Difference between revisions of "Team:NEFU China/Design"

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<a href="https://2018.igem.org/Team:NEFU_China"><img id="home" src="https://static.igem.org/mediawiki/2018/a/a9/T--NEFU_China--_Home.png">HOME</a>
 
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<a href="https://2018.igem.org/Team:NEFU_China/Background"><img id="project" src="https://static.igem.org/mediawiki/2018/1/14/T--NEFU_China--_PROJECT.png">PROJECT</a>
 
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<li><a href="https://2018.igem.org/Team:NEFU_China/Background" target="_self">BACKGROUND</a></li>
 
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<li><a href="https://2018.igem.org/Team:NEFU_China/Description" target="_self">DESCRIPTION</a></li>
 
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<li><a href="https://2018.igem.org/Team:NEFU_China/Design" target="_self">DESIGN</a></li>
 
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<li><a href="https://2018.igem.org/Team:NEFU_China/Coding book" target="_self">CODING BOOK</a></li>
 
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  <a href="https://2018.igem.org/Team:NEFU_China/Basic parts"><img id="parts" src="https://static.igem.org/mediawiki/2018/5/58/T--NEFU_China--_PARTS.png">PARTS</a>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Basic parts" target="_self">BASIC PARTS</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Composite parts" target="_self">COMPOSITE PARTS</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Improve" target="_self">IMPROVEMENT PARTS</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Parts collection" target="_self">PARTS COLLECTION</a></li>
 
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  <a href="https://2018.igem.org/Team:NEFU_China/Lock_Key"><img id="results" src="https://static.igem.org/mediawiki/2018/6/62/T--NEFU_China--_RESULTS.png">RESULTS</a>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Lock_Key" target="_self">LOCK &amp; KEY</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Suicide" target="_self">SUICIDE</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Splicing" target="_self">SPLICING</a></li>
 
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  <a href="https://2018.igem.org/Team:NEFU_China/Model"><img id="model" src="https://static.igem.org/mediawiki/2018/0/0c/T--NEFU_China--_MODEL.png">MODEL</a>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Model" target="_self">OVERVIEW</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Model1" target="_self">MODEL1</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Model2" target="_self">MODEL2</a></li>
 
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  <a href="https://2018.igem.org/Team:NEFU_China/Software"><img id="software" src="https://static.igem.org/mediawiki/2018/c/c0/T--NEFU_China--_SOFTWARE.png">SOFTWARE</a>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Software" target="_self">OVERVIEW</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Software1" target="_self">SOFTWARE1</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Software2" target="_self">SOFTWARE2</a></li>
 
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  <a href="https://2018.igem.org/Team:NEFU_China/Attributions"><img id="team" src="https://static.igem.org/mediawiki/2018/5/50/T--NEFU_China--_TEAM.png">TEAM</a>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Attributions" target="_self">ATTRIBUTIONS</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Members" target="_self">MEMBERS</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Sponsoring" target="_self">SPONSORING</a></li>
 
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  <a href="https://2018.igem.org/Team:NEFU_China/Human_Practices"><img id="humanpractice" src="https://static.igem.org/mediawiki/2018/9/91/T--NEFU_China--_HUMANPRACTICE.png">HUMAN PRACTICE</a>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Silver" target="_self">SILVER</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Collaborations" target="_self">COLLABORTION</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Public_Engagement" target="_self">EDUCATION &amp; PUBLIC ENGAGEMENT</a></li>
 
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  <a href="https://2018.igem.org/Team:NEFU_China/Notebook"><img id="notebook" src="https://static.igem.org/mediawiki/2018/c/cb/T--NEFU_China--_NOTEBOOK.png">NOTEBOOK</a>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Notebook" target="_self">OVERVIRW</a></li>
 
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  <li><a href="https://2018.igem.org/Team:NEFU_China/Protocol" target="_self">PROTOCOL</a></li>
 
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<h1>Design</h1>
 
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    <p>
 
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To build the system, we first established the one-to-one matches between the English alphabets and the codons in yeast; then the expressed information was written in the mRNA sequences. Afterwards, we transferred and integrated the encoding DNA sequences into the yeast genome to store and deliver the message. To prevent deciphering of the information, we have added introns that can be spliced to confuse the stealers. We included additional measures of molecular biology, which are can block unauthorized access and ensure the safety of stored information. Compared to the electronic or digital storage and transfer systems, ours approach is extremely secure since it cannot be affected by cyber attacks. Moreover, our system can easily provide customized services, because it is not difficult to adjust the “message & keys” and the biosecurity layers according to different requirements.<br>
 
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So far, the national trends in costs for wages, salaries, and benefits have glossed over these concerns. The growth in labor costs continued to slow in the second quarter - a pattern that held true in all major regions. However, the slowdown in labor costs is due solely to sharp cutbacks in what companies, mainly large corporations, are paying for benefits, which make up about a fourth of total compensation costs nationally. Because of slower growth in health care costs, workers' compensation, and state unemployment insurance, benefits grew only 2.6% during the past year, the lowest pace on record.
 
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</li>
 
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<li>
 
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So far, the national trends in costs for wages, salaries, and benefits have glossed over these concerns. The growth in labor costs continued to slow in the second quarter - a pattern that held true in all major regions. However, the slowdown in labor costs is due solely to sharp cutbacks in what companies, mainly large corporations, are paying for benefits, which make up about a fourth of total compensation costs nationally. Because of slower growth in health care costs, workers' compensation, and state unemployment insurance, benefits grew only 2.6% during the past year, the lowest pace on record.
 
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<p>
 
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The Japanese have their electronics, the Germans their engineering. But when it comes to command of global markets, the U.S. owns the service sector.<br>
 
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</p>
 
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<img src="https://static.igem.org/mediawiki/2018/5/58/T--NEFU_China--Figure_1.png" alt="Figure1" id="Figure1-img">
 
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<h2 id="Figure1-title">Figure 1: This is Figure 1.</h2>
 
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<p>
 
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So far, the national trends in costs for wages, salaries, and benefits have glossed over these concerns. The growth in labor costs continued to slow in the second quarter - a pattern that held true in all major regions. However, the slowdown in labor costs is due solely to sharp cutbacks in what companies, mainly large corporations, are paying for benefits, which make up about a fourth of total compensation costs nationally. Because of slower growth in health care costs, workers' compensation, and state unemployment insurance, benefits grew only 2.6% during the past year, the lowest pace on record.<br>
 
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<hr>
 
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<br>
 
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<h1>CODING</h1>
 
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<p>
 
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First, we were planning to convert English sentences into oligonucleotide sequences. So we designed the CODING module as following:
 
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<br>
 
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Every letter has its own frequency in English words, so does each codon in organisms. Therefore, we created a coding list, in which each letter corresponds to several codons with the same frequencies. In addition, we composed a program that can easily convert sentences into DNA sequences. Through this module, we achieved the transformation from English words to oligonucleotide sequences.（配图）
 
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</p>
 
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<p>
 
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So far, the national trends in costs for wages, salaries, and benefits have glossed over these concerns. The growth in labor costs continued to slow in the second quarter - a pattern that held true in all major regions. However, the slowdown in labor costs is due solely to sharp cutbacks in what companies, mainly large corporations, are paying for benefits, which make up about a fourth of total compensation costs nationally. Because of slower growth in health care costs, workers' compensation, and state unemployment insurance, benefits grew only 2.6% during the past year, the lowest pace on record.<br>
 
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So far, the national trends in costs for wages, salaries, and benefits have glossed over these concerns. The growth in labor costs continued to slow in the second quarter - a pattern that held true in all major regions. However, the slowdown in labor costs is due solely to sharp cutbacks in what companies, mainly large corporations, are paying for benefits, which make up about a fourth of total compensation costs nationally. Because of slower growth in health care costs, workers' compensation, and state unemployment insurance, benefits grew only 2.6% during the past year, the lowest pace on record.<br>
 
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</p>
 
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<img src="https://static.igem.org/mediawiki/2018/2/2f/T--NEFU_China--Figure_2.png" alt="Figure2" id="Figure2-img">
 
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<h2 id="Figure2-title">Figure 2: This is Figure 2.</h2>
 
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</td>
 
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</table>
 
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<p>
 
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The Japanese have their electronics, the Germans their engineering. But when it comes to command of global markets, the U.S. owns the service sector.<br>
 
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</p>
 
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<br>
 
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<hr>
 
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<br>
 
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<h1>WRITE IN</h1>
 
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<p>
 
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In the WRITE IN module, we transferred and integrated the DNA sequences carrying the information into the yeast for message storage and transmission.
 
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<br>
 
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First, after finding an appropriate homology region in the yeast genome, we added homology arm sequences to flank the message-carrying DNA sequence. Then, we inserted the DNA sequence into the yeast genome by homologous recombination.
 
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<h1>LOCKING</h1>
 
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<p>
 
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Just encrypting the information by CODING is not safe enough. To strengthen the security of the message, we designed the LOCKING module as following:
 
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<br>
 
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The main part of the LOCKING module is a DNA fragment with a stem loop structure generated by introducing the stem loop in the upstream of the message-carrying DNA sequence . The stem loop structure blocked the movement of RNAP, which caused transcription abortion. In this way, we prohibited the unnecessary expressions of the message. (配图）
 
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<br>
 
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<h1>MISLEADING</h1>
 
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<p>
 
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In order to prevent the information in DNA from being stolen, we integrated a MISLEADING module into the system, which is capable of confusing the stealers by the following measures:
 
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<br>
 
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<h1>Multi-carrier</h1>
 
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<p>
 
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Our system includes different types of defective yeast spores as the information carriers which harbored distinctive message, and only one of them carried the right information. (配动图）
 
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<br>
 
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<hr>
 
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<br>
 
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<h1>Insertion of introns</h1>
 
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<p>
 
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By inserting introns into the message-carrying DNA sequences , we changed the contents of the information. If the stealers are trying to extract the information by DNA sequencing directly, only the wrong message can be read out. (配动图）
 
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<hr>
 
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<br>
 
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<h1>Mutant</h1>
 
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<p>
 
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We also used EMS mutagenesis to increase the polymorphism of the yeast genome sequences, which further raised the difficulties for deciphering the information.
 
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<hr>
 
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<br>
 
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<h1>TIME DELAY SUICIDE</h1>
 
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<p>
 
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As we know, any puzzle will be solved eventually as long as the research time is long enough. With the time going by, all of our barriers could be eventually defeated. Therefore, we added the module for limiting the time of reading out the information by the suicide of yeast spores:
 
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<br>
 
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While the carrier yeast spore was type a, we also used another one called type α. Both types of yeast have receptors that reciprocally recognize each other. When the two types of yeast were co-cultured to a certain density, type α secreted α factor that bound to the membrane proteins on the cell surfaces of type a to pass signals. Then the cells of type a receiving the signals induced the expression of Bax(α) that has been engineered into the yeast genome. The product of the suicide gene Bax(α) could lead to apoptosis of the message-carrying yeast. (配动图）
 
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</p>
 
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<br>
 
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<hr>
 
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<br>
 
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<h1>READ OUT</h1>
 
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<p>
 
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We used the appropriate medium to select the yeast carrying the true information. After getting the right yeast, we added the "key" (a plasmid that can transcribe siRNA) transformed into yeast cells to bind and resolve the stem-loop structure, leading to RNA transcription of the stored message. Only the person with the right key to a given lock can obtain the information that we wanted to convey. Then, the message can be acquired by DNA sequencing and data analysis.
 
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<div id="background-reference">
 
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<h1>Reference</h1>
 
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<p> <a href="#"> [1] Pu, Jinyue and Zinkus-Boltz, Julia and Dickinson, Bryan C. (2017) Evolution of a split RNA polymerase as a versatile biosensor platform. <em><em>Nat Chem Biol 13</em></em> , 432-438 </a>
 
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<br>
 
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<a href="#"> [2] Pu, Jinyue and Zinkus-Boltz, Julia and Dickinson, Bryan C. (2017) Evolution of a split RNA polymerase as a versatile biosensor platform. <em><em>Nat Chem Biol 13</em></em> , 432-438 </a>
 
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<br>
 
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<a href="#"> [3] Pu, Jinyue and Zinkus-Boltz, Julia and Dickinson, Bryan C. (2017) Evolution of a split RNA polymerase as a versatile biosensor platform. <em><em>Nat Chem Biol 13</em></em> , 432-438 </a>
 
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<br>
 
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<a href="#"> [4] Pu, Jinyue and Zinkus-Boltz, Julia and Dickinson, Bryan C. (2017) Evolution of a split RNA polymerase as a versatile biosensor platform. <em><em>Nat Chem Biol 13</em></em> , 432-438 </a>
 
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<br>
 
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<a href="#"> [5] Pu, Jinyue and Zinkus-Boltz, Julia and Dickinson, Bryan C. (2017) Evolution of a split RNA polymerase as a versatile biosensor platform. <em><em>Nat Chem Biol 13</em></em> , 432-438 </a>
 
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<br>
 
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<a href="#"> [6] Pu, Jinyue and Zinkus-Boltz, Julia and Dickinson, Bryan C. (2017) Evolution of a split RNA polymerase as a versatile biosensor platform. <em><em>Nat Chem Biol 13</em></em> , 432-438 </a>s
 
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<h1>Userfull links</h1>
 
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<h2>
 
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<a href="https://2018.igem.org/Team:NEFU_China/NEFU_China">Home</a>
 
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&nbsp;&nbsp;&nbsp;&nbsp;
 
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<a href="https://2018.igem.org/Team:NEFU_China/MODEL/Overview">Model</a>
 
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&nbsp;&nbsp;&nbsp;
 
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<a href="https://2018.igem.org/Team:NEFU_China/PROJECT/Description">Project</a>
 
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    <a href="https://2018.igem.org/Team:NEFU_China/SOFTWARE/Overview">Software</a>
 
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</h2>
 
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<a href="https://2018.igem.org/Team:NEFU_China/PARTS/Basic parts">Parts</a>
 
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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<a href="https://2018.igem.org/Team:NEFU_China/TEAM/Members">Teams</a>
 
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&nbsp;&nbsp;
 
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<a href="https://2018.igem.org/Team:NEFU_China/RESULTS/Leaders">Results</a>
 
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<a href="https://2018.igem.org/Team:NEFU_China/NOTEBOOK/Overview">Notebook</a>
 
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<a href="https://2018.igem.org/Team:NEFU_China/HUMAN PRACTICE/Gold_integrated">Human &nbsp;Practice</a>
 
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<h1>Follow us</h1>
 
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<img alt="facebook" src="https://static.igem.org/mediawiki/2018/b/b5/T--NEFU_China--facebook.png">
 
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<img alt="wehchat" src="https://static.igem.org/mediawiki/2018/c/ca/T--NEFU_China--wechat.png">
 
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        <img alt="facebook" src="https://static.igem.org/mediawiki/2018/b/b5/T--NEFU_China--facebook.png">
 
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&nbsp;&nbsp;&nbsp;
 
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        <img alt="twitter" src="https://static.igem.org/mediawiki/2018/3/36/T--NEFU_China--twitter.png">
 
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<img alt="wehchat" src="https://static.igem.org/mediawiki/2018/c/ca/T--NEFU_China--wechat.png">
 
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<h1>Contact us</h1>
 
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<h2>iGEM-NEFU_China2018</h2>
 
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<h2>Email: hexinglu@nefu.edu.cn</h2>
 
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<h3>No.26 Hexing Road, Xiangfang <br>District, Harbin, Heilongjiang <br>Province 150000</h3>
 
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Latest revision as of 12:44, 17 October 2018