Difference between revisions of "Team:FJNU-China/Model"

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             <h2 >Overview</h2>
 
             <h2 >Overview</h2>
             <p>. As we know, the purpose of modeling is mainly to provide guidance and solve problems for the team experiment. So, before we designed the model, we sorted out some of the problems the team was facing. Based on these three problems, we designed the following models.<a href="#first">The first one</a> &nbsp;is about The effect of PLA concentration on the quantity Staphylococcus epidermidis.Because The effect of PLA concentration on the quantity Staphylococcus epidermidis.<a href="#second">The second one</a>&nbsp; is about PLA yield curves.Because The effect of PLA concentration on the quantity Staphylococcus epidermidis.<a href="#third"> The third one</a>&nbsp;is about Effect of arabinose concentration on mazF
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             <p>
.Because The effect of PLA concentration on the quantity Staphylococcus epidermidis.Vestibulum quis quam ut magna consequat faucibus. Pellentesque eget nisi a mi suscipit tincidunt. Ut tempus dictum risus. Pellentesque viverra sagittis quam at mattis. Suspendisse potenti. Aliquam sit amet gravida nibh, facilisis gravida odio. Phasellus auctor velit at lacus blandit, commodo iaculis justo viverra. Etiam vitae est arcu.
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In order to meet the requirements of iGEM, models of our projects are dedicated to solving the problems in experiment and providing guidance for the products. Our project is mainly based on bacteriostasis and incense production, while PLA is the major bacteriostatic material, so we have built two models about mechanism and yield of PLA with innovation and practicability of development as the following.The first model is about <a href="#first">Mechanism of PLA </a>.The second model is about <a href="#second">PLA yield curve</a>. The result of our models has a <a href="#third">application</a>.
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</p>
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            <hr>
  
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              <h2> Mechanism of PLA</h2>
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<h3>Effect of different concentration of PLA on the number of Staphylococcus epidermidis.</h3>
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            <p ><span style="font-size:25px;font-weight:bold;">Introduce</span></br><span style=" font-style:italic;">we had planned to established a dynamic equation to describe the effect of PLA on staphylococcus epidermidis which is the main bacteria that cause the armpit order. We gave several candidate forms of function for describing this process and finally found the best one which fit the experimental data quite well. By using the data from the experiment,we continually refine our models and guide our project through this models. Besides, this model, of which type has never been built before, also makes us learning the mechanism of PLA and solved problems as following:</br>(1) How many PLA should we put in our products that can kill the desired amount of Staphylococcus epidermidis?</br>
 +
(2) What is the effect of concentration of PLA on the number of Staphylococcus epidermidis over time.</br>
 +
(3)What is the growth of bacteria at any concentration of PLA?
 
</p>
 
</p>
 +
            <p ><span style="font-size:25px;font-weight:bold;">Method</span></br>To solve the problems above, we used different concentration of PLA to react with Staphylococcus epidermidis, then we measured the rest of bacteria every hour for a total of 8 hours. Through fitting the initial data, we got the following chary and found the appropriate function to describe this figure.
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</p>
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<div class="tz-gallery">
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<div class="row" style="display:block; margin-left:auto; margin-right:auto;margin-top: -75px;">
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<div class="col-sm-12 col-md-12">
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<a class="lightbox" href="https://static.igem.org/mediawiki/2018/d/de/T--FJNU-China--Interlab-figue12.png">
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<img src="https://static.igem.org/mediawiki/2018/d/de/T--FJNU-China--Interlab-figue12.png" alt="table1">
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</a>
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</div>
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</div>
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</div>
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            <p ><span style="font-size:20px;font-weight:bold;">Machine</span></br>Molecular Devices SpectraMax i3x
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</p>
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             <hr>
 
             <hr>
  
             <h2 name="first" class="target-1">PLA</h2>
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             <h2 >Methods</h2>
             <p >Nullam hendrerit justo non leo aliquet imperdiet. Etiam in sagittis lectus. Suspendisse ultrices placerat accumsan. Mauris quis dapibus orci. In dapibus velit blandit pharetra tincidunt. Quisque non sapien nec lacus condimentum facilisis ut iaculis enim. Sed viverra interdum bibendum. Donec ac sollicitudin dolor. Sed fringilla vitae lacus at rutrum. Phasellus congue vestibulum ligula sed consequat.</p>
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             <p>&nbsp;&nbsp;We followed this <a href="https://static.igem.org/mediawiki/2018/3/3e/T--FJNU-China--Interlab-Protocol.pdf">protocol</a> to do the Interlab Study.</br>&nbsp;&nbsp;When we completed three of the calibration measurements, performing the cell measurements. Used the same plates, volumes and settings that we used in calibration protocol. We transformed E.coli DH5α competent cells with the 8 plasmids and picked 2 colonies from each of plates into 5 mL LB medium + Chloramphenicol. After culturing the cells overnight at 37°C and 220 rpm, we used plate reader to measure the Abs600 and fluorescence of samples at 0, 6 hours.</p>
            <img src="https://static.igem.org/mediawiki/2017/8/8b/ED_OG_Interlab_Fig1.png"  style="display:block; margin:0 auto;padding-bottom: 1em;">
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            <img src=" https://static.igem.org/mediawiki/2017/7/71/T--Edinburgh_OG--model_res_eq1.png"  style="display:block; margin:0 auto;padding-bottom: 1em; width: 80%">
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            <p>Vestibulum consectetur scelerisque lacus, ac fermentum lorem convallis sed. Nam odio tortor, dictum quis malesuada at, pellentesque vitae orci. Vivamus elementum, felis eu auctor lobortis, diam velit egestas lacus, quis fermentum metus ante quis urna. Sed at facilisis libero. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Vestibulum bibendum blandit dolor. Nunc orci dolor, molestie nec nibh in, hendrerit tincidunt ante. Vivamus sem augue, hendrerit non sapien in, mollis ornare augue.</p>
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             <hr>
 
             <hr>
  
             <h2 ><a name="second" class="target-1"><img src="../img/title.jpg" style="width: 30%;height: 10%;">
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             <h2 >Result</h2>
</a></h2>
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          <p ><span style="font-size:20px;font-weight:bold;">Calibration</span></br>Calibration 1: OD600 reference point</p>
            <p >Nullam hendrerit justo non leo aliquet imperdiet. Etiam in sagittis lectus. Suspendisse ultrices placerat accumsan. Mauris quis dapibus orci. In dapibus velit blandit pharetra tincidunt. Quisque non sapien nec lacus condimentum facilisis ut iaculis enim. Sed viverra interdum bibendum. Donec ac sollicitudin dolor. Sed fringilla vitae lacus at rutrum. Phasellus congue vestibulum ligula sed consequat.</p>
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    <div>
            <img src="https://static.igem.org/mediawiki/2017/8/8b/ED_OG_Interlab_Fig1.png"  style="display:block; margin:0 auto;padding-bottom: 1em;">
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            <img src="https://static.igem.org/mediawiki/2018/3/3a/T--FJNU-China--Interlab-table1.png"  style="display:block; margin:0 auto;padding-bottom: 2em;">
            <img src=" https://static.igem.org/mediawiki/2017/7/71/T--Edinburgh_OG--model_res_eq1.png"  style="display:block; margin:0 auto;padding-bottom: 1em; width: 80%">
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            <p>Vestibulum consectetur scelerisque lacus, ac fermentum lorem convallis sed. Nam odio tortor, dictum quis malesuada at, pellentesque vitae orci. Vivamus elementum, felis eu auctor lobortis, diam velit egestas lacus, quis fermentum metus ante quis urna. Sed at facilisis libero. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Vestibulum bibendum blandit dolor. Nunc orci dolor, molestie nec nibh in, hendrerit tincidunt ante. Vivamus sem augue, hendrerit non sapien in, mollis ornare augue.</p>
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          </br><p >Calibration 2: Particle Standard Curve</p>
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<div class="tz-gallery">
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<div class="row" style="display:block; margin-left:auto; margin-right:auto;margin-top: -75px;">
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<div class="col-sm-12 col-md-12">
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<a class="lightbox" href="https://static.igem.org/mediawiki/2018/d/de/T--FJNU-China--Interlab-figue12.png">
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<img src="https://static.igem.org/mediawiki/2018/d/de/T--FJNU-China--Interlab-figue12.png" alt="table1">
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</a>
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</div>
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<div class="tz-gallery">
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<div class="row" style="display:block; margin-left:auto; margin-right:auto;margin-top: -75px;">
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<div class="col-sm-12 col-md-12">
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<a class="lightbox" href="https://static.igem.org/mediawiki/2018/e/ee/T--FJNU-China--Interlab-figue34.png">
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<img src="https://static.igem.org/mediawiki/2018/e/ee/T--FJNU-China--Interlab-figue34.png" alt="figue34">
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</a>
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          <p ><span style="font-size:20px;font-weight:bold;">Cell measurement</span></p>
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<div class="tz-gallery">
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<div class="row" style="display:block; margin-left:auto; margin-right:auto;margin-top: -75px;">
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<div class="col-sm-12 col-md-12">
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<a class="lightbox" href="https://static.igem.org/mediawiki/2018/3/35/T--FJNU-China--Interlab-table2.png">
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<img src="https://static.igem.org/mediawiki/2018/3/35/T--FJNU-China--Interlab-table2.png">
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</a>
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<div class="col-sm-12 col-md-12">
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<a class="lightbox" href="https://static.igem.org/mediawiki/2018/5/56/T--FJNU-China--Interlab-figue56.png">
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<img src="https://static.igem.org/mediawiki/2018/5/56/T--FJNU-China--Interlab-figue56.png" alt="figue56">
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             <hr>
 
             <hr>
  
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            <h2 >Analyse</h2>
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            <p style="margin-bottom: 5px;">&nbsp;&nbsp;A standard curve in a linear relationship can be obtained by calibration experiments.</br>
 +
By comparing and analyzing the fluorescence values and Absorbance value of the different test devices at 0 and 6 hours, we can draw the following conclusions: the negative control and the positive control showed significant differences in the 6h fluorescence measurement results. Among the six different test equipment, Device 4 has the strongest fluorescence, while Device 3 has the lowest fluorescence. Compared with the relation between absorbance and fluorescence value, we can't get the relationship, and we need to improve on the control variables during the experiment.
 +
</p>
  
            <h2 ><a name="third" class="target-1"><img src="../img/title.jpg" style="width: 30%;height: 10%;">
 
</a></h2>
 
            <p >Nullam hendrerit justo non leo aliquet imperdiet. Etiam in sagittis lectus. Suspendisse ultrices placerat accumsan. Mauris quis dapibus orci. In dapibus velit blandit pharetra tincidunt. Quisque non sapien nec lacus condimentum facilisis ut iaculis enim. Sed viverra interdum bibendum. Donec ac sollicitudin dolor. Sed fringilla vitae lacus at rutrum. Phasellus congue vestibulum ligula sed consequat.</p>
 
            <img src="https://static.igem.org/mediawiki/2017/8/8b/ED_OG_Interlab_Fig1.png"  style="display:block; margin:0 auto;padding-bottom: 1em;">
 
            <img src=" https://static.igem.org/mediawiki/2017/7/71/T--Edinburgh_OG--model_res_eq1.png"  style="display:block; margin:0 auto;padding-bottom: 1em; width: 80%">
 
           
 
            <p>Vestibulum consectetur scelerisque lacus, ac fermentum lorem convallis sed. Nam odio tortor, dictum quis malesuada at, pellentesque vitae orci. Vivamus elementum, felis eu auctor lobortis, diam velit egestas lacus, quis fermentum metus ante quis urna. Sed at facilisis libero. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Vestibulum bibendum blandit dolor. Nunc orci dolor, molestie nec nibh in, hendrerit tincidunt ante. Vivamus sem augue, hendrerit non sapien in, mollis ornare augue.</p>
 
 
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Revision as of 08:36, 7 October 2018

Models

Overview

In order to meet the requirements of iGEM, models of our projects are dedicated to solving the problems in experiment and providing guidance for the products. Our project is mainly based on bacteriostasis and incense production, while PLA is the major bacteriostatic material, so we have built two models about mechanism and yield of PLA with innovation and practicability of development as the following.The first model is about Mechanism of PLA .The second model is about PLA yield curve. The result of our models has a application.


Mechanism of PLA

Effect of different concentration of PLA on the number of Staphylococcus epidermidis.

Introduce
we had planned to established a dynamic equation to describe the effect of PLA on staphylococcus epidermidis which is the main bacteria that cause the armpit order. We gave several candidate forms of function for describing this process and finally found the best one which fit the experimental data quite well. By using the data from the experiment,we continually refine our models and guide our project through this models. Besides, this model, of which type has never been built before, also makes us learning the mechanism of PLA and solved problems as following:
(1) How many PLA should we put in our products that can kill the desired amount of Staphylococcus epidermidis?
(2) What is the effect of concentration of PLA on the number of Staphylococcus epidermidis over time.
(3)What is the growth of bacteria at any concentration of PLA?

Method
To solve the problems above, we used different concentration of PLA to react with Staphylococcus epidermidis, then we measured the rest of bacteria every hour for a total of 8 hours. Through fitting the initial data, we got the following chary and found the appropriate function to describe this figure.

Machine
Molecular Devices SpectraMax i3x


Methods

  We followed this protocol to do the Interlab Study.
  When we completed three of the calibration measurements, performing the cell measurements. Used the same plates, volumes and settings that we used in calibration protocol. We transformed E.coli DH5α competent cells with the 8 plasmids and picked 2 colonies from each of plates into 5 mL LB medium + Chloramphenicol. After culturing the cells overnight at 37°C and 220 rpm, we used plate reader to measure the Abs600 and fluorescence of samples at 0, 6 hours.


Result

Calibration
Calibration 1: OD600 reference point


Calibration 2: Particle Standard Curve

Cell measurement


Analyse

  A standard curve in a linear relationship can be obtained by calibration experiments.
By comparing and analyzing the fluorescence values and Absorbance value of the different test devices at 0 and 6 hours, we can draw the following conclusions: the negative control and the positive control showed significant differences in the 6h fluorescence measurement results. Among the six different test equipment, Device 4 has the strongest fluorescence, while Device 3 has the lowest fluorescence. Compared with the relation between absorbance and fluorescence value, we can't get the relationship, and we need to improve on the control variables during the experiment.


Summary

Suspendisse a orci facilisis, dignissim tortor vitae, ultrices mi. Vestibulum a iaculis lacus. Phasellus vitae convallis ligula, nec volutpat tellus. Vivamus scelerisque mollis nisl, nec vehicula elit egestas a. Sed luctus metus id mi gravida, faucibus convallis neque pretium. Maecenas quis sapien ut leo fringilla tempor vitae sit amet leo. Donec imperdiet tempus placerat. Pellentesque pulvinar ultrices nunc sed ultrices. Morbi vel mi pretium, fermentum lacus et, viverra tellus. Phasellus sodales libero nec dui convallis, sit amet fermentum sapien auctor. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Sed eu elementum nibh, quis varius libero.