Difference between revisions of "Team:CGU Taiwan/Parts"

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<h1>Parts</h1>
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/InterLab">INTERLAB</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/Parts">PARTS</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/Acknowledgement">ACKNOWLEDGEMENT</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/Engagement">PUBLIC ENGAGEMENT</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/TWConference">2017 iGEM TAIWAN CONFERENCE</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/Applied_Design">APPLIED DESIGN</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/Entrepreneurship">ENTREPRENEURSHIP</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/Hardware">HARDWARE</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/Measurement">MEASUREMENT</a>
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      <a href="https://2017.igem.org/Team:CGU_Taiwan/InterLab">INTERLAB</a>
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<h1>Introduction</h1>
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<p style="font-size:150%"> To achieve the localize deinking, we built a system that can detect the ink on the paper and using red light LED matrix to stimulate the yeast in some specific locations to produce enzymes.
 +
The paper will be photographed and sent to computer before we spread the yeast on it. Our image process program using OpenCV function library to decode the JPG image file and do the edge offset, then decide which area have ink. After the LED matric data be calculated, the program using RS-232 serial communication standard sends this data to Arduino. Arduino collects the data and then sends it to Max7219 microcontroller to light up the LED matrix to stimulate the yeast produce enzymes.
 +
The system accepts any shape of paper which is under the size of the device, and the device can be easily scale up by connecting more led matric. This shows the possibility of factory scale localize deinking. </p>
 +
<h1>Parts</h1>
 +
<p style="font-size:150%"> We had designed eight new biobricks in our project, three of them are composite
 +
parts and the rest are single biobricks. Our parts were designed to be use as a light
 +
inducible deinking enzyme secreting system, the codons were optimized and
 +
designed for expression in Saccharomyces cerevisiae.</p>
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<p align="center"><img src="https://static.igem.org/mediawiki/2017/f/f3/CguPart.png" width="40%"></p>
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<h2>BBa_K2376000</h2>
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<h3>endo-1,4-beta-xylanase A</h3>
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<p style="font-size:150%"> endo-1,4-beta-xylanase A ORF sequence took from Neocallimastix patriciarum (http://www.uniprot.org/uniprot/P29127), a rumen fungi normally found in goat rumen. This enzyme digests xylan (hemicellulose) into oligosaccharides (xylobiose and xylose) in the working condition of 30-35-degree Celcius and pH4.5-5.5. The sequence had been optimized to a Saccharomyces cerevisiae codon and had replaced the original signal peptide (1-18 amino acids) into Saccharomyces cerevisiae SUC2 secreting signal. This enzyme was used for digesting paper fibers in our project, it could be used in paper pulping, deinking, cleaning processes or other fiber related digestion.</p>
  
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<h2>BBa_K2376001
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</h2>
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<h3>endo-beta-1,4-glucanase B
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</h3>
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<p style="font-size:150%"> endo-beta-1,4-glucanase B ORF sequence took from Aspergillus oryzae (http://www.uniprot.org/uniprot/Q2UPQ4). This enzyme digests cellulose into oligosaccharides in the working condition of 30-35-degree Celcius and pH4.5-5.5. The sequence had been optimized to a Saccharomyces cerevisiae codon and had replaced the original signal peptide (1-17 amino acids) into Saccharomyces cerevisiae SUC2 secreting signal. This enzyme was used for digesting paper fibers in our project, it could be used in paper pulping, deinking, cleaning processes or other fiber related digestion.
 +
</p>
  
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<h2>BBa_K2376002
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</h2>
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<h3>Lipase
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</h3>
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<p style="font-size:150%">Lipase ORF sequence took from Rhizopus niveus (http://www.uniprot.org/uniprot/P61871). This enzyme hydrolyzes ester bonds of triglycerides in the working condition of 30-35-degree Celcius and pH4.5-5.5. The sequence had been optimized to a Saccharomyces cerevisiae codon and had replaced the original signal peptide (1-26 amino acids) into Saccharomyces cerevisiae SUC2 secreting signal. This enzyme was used for digesting ink in our project (such as soil bean ink), it could deinking process or lipid digesting.
 +
</p>
  
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<h2>BBa_K2376003
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</h2>
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<h3>ste12 promoter
 +
</h3>
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<p style="font-size:150%"> Upstream 500bp of a pheromone related pathway transcription factor of Saccharomyces cerevisiae (http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2010.07728.x/full). This promoter contains four PREs (pheromone-response element) that allows STE12 protein dimer binds on it. This is a very complex pathway induced by alpha or a factors, note that several inhibiting and antagonist pathway involves in the ste12 expression. However, the positive up-regulation feedback of the ste12 itself gives the potential of acting as an amplifier in various response pathway. We had designed this promoter for improving the expression of protein level after light inducing promoter systems. (https://www.ncbi.nlm.nih.gov/pubmed/2193847)
 +
</p>
  
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<h5>Adding parts to the registry</h5>
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<h2>BBa_K2376004
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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</h2>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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<h3>ste12 protein
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</div>
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</h3>
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<p style="font-size:150%">STE12 is a pheromone related pathway transcription factor of Saccharomyces cerevisiae (http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2010.07728.x/full), it acts as the final controller of several pheromone induced protein expression. This protein would form a dimer and can bind to PREs (pheromone-response element) sequence. This is a very complex pathway induced by alpha or a factors in haploid budding yeast, note that several inhibiting and antagonist pathway involves in the ste12 expression. However, the positive up-regulation feedback of the ste12 itself gives the potential of acting as an amplifier in various response pathway. We had designed this promoter for improving the expression of protein level after light inducing promoter systems. (https://www.ncbi.nlm.nih.gov/pubmed/2193847)
 +
</p>
  
 +
<h2>BBa_K2376005
 +
</h2>
 +
<h3>Glucanase and Xylanase with ste12 promoter
 +
</h3>
 +
<p style="font-size:150%"> This is a composite part combining endo-1,4-beta-xylanase A and Probable endo-beta-1,4-glucanase B from Neocallimastix patriciarum and Aspergillus oryzae, respectively. The protein codon had been optimized to Saccharomyces cerevisiae codon and had added a SUC2 secrete signal. Xylanase (BBa_K2376000) and glucanase (BBa_K2376001) were both promote by a ste12 promoter (BBa_K2376003) and followed by a TEF terminator (BBa_K801011). Kozak sequence was added in front of the start codon of both proteins. This composite part is used to induce the expression of deinking enzymes, it can be either activated by the induction of pheromone or any pathway that overexpress ste12 protein (BBa_K2376004). The ste12 transcription factor could bind to the ste12 promoter which has PREs, there is also a ste12 sequence in the yeast genome, which could cause a positive feedback of ste12 for binding and promote itself. The sequence of expression two proteins was reversed and formed a head-to-head sequence, wishing to lower the stereo obstacle the entry of RNA polymerase II while transcription. This composite biobrick remains central to our project. The two enzymes are the main enzymes that deink the recycled paper.
 +
</p>
  
 +
<h2>BBa_K2376006
 +
</h2>
 +
<h3></h3>
 +
<p style="font-size:150%">In this biobrick, STE12 protein, a transcription factor, can be driven by the system we made or the pheromone response system originally in yeast. Once the STE12 protein has been made, it initiates the positive feedback in yeast genome. The mass production of STE12 protein helps increase STE12 promoter to lift the expression of downstream gene, Lipase, Xylanase and Glucanase. Besides, Lipase is also constructed in this biobrick.
 +
</p>
  
 +
<h2>BBa_K2376007
 +
</h2>
 +
<h3>improved GAL4 based yeast light-switchable promoter system</h3>
 +
<p style="font-size:150%">This biobricks was made from BBa_K801042. Which was originally designed for a red light inducible protein expression system. In order to improve the funtionality and the efficiency, we tried to reverse half of the sequence, forming a head-to-head stricture, this mAy lower the stereo effect of RNA polymerase II.
 +
</p>
  
  
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<h5>What information do I need to start putting my parts on the Registry?</h5>
 
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<p>The information needed to initially create a part on the Registry is:</p>
 
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<ul>
 
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<li>Part Name</li>
 
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<li>Part type</li>
 
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<li>Creator</li>
 
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<li>Sequence</li>
 
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<li>Short Description (60 characters on what the DNA does)</li>
 
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<li>Long Description (Longer description of what the DNA does)</li>
 
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<li>Design considerations</li>
 
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<p>
 
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
 
  
 
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<footer align="right">
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<h5>Inspiration</h5>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
+
 
<ul>
 
<ul>
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
+
<li><a href="http://www.cgu.edu.tw"><img src="https://static.igem.org/mediawiki/2017/1/13/Cgucopyright0915.png" width="40%"></a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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</ul>  
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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<h5>Part Table </h5>
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
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<div class="highlight">
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<groupparts>iGEM17 CGU_Taiwan</groupparts>
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Revision as of 03:52, 2 November 2017

iGem CGU_Taiwan 2017 - Parts

Introduction

To achieve the localize deinking, we built a system that can detect the ink on the paper and using red light LED matrix to stimulate the yeast in some specific locations to produce enzymes. The paper will be photographed and sent to computer before we spread the yeast on it. Our image process program using OpenCV function library to decode the JPG image file and do the edge offset, then decide which area have ink. After the LED matric data be calculated, the program using RS-232 serial communication standard sends this data to Arduino. Arduino collects the data and then sends it to Max7219 microcontroller to light up the LED matrix to stimulate the yeast produce enzymes. The system accepts any shape of paper which is under the size of the device, and the device can be easily scale up by connecting more led matric. This shows the possibility of factory scale localize deinking.

Parts

We had designed eight new biobricks in our project, three of them are composite parts and the rest are single biobricks. Our parts were designed to be use as a light inducible deinking enzyme secreting system, the codons were optimized and designed for expression in Saccharomyces cerevisiae.

BBa_K2376000

endo-1,4-beta-xylanase A

endo-1,4-beta-xylanase A ORF sequence took from Neocallimastix patriciarum (http://www.uniprot.org/uniprot/P29127), a rumen fungi normally found in goat rumen. This enzyme digests xylan (hemicellulose) into oligosaccharides (xylobiose and xylose) in the working condition of 30-35-degree Celcius and pH4.5-5.5. The sequence had been optimized to a Saccharomyces cerevisiae codon and had replaced the original signal peptide (1-18 amino acids) into Saccharomyces cerevisiae SUC2 secreting signal. This enzyme was used for digesting paper fibers in our project, it could be used in paper pulping, deinking, cleaning processes or other fiber related digestion.

BBa_K2376001

endo-beta-1,4-glucanase B

endo-beta-1,4-glucanase B ORF sequence took from Aspergillus oryzae (http://www.uniprot.org/uniprot/Q2UPQ4). This enzyme digests cellulose into oligosaccharides in the working condition of 30-35-degree Celcius and pH4.5-5.5. The sequence had been optimized to a Saccharomyces cerevisiae codon and had replaced the original signal peptide (1-17 amino acids) into Saccharomyces cerevisiae SUC2 secreting signal. This enzyme was used for digesting paper fibers in our project, it could be used in paper pulping, deinking, cleaning processes or other fiber related digestion.

BBa_K2376002

Lipase

Lipase ORF sequence took from Rhizopus niveus (http://www.uniprot.org/uniprot/P61871). This enzyme hydrolyzes ester bonds of triglycerides in the working condition of 30-35-degree Celcius and pH4.5-5.5. The sequence had been optimized to a Saccharomyces cerevisiae codon and had replaced the original signal peptide (1-26 amino acids) into Saccharomyces cerevisiae SUC2 secreting signal. This enzyme was used for digesting ink in our project (such as soil bean ink), it could deinking process or lipid digesting.

BBa_K2376003

ste12 promoter

Upstream 500bp of a pheromone related pathway transcription factor of Saccharomyces cerevisiae (http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2010.07728.x/full). This promoter contains four PREs (pheromone-response element) that allows STE12 protein dimer binds on it. This is a very complex pathway induced by alpha or a factors, note that several inhibiting and antagonist pathway involves in the ste12 expression. However, the positive up-regulation feedback of the ste12 itself gives the potential of acting as an amplifier in various response pathway. We had designed this promoter for improving the expression of protein level after light inducing promoter systems. (https://www.ncbi.nlm.nih.gov/pubmed/2193847)

BBa_K2376004

ste12 protein

STE12 is a pheromone related pathway transcription factor of Saccharomyces cerevisiae (http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2010.07728.x/full), it acts as the final controller of several pheromone induced protein expression. This protein would form a dimer and can bind to PREs (pheromone-response element) sequence. This is a very complex pathway induced by alpha or a factors in haploid budding yeast, note that several inhibiting and antagonist pathway involves in the ste12 expression. However, the positive up-regulation feedback of the ste12 itself gives the potential of acting as an amplifier in various response pathway. We had designed this promoter for improving the expression of protein level after light inducing promoter systems. (https://www.ncbi.nlm.nih.gov/pubmed/2193847)

BBa_K2376005

Glucanase and Xylanase with ste12 promoter

This is a composite part combining endo-1,4-beta-xylanase A and Probable endo-beta-1,4-glucanase B from Neocallimastix patriciarum and Aspergillus oryzae, respectively. The protein codon had been optimized to Saccharomyces cerevisiae codon and had added a SUC2 secrete signal. Xylanase (BBa_K2376000) and glucanase (BBa_K2376001) were both promote by a ste12 promoter (BBa_K2376003) and followed by a TEF terminator (BBa_K801011). Kozak sequence was added in front of the start codon of both proteins. This composite part is used to induce the expression of deinking enzymes, it can be either activated by the induction of pheromone or any pathway that overexpress ste12 protein (BBa_K2376004). The ste12 transcription factor could bind to the ste12 promoter which has PREs, there is also a ste12 sequence in the yeast genome, which could cause a positive feedback of ste12 for binding and promote itself. The sequence of expression two proteins was reversed and formed a head-to-head sequence, wishing to lower the stereo obstacle the entry of RNA polymerase II while transcription. This composite biobrick remains central to our project. The two enzymes are the main enzymes that deink the recycled paper.

BBa_K2376006

In this biobrick, STE12 protein, a transcription factor, can be driven by the system we made or the pheromone response system originally in yeast. Once the STE12 protein has been made, it initiates the positive feedback in yeast genome. The mass production of STE12 protein helps increase STE12 promoter to lift the expression of downstream gene, Lipase, Xylanase and Glucanase. Besides, Lipase is also constructed in this biobrick.

BBa_K2376007

improved GAL4 based yeast light-switchable promoter system

This biobricks was made from BBa_K801042. Which was originally designed for a red light inducible protein expression system. In order to improve the funtionality and the efficiency, we tried to reverse half of the sequence, forming a head-to-head stricture, this mAy lower the stereo effect of RNA polymerase II.