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@@ -25,14 +25,39 @@
<div class="row">
<div class="col-md-2 sidenav-wrapper">
<div class="sidenav">
- <a href="#background"><p><b>Background</b></p></a>
- <a href="#plastic"><p>Plastic pollution</p></a>
- <a href="#phb"><p>Biodegradable plastic and PHB</p></a>
- <a href="#solutions"><p><b>Our Solutions</b></p></a>
- <a href="#esa"><p>Esa I/R system</p></a>
- <a href="#autolysis"></a><p>Autolysis system of phage</p></a>
- <a href="#model"><p>Three-layer dynamic regulation model</p></a>
- <a href="#ref"><p><b>References</b></p></a>
+ <a href="#over"
+ ><p><b>Overview</b></p></a
+ >
+ <a href="#why"
+ ><p><b>Why</b></p></a
+ >
+ <a href="#ci"
+ ><p><strong>Current issues with plastic</strong></p></a
+ >
+ <a href="#bp"
+ ><p><strong>Biodegradable plastic and PHB</strong></p></a
+ >
+ <a href="#how"
+ ><p><b>How</b></p></a
+ >
+ <a href="#two"
+ ><p><strong>Focusing on two problems</strong></p></a
+ >
+ <a href="#esa"
+ ><p><strong>Esa I/R system</strong></p></a
+ >
+ <a href="#aut"
+ ><p><strong>Autolysis system of phage</strong></p></a
+ >
+ <a href="#tl"
+ ><p><strong>Three-layer dynamic regulation model</strong></p></a
+ >
+ <a href="#fd"
+ ><p><b>Further development</b></p></a
+ >
+ <a href="#ref"
+ ><p><b>References</b></p></a
+ >
</div>
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@@ -40,348 +65,441 @@
</div>
<div class="col-sm-9 wiki-content">
<div>
- <h1 style="font-family: Chillax-Bold; text-align: center">
- <a name="background" >Background</a>
- </h1>
+ <div>
+ <ul class="gd-t1">
+ <a name="over"> <br /></a>
+ <li>Overview</li>
+ </ul>
+ </div>
+ <div>
+ <p>
+ Faced with the current serious plastic pollution problem, we have
+ chosen to contribute by improving the production of degradable
+ plastics through a three-layer dynamic regulation.
+ </p>
+ </div>
</div>
<div>
+ <ul class="gd-t1">
+ <a name="why"> <br /></a>
+ <li>Why</li>
+ </ul>
+ <div>
+ <ul class="gd-t2">
+ <a name="ci"> <br /></a>
+ <li>Current issues with plastic</li>
+ </ul>
+ </div>
<div>
- <hr
- style="height: 5vh; border: none; border-top: 5vh groove skyblue"
- />
- <br />
- <h2 style="text-align: center"><a name="plastic" >Plastic pollution</a></h2>
- <br />
<p>
Because of its advantages such as durability, flexibility, and
- affordability, plastic has become an important part of our
- lives<sub>[1]</sub>. Traditional petroleum-based plastics typically
- include polypropylene (PP), polystyrene (PS), polyethylene
- terephthalate (PET), polyvinyl chloride (PVC), low density
- polyethylene (LDPE), or high-density polyethylene (HDPE), which are
- accumulate in environment at a very high rate and are harmful to our
- human being (Fig.1).
+ affordability, <b>plastic</b> has become an important part of our
+ lives[1]. Traditional petroleum-based plastics typically include
+ polypropylene (PP), polystyrene (PS), polyethylene terephthalate
+ (PET), polyvinyl chloride (PVC), low density polyethylene (LDPE), or
+ high-density polyethylene (HDPE), which are
+ <b>accumulate in environment at a very high rate</b> and are
+ <b>harmful to our human being</b> (Fig.1).
</p>
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/1.jpg"
- alt="Fig.1 the situation of plastic pollution"
- width="900"
+ alt="Fig.1 The situation of plastic pollution"
+ width="50%"
style="display: block; margin: 0 auto"
/>
- <figcaption>Fig.1 the situation of plastic pollution</figcaption>
+ <figcaption>
+ <b>Fig.1 | </b> The situation of plastic pollution
+ </figcaption>
<p>
The School of Life Science of Shandong University is located in
- Qingdao, Shandong Province, which is closed to the sea. Thus, we
- have many opportunities to go to the seaside for internship and
- investigation. We found that plastic pollution is not a topic that
- far away from us. When not cleaned up in time, large amounts of
+ Qingdao, Shandong Province, which is closed to the <b>sea</b>. Thus,
+ we have many opportunities to go to the seaside for internship and
+ investigation. We found that <b>plastic pollution</b> is not a topic
+ that far away from us. When not cleaned up in time, large amounts of
plastic can accumulate on the beach.
</p>
<p>
- Plastic pollution is all around us, but we wanted to understand the
- problem from a more comprehensive perspective, so we decided to
- conduct a series of preliminary human practices.
+ <b>Plastic pollution is all around us</b>, but we wanted to
+ understand the problem from a more comprehensive perspective, so we
+ decided to conduct a series of <b>preliminary human practices</b>.
+ </p>
+ <p>
+ Meanwhile, it is important to note that plastics are derived from
+ <b>fossil fuels</b>. The World Economic Forum has reported that
+ 4%—8% of annual worldwide oil consumption is now connected to
+ plastics. If we continue to depend on plastics, it is projected that
+ <b
+ >they will contribute to 20% of all global oil consumption by
+ 2050</b
+ >.
+ </p>
+ <p>
+ First, we collaborated with the "Life Sandbar" team at Shandong
+ University to organize <b>beach cleaning activities</b>. This not
+ only improves our environment, but also gives us a clearer
+ understanding of the plastic waste situation around us.
</p>
+
+ <img
+ src=" https://static.igem.wiki/teams/4583/wiki/hp/hp-3.png"
+ alt="Fig.2 The first part of our Human Practice: Plastic pollution and us. Our initial human practice was mainly divided into three parts: sampling and analysis, questionnaire and interviews."
+ width="75%"
+ style="display: block; margin: 0 auto"
+ />
+ <br />
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/2.jpg"
- alt="Fig.2 the first part of our Human Practice: Plastic pollution and us. Our initial human practice was mainly divided into three parts: sampling and analysis, questionnaire and interviews."
- width="900"
+ alt="Fig.2 The first part of our Human Practice: Plastic pollution and us. Our initial human practice was mainly divided into three parts: sampling and analysis, questionnaire and interviews."
+ width="75%"
style="display: block; margin: 0 auto"
/>
<figcaption>
- Fig.2 the first part of our Human Practice: Plastic pollution and
- us. Our initial human practice was mainly divided into three parts:
- sampling and analysis, questionnaire and interviews.
+ <b>Fig.2 | </b> The first part of our Human Practice: Plastic
+ pollution and us. Our initial human practice was mainly divided into
+ three parts: sampling and analysis, questionnaire and interviews.
</figcaption>
<p>
- In the early stage, we will work with other iGEM teams in various
- regions to collect water or soil samples and investigate plastic
- pollution in various regions through a series of experiments. At the
- same time, with permission, we will conduct questionnaires,
- interviews and visits to get a deeper understanding of plastic
- pollution. We hope to provide solid advice for government and
- environmental organizations.
+ And, we worked with other iGEM teams in various regions to
+ <b>collect soil samples</b> and
+ <b>detected microplastic pollution</b> in various regions through a
+ series of experiments. At the same time, with permission, we
+ conducted <b>questionnaires, interviews and visits</b> to get a
+ deeper understanding of plastic pollution. Then,we conducted
+ correlation analysis to find the inner link.
</p>
</div>
-
<div>
- <br />
- <hr
- style="height: 5vh; border: none; border-top: 5vh groove skyblue"
- />
- <br />
- <h2 style="text-align: center"><a name="phb" >Biodegradable plastic and PHB</a></h2>
- <br />
+ <ul class="gd-t2">
+ <a name="bp"> <br /></a>
+ <li>Biodegradable plastic and PHB</li>
+ </ul>
+ </div>
+ <div>
<p>
- Biodegradable plastics have gained widespread attention in recent
- years, among which bacterial polyhydroxyalkanoates (PHAs) have shown
- great potential. PHAs are biodegradable thermoplastics, and they are
- produced by bacterial as a kind of intracellular carbon storage
- compounds (Fig.3).
+ <b>Biodegradable plastics</b> have gained widespread attention in
+ recent years, among which bacterial polyhydroxyalkanoates (PHAs)
+ have shown great potential. <b>PHAs</b> are biodegradable
+ thermoplastics, and they are produced by bacterial as a kind of
+ <b>intracellular carbon storage compounds</b> (Fig.3).
</p>
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/3.jpg"
alt="Fig.3 PHB granule in the cell"
- width="900"
+ width="80%"
style="display: block; margin: 0 auto"
/>
- <figcaption>Fig.3 PHB granule in the cell</figcaption>
+ <figcaption><b>Fig.3 | </b> PHB granule in the cell</figcaption>
<p>
- PHB (poly-β-hydroxybutyrate) is a class of PHAs<sub>[2]</sub>. PHB
- possesses better physical properties than polypropylene for
- applications such as food packaging and is completely nontoxic.
+ <b>PHB (poly-β-hydroxybutyrate)</b> is a class of PHAs[2]. PHB
+ possesses better <b>physical properties</b> than polypropylene for
+ applications such as food packaging and is completely
+ <b>nontoxic</b>.
</p>
<p>
- We found that PHB product can be used in extensive aspects, ranging
- from medical industrial to household items (Fig.4).
+ We found that PHB product can be used in <b>extensive aspects</b>,
+ ranging from medical industrial to household items (Fig.4).
</p>
- <div
- style="
- display: grid;
- max-height: 50vh;
- min-height: 320px;
- align-content: center;
- justify-content: center;
- overflow: hidden;
- "
- >
- <img
- src="https://static.igem.wiki/teams/4583/wiki/project-description/9.png"
- alt="Fig.4 The extensive applications of PHB products"
- width="auto"
- />
- </div>
+ <img
+ src="https://static.igem.wiki/teams/4583/wiki/project-description/de-00.png"
+ alt="Fig.4 The extensive applications of PHB products"
+ width="70%"
+ style="display: block; margin: 0 auto"
+ />
<figcaption>
- Fig.4 The extensive applications of PHB products
+ <b>Fig.4 | </b> The extensive applications of PHB products
</figcaption>
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/3.jpg"
alt="Fig.5 Comparison of the biodegradability between bio-based plastics and petroleum-based plastics."
- width="900"
+ width="70%"
style="display: block; margin: 0 auto"
/>
<figcaption>
- Fig.5 Comparison of the biodegradability between bio-based plastics
- and petroleum-based plastics.
+ <b>Fig.5 | </b> Comparison of the biodegradability between bio-based
+ plastics and petroleum-based plastics.
</figcaption>
<p>
After understanding the disadvantages of traditional plastics, we
- decided to choose degradable plastics as the general direction of
- our project.
+ decided to choose <b>degradable plastics</b> as the general
+ <b>direction</b> of our project.
</p>
<p>
Through the investigation of the types, properties and production
- costs of biodegradable plastics, we found that the commercial
- production of PHB, as a good biodegradable plastic, is greatly
- limited.
+ costs of biodegradable plastics, we found that the
+ <b>commercial production</b> of PHB, as a good biodegradable
+ plastic, <b>is greatly limited</b>.
</p>
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/5.jpg"
alt="Fig.6 Two difficulties in PHB Production"
- width="900"
+ width="80%"
style="display: block; margin: 0 auto"
/>
- <figcaption>Fig.6 Two difficulties in PHB Production</figcaption>
+ <figcaption>
+ <b>Fig.6 | </b> Two difficulties in PHB Production
+ </figcaption>
<p>
- One reason is that the PHB production pathway conflicts with the
- central metabolic pathway. Another reason is that PHB is an
- intracellular product, which cannot be released automatically and
- needs to be artificially lysed. So, we decide turn to these two
- problems.
+ One reason is that the PHB production pathway
+ <b>conflicts with the central metabolic pathway</b>. Another reason
+ is that PHB is an intracellular product, which
+ <b>cannot be released automatically</b> and needs to be artificially
+ lysed. So, we decide turn to these two problems.
</p>
</div>
</div>
-
<div>
+ <ul class="gd-t1">
+ <a name="how"> <br /></a>
+ <li>How</li>
+ </ul>
+ <div>
+ <ul class="gd-t2">
+ <a name="two"> <br /></a>
+ <li>Focusing on two problems</li>
+ </ul>
+ </div>
<div>
- <br />
- <hr
- style="height: 10vh; border: none; border-top: 10vh groove skyblue"
- />
- <br />
- <h1 style="font-family: Chillax-Bold; text-align: center">
- <a name="solutions" >Our Solutions</a>
- </h1>
- <br />
- <h3>Focusing on two problems</h3>
- <br />
<p>
We are going to addressing these two specific problems using
different tools:
</p>
- <h4>
- <b>Problem 1</b>: The PHB production pathway conflicts with the
- central metabolic pathway.
- </h4>
- <br />
- <p>
- Both TCA cycle and PHB production pathways use acetyl-coA as raw
- material, so if only the PHB production gene circuit is simply added
- to the engineered bacteria, the growth of the bacteria will be
- greatly affected, and the final result is low PHB production.
- </p>
- <p>
- We turn to <strong>Quorum Sensing (QS) system</strong>, a
- traditional regulation tool in synthetic biology, for help. Quorum
- sensing system can automatically sense cell density to regulate
- downstream genetic on/off. It is independent of metabolic pathways
- and do not need exogenous inducers, which make it a perfect tool for
- our project.
- </p>
- <br />
- <h4>
- <b>Problem 2</b>: As an intracellular product, PHB cannot be
- released on its own.
- </h4>
- <br />
- <p>
- PHB are a form of carbon storage by bacteria. PHB products take up
- most of the space inside the cell, but will not be released from the
- cell. The method of mechanical crushing or chemical solvent
- extraction used in traditional industry is not only expensive, but
- also brings great pressure to the environment, so we hope to design
- a auto-lysis system with specific expression time.
- </p>
+ <div class="table">
+ <ul class="table-text">
+ <li>
+ <p>
+ Problem 1: The PHB production pathway conflicts with the
+ central metabolic pathway.
+ </p>
+ </li>
+ </ul>
+ <img
+ id="table-pf-switch"
+ src="https://static.igem.wiki/teams/4583/wiki/graphic-design/button-close.png"
+ alt="These 6 strains are for QS- switch characterization"
+ style="display: block; margin: 0 auto"
+ />
+ </div>
+ <div id="table-pf" class="table-wrapper hide">
+ <div class="table-pf" style="text-align: left">
+ <p>
+ Both TCA cycle and PHB production pathways use
+ <b>acetyl-coA</b> as raw material, so if only the PHB production
+ gene circuit is simply added to the engineered bacteria, the
+ growth of the bacteria will be greatly affected, and the final
+ result is low PHB production.
+ </p>
+ <p>
+ We turn to <b>Quorum Sensing (QS) system</b>, a traditional
+ regulation tool in synthetic biology, for help. Quorum sensing
+ system can automatically sense cell density to regulate
+ downstream genetic on/off. It is
+ <b>independent of metabolic pathways</b> and
+ <b>do not need exogenous inducers</b>, which make it a perfect
+ tool for our project.
+ </p>
+ </div>
+ </div>
+ <div class="table">
+ <ul class="table-text">
+ <li>
+ <p>
+ Problem 2: As an intracellular product, PHB cannot be released
+ on its own.
+ </p>
+ </li>
+ </ul>
+ <img
+ id="table-fo-switch"
+ src="https://static.igem.wiki/teams/4583/wiki/graphic-design/button-close.png"
+ alt="These 6 strains are for QS- switch characterization"
+ style="display: block; margin: 0 auto"
+ />
+ </div>
+ <div id="table-fo" class="table-wrapper hide">
+ <div class="table-pf" style="text-align: left">
+ <p>
+ PHB are a form of carbon storage by bacteria. PHB products take
+ up most of the space inside the cell, but will not be released
+ from the cell. The method of mechanical crushing or chemical
+ solvent extraction used in traditional industry is not only
+ <b>expensive</b>, but also brings great <b>pressure</b> to the
+ environment, so we hope to design a <b>auto-lysis</b> system
+ with specific expression time.
+ </p>
+ </div>
+ </div>
+ </div>
+ <div>
+ <ul class="gd-t2">
+ <a name="two"> <br /></a>
+ <li>Esa I/R system</li>
+ </ul>
</div>
-
<div>
- <br />
- <hr
- style="height: 5vh; border: none; border-top: 5vh groove skyblue"
- />
- <br />
- <h2 style="text-align: center"><a name="esa">Esa I/R system</a></h2>
- <br />
<p>
- The Esa I/R system is quite special from traditional QS system. The
- EsaI/R QS system is homologous to the LuxI/R QS system and
- originates the maize pathogen--Pantoea stewartii subsp. stewartia.
- EsaR can act as both transcriptional activator and repressor.
+ <b>The Esa I/R system</b> is quite special from traditional QS
+ system. The EsaI/R QS system is homologous to the LuxI/R QS system
+ and originates the maize pathogen--Pantoea stewartii subsp.
+ stewartia. EsaR can act as
+ <b>both transcriptional activator and repressor</b>.
</p>
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/6.jpg"
- alt="Fig.7 schematic illustration of Esa I/R system"
- width="900"
+ alt="Fig.7 Schematic illustration of Esa I/R system"
+ width="80%"
style="display: block; margin: 0 auto"
/>
<figcaption>
- Fig.7 schematic illustration of Esa I/R system
+ <b>Fig.7 | </b> Schematic illustration of Esa I/R system
</figcaption>
<p>
P<sub>esaR</sub> is a natural EsaR-repressed promoter, whereas P<sub
>esaS</sub
>
- is anatural EsaR-activated promoter. At low cell density (low Ï),
- EsaR binds to its esa box to turn off PesaR and turn on
- P<sub>esaS</sub>. In the presence of AHL, EsaR can bind to AHL and
- release from the DNA. Thus, at high cell density(high Ï), the P<sub
- >esaR</sub
- >
- is turned on and the P<sub>esaS</sub> is turned off<sub>[3]</sub>.
+ is anatural EsaR-activated promoter.
+ <b>At low cell density (low Ï)</b>, EsaR binds to its esa box to
+ turn off PesaR and turn on P<sub>esaS</sub>. In the presence of AHL,
+ EsaR can bind to AHL and release from the DNA. Thus,
+ <b>at high cell density(high Ï)</b>, the P<sub>esaR</sub> is turned
+ on and the P<sub>esaS</sub> is turned off<sub>[3]</sub>.
</p>
</div>
<div>
- <br />
- <hr
- style="height: 5vh; border: none; border-top: 5vh groove skyblue"
- />
- <br />
- <h2 style="text-align: center"><a name="autolysis" >Autolysis system of phage</a></h2>
- <br />
+ <ul class="gd-t2">
+ <a name="aut"> <br /></a>
+ <li>Autolysis system of phage</li>
+ </ul>
+ </div>
+ <div>
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/7.jpg"
- alt="Fig.8 the lambda phage lysis gene cassette"
- width="900"
+ alt="Fig.8 The lambda phage lysis gene cassette"
+ width="70%"
style="display: block; margin: 0 auto"
/>
- <figcaption>Fig.8 the lambda phage lysis gene cassette</figcaption>
+ <figcaption>
+ <b>Fig.8 | </b> The lambda phage lysis gene cassette
+ </figcaption>
<p>
- We will use the lambda phage lysis gene cassette to design our
- auto-lysis system<sub>[4, 5]</sub>.
+ We will use <b>the lambda phage lysis gene cassette</b> to design
+ our auto-lysis system<sub>[4, 5]</sub>.
</p>
</div>
<div>
- <br />
- <hr
- style="height: 5vh; border: none; border-top: 5vh groove skyblue"
- />
- <br />
- <h2 style="text-align: center">
- <a name="model" >Three-layer dynamic regulation model</a>
- </h2>
- <br />
+ <ul class="gd-t2">
+ <a name="two"> <br /></a>
+ <li>Three-layer dynamic regulation model</li>
+ </ul>
+ </div>
+ <div>
<p>
- All in all, We have designed a three-layer dynamic regulation model
- to solve our problems:
+ All in all, we design
+ <b>a three-layer dynamic regulation model</b> to solve our problems:
</p>
<img
src="https://static.igem.wiki/teams/4583/wiki/project-description/8.jpg"
alt="Fig.9 The three-layer dynamic regulation"
- width="900"
+ width="80%"
style="display: block; margin: 0 auto"
/>
- <figcaption>Fig.9 The three-layer dynamic regulation</figcaption>
+ <figcaption>
+ <b>Fig.9 | </b> The three-layer dynamic regulation
+ </figcaption>
<p>
- In the first and second layer, we using a QS-switch to regulate the
- flow of acetyl-coA. At the early stage of growth, using QS-switch
- turn on the TCA cycle and turn off the PHB production pathway, so
- that acetyl-coA flowed into the TCA cycle and the cells grew. When
- the cell grows to a certain extent, the TCA cycle is turned off,
- while the PHB production pathway is turned on, and the acetyl-coA
- flows to the PHB production pathway for PHB production.
+ <b>In the first and second layer</b>, we using a <b>QS-switch</b> to
+ <b>regulate the flow of acetyl-coA</b>. At the early stage of
+ growth, using QS-switch turn on the TCA cycle and turn off the PHB
+ production pathway, so that acetyl-coA flowed into the TCA cycle and
+ the cells grew. <b>When the cell grows to a certain extent</b>, the
+ TCA cycle is turned off, while the PHB production pathway is turned
+ on, and the acetyl-coA flows to the PHB production pathway for
+ <b>PHB production</b>.
</p>
<p>
- In the third layer, we decide to use a stationary phase promoter and
- an auto-lysis system. The stationary phase promoter is used to
- regulate the expressing time of the downstream gene. When the
- bacterial reach the stationary phase, the promoter will turn on and
- then the cell lysis.
+ <b>In the third layer</b>, we decide to use
+ <b>a stationary phase promoter</b> and <b>an auto-lysis system</b>.
+ The stationary phase promoter is used to regulate the expressing
+ time of the downstream gene.<b
+ >When the bacterial reach the stationary phase</b
+ >, the promoter will turn on and then <b>the cell lysis</b>.
</p>
</div>
+ <div>
+ <ul class="gd-t1">
+ <a name="fd"> <br /></a>
+ <li>Further development</li>
+ </ul>
+ <div>
+ <p>
+ During conducting experience，we made a lot of effort to promote
+ industrialization.
+ </p>
+ <p>
+ We visit Henglu Technology and Continent Biotech group to know
+ more about <b>actual production</b>. Professor Xia Wang helped us
+ improve fermentation process. Besides, we asked for
+ <b>legal help</b> to know more about industrialization. After
+ that, we connected <b>downstream industries</b>, including medical
+ industry, Packaging industry agricultural mulch industry and so
+ on.
+ </p>
+ <p>
+ After all these efforts, we believed that our project could
+ contribute to <b>the reduction of plastic</b> in the world.
+ </p>
+ </div>
+ </div>
<div>
- <br />
- <hr
- style="height: 10vh; border: none; border-top: 10vh groove skyblue"
+ <a name="ref"><br /></a>
+ </div>
+ <div class="table">
+ <ul class="table-text" style="margin-left: 0">
+ <li><p>References</p></li>
+ </ul>
+ <img
+ id="table-re-switch"
+ src="https://static.igem.wiki/teams/4583/wiki/graphic-design/button-close.png"
+ alt="bottun"
+ style="display: block; margin: 0 auto"
/>
- <br />
- <h1 style="font-family: Chillax-Bold; text-align: center">
- <a name="ref">References</a>
- </h1>
- <br />
- <p>
- 1. Andrady, A.L. and M.A. Neal, Applications and societal benefits
- of plastics. Philos Trans R Soc Lond B Biol Sci, 2009. 364(1526): p.
- 1977-84.
- </p>
- <p>
- 2. McAdam, B., et al., Production of Polyhydroxybutyrate (PHB) and
- Factors Impacting Its Chemical and Mechanical Characteristics.
- Polymers (Basel), 2020. 12(12).
- </p>
- <p>
- 3. Gu, F., et al., Quorum Sensing-Based Dual-Function Switch and Its
- Application in Solving Two Key Metabolic Engineering Problems. ACS
- Synth Biol, 2020. 9(2): p. 209-217.
- </p>
- <p>
- 4. Gao, Y., et al., Inducible cell lysis systems in microbial
- production of bio-based chemicals. Appl Microbiol Biotechnol, 2013.
- 97(16): p. 7121-9.
- </p>
- <p>
- 5. Rajaure, M., et al., Membrane fusion during phage lysis. Proc
- Natl Acad Sci U S A, 2015. 112(17): p. 5497-502.
- </p>
- <br />
+ </div>
+ <div id="table-re" class="table-wrapper hide">
+ <div class="table-fo" id="reference">
+ <p>
+ 1. Andrady, A.L. and M.A. Neal, Applications and societal benefits
+ of plastics. Philos Trans R Soc Lond B Biol Sci, 2009. 364(1526):
+ p. 1977-84.
+ </p>
+ <p>
+ 2. McAdam, B., et al., Production of Polyhydroxybutyrate (PHB) and
+ Factors Impacting Its Chemical and Mechanical Characteristics.
+ Polymers (Basel), 2020. 12(12).
+ </p>
+ <p>
+ 3. Gu, F., et al., Quorum Sensing-Based Dual-Function Switch and
+ Its Application in Solving Two Key Metabolic Engineering Problems.
+ ACS Synth Biol, 2020. 9(2): p. 209-217.
+ </p>
+ <p>
+ 4. Gao, Y., et al., Inducible cell lysis systems in microbial
+ production of bio-based chemicals. Appl Microbiol Biotechnol,
+ 2013. 97(16): p. 7121-9.
+ </p>
+ <p>
+ 5. Rajaure, M., et al., Membrane fusion during phage lysis. Proc
+ Natl Acad Sci U S A, 2015. 112(17): p. 5497-502.
+ </p>
+ <br />
+ </div>
</div>
</div>
</div>
</div>
-</div>
-<!-- Inside Pages -->
-<script src="{{ url_for('static', filename = 'inside.pages.js')}}"></script>
+ <!-- Inside Pages -->
+ <script src="{{ url_for('static', filename = 'inside.pages.js')}}"></script>
-{% endblock %}
+ {% endblock %}
+</div>
diff --git a/wiki/pages/human-practices.html b/wiki/pages/human-practices.html
index 0fb8fc819cd6c887150aebd9eebcc4f239330786..e55f814510a7bd070f54444bde36942fc6cc25f1 100644
--- a/wiki/pages/human-practices.html
+++ b/wiki/pages/human-practices.html
@@ -365,7 +365,7 @@ header %}
</p>
<li>Australia:</li>
<img
- src="https://static.igem.wiki/teams/4583/wiki/hp/hp-f-2.png"
+ src="https://static.igem.wiki/teams/4583/wiki/hp/hp-f-3.png"
alt="Flag of Australia"
width="50%"
style="display: block; margin: 0 auto"
@@ -378,7 +378,7 @@ header %}
</p>
<li>China:</li>
<img
- src="https://static.igem.wiki/teams/4583/wiki/hp/hp-f-2.png"
+ src="https://static.igem.wiki/teams/4583/wiki/hp/hp-f-4.png"
alt="Flag of China"
width="50%"
style="display: block; margin: 0 auto"
@@ -400,22 +400,22 @@ header %}
<th>Element</th>
</tr>
<tr>
- <th>Irish</th>
- <th>2002</th>
- <th>Levy of VAT on plastics.</th>
+ <td>Irish</td>
+ <td>2002</td>
+ <td>Levy of VAT on plastics.</td>
</tr>
<tr>
- <th>Italy</th>
- <th>2006</th>
- <th>
+ <td>Italy</td>
+ <td>2006</td>
+ <td>
Legislation to heavily tax producers of common
plastics.
- </th>
+ </td>
</tr>
<tr>
- <th>China</th>
- <th>2007</th>
- <th>
+ <td>China</td>
+ <td>2007</td>
+ <td>
The General Office of the State Council on the
restriction of the production, sale and use of plastic
shopping bags notice: from June 1, 2008 onwards,
@@ -426,127 +426,127 @@ header %}
shopping bags paid for the use of plastic shopping
bags shall not be free of charge to provide plastic
shopping bags.
- </th>
+ </td>
</tr>
<tr>
- <th>Italy</th>
- <th>2011</th>
- <th>
+ <td>Italy</td>
+ <td>2011</td>
+ <td>
Legislate a total ban on the use of non-biodegradable
single-use plastic bags.
- </th>
+ </td>
</tr>
<tr>
- <th>Germany Netherlands Belgium</th>
- <th>2011-2014</th>
- <th>
+ <td>Germany Netherlands Belgium</td>
+ <td>2011-2014</td>
+ <td>
Formulate favorable tax policies to encourage the
application of biodegradable plastics and impose a
disposal fee on traditional plastics.
- </th>
+ </td>
</tr>
<tr>
- <th>China</th>
- <th>2015</th>
- <th>
+ <td>China</td>
+ <td>2015</td>
+ <td>
Jilin Province prohibits the production, sale and
provision of disposable non-degradable plastic
shopping bags and plastic tableware.
- </th>
+ </td>
</tr>
<tr>
- <th>French</th>
- <th>2017</th>
- <th>
+ <td>French</td>
+ <td>2017</td>
+ <td>
A total ban on plastic bags in supermarkets and a
complete ban on single-use plastic bags and plastic
tableware by 2020.
- </th>
+ </td>
</tr>
<tr>
- <th>United States of America</th>
- <th>2017</th>
- <th>
+ <td>United States of America</td>
+ <td>2017</td>
+ <td>
California referendum passes Proposition 67, banning
free single-use plastic bags from large supermarkets
and pharmacies.
- </th>
+ </td>
</tr>
<tr>
- <th>Malaysia</th>
- <th>2017</th>
- <th>
+ <td>Malaysia</td>
+ <td>2017</td>
+ <td>
Selangor government to fully implement Plastic Bag
Free Day from January , 2017
- </th>
+ </td>
</tr>
<tr>
- <th>Australia</th>
- <th>2017</th>
- <th>
+ <td>Australia</td>
+ <td>2017</td>
+ <td>
Plain plastic shopping bags have been banned in South
Australia, Western Australia, Tasmania, Queensland,
the Northern Territory and regional Canberra A
national ban will be introduced after 2018.
- </th>
+ </td>
</tr>
<tr>
- <th>Mongolia</th>
- <th>2018</th>
- <th>
+ <td>Mongolia</td>
+ <td>2018</td>
+ <td>
March 1, 2019 ban on the sale or use of single-use
plastic bags.
- </th>
+ </td>
</tr>
<tr>
- <th>Chile</th>
- <th>2018</th>
- <th>
+ <td>Chile</td>
+ <td>2018</td>
+ <td>
he "Plastic Prohibition Law" was officially enacted,
and since February , 2019, all large supermarkets and
shopping malls provide free or paid pl astic bags to
buyers, and the maximum fine for each illegal plastic
bag provided is up to 370 U.S. dollars; August 3,
2020, Chile will be a total an on plastic.
- </th>
+ </td>
</tr>
<tr>
- <th>Philippine</th>
- <th>2019</th>
- <th>
+ <td>Philippine</td>
+ <td>2019</td>
+ <td>
Philippine President Rodrigo Duterte has proposed a
ban on single-use plastics.
- </th>
+ </td>
</tr>
<tr>
- <th>Canadian</th>
- <th>2019</th>
- <th>
+ <td>Canadian</td>
+ <td>2019</td>
+ <td>
Plastic straws will be banned from April 2020 and
plastic bags from New Year's Day 2021.
- </th>
+ </td>
</tr>
<tr>
- <th>French</th>
- <th>2020</th>
- <th>
+ <td>French</td>
+ <td>2020</td>
+ <td>
As of January 1, 2020, France banned the sale of some
single-use plastic products, including plastic
products such as disposable cotton buds, disposable
cups and plates, and school cafeterias banned the use
of plastic bottles for purified water.
- </th>
+ </td>
</tr>
<tr>
- <th>China</th>
- <th>2021</th>
- <th>
+ <td>China</td>
+ <td>2021</td>
+ <td>
Promote degradable plastics according to local
conditions, actively and s teadily, improve the
standard system, and enhance the inspection. Testing
and detection capabilities, standardized application
and disposal.
- </th>
+ </td>
</tr>
</table>
<figcaption>
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index 11dcc79a1c4c94d73253e55d74a85cf209195b99..83b616decc86dcb13c5251709005cfc714b5f624 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -60,7 +60,7 @@
<div>
<p>
<b>Firstly</b>, we examined the intricate interaction mechanism
- between the <b>EsaR protein</b> and <b>AHL</b> (3-O-C 12-HSL). For
+ between the <b>EsaR protein</b> and <b>AHL</b> (3-O-C 6-HSL). For
enhanced precision control, we introduced
<b>19 point mutations</b> in EsaR and predicted the subsequent
three-dimensional structures using the <b>AlphaFold2 algorithm</b>.
@@ -138,7 +138,7 @@
</figcaption>
<p>
The table below presents the results of our
- <b>molecular dynamics simulations</b> conducted on 11 EsaR protein
+ <b>molecular dynamics simulations</b> conducted on 19 EsaR protein
mutants. The data clearly reveal that among all the studied EsaR
mutants,
<b>EsaR/125V/170V has the strongest binding affinity with AHL</b>,
@@ -504,13 +504,14 @@
expression of each promoter
</figcaption>
<p>
- Moreover, we validate our dual promoter switch using genes we have
- tagged with fluorescent proteins. By fitting the differential
- equations to the experimental data, we also acquire curves related
- to
- <b>the changes in the concentrations of the small molecules</b>.
- This likewise demonstrates that our switch dual promoter system
- exhibits commendable switch control capabilities.
+ Additionally, we employed genes labeled with fluorescent proteins
+ to validate our dual-promoter switch. By fitting the experimental
+ data to the differential equations we previously outlined, we
+ obtained curves related to
+ <b>the changes in small molecule concentration</b>. This also
+ confirmed that our dual-promoter switch system possesses excellent
+ switch control capabilities. The fit between the modeled results
+ and experimental findings is highly consistent.
</p>
<img
src="https://static.igem.wiki/teams/4583/wiki/modeling/md-4.png"
@@ -522,6 +523,16 @@
<b>Fig.2.2 |</b> QS Switch alters the intensity change in the
expression of each promoter (plotted after fitting the parameters)
</figcaption>
+ <img
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-33.png"
+ alt="Fig.2.3: Expression intensity of fluorescently labeled dual promoter switches (Experimental results)"
+ width="40%"
+ style="display: block; margin: 0 auto"
+ />
+ <figcaption>
+ <b>Fig.2.3 |</b> Expression intensity of fluorescently labeled
+ dual promoter switches (Experimental results)
+ </figcaption>
</div>
</div>
<div>
@@ -548,18 +559,17 @@
<div>
<ul class="gd-t2">
<a name="dn"> <br /></a>
- <li>Data Note</li>
+ <li>Data Description</li>
</ul>
<div>
<p>
- The data used in this section are all derived from either
+ All data used in this section are sourced from either
literature or the experimental records of this project. Here,
- we assume that E. coli proliferate according to a logistic
- equation model. After entering the lysis state, the population
- undergoes lysis at a constant rate. By calculating the cost
- consumption and the gain of PHB at each moment, we seek to
- find
- <b>the optimal time to cease fermentation</b>.
+ we simulate the proliferation of E. coli based on the logistic
+ equation model and utilize polynomial fitting for the lysis
+ process. By calculating the cost consumption and the revenue
+ from PHB at each moment, we aim to find
+ <b>the optimal fermentation termination time</b>.
</p>
<div id="table-pf" class="table-wrapper">
<table class="table-pf" style="text-align: center">
@@ -585,7 +595,7 @@
Rate of glucose consumption by E. coli in the first
stage (growth phase)
</td>
- <td>3.44e-12</td>
+ <td>3.44e-13</td>
<td>g L<sup>-1</sup> min<sup>-1</sup>CFU<sup>-1</sup></td>
</tr>
<tr>
@@ -594,7 +604,7 @@
Rate of glucose consumption by E. coli in the second
stage (productive phase)
</td>
- <td>5.45e-12</td>
+ <td>5.43e-13</td>
<td>g L<sup>-1</sup> min<sup>-1</sup>CFU<sup>-1</sup></td>
</tr>
<tr>
@@ -603,26 +613,44 @@
Rate of glucose consumption by E. coli in the late stage
(lysis phase)
</td>
- <td>2.39e-12</td>
+ <td>2.37e-13</td>
<td>g L<sup>-1</sup> min<sup>-1</sup>CFU<sup>-1</sup></td>
</tr>
<tr>
<td>k<sub>5</sub></td>
- <td>The rate of E.coli lysis</td>
- <td>23961</td>
- <td>CFU min<sup>-1</sup></td>
+ <td>E.coli lysis constant</td>
+ <td>2.52</td>
+ <td>-</td>
+ </tr>
+ <tr>
+ <td>k<sub>6</sub></td>
+ <td>E.coli lysis constant</td>
+ <td>-19938</td>
+ <td>-</td>
+ </tr>
+ <tr>
+ <td>k<sub>7</sub></td>
+ <td>E.coli lysis constant</td>
+ <td>2.4498×107</td>
+ <td>-</td>
</tr>
<tr>
<td>K</td>
<td>The carrying capacity of E.coli</td>
<td>68627256</td>
- <td>CFU min<sup>-1</sup></td>
+ <td>CFU mL<sup>-1</sup></td>
</tr>
<tr>
<td>r</td>
<td>The intrinsic growth rate</td>
<td>0.01843</td>
- <td>M<sup>−1</sup>min<sup>−1</sup></td>
+ <td>min<sup>−1</sup></td>
+ </tr>
+ <tr>
+ <td>N<sub>0</sub></td>
+ <td>Initial number of E. coli</td>
+ <td>1302355</td>
+ <td>CFU mL<sup>-1</sup></td>
</tr>
<tr>
<td>T<sub>1</sub></td>
@@ -743,7 +771,19 @@
</p>
<div class="formula">
<img
- src="https://static.igem.wiki/teams/4583/wiki/modeling/md-fo-11.png"
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-211.png"
+ alt="Modeling formula 11: Third"
+ width="30%"
+ style="display: block; margin: 0 auto"
+ />
+ <img
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-23.png"
+ alt="Modeling formula 11: Third"
+ width="50%"
+ style="display: block; margin: 0 auto"
+ />
+ <img
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-212.png"
alt="Modeling formula 11: Third"
width="30%"
style="display: block; margin: 0 auto"
@@ -757,21 +797,68 @@
decrease. Below is the result of our modeling:
</p>
<img
- src="https://static.igem.wiki/teams/4583/wiki/modeling/temp2.png"
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-11.png"
alt="Fig.3.1: The result of modeling "
width="40%"
style="display: block; margin: 0 auto"
/>
<figcaption><b>Fig.3.1 |</b> The result of modeling</figcaption>
<p>
- <b>At the 3,830th minute</b>, the dynamic revenue falls below
+ <b>At the 3,778th minute</b>, the dynamic revenue falls below
the dynamic costs, so operations should ideally be halted.
</p>
<p><b>By the 4,104th minute</b>, all bacteria have died.</p>
<p>
The <b>total profit</b> amounts to
- <b>751.9341748649531 yuan</b>.
+ <b>85.00776820637935 yuan</b>.
+ </p>
+ <p>
+ In addition, based on the experimental data obtained from
+ simulated fermentation, we modeled the changes in glucose
+ concentration and derived a function representing glucose
+ changes over time. This can provide data references for our
+ hardware—the glucose automatic monitoring and supplementation
+ system based on human-computer interaction. Meanwhile, based on
+ the modeled glucose concentration indications, we can provide
+ predictions for software testing. In the same vein, we will
+ optimize our model according to updates from both hardware and
+ software, aiming to achieve more accurate model parameters.
+ Glucose concentration consumption：
</p>
+ <div class="formula">
+ <img
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-23.png"
+ alt="Modeling formula 11: Third"
+ width="50%"
+ style="display: block; margin: 0 auto"
+ />
+ </div>
+ <div>
+ <ul class="gd-t2">
+ <a name="dn"> <br /></a>
+ <li>The function of total glucose concentration:</li>
+ </ul>
+ <div>
+ <div class="formula">
+ <img
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-24.png"
+ alt="Modeling formula 11: Third"
+ width="50%"
+ style="display: block; margin: 0 auto"
+ />
+ </div>
+ <br />
+ <img
+ src="https://static.igem.wiki/teams/4583/wiki/modeling/md-22.png"
+ alt="Fig.3.2: Glucose change curve (C0 = 56.25)"
+ width="40%"
+ style="display: block; margin: 0 auto"
+ />
+ <figcaption>
+ <b>Fig.3.2 |</b> Glucose change curve (C0 = 56.25)
+ </figcaption>
+ </div>
+ </div>
</div>
</div>
</div>
@@ -853,16 +940,15 @@
</ul>
<ul class="gd-t3">
<li>
- "Average Disposable Income" and "GDP" show
- <b>a certain positive correlation</b> with "Microplastics
+ "<b>Average Disposable Income</b>" and "<b>GDP</b>" show a
+ certain positive correlation with "Microplastics
Abundance".
</li>
</ul>
<ul class="gd-t3">
<li>
- "Industrial Electricity Consumption" is
- <b>negatively correlated</b> with "Microplastics
- Abundance".
+ "<b>Industrial Electricity Consumption</b>" is negatively
+ correlated with "Microplastics Abundance".
</li>
</ul>
</div>