output and easy storage. Moreover, it requires no expertise of medicine to use. Therefore, the detector in test paper form is a desired candidate to fit the idea of Mobile Health. However, what can be used as the main components to sense the pathogen as well as output the color change?  
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<p>We are inspired by the idea of synthetic biology, in which living organisms are modified for various purpose and applications. Synthetic organisms are easy to manipulate and modify, which serves as the ideal candidate components for our detector. In our project, genetically modified S. cerevisiae (budding yeast) is utilized as the main component in the test paper. The yeast detects the signal of the bacteria and then reports it by expressing reporter genes. The yeast system is chosen generally based on four reasons: 1) Yeasts are small, fast proliferating organisms, whose genetic background are well understood. 2) Yeasts are eukaryotes, different from the target bacteria. It sets proper orthogonality between the detector and the target. 3) Being widely used in food and drinks manufacturing, yeasts are fundamentally friendlier to human health than other microorganisms. 4) Yeasts have the dramatic mechanism of mating. We take advantage of this mechanism to separate the sensor and reporter in our detector, increasing the flexibility and effectiveness of the system.  
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Figure 1. Explore possible approach to overcome the challenge<br/>
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<p>Then the next question is that, how will the yeast in our test paper detect the pathogen? Our first inspiration is to use the classic antigen-antibody reaction, in which specific antibodies are introduced in the detector to target and recognize the antigen of the pathogen. However, novel pathways are difficult to design in yeast to simultaneous include the input and output. Therefore, we asked the question: can we find and use pathways functioning in nature which detects specific bacteria populations? Qurom sensing, a conserved mechanism in bacteria to sense the population around, is detected and then used to suggest the appearance of the pathogen. In gram-negative bacteria, a small molecular in qurom sensing, called N-Acyl Homoserine Lactone (AHL), is release by the bacteria and convey the communicating message among the entire group. By using AHL, direct contact of pathogen and yeasts are avoided, reduce the possibility of contamination. Moreover, each species has its own specific AHL molecular, underling the specificity of the detector. Therefore, AHL is a potential candidate to identify the appearance as well as the size of a specific pathogen population. If the AHL sensing system of one pathogen is introduced in the yeast, then the yeast will work as the detector and sense the pathogen. Downstream reporter gene is expressed and it changes the color of the test paper.  
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(<i>Picture by Tsinghua iGEM team 2013</i>)
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<p>Additionally, one unique feature of yeast against other microorganisms is that is has “gender”. Haploid yeasts with a type and α type can mate with each other to form a diploid. We use this feature of yeast to revise our detector system. Yeast in a type is utilized as the sensor, while Yeast in α type is in charge of the reporter. The sensor specificity target to interested pathogen and its AHL, while α type yeasts with different reporter colors is selected as the output. There are at least four main advantage of this: 1) the whole system is divided into two subparts, reducing the difficulty and time to build each part. 2) The flexibility of the system is increased. Different combination of sensors and reporter is accessible, making the system used as a potable toolbox and increasing the number of applicable detectors. 3) During the two-step process, the signal is amplified and easier to be detected. 4) New subparts are convenient to be added to the system, as it needs exclusively modification for only one part.  
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<p>To summarize our idea, a potable detector in test paper form is designed with genetically modified yeasts. The sensor yeasts are able to sense the AHL signal of the pathogen and then the reporter yeasts reveal the signal with color change. We believe the system is an ideal model to fit the design of Mobile Health, making a potable and effective pathogen detector.  
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To meet the foregoing challenges, a portable pathogen detector which could be kept within reach is required. The detector is designed as test paper. When pathogen appears, its existence is reported by the color change of the detector. But what can be used as the components to sense the pathogen as well as output the color change?
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Figure 2. Budding yeast is wildly utilized in manufacturing<br/>
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(<i>Picture by Tsinghua iGEM team 2013</i>)
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In our project, <b>genetically modified <i>S. cerevisiae</i> (budding yeast)</b> is utilized as the main component on the <b>test paper</b>. The yeast <b>detects</b> the signals of bacteria and then <b>reports</b> them by expressing reporter genes. The yeast system is chosen generally based on four reasons: 1) Living organisms such as yeast are easy to <b>modify genetically</b>. 2) Yeast is eukaryote, different from target bacteria. It sets proper <b>orthogonality</b> between the detector and the target. 3) Being widely used in food and drink manufacturing, yeast is <b>fundamentally friendlier to human health</b> and <b>easier to be accepted</b> than other microorganisms. 4) Yeast has the dramatic mechanism of <b>mating</b>. We took advantage of this mechanism to separate the sensor and reporter in our detector, increasing the diversity and effectiveness of the system.  
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The next question is - how will the yeast on our test paper detect pathogens? <b>Quorum sensing</b>, a conserved mechanism in bacteria to sense the population around, is used to suggest the existence of the pathogen. In <b>gram-negative bacteria</b>, a small molecule important in quorum sensing called <b>N-Acyl homoserine lactone (AHL)</b> is released by bacteria and conveys communicating messages among the <b>entire group</b>. Moreover, each species has its own specific AHL molecule. Therefore, AHL is an ideal candidate to identify the existence as well as the size of a specific pathogen population. If the AHL sensing system of one pathogen is introduced into the yeast, the yeast will work as the detector and sense the pathogen. Downstream reporter genes will then be expressed and change the color of the <b>test paper</b>.  
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Figure 3. The principle of quorum sensing system<br/>
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(<i>Picture by Tsinghua iGEM team 2013</i>)
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Additionally, one feature of yeast unique from other microorganisms is that it has “<b>gender</b>”. <b>Haploid</b> yeasts of <b>type a</b> and <b>type α</b> can mate with each other to form a <b>diploid</b>. We used this feature of yeast to revise our detecting system. Yeasts of type a are utilized as <b>sensors</b>, while yeasts of type α act as <b>reporters</b>. The sensor is targeted to the pathogen of interest and its AHL specifically, while one of the type α yeasts with different reporting colors is selected as the output. There are at least four main advantages of this design: 1) the whole system is divided into <b>two subparts</b>, reducing the difficulty and time to complete each part. 2) The <b>flexibility</b> of the system is increased. Different combinations of <b>sensors</b> and <b>reporters</b> increase the number of possible <b>detectors</b>. 3) During the two-step process, the signal is <b>amplified</b> and easier to be observed. 4) New <b>subparts</b> are convenient to be added to the system, as modification is needed for only one part.  
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Figure 4. The principle of our portable pathogen detector<br/>
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(<i>Picture by Tsinghua iGEM team 2013</i>)
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To summarize our idea, a <b>portable detector</b> in the form of <b>test paper</b> is designed with genetically modified yeasts on it. The sensing yeast is able to sense the signal AHL from the pathogen and then the reporting yeast will reveal the signal with color change.  
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<img class="center" src="https://static.igem.org/mediawiki/2013/d/d3/Tsinghua-OurIdea5.png"/>
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Figure 5. Portable test paper is designed for pathogen detection<br/>
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(<i>Picture by Tsinghua iGEM team 2013</i>)
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<h3>Reference</h3>
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[1] Lazcka O, Campo F, Munoz F X. Pathogen detection: a perspective of traditional methods and biosensors[J]. Biosensors and Bioelectronics, 2007, 22(7): 1205-1217.
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[2] Nassif X. A revolution in the identification of pathogens in clinical laboratories[J]. Clinical infectious diseases, 2009, 49(4): 552-553.
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Latest revision as of 19:54, 27 September 2013

Our Idea

Figure 1. Explore possible approach to overcome the challenge
(Picture by Tsinghua iGEM team 2013)

To meet the foregoing challenges, a portable pathogen detector which could be kept within reach is required. The detector is designed as test paper. When pathogen appears, its existence is reported by the color change of the detector. But what can be used as the components to sense the pathogen as well as output the color change?

Figure 2. Budding yeast is wildly utilized in manufacturing
(Picture by Tsinghua iGEM team 2013)

In our project, genetically modified S. cerevisiae (budding yeast) is utilized as the main component on the test paper. The yeast detects the signals of bacteria and then reports them by expressing reporter genes. The yeast system is chosen generally based on four reasons: 1) Living organisms such as yeast are easy to modify genetically. 2) Yeast is eukaryote, different from target bacteria. It sets proper orthogonality between the detector and the target. 3) Being widely used in food and drink manufacturing, yeast is fundamentally friendlier to human health and easier to be accepted than other microorganisms. 4) Yeast has the dramatic mechanism of mating. We took advantage of this mechanism to separate the sensor and reporter in our detector, increasing the diversity and effectiveness of the system.

The next question is - how will the yeast on our test paper detect pathogens? Quorum sensing, a conserved mechanism in bacteria to sense the population around, is used to suggest the existence of the pathogen. In gram-negative bacteria, a small molecule important in quorum sensing called N-Acyl homoserine lactone (AHL) is released by bacteria and conveys communicating messages among the entire group. Moreover, each species has its own specific AHL molecule. Therefore, AHL is an ideal candidate to identify the existence as well as the size of a specific pathogen population. If the AHL sensing system of one pathogen is introduced into the yeast, the yeast will work as the detector and sense the pathogen. Downstream reporter genes will then be expressed and change the color of the test paper.

Figure 3. The principle of quorum sensing system
(Picture by Tsinghua iGEM team 2013)

Additionally, one feature of yeast unique from other microorganisms is that it has “gender”. Haploid yeasts of type a and type α can mate with each other to form a diploid. We used this feature of yeast to revise our detecting system. Yeasts of type a are utilized as sensors, while yeasts of type α act as reporters. The sensor is targeted to the pathogen of interest and its AHL specifically, while one of the type α yeasts with different reporting colors is selected as the output. There are at least four main advantages of this design: 1) the whole system is divided into two subparts, reducing the difficulty and time to complete each part. 2) The flexibility of the system is increased. Different combinations of sensors and reporters increase the number of possible detectors. 3) During the two-step process, the signal is amplified and easier to be observed. 4) New subparts are convenient to be added to the system, as modification is needed for only one part.

Figure 4. The principle of our portable pathogen detector
(Picture by Tsinghua iGEM team 2013)

To summarize our idea, a portable detector in the form of test paper is designed with genetically modified yeasts on it. The sensing yeast is able to sense the signal AHL from the pathogen and then the reporting yeast will reveal the signal with color change.

Figure 5. Portable test paper is designed for pathogen detection
(Picture by Tsinghua iGEM team 2013)

Reference

[1] Lazcka O, Campo F, Munoz F X. Pathogen detection: a perspective of traditional methods and biosensors[J]. Biosensors and Bioelectronics, 2007, 22(7): 1205-1217.

[2] Nassif X. A revolution in the identification of pathogens in clinical laboratories[J]. Clinical infectious diseases, 2009, 49(4): 552-553.

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