Team:Korea U Seoul/Project/Description

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<h4><p id="title">Rice Guardian</p></h4>
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    <dt>
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<b> A. Background and Abstract </b>
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</dt>
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        <dd>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Bacterial leaf blight disease (BLB) is one of the prominent vascular diseases in irrigated rice. This disease can cause up to 50% yield reduction. Bacterial leaf blight in rice is caused by infection of bacteria known as <i> X. oryzae pv. oryzae </i> (Korean specie: <i> Xanthomonas oryzae </i> KACC10331), a yellow, slime-producing, motile, gram negative rod with a polar flagellum. It reaches the vascular tissue, particularly the xylem, from where it multiplies and spreads throughout the plant. An infected leaf has yellow watersoaked lesions at the margin of its leaf blade. The lesions run parallel along the leaf and when they join together may cover the whole leaf. The infection also accompanies notable symptoms such as seeding wilt, yellow leaf, and panicles sterile.
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</p>
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            <img src="https://static.igem.org/mediawiki/2012/a/ab/KUS_description1.jpg" width="300" />
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            <br>Figure 1. Bacterial leaf blight rice infected by <i> Xanthomonas oryzae </i> KACC10331 <br><font size=0.1>(image source : http://www.knowledgebank.irri.org/RiceDoctor/information-sheets-mainmenu-2730/diseases-mainmenu-2735.html)</font>
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            <br>
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<h3>Binary Full Adder Using Biological Logic Gate System Application</h3>
 
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<br>
 
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<dd>
 
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; An idea which biological component can compute and process data first appeared in 1962. Since then, a number of researches about bio-computing had increased to reach its peak in 2009. Though significant improvement was made, it is still ongoing project and needs support and public interest. Now, bio-computing is subdivided into bio-sensors, databases, bio-informatics, and so on.
 
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</dd>
 
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<br><br><br>
 
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Bacterial leaf blight severely damages agriculture and nation’s economy. BLB is a major concern in countries where the staple food is rice. Bacterial blight is reported to have reduced Asia's annual rice production by as much as 60%. For example, in Japan, about 300,000 to 400,000 hectares of rice were affected by the disease in recent years. There were 20% to 50% yield losses reported in severely infected fields. In Indonesia, losses were higher than those reported in Japan. In India, millions of hectares were severely infected, causing yield losses from 6% to 60%.
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[Figure1.A number of thesis about bio-computing.]  
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</p>
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            <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Because of its devastating impact on rice production, researchers in Korea sequenced full genomic map of some strains in <i>X. oryzae pv. oryzae</i> species, and one of them is <i> Xanthomonas oryzae </i> KACC10331. Still majority of protein functions and mechanisms are unknown, previous researches give us insight on how <i> X. oryzae pv. oryzae </i> causes BLB. Based on previous researches, it was proven that bacterial rax genes (rax A, B, C, P, Q, R, H) and its protein products are responsible for BLB. In fact, RaxP and Q proteins modify proteins called Ax21, a short oligopeptide with a sulfate group, inducing disease and provoking immune response. Then Ax21 is secreted by RaxA, B and C complex. It is known that Ax21 also acts not only as a ligand for plant receptor Xa21, but also as a quorum sensing molecule. Ax21 is then detected by RaxR and H proteins informing the presence of plant host nearby. Yet, the mechanism how Ax21 induces BLB in rice remains unclear.
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[Figure 2. The IBM 702: a computer used by the first generation of AI researchers]
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            <img src="https://static.igem.org/mediawiki/2012/a/a7/KUS_description2.png" width="500" />
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<br><br><br>
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            <br>Figure 2. Genes responsible for Ax21 production, a main source of pathogen induced BLB (figure adapted from ref. 5)
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<b>1) Cell-based computer development</b>
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            </div>
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</dd>
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        <br><br><br>
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        <dt>
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<b> B. Project overview </b>
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</dt>
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        <dd>
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<p>
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            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Unfortunately, there is no way to stop BLB. Only several precautionary measures were given to farmers. Several attempts to tackle spreading of disease were ineffective; for example, genetically modified rice was not effective. It is evident that solution for reducing BLB is in killing pathogen, not in rice. Thus we decided to create bacteria that are able to detect and kill <i> X. oryzae </i> KACC10331 (Korean specie). Since Ax21 is the major cause that induces BLB and ever present molecule that signifies presence of <i> X. oryzae </i> KACC10331, we decided to make synthetic bacteria that detects Ax21 and furthermore kill them. We will use the promoter of raxR to detect Ax21. As a result of transcription activation, gene will synthesize bacteriocin to kill the bacteria. We hope our project can minimize the damage caused by the bacteria.
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</p>
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            <img src="https://static.igem.org/mediawiki/2012/1/1a/KUS_Rax_mrfp.png" width="500" />
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            <br>Figure 3. Plasmid construction of Rice Guardian
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</dd>
<br><br>
<br><br>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Our project, Bacterial Logic Gate, is to design 2 binary full adder by using cellular component. Our team thinks making computer out of biological component is possible in the future. The bacterial calculator is the first one. Although many researches and experiment should be done in order to make cell-based computer, completing 2 bit adder is the starter. <br>
 
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No one in 1940 believed it was possible for non-organic material to process data. When the computer was invented,it was a revolutionary remark. Like the first computer, ENIAC, took one day to process its data, bacterial calculator may seem useless at this moment. <br>However, sum of these small changes the world. When researches discover more about biology, advancement on bio-computing will be realized. 
 
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<b>2) Application of AND, XOR, OR gate into other area</b>
 
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Binary full adder is composed of AND, XOR, and OR gate. Each gate is separable and independent from each other. On the other hand, adding each gate is also possible and its alignment leads to different outcome. That is to say, combination of AND, XOR, and OR gate may lead to other application such as Hash function. Hash function is encryption of data and commonly used. Many iGEM teams developed this idea and it was successful. Apart for this, we believe combination AND, XOR, and OR gate can imitate already existing cellular mechanism.
 
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</dd>
 
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<br><br><br>
 
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<h3>Rice Guardian Application</h3>
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<h4><p id="title">Binary Full Adder Using Bacterial Logic Gate System</p></h4>
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<hr width=1>
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    <dt>
<br>
<br>
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<b>A. Background and Abstract</b>
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</dt>
<dd>
<dd>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Recently there are many problems regarding bacterial leaf blight disease(BLB). Bacterial leaf blight, an example of plant disease, is an infamous vascular disease in irrigated rice. This disease can cause up to 50% yield reduction. Bacterial leaf blight in rice is caused by infection of bacteria known as Xanthomonas oryzae KACC10331.<br>
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<p>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Bacterial leaf blight severely damages agriculture and nation’s economy. BLB is a major concern in countries where the staple food is rice. Bacterial blight is reported to have reduced Asia's annual rice production by as much as 60%. For example, in Japan, about 300,000 to 400,000 hectares of rice were affected by the disease in recent years. There were 20% to 50% yield losses reported in severely infected fields. In Indonesia, losses were higher than those reported in Japan. In India, millions of hectares were severely infected, causing yield losses from 6% to 60%. <br>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Logic circuit is an operation system consists of sets of various logic gates such as AND, OR, XOR, NOR etc.. that interact with each other to draw certain outputs from input signals. Attempts to make biological logic gates have been tried by a lot of researchers due to their lots of applications and some meaningful results have been introduced. Our project adopted some methods to build biological XOR, AND, and OR gates, and by arranging the gates in proper order with certain supplementary system our team has designed, we are expecting a working full adder to complete biologically operating binary adder.
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; To solve this problem, we performed gene manipulation which can kill Xanthomonas oryzae KACC10331, the causing bacteria of BLB. We designed genetically modified E. coli which can recognize the particles from Xanthomonas oryzae KACC10331and after recognizing them, secreting substance that kills Xanthomonas oryzae KACC10331. By this method, we think we can partially prevent BLB.
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</p>
</dd>
</dd>
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<br><br>
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<br>&nbsp;
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<b>1) Solution for Food Shortage</b>
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<br><br>
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<dt>
<dt>
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Eco-friendly
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<b>B. Project overview</b>
</dt>
</dt>
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<br>
 
<dd>
<dd>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Advantage of Rice Guardian is eco-friendly.Because agricultural chemicals such as pesticide and herbicide aren't used, it doesn’t damage ecosystem. Since agricultural chemicals are bad for human health, the use of Rice Guardian may contribute to longer lifespan.  
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<p>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; In our project, a kind of major quorum sensing molecules, AHLs, were used as signaling molecules mediating delivery of information or data. For different input signals 3OC6 - 3-oxo-C6 HSL, 3OC12 - 3-oxo-C12 HSL and products of hrpR and S genes were used. Also, as a common mediator in signal transduction between logic gates, C4 AHL was used. For the project, our team used 9 types of bricks and semi-permeable membranes to complete the circuit. We made a model for the project adopting Hall equation and setting some key variables. Then we proceeded simulation for the model. Due to conditions in our laboratory and time limit, we were unable to do actual wet-lab experiments that show how well our model predicted the results and give some key variables which could provide us more sophisticated information to elaborate our model.
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</p>
</dd>
</dd>
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<br><br>
 
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<dt>
 
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Application into other crops<br>
 
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</dt>
 
<br>
<br>
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<dd>
 
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Rice Guardian can be used in variety of crops as well. Xanthomonas species can infect as a wide variety of species including pepper, citrus, cotton, tomato, broccoli, cabbage, and soybeans as well as rice. Rice Guardian can play an important role in reducing the infection of many other crop.
 
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<b>Increase in Crop productivity</b>
 
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<br>
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<dd>
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<h4><p id="title">References</p></h4>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Increase in crop production is expected. By killing Xanthomonas oryzae KACC10331, other diseases caused by Xanthomonas genus such as bacterial canker, bacterial shot hole, black rot can be prevented. Eventually the strongest effect is increasing the crop production . It could be the solution for food shortage.
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    <dt>
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</dd>
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<ul>
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<br><br>
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                  <li>Sang-Wook Han, Pamela C. Ronald et al. 2011. Small protein-mediated quorum sensing in a gram-negative bacterium. PLoS ONE. 6:12</li>
 +
            <li>A. Elings,,P.R. Reddy, T. Marimuthuc, W.A.H. Rossing, M.J.W. Jansene, P.S. Tengf, Ricebacterialleafblight: field experiments, systems analysis and damage coefficients, Elsevier, volume 51, issue 2-1</li>
 +
                <li>S. S. Gnanamanickam, V. BrindhaPriyadarisini, N. N. Narayanan, PreetiVasudevan and S. Kavitha, . 1999. An overview of bacterial blight disease of rice and strategies for its management , CURRENT SCIENCE, VOL. 77, NO. 11</li>
 +
                <li>Suparyono, JLA Catindig, FA dela Peña, and IP Oña, Rice knowledge bank, IRRE</li>
 +
                <li>Sang-Wook Han, Sang-Won Lee and Pamela C Ronald. 2011. Secretion, modification, and regulation of Ax21, Current Opinion in Microbiology. 14:62–67</li>
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            </ul>       
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</dt>
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        <dd>
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<br>
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<b>2) Protecting Endangered Species –Cyperussemifertilis(Sedge)</b>
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                <a href="http://korea.ac.kr">  
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<img src="https://static.igem.org/mediawiki/2012/a/ab/KUS_Ku.jpg" style="padding-top:10px;" width="80px" ></a>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Cyperus is a large genus of about 600 species of sedges, distributed throughout all continents in both tropical and temperate regions. They are annual or perennial plants, mostly aquatic and growing in still or slow-moving water up to 0.5 m deep. The species vary greatly in size, with small species only 5 cm tall, while others can reach 5 m in height. Common names include papyrus sedges, flatsedges, nutsedges, umbrella-sedges and galingales.<br>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The stems are circular in cross-section in some, triangular in others, usually leafless for most of their length, with the slender grass-like leaves at the base of the plant, and in a whorl at the apex of the flowering stems. The flowers are greenish, and wind pollinated; they are produced in clusters among the apical leaves. The seed is a small nutlet. <br>
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                <a href="http://compbio.korea.ac.kr/wiki/index.php/Main_Page"> <img src="https://static.igem.org/mediawiki/2012/5/5d/KUS_Csbl.jpg" width="82px" ></a>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; The Scientific Committee, established by the Threatened Species Conservation Act, has made a Final Determination to list the sedgeCyperussemifertilis S.T. Blake as an ENDANGERED SPECIES on Part 1 of Schedule 1 of the Act. Listing of Endangered Species is provided for by Part 2 of the Act. <br>
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Cyperussemifertilis is subspecies of sadge and is also attacked by Xanthomonas oryzae KACC10331. Since it is endangered species, Rice guardian may prevent infection by Xanthomonas oryzae KACC10331. Many other plant species also attacked by Xanthomonas oryzae KACC10331 can be protected.<br>
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                <a href="http://ctl.korea.ac.kr/index.ctl"> <img src="https://static.igem.org/mediawiki/2012/4/49/KUS_Ctl.jpg" width="75px" ></a>
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                <a href="http://www.cosmogenetech.com/ko">
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<img src="https://static.igem.org/mediawiki/2012/8/81/KUS_Cosmo.jpg" width="75px" height="70"></a>
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                <a href="http://www.youtube.com/watch?v=vr7TlPjyAEg">
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<img src="https://static.igem.org/mediawiki/2012/c/c4/KUS_Youtube.jpg" width="65px" ></a>
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                <a href="http://www.facebook.com/2012iGEM.KU"> <img src="https://static.igem.org/mediawiki/2012/7/71/KUS_Facebook.jpg" width="52px"></a>
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                <a href="https://twitter.com/iGEM_KU2012"> <img src="https://static.igem.org/mediawiki/2012/4/4d/KUS_Twitter.jpg" width="63px"></a>   
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Latest revision as of 03:20, 27 September 2012

Rice Guardian

A. Background and Abstract

     Bacterial leaf blight disease (BLB) is one of the prominent vascular diseases in irrigated rice. This disease can cause up to 50% yield reduction. Bacterial leaf blight in rice is caused by infection of bacteria known as X. oryzae pv. oryzae (Korean specie: Xanthomonas oryzae KACC10331), a yellow, slime-producing, motile, gram negative rod with a polar flagellum. It reaches the vascular tissue, particularly the xylem, from where it multiplies and spreads throughout the plant. An infected leaf has yellow watersoaked lesions at the margin of its leaf blade. The lesions run parallel along the leaf and when they join together may cover the whole leaf. The infection also accompanies notable symptoms such as seeding wilt, yellow leaf, and panicles sterile.


Figure 1. Bacterial leaf blight rice infected by Xanthomonas oryzae KACC10331
(image source : http://www.knowledgebank.irri.org/RiceDoctor/information-sheets-mainmenu-2730/diseases-mainmenu-2735.html)

     Bacterial leaf blight severely damages agriculture and nation’s economy. BLB is a major concern in countries where the staple food is rice. Bacterial blight is reported to have reduced Asia's annual rice production by as much as 60%. For example, in Japan, about 300,000 to 400,000 hectares of rice were affected by the disease in recent years. There were 20% to 50% yield losses reported in severely infected fields. In Indonesia, losses were higher than those reported in Japan. In India, millions of hectares were severely infected, causing yield losses from 6% to 60%.

     Because of its devastating impact on rice production, researchers in Korea sequenced full genomic map of some strains in X. oryzae pv. oryzae species, and one of them is Xanthomonas oryzae KACC10331. Still majority of protein functions and mechanisms are unknown, previous researches give us insight on how X. oryzae pv. oryzae causes BLB. Based on previous researches, it was proven that bacterial rax genes (rax A, B, C, P, Q, R, H) and its protein products are responsible for BLB. In fact, RaxP and Q proteins modify proteins called Ax21, a short oligopeptide with a sulfate group, inducing disease and provoking immune response. Then Ax21 is secreted by RaxA, B and C complex. It is known that Ax21 also acts not only as a ligand for plant receptor Xa21, but also as a quorum sensing molecule. Ax21 is then detected by RaxR and H proteins informing the presence of plant host nearby. Yet, the mechanism how Ax21 induces BLB in rice remains unclear.



Figure 2. Genes responsible for Ax21 production, a main source of pathogen induced BLB (figure adapted from ref. 5)



B. Project overview

     Unfortunately, there is no way to stop BLB. Only several precautionary measures were given to farmers. Several attempts to tackle spreading of disease were ineffective; for example, genetically modified rice was not effective. It is evident that solution for reducing BLB is in killing pathogen, not in rice. Thus we decided to create bacteria that are able to detect and kill X. oryzae KACC10331 (Korean specie). Since Ax21 is the major cause that induces BLB and ever present molecule that signifies presence of X. oryzae KACC10331, we decided to make synthetic bacteria that detects Ax21 and furthermore kill them. We will use the promoter of raxR to detect Ax21. As a result of transcription activation, gene will synthesize bacteriocin to kill the bacteria. We hope our project can minimize the damage caused by the bacteria.


Figure 3. Plasmid construction of Rice Guardian


Binary Full Adder Using Bacterial Logic Gate System


A. Background and Abstract

          Logic circuit is an operation system consists of sets of various logic gates such as AND, OR, XOR, NOR etc.. that interact with each other to draw certain outputs from input signals. Attempts to make biological logic gates have been tried by a lot of researchers due to their lots of applications and some meaningful results have been introduced. Our project adopted some methods to build biological XOR, AND, and OR gates, and by arranging the gates in proper order with certain supplementary system our team has designed, we are expecting a working full adder to complete biologically operating binary adder.


 
B. Project overview

          In our project, a kind of major quorum sensing molecules, AHLs, were used as signaling molecules mediating delivery of information or data. For different input signals 3OC6 - 3-oxo-C6 HSL, 3OC12 - 3-oxo-C12 HSL and products of hrpR and S genes were used. Also, as a common mediator in signal transduction between logic gates, C4 AHL was used. For the project, our team used 9 types of bricks and semi-permeable membranes to complete the circuit. We made a model for the project adopting Hall equation and setting some key variables. Then we proceeded simulation for the model. Due to conditions in our laboratory and time limit, we were unable to do actual wet-lab experiments that show how well our model predicted the results and give some key variables which could provide us more sophisticated information to elaborate our model.



References

  • Sang-Wook Han, Pamela C. Ronald et al. 2011. Small protein-mediated quorum sensing in a gram-negative bacterium. PLoS ONE. 6:12
  • A. Elings,,P.R. Reddy, T. Marimuthuc, W.A.H. Rossing, M.J.W. Jansene, P.S. Tengf, Ricebacterialleafblight: field experiments, systems analysis and damage coefficients, Elsevier, volume 51, issue 2-1
  • S. S. Gnanamanickam, V. BrindhaPriyadarisini, N. N. Narayanan, PreetiVasudevan and S. Kavitha, . 1999. An overview of bacterial blight disease of rice and strategies for its management , CURRENT SCIENCE, VOL. 77, NO. 11
  • Suparyono, JLA Catindig, FA dela Peña, and IP Oña, Rice knowledge bank, IRRE
  • Sang-Wook Han, Sang-Won Lee and Pamela C Ronald. 2011. Secretion, modification, and regulation of Ax21, Current Opinion in Microbiology. 14:62–67