From d2a9476c7223729685d36577238fd7e22561d7d2 Mon Sep 17 00:00:00 2001
From: Ruby Chang <ruby931109@gmail.com>
Date: Tue, 11 Oct 2022 07:57:45 +0800
Subject: [PATCH] modified: static/style.css modified:
wiki/pages/collaborations.html modified:
wiki/pages/communication.html modified: wiki/pages/contribution.html
modified: wiki/pages/description.html modified:
wiki/pages/education.html modified: wiki/pages/engineering.html
modified: wiki/pages/entrepreneurship.html modified:
wiki/pages/experiments.html modified: wiki/pages/hardware.html
modified: wiki/pages/human-practices.html modified:
wiki/pages/implementation.html modified: wiki/pages/improve.html
modified: wiki/pages/inclusivity.html modified:
wiki/pages/measurement.html modified: wiki/pages/model.html
modified: wiki/pages/part-collection.html modified:
wiki/pages/partnership.html modified: wiki/pages/parts.html
modified: wiki/pages/plant.html modified:
wiki/pages/proof-of-concept.html modified: wiki/pages/results.html
modified: wiki/pages/safety.html modified: wiki/pages/software.html
modified: wiki/pages/sustainable.html
---
static/style.css | 35 +-
wiki/pages/collaborations.html | 710 ++++++++--------
wiki/pages/communication.html | 84 +-
wiki/pages/contribution.html | 603 +++++++-------
wiki/pages/description.html | 701 ++++++++--------
wiki/pages/education.html | 1055 ++++++++++++------------
wiki/pages/engineering.html | 2 +
wiki/pages/entrepreneurship.html | 84 +-
wiki/pages/experiments.html | 84 +-
wiki/pages/hardware.html | 702 ++++++++--------
wiki/pages/human-practices.html | 1029 ++++++++++++------------
wiki/pages/implementation.html | 825 +++++++++----------
wiki/pages/improve.html | 84 +-
wiki/pages/inclusivity.html | 84 +-
wiki/pages/measurement.html | 84 +-
wiki/pages/model.html | 1291 +++++++++++++++---------------
wiki/pages/part-collection.html | 47 +-
wiki/pages/partnership.html | 392 ++++-----
wiki/pages/parts.html | 84 +-
wiki/pages/plant.html | 84 +-
wiki/pages/proof-of-concept.html | 139 ++--
wiki/pages/results.html | 84 +-
wiki/pages/safety.html | 427 +++++-----
wiki/pages/software.html | 234 +++---
wiki/pages/sustainable.html | 84 +-
25 files changed, 4230 insertions(+), 4802 deletions(-)
diff --git a/static/style.css b/static/style.css
index 7fa6131..8a71411 100644
--- a/static/style.css
+++ b/static/style.css
@@ -1,6 +1,5 @@
-@import url('https://fonts.googleapis.com/css?family=Lora');
* {
- font-family: 'Playfair Display';
+ font-family: 'Brush Script Std';
scroll-behavior: smooth;
}
body {
@@ -19,9 +18,6 @@ html {
.bg-hero {
background-color: #7952b3;
}
-.container {
- width: 100%;
-}
/* CALLOUT */
.bd-callout {
padding: 1.25rem;
@@ -227,7 +223,8 @@ html {
font-weight: 700;
margin-bottom: 30px;
font-size: 40px;
- font-family: 'Playfair Display';
+
+ font-family: 'Brush Script Std';
}
.introwrap {
margin: 0 auto;
@@ -376,7 +373,8 @@ html {
}
.impldesc_name {
font-size: 25px;
- font-family: 'Playfair Display';
+
+ font-family: 'Brush Script Std';
}
.pageswrap {
@@ -492,7 +490,8 @@ html {
align-items: center;
justify-content: center;
height: 600px;
- font-family: 'Playfair Display';
+
+ font-family: 'Brush Script Std';
color: #082076;
}
.video_hardware {
@@ -506,7 +505,8 @@ html {
align-items: center;
justify-content: center;
height: 600px;
- font-family: 'Playfair Display';
+
+ font-family: 'Brush Script Std';
}
#ourprojectwrap {
margin-top: 250px;
@@ -1724,6 +1724,12 @@ html {
text-transform: uppercase;
color: #e8a353;
}
+.info_contents_centered_contribution {
+ font-size: 25px;
+ margin-top: 35px;
+ align-self: center;
+ text-align: center;
+}
#implcentered {
margin-top: 100px;
}
@@ -2103,11 +2109,18 @@ html {
color: #8a86df;
transition: 150ms;
}
+#partlink {
+ color: #77c1c6;
+ transition: 150ms;
+}
+#partlink:hover {
+ color: #b2d9d7;
+}
#hardwarelink:hover {
color: #869adf;
}
#collablink {
- color: #6eb291;
+ color: #98d1b5;
transition: 150ms;
}
#collablink:hover {
@@ -2208,7 +2221,7 @@ html {
}
@media screen and (max-width: 980px) {
.constant_height,
- #lower_height{
+ #lower_height {
height: 200px;
}
.enlarged_constant_height,
diff --git a/wiki/pages/collaborations.html b/wiki/pages/collaborations.html
index ae960b1..96e097f 100644
--- a/wiki/pages/collaborations.html
+++ b/wiki/pages/collaborations.html
@@ -1,397 +1,405 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
+ </div>
+
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src=" https://static.igem.wiki/teams/4271/wiki/collaboration.png"
+ />
+ </div>
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
+ </div>
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="collabpointer" href="#overview">Overview</a>
+ <a class="pointer" id="collabpointer" href="#onlinemeet">
+ Online meetings
+ </a>
+ <a class="pointer" id="collabpointer" href="#koreahs">Korea_HS</a>
+ <a class="pointer" id="collabpointer" href="#podcast">Podcast</a>
+ <a class="pointer" id="collabpointer" href="#puzzle">Puzzle book</a>
+ <a class="pointer" id="collabpointer" href="#collabvid">
+ Collaboration video
+ </a>
+ <a class="pointer" id="collabpointer" href="#conclusion">Conclusion</a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+
+ <b class="heading1" id="collabheading1">
+ Collaboration
+ </b>
+
+ <div class="index_container" id="overview"></div>
+ <div class="heading2" id="collabheading2">
+ Overview
+ </div>
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src=" https://static.igem.wiki/teams/4271/wiki/collaboration.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="collabpointer" href="#overview">Overview</a>
- <a class="pointer" id="collabpointer" href="#onlinemeet">Online meetings</a>
- <a class="pointer" id="collabpointer" href="#koreahs">Korea_HS</a>
- <a class="pointer" id="collabpointer" href="#podcast">Podcast</a>
- <a class="pointer" id="collabpointer" href="#puzzle">Puzzle book</a>
- <a class="pointer" id="collabpointer" href="#collabvid">
- Collaboration video
- </a>
- <a class="pointer" id="collabpointer" href="#conclusion">Conclusion</a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
-
- <b class="heading1" id="collabheading1">
- Collaboration
- </b>
-
- <div class="index_container" id="overview"></div>
- <div class="heading2" id="collabheading2">
- Overview
- </div>
+ <div class="info_contents" id="greencontents">
+ To improve our project, exchange ideas, and find innovation, we reached
+ out to other iGEM teams for collaborations and ultimately connected with
+ the iGEM community. We collaborated in different styles by hosting online
+ meetings, recording episodes of podcasts, creating a puzzle book, and
+ producing a promotional video. The scale of our collaboration ranges from
+ levels of international university teams to local high school teams. In
+ the following sections of this page, we will go in-depth into each
+ collaboration with each iGEM team.
+ </div>
- <div class="info_contents" id="greencontents">
- To improve our project, exchange ideas, and find innovation, we reached out
- to other iGEM teams for collaborations and ultimately connected with the
- iGEM community. We collaborated in different styles by hosting online
- meetings, recording episodes of podcasts, creating a puzzle book, and
- producing a promotional video. The scale of our collaboration ranges from
- levels of international university teams to local high school teams. In the
- following sections of this page, we will go in-depth into each collaboration
- with each iGEM team.
- </div>
+ <div class="index_container" id="onlinemeet"></div>
+ <div class="heading2" id="collabheading2">
+ Online meetings
+ </div>
- <div class="index_container" id="onlinemeet"></div>
- <div class="heading2" id="collabheading2">
- Online meetings
- </div>
+ <em class="info_contents_italics" id="greencontents">
+ Overview
+ </em>
- <em class="info_contents_italics" id="greencontents">
- Overview
- </em>
-
- <div class="info_contents" id="greencontents">
- The purpose of online meetings was to promote more interactions with teams
- in the iGEM community and broaden our visions through this style of
- collaboration. By understanding the problems of other teams, we brainstormed
- ideas to empower our solutions and come up with better ideas. Possibly, we
- hope for partnerships and potentially reach out even further for other
- collaborations with more iGEM teams.
- </div>
+ <div class="info_contents" id="greencontents">
+ The purpose of online meetings was to promote more interactions with teams
+ in the iGEM community and broaden our visions through this style of
+ collaboration. By understanding the problems of other teams, we
+ brainstormed ideas to empower our solutions and come up with better ideas.
+ Possibly, we hope for partnerships and potentially reach out even further
+ for other collaborations with more iGEM teams.
+ </div>
- <div class="heading4" id="collabheading4">
- NYCU
- </div>
+ <div class="heading4" id="collabheading4">
+ NYCU
+ </div>
- <em class="info_contents_italics" id="greencontents">
- 2022.8.14
- </em>
-
- <div class="info_contents" id="greencontents">
- Through the sharing of our projects and exchanging of our ideas, we
- understood their project “E.Color†and they comprehended our project dealing
- with eutrophication. This collaboration was vital for both teams to impart
- their knowledge and exchange bateria to implement into the projects of both
- teams. Therefore, we decided extending our collaboration even further to a
- long-run
- <a
- class="content_link"
- id="collablink"
- href="{{ url_for('pages', page='partnership') }}"
- >
- partnership
- </a>
- .
- </div>
+ <em class="info_contents_italics" id="greencontents">
+ 2022.8.14
+ </em>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/nycu.png"
- />
+ <div class="info_contents" id="greencontents">
+ Through the sharing of our projects and exchanging of our ideas, we
+ understood their project “E.Color†and they comprehended our project
+ dealing with eutrophication. This collaboration was vital for both teams
+ to impart their knowledge and exchange bateria to implement into the
+ projects of both teams. Therefore, we decided extending our collaboration
+ even further to a long-run
+ <a
+ class="content_link"
+ id="collablink"
+ href="{{ url_for('pages', page='partnership') }}"
+ >
+ partnership
+ </a>
+ .
+ </div>
- <div class="heading4" id="collabheading4">
- KCIS
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/nycu.png"
+ />
- <em class="info_contents_italics" id="greencontents">
- 2022.8.21
- </em>
- <div class="info_contents" id="greencontents">
- KCIS was a fitting team to collaborate with because we shared same level and
- background knowledge in synthetic biology. It was a great experience for us
- to encompass different biology fields. KCIS introduced their project related
- to obesity and human health while our team talked about our project about
- aquatic issues, specifically eutrophication. Finally, we delved into
- experimental experiences of both teams and took some suggestions on how to
- enhance our project. Despites the differences in our experimental designs,
- our team values this experience to share insights with KCIS iGEM team.
- </div>
+ <div class="heading4" id="collabheading4">
+ KCIS
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/kcis.png"
- />
+ <em class="info_contents_italics" id="greencontents">
+ 2022.8.21
+ </em>
+ <div class="info_contents" id="greencontents">
+ KCIS was a fitting team to collaborate with because we shared same level
+ and background knowledge in synthetic biology. It was a great experience
+ for us to encompass different biology fields. KCIS introduced their
+ project related to obesity and human health while our team talked about
+ our project about aquatic issues, specifically eutrophication. Finally, we
+ delved into experimental experiences of both teams and took some
+ suggestions on how to enhance our project. Despites the differences in our
+ experimental designs, our team values this experience to share insights
+ with KCIS iGEM team.
+ </div>
- <div class="heading4" id="collabheading4">
- HNU_China
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/kcis.png"
+ />
- <em class="info_contents_italics" id="greencontents">
- 2022.9.4
- </em>
- <div class="info_contents" id="greencontents">
- It is a unique opportunity to collaborate with team HNU_China who utilize a
- different approach to deal with eutrophication. Their method was to create a
- genetic circuit that has the ability to absorb and extract inorganic
- phosphate. Throughout the meeting, our team asked HNU_China technical
- questions regarding
- <a
- class="content_link"
- href="{{ url_for('pages', page='implementation') }}"
- >
- our product
- </a>
+ <div class="heading4" id="collabheading4">
+ HNU_China: P Pack
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ 2022.9.4
+ </em>
<div class="info_contents" id="greencontents">
- since they were more experienced in implementation techniques. Finally, we
- discussed some aspects of human practice and came to a decision to make a
- podcast together.
+ It is a unique opportunity to collaborate with team HNU_China who utilize
+ a different approach to deal with eutrophication. Their method was to
+ create a genetic circuit that has the ability to absorb and extract
+ inorganic phosphate. Throughout the meeting, our team asked HNU_China
+ technical questions regarding
+ <a
+ class="content_link"
+ id="collablink"
+ href="{{ url_for('pages', page='implementation') }}"
+ >
+ our product
+ </a>
+ <div class="info_contents" id="greencontents">
+ since they were more experienced in implementation techniques. Finally,
+ we discussed some aspects of human practice and came to a decision to
+ make a podcast together.
+ </div>
</div>
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/china.png"
- />
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/china.png"
+ />
- <div class="index_container" id="koreahs"></div>
- <div class="heading2" id="collabheading2">
- Korea_HS (Business and Technology Conference)
- </div>
- <div class="info_contents" id="greencontents">
- Our team seeks a shared space for discussions. The Business and Technology
- Conference held by team Korea_HS gather different iGEM teams to share their
- inspirations in creating their products. The conference involved team Empire
- Gene, Insa Lyon1, iGEM Patras, and Korea_HS.
- </div>
+ <div class="index_container" id="koreahs"></div>
+ <div class="heading2" id="collabheading2">
+ Korea_HS (Business and Technology Conference)
+ </div>
+ <div class="info_contents" id="greencontents">
+ Our team seeks a shared space for discussions. The Business and Technology
+ Conference held by team Korea_HS gather different iGEM teams to share
+ their inspirations in creating their products. The conference involved
+ team Empire Gene, Insa Lyon1, iGEM Patras, and Korea_HS.
+ </div>
- <div class="info_contents" id="greencontents">
- Through ten minute long presentations for every team, we were inspired by
- unprecedented ideas and novel manufacturing processes. Even though each team
- concentrated in different issues, we were driven by the same passion for
- synthetic biology and the strong networks behind the competition. Some teams
- shared their ten plus interviews with different medical and synbio experts;
- another explained fervently their ideas to use DNA to store information. The
- active interactions and communications kept elevating the conversation to a
- professional level.
- </div>
+ <div class="info_contents" id="greencontents">
+ Through ten minute long presentations for every team, we were inspired by
+ unprecedented ideas and novel manufacturing processes. Even though each
+ team concentrated in different issues, we were driven by the same passion
+ for synthetic biology and the strong networks behind the competition. Some
+ teams shared their ten plus interviews with different medical and synbio
+ experts; another explained fervently their ideas to use DNA to store
+ information. The active interactions and communications kept elevating the
+ conversation to a professional level.
+ </div>
- <div class="info_contents" id="greencontents">
- Our team was grateful to gain the best entrepreneur at the conference. In
- our eyes, every innovative product we saw at the conference showcases the
- stories and efforts behind every team. With the advice and inspiration we
- learned from them, our team would continue to explore and find a unique
- position for our product in the market.
- </div>
+ <div class="info_contents" id="greencontents">
+ Our team was grateful to gain the best entrepreneur at the conference. In
+ our eyes, every innovative product we saw at the conference showcases the
+ stories and efforts behind every team. With the advice and inspiration we
+ learned from them, our team would continue to explore and find a unique
+ position for our product in the market.
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/biz-tech1.png"
- />
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/biz-tech1.png"
+ />
- <div class="image_description" id="greencontents">
- Fig. 1 The product score our group got.
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 1 The product score our group got.
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/biz-tech2.png"
- />
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/biz-tech2.png"
+ />
- <div class="image_description" id="greencontents">
- Fig. 2 An image of getting Best Entrepreneur.
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 2 An image of getting Best Entrepreneur.
+ </div>
- <div class="index_container" id="podcast"></div>
- <div class="heading2" id="collabheading2">
- Podcast
- </div>
+ <div class="index_container" id="podcast"></div>
+ <div class="heading2" id="collabheading2">
+ Podcast
+ </div>
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/podcast-cover.png"
- />
-
- <div class="info_contents" id="greencontents">
- By making a collection of podcast episodes, we aimed at delivering potential
- issues in real-world settings. The podcast collaboration consists of
- interviews and project sharings. Through the interviews, we informed and
- reminded the general public about the seriousness of global issues and how
- would those problems affect society. In every episode, we invited iGEM teams
- to talk about their projects and, most importantly, give the general public
- notion of ceasing global issues concerns.
- </div>
+ <img
+ class="constant_width"
+ src="https://static.igem.wiki/teams/4271/wiki/podcast-cover.png"
+ />
- <a
- class="button_collab"
- target="_blank"
- href="https://open.spotify.com/show/0C2VM4MngWrLqsO1IEMLk6"
- >
- Click here to listen to our podcast!
- </a>
+ <div class="info_contents" id="greencontents">
+ By making a collection of podcast episodes, we aimed at delivering
+ potential issues in real-world settings. The podcast collaboration
+ consists of interviews and project sharings. Through the interviews, we
+ informed and reminded the general public about the seriousness of global
+ issues and how would those problems affect society. In every episode, we
+ invited iGEM teams to talk about their projects and, most importantly,
+ give the general public notion of ceasing global issues concerns.
+ </div>
- <div class="heading4" id="collabheading4">
- NYCU: E.Color
- </div>
+ <a
+ class="button_collab"
+ target="_blank"
+ href="https://open.spotify.com/show/0C2VM4MngWrLqsO1IEMLk6"
+ >
+ Click here to listen to our podcast!
+ </a>
- <div class="info_contents" id="greencontents">
- In the second episode of our podcast, we invited team NYCU_Taipei to finish
- a recording with us. NYCU talked about their project called “E.Color†along
- with their inspirations and project significance. Their aim was to indicate
- the growth status of different E.coli by expressing the bacteria with
- different colors. From this collaboration, we saw great possibilities that
- their project could be applied in environmental and clinical applications to
- contribute to the society.
- </div>
+ <div class="heading4" id="collabheading4">
+ NYCU: E.Color
+ </div>
- <div class="heading4" id="collabheading4">
- Korea_HS: Tfam DNA Enhancement Kit
- </div>
+ <div class="info_contents" id="greencontents">
+ In the second episode of our podcast, we invited team NYCU_Taipei to
+ finish a recording with us. NYCU talked about their project called
+ “E.Color†along with their inspirations and project significance. Their
+ aim was to indicate the growth status of different E.coli by expressing
+ the bacteria with different colors. From this collaboration, we saw great
+ possibilities that their project could be applied in environmental and
+ clinical applications to contribute to the society.
+ </div>
- <div class="info_contents" id="greencontents">
- Korea_HS came up with a project to improve the stability of data stored in
- DNA. They called their project “Tfam DNA Enhancement Kit.†Unlike other DNA
- storage systems, their project is environmentally friendly because their
- method does not emit COâ‚‚ or use excess energy. Therefore, after they
- imparting their knowledge in technology and synthetic biology, DNA storage
- would become more stable and harmless to the environment. Though their
- project is not directly related to environmental issues, it is a good
- example of benefitting the environment from a different facet.
- </div>
+ <div class="heading4" id="collabheading4">
+ Korea_HS: Tfam DNA Enhancement Kit
+ </div>
- <div class="heading4" id="collabheading4">
- HNU_China: not yet
- </div>
+ <div class="info_contents" id="greencontents">
+ Korea_HS came up with a project to improve the stability of data stored in
+ DNA. They called their project “Tfam DNA Enhancement Kit.†Unlike other
+ DNA storage systems, their project is environmentally friendly because
+ their method does not emit COâ‚‚ or use excess energy. Therefore, after they
+ imparting their knowledge in technology and synthetic biology, DNA storage
+ would become more stable and harmless to the environment. Though their
+ project is not directly related to environmental issues, it is a good
+ example of benefitting the environment from a different facet.
+ </div>
- <div class="info_contents" id="greencontents">
- In China (Hunan), a large proportion of water is eutrophic. Similar to our
- topic, they also came up with an idea to cope with eutrophication. Their
- project “P Pact†was to build up a genetic circuit to absorb and export
- inorganic phosphate to lessen eutrophication. Their final goal is to reach
- sustainable development, purifying water bodies in their region (Hunan).
- Thanks to them, we learned a different application of synthetic biology to
- deal with eutrophication.
- </div>
+ <div class="heading4" id="collabheading4">
+ HNU_China: not yet
+ </div>
- <div class="heading4" id="collabheading4">
- MSP Maastricht iGEM: not yet
- </div>
+ <div class="info_contents" id="greencontents">
+ In China (Hunan), a large proportion of water is eutrophic. Similar to our
+ topic, they also came up with an idea to cope with eutrophication. Their
+ project “P Pact†was to build up a genetic circuit to absorb and export
+ inorganic phosphate to lessen eutrophication. Their final goal is to reach
+ sustainable development, purifying water bodies in their region (Hunan).
+ Thanks to them, we learned a different application of synthetic biology to
+ deal with eutrophication.
+ </div>
- <div class="info_contents" id="greencontents">
- MSP iGEM's target problem is water scarcity. With their solution, it is
- possible to not use energy, emit greenhouse gases, and obtain water with a
- cheap and sustainable price. Similar to our project, our projects focus on
- water issues and make sure our methods are friendly to the environment.
- </div>
+ <div class="heading4" id="collabheading4">
+ MSP Maastricht iGEM: not yet
+ </div>
- <div class="heading4" id="collabheading4">
- iGEM Aachen 2022: not yet
- </div>
- <div class="index_container" id="puzzle"></div>
+ <div class="info_contents" id="greencontents">
+ MSP iGEM's target problem is water scarcity. With their solution, it is
+ possible to not use energy, emit greenhouse gases, and obtain water with a
+ cheap and sustainable price. Similar to our project, our projects focus on
+ water issues and make sure our methods are friendly to the environment.
+ </div>
- <div class="heading2" id="collabheading2">
- Puzzle book
- </div>
+ <div class="index_container" id="puzzle"></div>
- <div class="info_contents" id="greencontents">
- Puzzle book was initiated by team Aestuarium MSP Maastricht and collaborated
- with 20 other iGEM teams. In this collaborative project, we included a
- 150-word project description and 10 words to introduce our team and project.
- With a brief and creative puzzle book, we hope our project could be easier
- to understand by the public.
- </div>
+ <div class="heading2" id="collabheading2">
+ Puzzle book
+ </div>
- <em class="info_contents_italics" id="greencontents">
- Words to describe our team:
- </em>
-
- <ul>
- <li>United</li>
- <li>Resilient</li>
- <li>Driven</li>
- <li>Cohesive</li>
- <li>Accountable</li>
- <li>Dedicated</li>
- </ul>
-
- <div class="info_contents" id="greencontents">
- Our team is like a
- <b>united family</b>
- : spent time working
- <b>cohesively</b>
- and supporting each other in many aspects. All 15 of us are equally
- determined to achieve the same goal, so everyone is
- <b>driven</b>
- and
- <b>dedicated</b>
- . While encountering problems, every single one of us is resilient and
- <b>accountable</b>
- to dissolve the obstacles.
- </div>
+ <div class="info_contents" id="greencontents">
+ Puzzle book was initiated by team Aestuarium MSP Maastricht and
+ collaborated with 20 other iGEM teams. In this collaborative project, we
+ included a 150-word project description and 10 words to introduce our team
+ and project. With a brief and creative puzzle book, we hope our project
+ could be easier to understand by the public.
+ </div>
- <em class="info_contents_italics" id="greencontents">
- Words to describe our project:
- </em>
-
- <ul>
- <li>Eco-friendly</li>
- <li>Measurable</li>
- <li>Innovative</li>
- <li>Practical</li>
- </ul>
-
- <div class="info_contents" id="greencontents">
- Our project is
- <b>measurable</b>
- and
- <b>practical</b>
- in terms of its benefits and achievements. It is not only achievable in
- monetary aspects, our plan is
- <b>innovative</b>
- and
- <b>eco-friendly</b>
- aiming at solving Eutrophication issues and providing a stable ecology in
- the global community.
- </div>
+ <em class="info_contents_italics" id="greencontents">
+ Words to describe our team:
+ </em>
- <div class="index_container" id="collabvid"></div>
- <div class="heading2" id="collabheading2">
- Collaboration video
- </div>
+ <ul>
+ <li>United</li>
+ <li>Resilient</li>
+ <li>Driven</li>
+ <li>Cohesive</li>
+ <li>Accountable</li>
+ <li>Dedicated</li>
+ </ul>
- <div class="info_contents" id="greencontents">
- iGEM team NCHU Taichung, a university in Taiwan, launched an activity to
- collaborate with all iGEM teams in Taiwan in order to create a video gallery
- about the projects of each team. The purpose of this collaboration was to
- let Taiwanese citizens understand local issues and the applications of
- synthetic biology. By explaining eutrophication and our approach to solving
- this issue through synthetic biology, our team could deliver our messages
- and raise public awareness through a
-
- <a class="content_link" target="_blank" href="https://youtu.be/2h4nfemK8W4">
- video
- </a>
- .
- </div>
+ <div class="info_contents" id="greencontents">
+ Our team is like a
+ <b>united family</b>
+ : spent time working
+ <b>cohesively</b>
+ and supporting each other in many aspects. All 15 of us are equally
+ determined to achieve the same goal, so everyone is
+ <b>driven</b>
+ and
+ <b>dedicated</b>
+ . While encountering problems, every single one of us is resilient and
+ <b>accountable</b>
+ to dissolve the obstacles.
+ </div>
- <div class="index_container" id="objective"></div>
- <div class="heading2" id="collabheading2">
- Conclusion
- </div>
+ <em class="info_contents_italics" id="greencontents">
+ Words to describe our project:
+ </em>
+
+ <ul>
+ <li>Eco-friendly</li>
+ <li>Measurable</li>
+ <li>Innovative</li>
+ <li>Practical</li>
+ </ul>
- <div class="info_contents" id="greencontents">
- To conclude, we hope we can have more interactions and communications with
- other iGEM teams. We hope to spread more ideas about the seriousness of
- aquatic issues and help out other iGEM teams to solve problems by working
- together, gathering ideas, and sharing experiences.
+ <div class="info_contents" id="greencontents">
+ Our project is
+ <b>measurable</b>
+ and
+ <b>practical</b>
+ in terms of its benefits and achievements. It is not only achievable in
+ monetary aspects, our plan is
+ <b>innovative</b>
+ and
+ <b>eco-friendly</b>
+ aiming at solving Eutrophication issues and providing a stable ecology in
+ the global community.
+ </div>
+
+ <div class="index_container" id="collabvid"></div>
+ <div class="heading2" id="collabheading2">
+ Collaboration video
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ iGEM team NCHU Taichung, a university in Taiwan, launched an activity to
+ collaborate with all iGEM teams in Taiwan in order to create a video
+ gallery about the projects of each team. The purpose of this collaboration
+ was to let Taiwanese citizens understand local issues and the applications
+ of synthetic biology. By explaining eutrophication and our approach to
+ solving this issue through synthetic biology, our team could deliver our
+ messages and raise public awareness through a
+
+ <a
+ class="content_link"
+ id="collablink"
+ target="_blank"
+ href="https://youtu.be/2h4nfemK8W4"
+ >
+ video
+ </a>
+ .
+ </div>
+
+ <div class="index_container" id="objective"></div>
+ <div class="heading2" id="collabheading2">
+ Conclusion
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ To conclude, we hope we can have more interactions and communications with
+ other iGEM teams. We hope to spread more ideas about the seriousness of
+ aquatic issues and help out other iGEM teams to solve problems by working
+ together, gathering ideas, and sharing experiences.
+ </div>
</div>
</div>
{% endblock %}
diff --git a/wiki/pages/communication.html b/wiki/pages/communication.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/communication.html
+++ b/wiki/pages/communication.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/contribution.html b/wiki/pages/contribution.html
index 33bddb3..1729ece 100644
--- a/wiki/pages/contribution.html
+++ b/wiki/pages/contribution.html
@@ -1,309 +1,314 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/contribution.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="conpointer" href="#hardware">
- Hardware
- </a>
- <a class="pointer" id="conpointer" href="#model">
- Model
- </a>
-
- <a class="pointer" id="conpointer" href="#wetlab">
- Wet Lab
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
-
- <b class="heading1" id="contributionheading1">
- Contribution
- </b>
-
- <div class="index_container" id="hardware"></div>
- <div class="heading2" id="contributionheading2">
- Hardware Contribution: 3D Printing
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-6.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 1. The designed structure of our filtering device
- </div>
-
- <div class="info_contents" id="greencontents">
- The filter tube is covered by filter paper, which is used to prevent
- bacterial leakage. We designed filter paper caps to fix the filter paper
- caps for further prevention of bacterial leakage. The caps have similar
- sizes to the tube’s opening, as indicated in Fig. 7, so when caps are locked
- on the tube with filter papers, the filter would be an isolated space. To
- prevent branches or stones from breaking the filter papers, we added filter
- webs outside the filter papers’ cabs and designed filter webs’ caps to fix
- the webs on the tube. The caps’ design and 3D printing are documented for
- future iGEM teams to reference when developing prototypes for their
- implementation device.
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-7.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 2. The design of the cap for the filter
- </div>
-
- <div class="info_contents" id="greencontents">
- We chose to use Acrylonitrile Butadiene Styrene (ABS) as the material of the
- 3D-printed caps because it is acid, base, and heat resistant, especially to
- phosphoric acid, which eutrophic water has a high concentration of.
- Therefore, when placed into the reservoirs, the caps made out of abs can
- keep the filter papers intact and prevent bacteria leakage.
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- How do we design the caps?
- </em>
-
- <div class="video_hardware">
- <iframe
- title="Wego_Taipei: The Design of Caps (2022) [English]"
- width="100%"
- height="100%"
- src="https://video.igem.org/videos/embed/b8780734-7c0f-469f-b9b7-c6a65650f587"
- frameborder="0"
- allowfullscreen=""
- sandbox="allow-same-origin allow-scripts allow-popups"
- ></iframe>
- </div>
- <div class="info_contents" id="greencontents">
- Here is a video about how we utilize 3D-printed caps in the design.
- </div>
-
- <div class="info_contents" id="greencontents">
- For more information about the hardware, please visit our
- <a
- class="content_link"
- id="conlink"
- href="{{ url_for('pages', page='hardware') }}"
- >
- Hardware Page.
- </a>
- </div>
- <div class="index_container" id="model"></div>
-
- <div class="heading2" id="contributionheading2">
- Model Contribution
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
- <div class="info_contents" id="greencontents">
- Our model was built to explain the results from the proof of concept
- experiment of the designed part organophosphorus hydrolase (OPH), in which
- the ability of optimized conditions for OPH to hydrolyze paraoxon (a form of
- organic phosphate pollutant) into p-nitrophenol (pNP) was tested. Due to the
- fact that the OPH construct (Part: BBa_K4271001) we engineered was recently
- published, there are limited resources regarding this variant of OPH. Among
- these studies on this OPH, there was no research that provides quantitative
- analysis for this OPH. Therefore we contributed to this OPH part by fitting
- our experimental data with our model to evaluate the rate reaction constants
- of this OPH quantitatively. We constructed this model using Enzyme Kinetics.
- On this basis, there are three reactions concerning OPH. One of them is the
- reversible reaction of paraoxon PXN binding with OPH, forming the complex
- OPH::PXN. The reaction rate constants for this reaction are kOPH_PXN_f and
- kOPH_PXN_r, denoting the forward and reverse reactions, respectively. The
- rest of the reactions are hydrolysis and degradation; their reaction rate
- constants are khydro, and kdOPH respectively. We used data collected in the
- experimentation of the OPH function under different concentrations of IPTG
- induction and fitted them with the model we constructed and yielded the
- values summarized in the table below.
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/contribution.png"
+ />
</div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/table-for-page.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 3. Proposed reaction rate constants
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
</div>
-
- <div class="info_contents" id="greencontents">
- We then used these constants to simulate a pNP curve for any other
- experimental data. The curve was plotted with the data and proved that our
- proposed kinetics are reasonable.
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/final-proof.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 4. pNP simulation curve
- </div>
- <div class="info_contents" id="greencontents">
- For more information about the model, please visit our
- <a
- class="content_link"
- id="conlink"
- href="{{ url_for('pages', page='model') }}"
- >
- Dry Lab (Model) Page.
- </a>
- </div>
- <div class="index_container" id="wetlab"></div>
- <div class="heading2" id="contributionheading2">
- Wet Lab Contribution
- </div>
- <div class="info_contents" id="greencontents">
- In order to detect the degree of paraoxon degradation by our target protein
- OPH into p-nitrophenol (pNP), we designed a biosensor based on the existing
- part: superfolder GFP coding sequence (Part:
- <a
- class="content_link"
- target="_blank"
- id="conlink"
- href="http://parts.igem.org/Part:BBa_I746916#"
- >
- BBa_I746916
- </a>
- ). Our construct design
- <a
- class="content_link"
- target="_blank"
- id="conlink"
- href="http://parts.igem.org/Part:BBa_K4271008"
- >
- (BBa_4271008)
- </a>
- was based on a research paper published in Nucleic Acids Research (Jha,
- Ramesh K., et al.). The pNP sensor indicates the amount of pNP produced
- during OPH hydrolysis via GFP fluorescence.
- </div>
-
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 5. The linear map of our pNP sensor plasmid
- </div>
-
- <div class="image_description" id="greencontents">
- Our sensor plasmid includes a dual-directional pobA/R promoter, pNP RBS,
- sfGFP, pobR operator, pNPmut1-1, and two double terminators that are
- composed of RrrnB1 terminator and T7 terminator
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/paraoxon-biosensor.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 6. Theoretical function of our biosensor upon IPTG induction (created
- by BioRender):
- </div>
-
- <div class="image_description_small" id="greencontents">
- Our biosensor contains an enzyme plasmid and a sensor plasmid that would
- enhance GFP expression, thereby indicating the amount of paraoxon detoxified
- by OPH
- </div>
-
- <div class="info_contents" id="greencontents">
- After cultivating normal E.coli colonies and E.coli engineered with the
- biosensor in the absence and presence of pNP, the result we acquired from
- the experiment was not consistent with the data published in the paper (Jha
- et al., 2016). The observed differences between the levels of GFP
- fluorescence before and after adding 125 µM of pNP were not significant
- enough to prove the effectiveness of the biosensor.
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/fluorescent-protein-expression-level.png"
- />
-
- <div class="chart" id="two_five">
- <b class="chart_header" id="greencontents">
- Groups
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="conpointer" href="#hardware">
+ Hardware
+ </a>
+ <a class="pointer" id="conpointer" href="#model">
+ Model
+ </a>
+
+ <a class="pointer" id="conpointer" href="#wetlab">
+ Wet Lab
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+
+ <b class="heading1" id="contributionheading1">
+ Contribution
</b>
- <b class="chart_header" id="greencontents">
- Fluorescence
- </b>
- <div class="chart_contents" id="greencontents">DH5alpha</div>
- <div class="chart_contents" id="greencontents">24870</div>
- <div class="chart_contents" id="greencontents">DH5alpha + pNP</div>
- <div class="chart_contents" id="greencontents">20650</div>
- <div class="chart_contents" id="greencontents">DH5alpha-sensor</div>
- <div class="chart_contents" id="greencontents">46867</div>
- <div class="chart_contents" id="greencontents">DH5alpha-sensor + pNP</div>
- <div class="chart_contents" id="greencontents">50783</div>
- </div>
- <div class="image_description" id="greencontents">
- Fig. 7. GFP fluorescence level of DH5 alpha and DH5 alpha with biosensor in
- the absence/presence of pNP
- </div>
- <div class="info_contents" id="greencontents">
- Since the genetic organization and sequence of our pNP sensor is identical
- to the plasmid design in the research paper, we concluded that there might
- be an error in the biosensor design. We believe this discovery would benefit
- and contribute to future research related to the application of the pNP
- biosensor.
- </div>
-
- <div class="info_contents" id="greencontents">
- For more information about the pNP biosensor design and experiments, please
- visit our
- <a
- class="content_link"
- id="conlink"
- href="{{ url_for('pages', page='engineering') }}"
- >
- Engineering Success Page
- </a>
- .
- </div>
-
- <div class="workscited" id="greencontents">References</div>
-
- <div class="info_contents" id="greencontents">
- Ramesh K. Jha, Theresa L. Kern, Youngchang Kim, Christine Tesar, Robert
- Jedrzejczak, Andrzej Joachimiak, Charlie E. M. Strauss, A microbial sensor
- for organophosphate hydrolysis exploiting an engineered specificity switch
- in a transcription factor, Nucleic Acids Research, Volume 44, Issue 17, 30
- September 2016, Pages 8490–8500, https://doi.org/10.1093/nar/gkw687
+ <div class="index_container" id="hardware"></div>
+ <div class="heading2" id="contributionheading2">
+ Hardware Contribution: 3D Printing
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-6.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 1. The designed structure of our filtering device
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ The filter tube is covered by filter paper, which is used to prevent
+ bacterial leakage. We designed filter paper caps to fix the filter paper
+ caps for further prevention of bacterial leakage. The caps have similar
+ sizes to the tube’s opening, as indicated in Fig. 7, so when caps are
+ locked on the tube with filter papers, the filter would be an isolated
+ space. To prevent branches or stones from breaking the filter papers, we
+ added filter webs outside the filter papers’ cabs and designed filter
+ webs’ caps to fix the webs on the tube. The caps’ design and 3D printing
+ are documented for future iGEM teams to reference when developing
+ prototypes for their implementation device.
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-7.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 2. The design of the cap for the filter
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ We chose to use Acrylonitrile Butadiene Styrene (ABS) as the material of
+ the 3D-printed caps because it is acid, base, and heat resistant,
+ especially to phosphoric acid, which eutrophic water has a high
+ concentration of. Therefore, when placed into the reservoirs, the caps
+ made out of abs can keep the filter papers intact and prevent bacteria
+ leakage.
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ How do we design the caps?
+ </em>
+
+ <div class="video_hardware">
+ <iframe
+ title="Wego_Taipei: The Design of Caps (2022) [English]"
+ width="100%"
+ height="100%"
+ src="https://video.igem.org/videos/embed/b8780734-7c0f-469f-b9b7-c6a65650f587"
+ frameborder="0"
+ allowfullscreen=""
+ sandbox="allow-same-origin allow-scripts allow-popups"
+ ></iframe>
+ </div>
+ <div class="info_contents_centered_contribution" id="greencontents">
+ Here is a video about how we utilize 3D-printed caps in the design.
+ </div>
+
+ <div class="info_contents_centered_contribution" id="greencontents">
+ For more information about the hardware, please visit our
+ <a
+ class="content_link"
+ id="conlink"
+ href="{{ url_for('pages', page='hardware') }}"
+ >
+ Hardware Page.
+ </a>
+ </div>
+ <div class="index_container" id="model"></div>
+
+ <div class="heading2" id="contributionheading2">
+ Model Contribution
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Our model was built to explain the results from the proof of concept
+ experiment of the designed part organophosphorus hydrolase (OPH), in which
+ the ability of optimized conditions for OPH to hydrolyze paraoxon (a form
+ of organic phosphate pollutant) into p-nitrophenol (pNP) was tested. Due
+ to the fact that the OPH construct (Part: BBa_K4271001) we engineered was
+ recently published, there are limited resources regarding this variant of
+ OPH. Among these studies on this OPH, there was no research that provides
+ quantitative analysis for this OPH. Therefore we contributed to this OPH
+ part by fitting our experimental data with our model to evaluate the rate
+ reaction constants of this OPH quantitatively. We constructed this model
+ using Enzyme Kinetics. On this basis, there are three reactions concerning
+ OPH. One of them is the reversible reaction of paraoxon PXN binding with
+ OPH, forming the complex OPH::PXN. The reaction rate constants for this
+ reaction are kOPH_PXN_f and kOPH_PXN_r, denoting the forward and reverse
+ reactions, respectively. The rest of the reactions are hydrolysis and
+ degradation; their reaction rate constants are khydro, and kdOPH
+ respectively. We used data collected in the experimentation of the OPH
+ function under different concentrations of IPTG induction and fitted them
+ with the model we constructed and yielded the values summarized in the
+ table below.
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/table-for-page.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 3. Proposed reaction rate constants
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ We then used these constants to simulate a pNP curve for any other
+ experimental data. The curve was plotted with the data and proved that our
+ proposed kinetics are reasonable.
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/final-proof.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 4. pNP simulation curve
+ </div>
+ <div class="info_contents_centered_contribution" id="greencontents">
+ For more information about the model, please visit our
+ <a
+ class="content_link"
+ id="conlink"
+ href="{{ url_for('pages', page='model') }}"
+ >
+ Dry Lab (Model) Page.
+ </a>
+ </div>
+ <div class="index_container" id="wetlab"></div>
+ <div class="heading2" id="contributionheading2">
+ Wet Lab Contribution
+ </div>
+ <div class="info_contents" id="greencontents">
+ In order to detect the degree of paraoxon degradation by our target
+ protein OPH into p-nitrophenol (pNP), we designed a biosensor based on the
+ existing part: superfolder GFP coding sequence (Part:
+ <a
+ class="content_link"
+ target="_blank"
+ id="conlink"
+ href="http://parts.igem.org/Part:BBa_I746916#"
+ >
+ BBa_I746916
+ </a>
+ ). Our construct design
+ <a
+ class="content_link"
+ target="_blank"
+ id="conlink"
+ href="http://parts.igem.org/Part:BBa_K4271008"
+ >
+ (BBa_4271008)
+ </a>
+ was based on a research paper published in Nucleic Acids Research (Jha,
+ Ramesh K., et al.). The pNP sensor indicates the amount of pNP produced
+ during OPH hydrolysis via GFP fluorescence.
+ </div>
+
+ <img
+ class="constant_width"
+ src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 5. The linear map of our pNP sensor plasmid
+ </div>
+
+ <div class="image_description" id="greencontents">
+ Our sensor plasmid includes a dual-directional pobA/R promoter, pNP RBS,
+ sfGFP, pobR operator, pNPmut1-1, and two double terminators that are
+ composed of RrrnB1 terminator and T7 terminator
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/paraoxon-biosensor.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 6. Theoretical function of our biosensor upon IPTG induction (created
+ by BioRender):
+ </div>
+
+ <div class="image_description_small" id="greencontents">
+ Our biosensor contains an enzyme plasmid and a sensor plasmid that would
+ enhance GFP expression, thereby indicating the amount of paraoxon
+ detoxified by OPH
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ After cultivating normal E.coli colonies and E.coli engineered with the
+ biosensor in the absence and presence of pNP, the result we acquired from
+ the experiment was not consistent with the data published in the paper
+ (Jha et al., 2016). The observed differences between the levels of GFP
+ fluorescence before and after adding 125 µM of pNP were not significant
+ enough to prove the effectiveness of the biosensor.
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/fluorescent-protein-expression-level.png"
+ />
+
+ <div class="chart" id="two_five">
+ <b class="chart_header" id="greencontents">
+ Groups
+ </b>
+ <b class="chart_header" id="greencontents">
+ Fluorescence
+ </b>
+ <div class="chart_contents" id="greencontents">DH5alpha</div>
+ <div class="chart_contents" id="greencontents">24870</div>
+ <div class="chart_contents" id="greencontents">DH5alpha + pNP</div>
+ <div class="chart_contents" id="greencontents">20650</div>
+ <div class="chart_contents" id="greencontents">DH5alpha-sensor</div>
+ <div class="chart_contents" id="greencontents">46867</div>
+ <div class="chart_contents" id="greencontents">DH5alpha-sensor + pNP</div>
+ <div class="chart_contents" id="greencontents">50783</div>
+ </div>
+ <div class="image_description" id="greencontents">
+ Fig. 7. GFP fluorescence level of DH5 alpha and DH5 alpha with biosensor
+ in the absence/presence of pNP
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Since the genetic organization and sequence of our pNP sensor is identical
+ to the plasmid design in the research paper, we concluded that there might
+ be an error in the biosensor design. We believe this discovery would
+ benefit and contribute to future research related to the application of
+ the pNP biosensor.
+ </div>
+
+ <div class="info_contents_centered_contribution" id="greencontents">
+ For more information about the pNP biosensor design and experiments,
+ please visit our
+ <a
+ class="content_link"
+ id="conlink"
+ href="{{ url_for('pages', page='engineering') }}"
+ >
+ Engineering Success Page
+ </a>
+ .
+ </div>
+
+ <div class="workscited" id="greencontents">References</div>
+
+ <div class="info_contents" id="greencontents">
+ Ramesh K. Jha, Theresa L. Kern, Youngchang Kim, Christine Tesar, Robert
+ Jedrzejczak, Andrzej Joachimiak, Charlie E. M. Strauss, A microbial sensor
+ for organophosphate hydrolysis exploiting an engineered specificity switch
+ in a transcription factor, Nucleic Acids Research, Volume 44, Issue 17, 30
+ September 2016, Pages 8490–8500, https://doi.org/10.1093/nar/gkw687
+ </div>
</div>
</div>
+
{% endblock %}
diff --git a/wiki/pages/description.html b/wiki/pages/description.html
index 2bf37bf..fc17434 100644
--- a/wiki/pages/description.html
+++ b/wiki/pages/description.html
@@ -1,373 +1,378 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src=" https://static.igem.wiki/teams/4271/wiki/description.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="descriptionpointer" href="#background">Background</a>
- <a class="pointer" id="descriptionpointer" href="#currentsolution">
- Current Solutions
- </a>
- <a class="pointer" id="descriptionpointer" href="#oursolution">
- Our Solution
- </a>
- <a class="pointer" id="descriptionpointer" href="#inspiration">
- Inspiration
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="descriptionheading1">The Dead Zone Poison</b>
- <div class="index_container" id="background"></div>
- <div class="heading2" id="descriptionheading2">Background</div>
- <em class="info_contents_italics" id="greencontents">
- What is Eutrophication?
- </em>
- <div class="info_contents" id="greencontents">
- Eutrophication is a process caused by the gradual increase in the
- concentration of phosphorus, nitrogen, and other plant nutrients in the
- biosystem, which are introduced into the ecosystem primarily when streams
- wash away soils from land. Debris, products of reproduction, and dead
- terrestrial organisms are then deposited in water bodies as they enter the
- ecosystem. The overabundance of nutrients in water bodies results in harmful
- environmental effects. As the organic materials break down into nutrients,
- the productivity or fertility in the ecosystem increases. A great
- concentration of algae and microscopic organisms in the water bodies feed on
- the nutrients, growing, propagating, and forming unsightly algae blooms on
- the water surface. When the scum on the water surface blocks light
- penetration, plants produce less oxygen for underwater life. Moreover, dead
- algae are decomposed by bacteria and produce putrid odors or even release
- toxins in the water. The bacteria will consume oxygen in the water during
- the decomposition process and deplete the oxygen needed to sustain life.
- Ultimately, without oxygen, bodies of water become "dead zones."
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/description-pic1.jpeg"
- />
- <div class="image_description" id="greencontents">
- Fig. 1 An image of marine polluted by the phytoplankton bloom
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src=" https://static.igem.wiki/teams/4271/wiki/description.png"
+ />
+ </div>
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
</div>
- <em class="info_contents_italics" id="greencontents">
- Why are excess phosphates a problem?
- </em>
- <div class="info_contents" id="greencontents">
- Ammonia (NH3), Ammonium (NH4+), nitrate (NO3-), and phosphates are the
- primary forms of nitrogen and phosphorus in water bodies. Phosphate is a
- limiting nutrient, which means only limited solubility of phosphates is
- required for organism growth in aquatic ecosystems. In other words, excess
- quantities of phosphorus will result in problems of water quality such as
- eutrophication and harmful algal growth.
- </div>
- <div class="info_contents" id="greencontents">
- In the past two decades, human activities exacerbated the release of
- phosphorus. Discharges of agricultural and industrial wastes, applications
- of inorganic fertilizers, along with increased soil erosion and landslides
- from fields result in accelerating phosphorus transport into aquatic
- systems. As described, restricted nutrient levels can often limit the
- productivity of bacterioplankton and algae. However, organic and inorganic
- phosphorus from soils has increased in the water system due to land erosion.
- As a result, the overall nutrient concentration in the water bodies rises to
- unnaturally high levels. Bacteria and algae, thus, are allowed to flourish
- and deplete oxygen in the system.
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/description-pic2.jpg"
- />
- <div class="image_description" id="greencontents">
- Fig. 2 Pollution of water bodies by chemical fertilizers
- </div>
-
- <em class="info_contents_italics" id="greencontents">A Global Issue</em>
- <div class="info_contents" id="greencontents">
- Given the widespread extent of water quality degradation caused by nutrient
- enrichment, eutrophication has been and continues to be a major global
- challenge. A study by the United Nations Environment Programme indicates
- that 30~40% of lakes and reservoirs around the world have been affected by
- eutrophication. Evidently, it poses a serious threat to the aquatic
- ecosystem, yet current solutions are either ineffective or extremely costly.
- Tainted drinking water supplies and the degradation of recreational
- opportunities, for example, can be detrimental to human health and
- well-being. Eutrophication as well contributes to the spread of
- gastrointestinal and dermatological diseases such as conjunctivitis and
- hypoxia. In the US alone, the combined costs of the treatments for
- eutrophication in freshwaters are approximately $2.2 billion annually
- (Dodds, et al).
- </div>
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="descriptionpointer" href="#background">
+ Background
+ </a>
+ <a class="pointer" id="descriptionpointer" href="#currentsolution">
+ Current Solutions
+ </a>
+ <a class="pointer" id="descriptionpointer" href="#oursolution">
+ Our Solution
+ </a>
+ <a class="pointer" id="descriptionpointer" href="#inspiration">
+ Inspiration
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+ <b class="heading1" id="descriptionheading1">The Dead Zone Poison</b>
+ <div class="index_container" id="background"></div>
+ <div class="heading2" id="descriptionheading2">Background</div>
+ <em class="info_contents_italics" id="greencontents">
+ What is Eutrophication?
+ </em>
+ <div class="info_contents" id="greencontents">
+ Eutrophication is a process caused by the gradual increase in the
+ concentration of phosphorus, nitrogen, and other plant nutrients in the
+ biosystem, which are introduced into the ecosystem primarily when streams
+ wash away soils from land. Debris, products of reproduction, and dead
+ terrestrial organisms are then deposited in water bodies as they enter the
+ ecosystem. The overabundance of nutrients in water bodies results in
+ harmful environmental effects. As the organic materials break down into
+ nutrients, the productivity or fertility in the ecosystem increases. A
+ great concentration of algae and microscopic organisms in the water bodies
+ feed on the nutrients, growing, propagating, and forming unsightly algae
+ blooms on the water surface. When the scum on the water surface blocks
+ light penetration, plants produce less oxygen for underwater life.
+ Moreover, dead algae are decomposed by bacteria and produce putrid odors
+ or even release toxins in the water. The bacteria will consume oxygen in
+ the water during the decomposition process and deplete the oxygen needed
+ to sustain life. Ultimately, without oxygen, bodies of water become "dead
+ zones."
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/description-pic1.jpeg"
+ />
- <div class="index_container" id="currentsolution"></div>
- <div class="heading2" id="descriptionheading2">Current Solutions</div>
- <div class="info_contents" id="greencontents">
- Eutrophication is one of the major environmental issues today. There have
- been studies that provide great notions and methods that can be applied to
- solve the problem of eutrophication.
- </div>
- <div class="info_contents" id="greencontents">
- According to Natural Resources 235, the best way to cope with eutrophication
- is to reduce and manage the amount of fertilizers humans use for
- agriculture. The use of fertilizers is one of the major reasons behind
- eutrophication. However, there are already a lot of dead zones, which are
- bodies of water that are hypoxic. Therefore, taking preventative measures
- would not be the most idealistic way to cope with the current condition.
- Most of the 27 reservoirs in Taiwan are affected by eutrophication (Lo Chi &
- Jake Chung). Mainly, the Taiwanese government has two current solutions to
- deal with eutrophication. The two methods being Multi-soil Layering (MSL)
- and Biomanipulation.
+ <div class="image_description" id="greencontents">
+ Fig. 1 An image of marine polluted by the phytoplankton bloom
+ </div>
+ <em class="info_contents_italics" id="greencontents">
+ Why are excess phosphates a problem?
+ </em>
<div class="info_contents" id="greencontents">
- Multi-soil Layering is a system introduced by Japanese researchers to
- decrease pollution and effectively remove phosphorus in the bodies of
- water (“水庫優養化剋星─多層複åˆæ¿¾æ–™(MSL)â€). MSL contains two layers to
- filter and extract phosphate. This system has the benefits, such as the
- use of natural materials and high efficiency. The total phosphorus (TP)
- removal efficiency is approximately 92% to 99.2% (Chia-Chun Ho & Pei-Hao
- Wang). In Taiwan, recently, MSL has been successfully implemented in
- Longtan Pond, Taoyuan. The system is placed near or juxtaposed to the
- reservoir, ensuring the cleanliness of the pond. Unfortunately, the cost
- of this system comes at a relatively high price. It is estimated that the
- whole cost is about $10,000 USD (Chia-Chun Ho & Pei-Hao Wang). Compared to
- the average cost for Annual Pond Maintenance Cleaning, which is about
- $2,000 USD, it is relatively expensive. Though this MSL is great, the main
- downside is the cost.
+ Ammonia (NH3), Ammonium (NH4+), nitrate (NO3-), and phosphates are the
+ primary forms of nitrogen and phosphorus in water bodies. Phosphate is a
+ limiting nutrient, which means only limited solubility of phosphates is
+ required for organism growth in aquatic ecosystems. In other words, excess
+ quantities of phosphorus will result in problems of water quality such as
+ eutrophication and harmful algal growth.
</div>
<div class="info_contents" id="greencontents">
- The other solution implemented by the Taiwanese government leans toward a
- biological approach, which is biomanipulation (æ士豪). Biomanipulation is
- the use of ecological techniques to solve environmental problems. By
- reducing the number of planktivorous fish, the density of large cladoceran
- zooplankton increases; hence, the growth of algae is reduced. (L.-A.
- Hansson, C. Brönmark). This method is known as the fish-stock
- biomanipulation. The cost, efficiency, and time of this approach is
- unforeseeable due to the environmental variability. The time needed to
- clear the water was four weeks in this fish-stock biomanipulation, which
- is efficient and effective in this example. In spite of that, the flaw
- that holds this method back is its lack of instability because
- biomanipulation is dependent on the environment. Some environments are
- suitable for biomanipulation, but others may not (Gerard ter Heerdt &
- Michiel Hootsmans). Therefore, the success rate of operating
- biomanipulation is uncertain.
+ In the past two decades, human activities exacerbated the release of
+ phosphorus. Discharges of agricultural and industrial wastes, applications
+ of inorganic fertilizers, along with increased soil erosion and landslides
+ from fields result in accelerating phosphorus transport into aquatic
+ systems. As described, restricted nutrient levels can often limit the
+ productivity of bacterioplankton and algae. However, organic and inorganic
+ phosphorus from soils has increased in the water system due to land
+ erosion. As a result, the overall nutrient concentration in the water
+ bodies rises to unnaturally high levels. Bacteria and algae, thus, are
+ allowed to flourish and deplete oxygen in the system.
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/description-pic2.jpg"
+ />
+ <div class="image_description" id="greencontents">
+ Fig. 2 Pollution of water bodies by chemical fertilizers
</div>
+ <em class="info_contents_italics" id="greencontents">A Global Issue</em>
<div class="info_contents" id="greencontents">
- To summarize above, both MSL and biomanipulation are considerable
- solutions to eutrophication. The major problem of MSL is the high price;
- meanwhile, biomanipulation lacks stability. Due to those problems, we
- designed our project to modify the MSL system into a better version.
+ Given the widespread extent of water quality degradation caused by
+ nutrient enrichment, eutrophication has been and continues to be a major
+ global challenge. A study by the United Nations Environment Programme
+ indicates that 30~40% of lakes and reservoirs around the world have been
+ affected by eutrophication. Evidently, it poses a serious threat to the
+ aquatic ecosystem, yet current solutions are either ineffective or
+ extremely costly. Tainted drinking water supplies and the degradation of
+ recreational opportunities, for example, can be detrimental to human
+ health and well-being. Eutrophication as well contributes to the spread of
+ gastrointestinal and dermatological diseases such as conjunctivitis and
+ hypoxia. In the US alone, the combined costs of the treatments for
+ eutrophication in freshwaters are approximately $2.2 billion annually
+ (Dodds, et al).
</div>
- </div>
- <div class="index_container" id="oursolution"></div>
- <div class="heading2" id="descriptionheading2">Our Solution</div>
- <div class="info_contents" id="greencontents">
- Our approach to solving eutrophication is to engineer cells of
- <em>Escherichia coli</em>
- to decline the external phosphorus level, which is the main reason behind
- eutrophic waters. The plan is to overexpress target genes, specifically
- Organophosphate Hydrolase (OPH) and an antisense mRNA for phoU (AsPhoU),
- that hydrolyze organic phosphate into inorganic phosphate (Pi), catalyze Pi
- transport, and polymerize Pi into Polyphosphate (PolyP), which can
- ultimately be stored in the bacteria to reduce the overall amount of
- phosphate in the surrounding bodies of water.
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/description-pic4.png"
- />
- <div class="image_description" id="greencontents">
- Fig. 3 AsPhoU System
- </div>
- <div class="info_contents" id="greencontents">
- Through overexpressing OPH, our E.coli is able to hydrolyze
- organophosphates, such as Paraoxon-methyl, into p-nitrophenol (pNP) and
- Dimethyl phosphate (DMP) (Grimsley JK). Glycerophosphodiesterase (GpdQ) then
- hydrolyzes DMP into inorganic phosphate for later use
- (“Glycerophosphodiester Phosphodiesterase Gpdq.â€).
- </div>
- <div class="info_contents" id="greencontents">
- By producing AsPhoU, we are able to eliminate phoU expression, thus
- enhancing PstSCAB expression. The PstSCAB proteins then transport Pi into
- the bacterial cytoplasm via the ABC-type transport systems – with PstS as
- the periplasmic Pi binding protein, PstC and PstA as integral membrane
- proteins, and PstB as the ATP binding protein (William R. McCleary).
- </div>
- <div class="info_contents" id="greencontents">
- Furthermore, the low concentration of Pi induces the expressions of PhoB and
- PhoR genes from the Phosphate regulons. The histidine kinase sensor PhoR
- subsequently catalyzes the activation of the response regulator PhoB,
- whereas the activated PhoB positively regulates the PstSCAB transcription
- operon and enhances Pi intake into
- <em>E. coli</em>
- , as explained above (William R. McCleary).
- </div>
+ <div class="index_container" id="currentsolution"></div>
+ <div class="heading2" id="descriptionheading2">Current Solutions</div>
+ <div class="info_contents" id="greencontents">
+ Eutrophication is one of the major environmental issues today. There have
+ been studies that provide great notions and methods that can be applied to
+ solve the problem of eutrophication.
+ </div>
+ <div class="info_contents" id="greencontents">
+ According to Natural Resources 235, the best way to cope with
+ eutrophication is to reduce and manage the amount of fertilizers humans
+ use for agriculture. The use of fertilizers is one of the major reasons
+ behind eutrophication. However, there are already a lot of dead zones,
+ which are bodies of water that are hypoxic. Therefore, taking preventative
+ measures would not be the most idealistic way to cope with the current
+ condition. Most of the 27 reservoirs in Taiwan are affected by
+ eutrophication (Lo Chi & Jake Chung). Mainly, the Taiwanese government has
+ two current solutions to deal with eutrophication. The two methods being
+ Multi-soil Layering (MSL) and Biomanipulation.
- <div class="info_contents" id="greencontents">
- After Pi is intaken,
- <em>E. coli</em>
- activates expressions of PhoB and PhoR genes from the Phosphate regulons.
- The histidine kinase sensor PhoR subsequently catalyzes the activation of
- the response regulator PhoB, whereas the activated PhoB positively regulates
- the PstSCAB transcription operon and enhances Pi intake into
- <em>E. coli</em>
- , as explained above (William R. McCleary).
- </div>
- <div class="info_contents" id="greencontents">
- Lastly, Polyphosphate kinase (PPK) is responsible for the synthesis of polyP
- in E.coli (Ye Zhu). As a result, excess polyphosphate is stored in bacteria,
- therefore diminishing the concentration of phosphate in the water body,
- reducing the overgrowth of algae, and inducing the amount of oxygen
- available for aquatic ecological growth.
- </div>
+ <div class="info_contents" id="greencontents">
+ Multi-soil Layering is a system introduced by Japanese researchers to
+ decrease pollution and effectively remove phosphorus in the bodies of
+ water (“水庫優養化剋星─多層複åˆæ¿¾æ–™(MSL)â€). MSL contains two layers to
+ filter and extract phosphate. This system has the benefits, such as the
+ use of natural materials and high efficiency. The total phosphorus (TP)
+ removal efficiency is approximately 92% to 99.2% (Chia-Chun Ho & Pei-Hao
+ Wang). In Taiwan, recently, MSL has been successfully implemented in
+ Longtan Pond, Taoyuan. The system is placed near or juxtaposed to the
+ reservoir, ensuring the cleanliness of the pond. Unfortunately, the cost
+ of this system comes at a relatively high price. It is estimated that
+ the whole cost is about $10,000 USD (Chia-Chun Ho & Pei-Hao Wang).
+ Compared to the average cost for Annual Pond Maintenance Cleaning, which
+ is about $2,000 USD, it is relatively expensive. Though this MSL is
+ great, the main downside is the cost.
+ </div>
+ <div class="info_contents" id="greencontents">
+ The other solution implemented by the Taiwanese government leans toward
+ a biological approach, which is biomanipulation (æ士豪).
+ Biomanipulation is the use of ecological techniques to solve
+ environmental problems. By reducing the number of planktivorous fish,
+ the density of large cladoceran zooplankton increases; hence, the growth
+ of algae is reduced. (L.-A. Hansson, C. Brönmark). This method is known
+ as the fish-stock biomanipulation. The cost, efficiency, and time of
+ this approach is unforeseeable due to the environmental variability. The
+ time needed to clear the water was four weeks in this fish-stock
+ biomanipulation, which is efficient and effective in this example. In
+ spite of that, the flaw that holds this method back is its lack of
+ instability because biomanipulation is dependent on the environment.
+ Some environments are suitable for biomanipulation, but others may not
+ (Gerard ter Heerdt & Michiel Hootsmans). Therefore, the success rate of
+ operating biomanipulation is uncertain.
+ </div>
- <div class="index_container" id="inspiration"></div>
- <div class="heading2" id="descriptionheading2">Inspiration</div>
- <div class="info_contents" id="greencontents">
- At the earliest stage of research, we came up with ideas spanning an
- impossibly wide area of expertise, from diagnostics and therapeutics to food
- and nutrition. Yet the more we expanded the scope of our topics, we realized
- that there is no better place to start than from our own living environment.
- We were astonished to learn that sixteen out of the twenty-six reservoirs in
- Taiwan are affected by the over-enrichment of nutrients (水質處生物組).
- Through synthetic biology, we hope to approach such a multifaceted issue
- from a different angle and develop a creative but feasible solution.
- </div>
- <div class="workscited" id="greencontents">References</div>
+ <div class="info_contents" id="greencontents">
+ To summarize above, both MSL and biomanipulation are considerable
+ solutions to eutrophication. The major problem of MSL is the high price;
+ meanwhile, biomanipulation lacks stability. Due to those problems, we
+ designed our project to modify the MSL system into a better version.
+ </div>
+ </div>
- <div class="info_contents" id="greencontents">
- Brönmark, & Hansson. (2009). Biomanipulation. Biomanipulation - an overview
- | ScienceDirect Topics. Retrieved April 22, 2022, from
- https://www.sciencedirect.com/topics/earth-and-planetary-sciences/biomanipulation#:~:text=Biomanipulation%20aims%20to%20prevent%20the,certain%20levels%20of%20nutrient%20loadings.
- </div>
- <div class="info_contents" id="greencontents">
- Chung, J., & Chi, L. (2021, August 1). Problematic water quality at Island
- Reservoirs: Report. Taipei Times. Retrieved April 22, 2022, from
- https://www.taipeitimes.com/News/taiwan/archives/2021/08/02/2003761878
- </div>
- <div class="info_contents" id="greencontents">
- Dodds, Walter K, et al. “Eutrophication of U.S. Freshwaters: Analysis of
- Potential Economic Damages.†Environmental Science & Technology, U.S.
- National Library of Medicine, 1 Jan. 2009,
- https://pubmed.ncbi.nlm.nih.gov/19209578/#:~:text= The%20
- combined%20costs%20were%20approximately,%2D1.16%20billion%20per%20year.
- </div>
- <div class="info_contents" id="greencontents">
- Ho, C.-C., & Wang, P.-H. (2015, March 23). Efficiency of a
- multi-soil-layering system on wastewater treatment using
- environment-friendly filter materials. International journal of
- environmental research and public health. Retrieved April 22, 2022, from
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377971/#:~:text=Therefore%2C%20the%20whole%20cost%20for,NTS%20is%20an%20economical%20solution.
- </div>
+ <div class="index_container" id="oursolution"></div>
+ <div class="heading2" id="descriptionheading2">Our Solution</div>
+ <div class="info_contents" id="greencontents">
+ Our approach to solving eutrophication is to engineer cells of
+ <em>Escherichia coli</em>
+ to decline the external phosphorus level, which is the main reason behind
+ eutrophic waters. The plan is to overexpress target genes, specifically
+ Organophosphate Hydrolase (OPH) and an antisense mRNA for phoU (AsPhoU),
+ that hydrolyze organic phosphate into inorganic phosphate (Pi), catalyze
+ Pi transport, and polymerize Pi into Polyphosphate (PolyP), which can
+ ultimately be stored in the bacteria to reduce the overall amount of
+ phosphate in the surrounding bodies of water.
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/description-pic4.png"
+ />
+ <div class="image_description" id="greencontents">
+ Fig. 3 AsPhoU System
+ </div>
+ <div class="info_contents" id="greencontents">
+ Through overexpressing OPH, our E.coli is able to hydrolyze
+ organophosphates, such as Paraoxon-methyl, into p-nitrophenol (pNP) and
+ Dimethyl phosphate (DMP) (Grimsley JK). Glycerophosphodiesterase (GpdQ)
+ then hydrolyzes DMP into inorganic phosphate for later use
+ (“Glycerophosphodiester Phosphodiesterase Gpdq.â€).
+ </div>
+ <div class="info_contents" id="greencontents">
+ By producing AsPhoU, we are able to eliminate phoU expression, thus
+ enhancing PstSCAB expression. The PstSCAB proteins then transport Pi into
+ the bacterial cytoplasm via the ABC-type transport systems – with PstS as
+ the periplasmic Pi binding protein, PstC and PstA as integral membrane
+ proteins, and PstB as the ATP binding protein (William R. McCleary).
+ </div>
+ <div class="info_contents" id="greencontents">
+ Furthermore, the low concentration of Pi induces the expressions of PhoB
+ and PhoR genes from the Phosphate regulons. The histidine kinase sensor
+ PhoR subsequently catalyzes the activation of the response regulator PhoB,
+ whereas the activated PhoB positively regulates the PstSCAB transcription
+ operon and enhances Pi intake into
+ <em>E. coli</em>
+ , as explained above (William R. McCleary).
+ </div>
- <div class="info_contents" id="greencontents">
- he%20whole%20cost%20for,NTS%20is%20an%20economical%20solution. JR;, Grimsley
- JK;Scholtz JM;Pace CN;Wild. “Organophosphorus Hydrolase Is a Remarkably
- Stable Enzyme That Unfolds through a Homodimeric Intermediate.â€
- Biochemistry, U.S. National Library of Medicine,
- https://pubmed.ncbi.nlm.nih.gov/9398154/.
- </div>
- <div class="info_contents" id="greencontents">
- McCleary, William R. “Chapter: Molecular Mechanisms of Phosphate Homeostasis
- in Escherichia Coli.†IntechOpen, IntechOpen, 12 July 2017,
- https://www.intechopen.com/chapters/53934.
- </div>
- <div class="info_contents" id="greencontents">
- Masunaga, T., Sato, K., Zennami, T., Fujii, S., & Wakatsuki, T. (n.d.).
- Direct treatment of polluted river ... - JSTAGE.JST.GO.JP. Retrieved April
- 22, 2022, from
- https://www.jstage.jst.go.jp/article/jwet/1/1/1_1_97/_pdf/-char/en
- </div>
+ <div class="info_contents" id="greencontents">
+ After Pi is intaken,
+ <em>E. coli</em>
+ activates expressions of PhoB and PhoR genes from the Phosphate regulons.
+ The histidine kinase sensor PhoR subsequently catalyzes the activation of
+ the response regulator PhoB, whereas the activated PhoB positively
+ regulates the PstSCAB transcription operon and enhances Pi intake into
+ <em>E. coli</em>
+ , as explained above (William R. McCleary).
+ </div>
+ <div class="info_contents" id="greencontents">
+ Lastly, Polyphosphate kinase (PPK) is responsible for the synthesis of
+ polyP in E.coli (Ye Zhu). As a result, excess polyphosphate is stored in
+ bacteria, therefore diminishing the concentration of phosphate in the
+ water body, reducing the overgrowth of algae, and inducing the amount of
+ oxygen available for aquatic ecological growth.
+ </div>
- <div class="info_contents" id="greencontents">
- “Phosphorus in The Environment: Natural Flows and Human Interferences.â€
- Annual Reviews,
- https://www.annualreviews.org/doi/10.1146/annurev.energy.25.1.53. Accessed
- 21 Apr. 2022.
- </div>
- <div class="info_contents" id="greencontents">
- Sato, K., Wakatsuki, T., Iwashima, N., & Masunaga, T. (2019, January 23).
- Evaluation of long-term wastewater treatment performances in
- multi-soil-layering systems in small rural communities. Applied and
- Environmental Soil Science. Retrieved April 22, 2022, from
- https://www.hindawi.com/journals/aess/2019/1214368/
- </div>
- <div class="info_contents" id="greencontents">
- Sato, K., Wakatsuki, T., Iwashima, N., & Masunaga, T. (2019, January 23).
- Evaluation of long-term wastewater treatment performances in
- multi-soil-layering systems in small rural communities. Applied and
- Environmental Soil Science. Retrieved April 22, 2022, from
- https://www.hindawi.com/journals/aess/2019/1214368/
- </div>
- <div class="info_contents" id="greencontents">
- Shultz, David. “Past Phosphorus Runoff Causes Present Oxygen Depletion in
- Lakes.†EOS, 24 July 2015,
- https://eos.org/research-spotlights/past-phosphorus-runoff-causes-
- present-oxygen-depletion-in-lakes. Accessed 20 Apr. 2022
- </div>
+ <div class="index_container" id="inspiration"></div>
+ <div class="heading2" id="descriptionheading2">Inspiration</div>
+ <div class="info_contents" id="greencontents">
+ At the earliest stage of research, we came up with ideas spanning an
+ impossibly wide area of expertise, from diagnostics and therapeutics to
+ food and nutrition. Yet the more we expanded the scope of our topics, we
+ realized that there is no better place to start than from our own living
+ environment. We were astonished to learn that sixteen out of the
+ twenty-six reservoirs in Taiwan are affected by the over-enrichment of
+ nutrients (水質處生物組). Through synthetic biology, we hope to approach
+ such a multifaceted issue from a different angle and develop a creative
+ but feasible solution.
+ </div>
+ <div class="workscited" id="greencontents">References</div>
- <div class="info_contents" id="greencontents">
- ter Heerdt, G., & Hootsmans, M. (2007, June). Why biomanipulation can be
- effective in Peaty Lakes - Hydrobiologia. SpringerLink. Retrieved April 22,
- 2022, from https://link.springer.com/article/10.1007/s10750-007-0594-9
- </div>
- <div class="info_contents" id="greencontents">
- UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information
- ResourceSIB Swiss Institute of Bioinformatics. “Glycerophosphodiester
- Phosphodiesterase Gpdq.†UniProt ConsortiumEuropean Bioinformatics
- InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics,
- 23 Feb. 2022, https://www.uniprot.org/uniprot/Q6XBH1.
- </div>
- <div class="info_contents" id="greencontents">
- Wang, P.-H., & Ho, C.-C. (n.d.). Efficiency of a multi-soil-layering system
- ... - researchgate. Retrieved April 22, 2022, from
- https://www.researchgate.net/publication/274092305_Efficiency_of_a_Multi-Soil-Layering_System_on_Wastewater_Treatment_Using_Environment-Friendly_Filter_Materials
- </div>
+ <div class="info_contents" id="greencontents">
+ Brönmark, & Hansson. (2009). Biomanipulation. Biomanipulation - an
+ overview | ScienceDirect Topics. Retrieved April 22, 2022, from
+ https://www.sciencedirect.com/topics/earth-and-planetary-sciences/biomanipulation#:~:text=Biomanipulation%20aims%20to%20prevent%20the,certain%20levels%20of%20nutrient%20loadings.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Chung, J., & Chi, L. (2021, August 1). Problematic water quality at Island
+ Reservoirs: Report. Taipei Times. Retrieved April 22, 2022, from
+ https://www.taipeitimes.com/News/taiwan/archives/2021/08/02/2003761878
+ </div>
+ <div class="info_contents" id="greencontents">
+ Dodds, Walter K, et al. “Eutrophication of U.S. Freshwaters: Analysis of
+ Potential Economic Damages.†Environmental Science & Technology, U.S.
+ National Library of Medicine, 1 Jan. 2009,
+ https://pubmed.ncbi.nlm.nih.gov/19209578/#:~:text= The%20
+ combined%20costs%20were%20approximately,%2D1.16%20billion%20per%20year.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Ho, C.-C., & Wang, P.-H. (2015, March 23). Efficiency of a
+ multi-soil-layering system on wastewater treatment using
+ environment-friendly filter materials. International journal of
+ environmental research and public health. Retrieved April 22, 2022, from
+ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377971/#:~:text=Therefore%2C%20the%20whole%20cost%20for,NTS%20is%20an%20economical%20solution.
+ </div>
- <div class="info_contents" id="greencontents">
- Zhu, Ye, et al. “Crystal Structure of a Polyphosphate Kinase and Its
- Implications for Polyphosphate Synthesis.†EMBO Reports, U.S. National
- Library of Medicine, July 2005,
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369109/.
- </div>
- <div class="info_contents" id="greencontents">
- æ 士豪. (2012, May 30). 阻æ¢å„ªé¤ŠåŒ–　交大有撇æ¥. å–€å ±. Retrieved April 22,
- 2022, from
- https://castnet.nctu.edu.tw/meichu2019/article/4628?issueID=171#:~:text=2012%2F05%2F30-,%E7%82%BA%E4%BA%86%E9%81%BF%E5%85%8D%E5%84%AA%E9%A4%8A%E5%8C%96%E7%99%BC%E7%94%9F%EF%BC%8C%E6%B8%9B%E5%B0%91%E5%90%AB%E6%B0%AE%E3%80%81%E7%A3%B7,%E5%B1%85%E6%B0%91%E7%9A%84%E4%BC%91%E9%96%92%E5%A5%BD%E5%8E%BB%E8%99%95%E3%80%82&text=%E5%9C%A8%E6%B1%99%E6%9F%93%E9%98%B2%E6%B2%BB%E4%B8%AD%EF%BC%8C%E6%B8%9B%E5%B0%91,%E5%8C%96%E7%99%BC%E7%94%9F%E7%9A%84%E9%A6%96%E8%A6%81%E6%A2%9D%E4%BB%B6%E3%80%82
- </div>
- <div class="info_contents" id="greencontents">
- 水質處生物組. “水庫優養化.†自來水全çƒè³‡è¨Šç¶², å°ç£è‡ªä¾†æ°´å…¬å¸, 22 Jan. 2022,
- www.water.gov.tw/ch/Subject/Detail/1123?nodeId=746.
- </div>
- <div class="info_contents" id="greencontents">
- 水庫優養化剋星─多層複åˆæ¿¾æ–™(MSL). ç’°ä¿æ–°èžå°ˆå€. (n.d.). Retrieved April 22,
- 2022, from
- https://enews.epa.gov.tw/Page/894720A1EB490390/4865463d-84a1-45e1-b332-9fd891adc14b
+ <div class="info_contents" id="greencontents">
+ he%20whole%20cost%20for,NTS%20is%20an%20economical%20solution. JR;,
+ Grimsley JK;Scholtz JM;Pace CN;Wild. “Organophosphorus Hydrolase Is a
+ Remarkably Stable Enzyme That Unfolds through a Homodimeric Intermediate.â€
+ Biochemistry, U.S. National Library of Medicine,
+ https://pubmed.ncbi.nlm.nih.gov/9398154/.
+ </div>
+ <div class="info_contents" id="greencontents">
+ McCleary, William R. “Chapter: Molecular Mechanisms of Phosphate
+ Homeostasis in Escherichia Coli.†IntechOpen, IntechOpen, 12 July 2017,
+ https://www.intechopen.com/chapters/53934.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Masunaga, T., Sato, K., Zennami, T., Fujii, S., & Wakatsuki, T. (n.d.).
+ Direct treatment of polluted river ... - JSTAGE.JST.GO.JP. Retrieved April
+ 22, 2022, from
+ https://www.jstage.jst.go.jp/article/jwet/1/1/1_1_97/_pdf/-char/en
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ “Phosphorus in The Environment: Natural Flows and Human Interferences.â€
+ Annual Reviews,
+ https://www.annualreviews.org/doi/10.1146/annurev.energy.25.1.53. Accessed
+ 21 Apr. 2022.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Sato, K., Wakatsuki, T., Iwashima, N., & Masunaga, T. (2019, January 23).
+ Evaluation of long-term wastewater treatment performances in
+ multi-soil-layering systems in small rural communities. Applied and
+ Environmental Soil Science. Retrieved April 22, 2022, from
+ https://www.hindawi.com/journals/aess/2019/1214368/
+ </div>
+ <div class="info_contents" id="greencontents">
+ Sato, K., Wakatsuki, T., Iwashima, N., & Masunaga, T. (2019, January 23).
+ Evaluation of long-term wastewater treatment performances in
+ multi-soil-layering systems in small rural communities. Applied and
+ Environmental Soil Science. Retrieved April 22, 2022, from
+ https://www.hindawi.com/journals/aess/2019/1214368/
+ </div>
+ <div class="info_contents" id="greencontents">
+ Shultz, David. “Past Phosphorus Runoff Causes Present Oxygen Depletion in
+ Lakes.†EOS, 24 July 2015,
+ https://eos.org/research-spotlights/past-phosphorus-runoff-causes-
+ present-oxygen-depletion-in-lakes. Accessed 20 Apr. 2022
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ ter Heerdt, G., & Hootsmans, M. (2007, June). Why biomanipulation can be
+ effective in Peaty Lakes - Hydrobiologia. SpringerLink. Retrieved April
+ 22, 2022, from https://link.springer.com/article/10.1007/s10750-007-0594-9
+ </div>
+ <div class="info_contents" id="greencontents">
+ UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information
+ ResourceSIB Swiss Institute of Bioinformatics. “Glycerophosphodiester
+ Phosphodiesterase Gpdq.†UniProt ConsortiumEuropean Bioinformatics
+ InstituteProtein Information ResourceSIB Swiss Institute of
+ Bioinformatics, 23 Feb. 2022, https://www.uniprot.org/uniprot/Q6XBH1.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Wang, P.-H., & Ho, C.-C. (n.d.). Efficiency of a multi-soil-layering
+ system ... - researchgate. Retrieved April 22, 2022, from
+ https://www.researchgate.net/publication/274092305_Efficiency_of_a_Multi-Soil-Layering_System_on_Wastewater_Treatment_Using_Environment-Friendly_Filter_Materials
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Zhu, Ye, et al. “Crystal Structure of a Polyphosphate Kinase and Its
+ Implications for Polyphosphate Synthesis.†EMBO Reports, U.S. National
+ Library of Medicine, July 2005,
+ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369109/.
+ </div>
+ <div class="info_contents" id="greencontents">
+ æ 士豪. (2012, May 30). 阻æ¢å„ªé¤ŠåŒ–　交大有撇æ¥. å–€å ±. Retrieved April 22,
+ 2022, from
+ https://castnet.nctu.edu.tw/meichu2019/article/4628?issueID=171#:~:text=2012%2F05%2F30-,%E7%82%BA%E4%BA%86%E9%81%BF%E5%85%8D%E5%84%AA%E9%A4%8A%E5%8C%96%E7%99%BC%E7%94%9F%EF%BC%8C%E6%B8%9B%E5%B0%91%E5%90%AB%E6%B0%AE%E3%80%81%E7%A3%B7,%E5%B1%85%E6%B0%91%E7%9A%84%E4%BC%91%E9%96%92%E5%A5%BD%E5%8E%BB%E8%99%95%E3%80%82&text=%E5%9C%A8%E6%B1%99%E6%9F%93%E9%98%B2%E6%B2%BB%E4%B8%AD%EF%BC%8C%E6%B8%9B%E5%B0%91,%E5%8C%96%E7%99%BC%E7%94%9F%E7%9A%84%E9%A6%96%E8%A6%81%E6%A2%9D%E4%BB%B6%E3%80%82
+ </div>
+ <div class="info_contents" id="greencontents">
+ 水質處生物組. “水庫優養化.†自來水全çƒè³‡è¨Šç¶², å°ç£è‡ªä¾†æ°´å…¬å¸, 22 Jan.
+ 2022, www.water.gov.tw/ch/Subject/Detail/1123?nodeId=746.
+ </div>
+ <div class="info_contents" id="greencontents">
+ 水庫優養化剋星─多層複åˆæ¿¾æ–™(MSL). ç’°ä¿æ–°èžå°ˆå€. (n.d.). Retrieved April
+ 22, 2022, from
+ https://enews.epa.gov.tw/Page/894720A1EB490390/4865463d-84a1-45e1-b332-9fd891adc14b
+ </div>
</div>
</div>
-
{% endblock %}
diff --git a/wiki/pages/education.html b/wiki/pages/education.html
index c70598a..fa86c99 100644
--- a/wiki/pages/education.html
+++ b/wiki/pages/education.html
@@ -1,613 +1,618 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/education.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="educationpointer" href="#objective">
- Objective
- </a>
- <a class="pointer" id="educationpointer" href="#lectures">
- Lectures
- </a>
- <a class="pointer" id="educationpointer" href="#inclusivity">
- Inclusivity
- </a>
- <a class="pointer" id="educationpointer" href="#postcards">
- Postcards
- </a>
- <a class="pointer" id="educationpointer" href="#socialmed">
- Social Media
- </a>
- <a class="pointer" id="educationpointer" href="#mediaout">
- Media Outreach
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
-
- <b class="heading1" id="educationheading1">
- EDUCATION
- </b>
-
- <div class="index_container" id="objective"></div>
- <div class="heading2" id="educationheading2">
- Objective
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
- <div class="info_contents" id="greencontents">
- From preteens to professors, from urban cities to rural areas, Wego_Taipei
- strove to spread awareness of issues related to eutrophication. Whether by
- in-person lectures or online campaigns, our team tried to take the
- initiative to educate the public. We aimed to diversify our media to reach a
- wider audience, as we believed everyone has an equally important role in
- environmental preservation. Our
- <a
- class="content_link"
- id="education_link"
- href="{{ url_for('pages', page='human-practices') }}"
- >
- public opinion survey
- </a>
- showed a significant improvement in the understanding of such topics after
- exposure to any one of the following:
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/education.png"
+ />
</div>
-
- <div class="index_container" id="lectures"></div>
- <div class="heading2" id="educationheading2">
- Lectures
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
</div>
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="educationpointer" href="#objective">
+ Objective
+ </a>
+ <a class="pointer" id="educationpointer" href="#lectures">
+ Lectures
+ </a>
+ <a class="pointer" id="educationpointer" href="#inclusivity">
+ Inclusivity
+ </a>
+ <a class="pointer" id="educationpointer" href="#postcards">
+ Postcards
+ </a>
+ <a class="pointer" id="educationpointer" href="#socialmed">
+ Social Media
+ </a>
+ <a class="pointer" id="educationpointer" href="#mediaout">
+ Media Outreach
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
- <div class="info_contents" id="greencontents">
- Our main approach was giving hour-long presentations in our local community.
- While each lecture was tailor-made to suit different age groups, the focus
- revolved around eutrophication, our solution, and a call to action. We
- handed out poll postcards at the end of each class.
- </div>
+ <b class="heading1" id="educationheading1">
+ EDUCATION
+ </b>
- <em class="info_contents_italics" id="greencontents">
- Elementary School 9/19
- </em>
-
- <b class="heading4">
- Tianmu Elementary School (天æ¯åœ‹æ°‘å°å¸)
- </b>
-
- <div class="info_contents" id="greencontents">
- Tianmu Elementary School is a public school located in the district of
- Shilin in Taipei, Taiwan. We started with an introduction to synthetic
- biology, went into detail about the causes and impacts of eutrophication,
- and gave an overview of our engineered TripleP cell. We alternated between
- Mandarin and English to better convey the science behind our solution. Since
- we hoped to spark their interest in science-related fields of study, we
- ended the class with a group activity.
- </div>
+ <div class="index_container" id="objective"></div>
+ <div class="heading2" id="educationheading2">
+ Objective
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/tianmu1.jpg"
- />
+ <div class="info_contents" id="greencontents">
+ From preteens to professors, from urban cities to rural areas, Wego_Taipei
+ strove to spread awareness of issues related to eutrophication. Whether by
+ in-person lectures or online campaigns, our team tried to take the
+ initiative to educate the public. We aimed to diversify our media to reach
+ a wider audience, as we believed everyone has an equally important role in
+ environmental preservation. Our
+ <a
+ class="content_link"
+ id="education_link"
+ href="{{ url_for('pages', page='human-practices') }}"
+ >
+ public opinion survey
+ </a>
+ showed a significant improvement in the understanding of such topics after
+ exposure to any one of the following:
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 1 The HP team leading the jeopardy.
- </div>
+ <div class="index_container" id="lectures"></div>
+ <div class="heading2" id="educationheading2">
+ Lectures
+ </div>
- <div class="info_contents" id="greencontents">
- (Translation)
- <br />
- Q: Why causes eutrophication? Please explain the process in detail.
- <br />
- A: An overabundance of phosphate accumulates in water bodies and causes
- rapid algae growth; algal bloom, in turn, decreases the oxygen concentration
- and kills organisms.
- </div>
+ <div class="info_contents" id="greencontents">
+ Our main approach was giving hour-long presentations in our local
+ community. While each lecture was tailor-made to suit different age
+ groups, the focus revolved around eutrophication, our solution, and a call
+ to action. We handed out poll postcards at the end of each class.
+ </div>
- <img
- class="constant_height"
- id="figure2_edu"
- src="https://static.igem.wiki/teams/4271/wiki/tianmu-figure2.jpg"
- />
+ <em class="info_contents_italics" id="greencontents">
+ Elementary School 9/19
+ </em>
+
+ <b class="heading4">
+ Tianmu Elementary School (天æ¯åœ‹æ°‘å°å¸)
+ </b>
+
+ <div class="info_contents" id="greencontents">
+ Tianmu Elementary School is a public school located in the district of
+ Shilin in Taipei, Taiwan. We started with an introduction to synthetic
+ biology, went into detail about the causes and impacts of eutrophication,
+ and gave an overview of our engineered TripleP cell. We alternated between
+ Mandarin and English to better convey the science behind our solution.
+ Since we hoped to spark their interest in science-related fields of study,
+ we ended the class with a group activity.
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 2 Fifth-graders enthusiastically participate in the interactive class.
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/tianmu1.jpg"
+ />
- <a
- class="button_education"
- target="_blank"
- href="https://docs.google.com/presentation/d/1tMPmAkuRw1-jiViIK7QDBYyrXp3IhRpYJBnVAQs79nM/edit"
- >
- Check out our presentation slides!
- </a>
+ <div class="image_description" id="greencontents">
+ Fig. 1 The HP team leading the jeopardy.
+ </div>
- <div class="info_contents_centered">
- Scroll for more photos!
- </div>
- <!-- Slideshow container -->
- <div class="slideshow-container">
- <!-- Full-width images with number and caption text -->
- <div class="mySlides">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/cover1.jpg"
- style="width: 100%;"
- />
+ <div class="info_contents" id="greencontents">
+ (Translation)
+ <br />
+ Q: Why causes eutrophication? Please explain the process in detail.
+ <br />
+ A: An overabundance of phosphate accumulates in water bodies and causes
+ rapid algae growth; algal bloom, in turn, decreases the oxygen
+ concentration and kills organisms.
</div>
- <div class="mySlides">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/tianmu-cover.jpg"
- style="width: 100%;"
- />
+ <img
+ class="constant_height"
+ id="figure2_edu"
+ src="https://static.igem.wiki/teams/4271/wiki/tianmu-figure2.jpg"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 2 Fifth-graders enthusiastically participate in the interactive
+ class.
</div>
- <div class="mySlides">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/tianmu2.jpg"
- style="width: 100%;"
- />
+ <a
+ class="button_education"
+ target="_blank"
+ href="https://docs.google.com/presentation/d/1tMPmAkuRw1-jiViIK7QDBYyrXp3IhRpYJBnVAQs79nM/edit"
+ >
+ Check out our presentation slides!
+ </a>
+
+ <div class="info_contents_centered">
+ Scroll for more photos!
</div>
+ <!-- Slideshow container -->
+ <div class="slideshow-container">
+ <!-- Full-width images with number and caption text -->
+ <div class="mySlides">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/cover1.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/tianmu-cover.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/tianmu2.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/tianmu3.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/tianmu4.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <!-- Next and previous buttons -->
+ <a class="prev" onclick="plusSlides(-1)">❮</a>
+ <a class="next" onclick="plusSlides(1)">❯</a>
+ </div>
+ <br />
- <div class="mySlides">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/tianmu3.jpg"
- style="width: 100%;"
- />
+ <!-- The dots/circles -->
+ <div class="dots_slideshow">
+ <span class="dot" onclick="currentSlide(1)"></span>
+ <span class="dot" onclick="currentSlide(2)"></span>
+ <span class="dot" onclick="currentSlide(3)"></span>
+ <span class="dot" onclick="currentSlide(4)"></span>
+ <span class="dot" onclick="currentSlide(5)"></span>
</div>
- <div class="mySlides">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/tianmu4.jpg"
- style="width: 100%;"
- />
+ <em class="info_contents_italics" id="greencontents">
+ Junior High & Middle School 9/7
+ </em>
+
+ <b class="heading4">
+ Taipei Wego Private Junior High School
+ </b>
+
+ <div class="info_contents" id="greencontents">
+ The international department of Wego Junior High provides bilingual
+ education from seventh through ninth grade. We were able to go in-depth
+ with an all-English presentation, building on previous knowledge the
+ students had already learnt. A fair amount of time was spent explaining
+ the names and functions of enzymes and proteins – such as AsPhoU, pNP, and
+ E. coli, among many others. During the Q&A session, students voiced
+ concerns ranging from the possibility of bacteria leakage to the
+ ethicality of bioengineering. These were addressed to the team and we made
+ changes accordingly.
</div>
- <!-- Next and previous buttons -->
- <a class="prev" onclick="plusSlides(-1)">❮</a>
- <a class="next" onclick="plusSlides(1)">❯</a>
- </div>
- <br />
-
- <!-- The dots/circles -->
- <div class="dots_slideshow">
- <span class="dot" onclick="currentSlide(1)"></span>
- <span class="dot" onclick="currentSlide(2)"></span>
- <span class="dot" onclick="currentSlide(3)"></span>
- <span class="dot" onclick="currentSlide(4)"></span>
- <span class="dot" onclick="currentSlide(5)"></span>
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/9th-grade.jpg"
+ />
- <em class="info_contents_italics" id="greencontents">
- Junior High & Middle School 9/7
- </em>
-
- <b class="heading4">
- Taipei Wego Private Junior High School
- </b>
-
- <div class="info_contents" id="greencontents">
- The international department of Wego Junior High provides bilingual
- education from seventh through ninth grade. We were able to go in-depth with
- an all-English presentation, building on previous knowledge the students had
- already learnt. A fair amount of time was spent explaining the names and
- functions of enzymes and proteins – such as AsPhoU, pNP, and E. coli, among
- many others. During the Q&A session, students voiced concerns ranging from
- the possibility of bacteria leakage to the ethicality of bioengineering.
- These were addressed to the team and we made changes accordingly.
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 3 A member explains the cloning cycle of E. coli.
+ </div>
+ <a
+ class="button_education"
+ target="_blank"
+ href="https://docs.google.com/presentation/d/1keHNXv32x3FAMLMrwYG1zusDGO-d0vN9PztQIKZW1PU/edit?usp=sharing"
+ >
+ Check out our presentation slides!
+ </a>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/9th-grade.jpg"
- />
+ <em class="info_contents_italics" id="greencontents">
+ High School & Teachers 9/19
+ </em>
+
+ <b class="heading4">
+ Taipei Wego Private Senior High School
+ </b>
+
+ <div class="info_contents" id="greencontents">
+ As juniors and seniors, our members invited their respective homeroom
+ classes and teachers to attend our final lecture. Looser time constraints
+ and a higher level of education meant that each team (Wet Lab, Dry Lab,
+ HP, Wiki) was able to thoroughly present its findings. Our peers expressed
+ interest in gene engineering as well as joining iGEM in the upcoming year.
+ They raised questions about whether the cost, feasibility, and
+ effectiveness of our project could set our project apart from existing
+ solutions. We, then, consulted professionals about product positioning.
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 3 A member explains the cloning cycle of E. coli.
- </div>
- <a
- class="button_education"
- target="_blank"
- href="https://docs.google.com/presentation/d/1keHNXv32x3FAMLMrwYG1zusDGO-d0vN9PztQIKZW1PU/edit?usp=sharing"
- >
- Check out our presentation slides!
- </a>
-
- <em class="info_contents_italics" id="greencontents">
- High School & Teachers 9/19
- </em>
-
- <b class="heading4">
- Taipei Wego Private Senior High School
- </b>
-
- <div class="info_contents" id="greencontents">
- As juniors and seniors, our members invited their respective homeroom
- classes and teachers to attend our final lecture. Looser time constraints
- and a higher level of education meant that each team (Wet Lab, Dry Lab, HP,
- Wiki) was able to thoroughly present its findings. Our peers expressed
- interest in gene engineering as well as joining iGEM in the upcoming year.
- They raised questions about whether the cost, feasibility, and effectiveness
- of our project could set our project apart from existing solutions. We,
- then, consulted professionals about product positioning.
- </div>
+ <div class="index_container" id="inclusivity"></div>
+ <div class="heading2" id="educationheading2">
+ Inclusivity
+ </div>
- <div class="index_container" id="inclusivity"></div>
- <div class="heading2" id="educationheading2">
- Inclusivity
- </div>
+ <div class="info_contents_centered">
+ Scroll for more photos!
+ </div>
+ <!-- Slideshow container -->
+ <div class="slideshow-container">
+ <!-- Full-width images with number and caption text -->
+ <div class="mySlides2">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/lecture1.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides2">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/lecture2.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides2">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/lecture3.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides2">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/lecture4.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides2">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/lecture5.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <!-- Next and previous buttons -->
+ <a class="prev" onclick="plusSlides2(-1)">❮</a>
+ <a class="next" onclick="plusSlides2(1)">❯</a>
+ </div>
+ <br />
- <div class="info_contents_centered">
- Scroll for more photos!
- </div>
- <!-- Slideshow container -->
- <div class="slideshow-container">
- <!-- Full-width images with number and caption text -->
- <div class="mySlides2">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/lecture1.jpg"
- style="width: 100%;"
- />
+ <!-- The dots/circles -->
+ <div class="dots_slideshow">
+ <span class="dot2" onclick="currentSlide2(1)"></span>
+ <span class="dot2" onclick="currentSlide2(2)"></span>
+ <span class="dot2" onclick="currentSlide2(3)"></span>
+ <span class="dot2" onclick="currentSlide2(4)"></span>
+ <span class="dot2" onclick="currentSlide2(5)"></span>
</div>
- <div class="mySlides2">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/lecture2.jpg"
- style="width: 100%;"
- />
+ <b class="heading4">
+ MeiHe Elementary School (美和國å°)
+ </b>
+
+ <div class="info_contents" id="greencontents">
+ Wego_Taipei firmly believes that education should have no boundaries. The
+ “general public†encompasses people of all ages and backgrounds;
+ socioeconomic status should play no part in education. To achieve this
+ vision, we collaborated with a student-founded scientific educational
+ group Science x Life to design a science-learning summer program for
+ elementary school kids in rural Taiwan. Mei-ho Elementary School is a
+ public school located in rural Taitung and has limited funding. By guiding
+ students to perform experiments, teaching them about reactions in
+ photosynthesis, and raising awareness to the local environmental issues,
+ we aimed to remove barriers in STEM education resulting from economic
+ inequality. Our goal was to inspire students to be curious about, develop
+ a passion for, and keep pursuing science in the future.
</div>
- <div class="mySlides2">
+ <div class="safety_image_wrap">
<img
- src="https://static.igem.wiki/teams/4271/wiki/lecture3.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/inclusivity1.jpg"
/>
- </div>
-
- <div class="mySlides2">
<img
- src="https://static.igem.wiki/teams/4271/wiki/lecture4.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/inclusivity2.jpg"
/>
</div>
- <div class="mySlides2">
+ <div class="image_description" id="greencontents">
+ Fig. 4 A member explains the experiment.
+ </div>
+
+ <div class="promo">
+ <img
+ class="constant_height"
+ id="education_image"
+ src="https://static.igem.wiki/teams/4271/wiki/inclusivity4.jpg"
+ />
<img
- src="https://static.igem.wiki/teams/4271/wiki/lecture5.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="education_image"
+ src="https://static.igem.wiki/teams/4271/wiki/inclusivity5.jpg"
/>
</div>
- <!-- Next and previous buttons -->
- <a class="prev" onclick="plusSlides2(-1)">❮</a>
- <a class="next" onclick="plusSlides2(1)">❯</a>
- </div>
- <br />
-
- <!-- The dots/circles -->
- <div class="dots_slideshow">
- <span class="dot2" onclick="currentSlide2(1)"></span>
- <span class="dot2" onclick="currentSlide2(2)"></span>
- <span class="dot2" onclick="currentSlide2(3)"></span>
- <span class="dot2" onclick="currentSlide2(4)"></span>
- <span class="dot2" onclick="currentSlide2(5)"></span>
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 5 Experiment preparation.
+ </div>
+ <a
+ class="button_education"
+ target="_blank"
+ href="https://docs.google.com/presentation/d/13ynpbW7nUfvJIZILTvNqPTSZ5vgUq-vsyDfOBBaJ03M/edit?usp=sharing"
+ >
+ Check out our presentation slides!
+ </a>
- <b class="heading4">
- MeiHe Elementary School (美和國å°)
- </b>
-
- <div class="info_contents" id="greencontents">
- Wego_Taipei firmly believes that education should have no boundaries. The
- “general public†encompasses people of all ages and backgrounds;
- socioeconomic status should play no part in education. To achieve this
- vision, we collaborated with a student-founded scientific educational group
- Science x Life to design a science-learning summer program for elementary
- school kids in rural Taiwan. Mei-ho Elementary School is a public school
- located in rural Taitung and has limited funding. By guiding students to
- perform experiments, teaching them about reactions in photosynthesis, and
- raising awareness to the local environmental issues, we aimed to remove
- barriers in STEM education resulting from economic inequality. Our goal was
- to inspire students to be curious about, develop a passion for, and keep
- pursuing science in the future.
- </div>
+ <div class="index_container" id="postcards"></div>
+ <div class="heading2" id="educationheading2">
+ Postcards
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ At the end of the elementary and middle school lectures, we collected
+ feedback by asking students to fill out the postcards we designed. Some
+ made illustrations and others wrote down lingering questions. Many thanked
+ us for giving an educational yet entertaining presentation. The postcard
+ activity was crucial because it gave the audience a chance to express
+ their thoughts, and it gave us space for improvement.
+ </div>
- <div class="safety_image_wrap">
- <img
- class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/inclusivity1.jpg"
- />
<img
class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/inclusivity2.jpg"
+ src="https://static.igem.wiki/teams/4271/wiki/s-21823509.jpg"
/>
- </div>
- <div class="image_description" id="greencontents">
- Fig. 4 A member explains the experiment.
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 6 Image drawn by Tianmu Elementary School students.
+ </div>
- <div class="promo">
- <img
- class="constant_height"
- id="education_image"
- src="https://static.igem.wiki/teams/4271/wiki/inclusivity4.jpg"
- />
- <img
- class="constant_height"
- id="education_image"
- src="https://static.igem.wiki/teams/4271/wiki/inclusivity5.jpg"
- />
- </div>
+ <div class="info_contents_centered">
+ Postcards written by Grade 9 students in Wego.
+ </div>
+ <!-- Slideshow container -->
+ <div class="slideshow-container">
+ <!-- Full-width images with number and caption text -->
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-0-0.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-41.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-23.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-15.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-10.jpg"
+ style="width: 100%;"
+ />
+ </div>
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-40.jpg"
+ style="width: 100%;"
+ />
+ </div>
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-11.jpg"
+ style="width: 100%;"
+ />
+ </div>
+ <div class="mySlides3">
+ <img
+ src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-16.jpg"
+ style="width: 100%;"
+ />
+ </div>
+
+ <!-- Next and previous buttons -->
+ <a class="prev" id="prev3" onclick="plusSlides3(-1)">❮</a>
+ <a class="next" id="prev3" onclick="plusSlides3(1)">❯</a>
+ </div>
+ <br />
- <div class="image_description" id="greencontents">
- Fig. 5 Experiment preparation.
- </div>
- <a
- class="button_education"
- target="_blank"
- href="https://docs.google.com/presentation/d/13ynpbW7nUfvJIZILTvNqPTSZ5vgUq-vsyDfOBBaJ03M/edit?usp=sharing"
- >
- Check out our presentation slides!
- </a>
-
- <div class="index_container" id="postcards"></div>
- <div class="heading2" id="educationheading2">
- Postcards
- </div>
+ <!-- The dots/circles -->
+ <div class="dots_slideshow">
+ <span class="dot3" onclick="currentSlide3(1)"></span>
+ <span class="dot3" onclick="currentSlide3(2)"></span>
+ <span class="dot3" onclick="currentSlide3(3)"></span>
+ <span class="dot3" onclick="currentSlide3(4)"></span>
+ <span class="dot3" onclick="currentSlide3(5)"></span>
+ <span class="dot3" onclick="currentSlide3(6)"></span>
+ <span class="dot3" onclick="currentSlide3(7)"></span>
+ <span class="dot3" onclick="currentSlide3(8)"></span>
+ </div>
- <div class="info_contents" id="greencontents">
- At the end of the elementary and middle school lectures, we collected
- feedback by asking students to fill out the postcards we designed. Some made
- illustrations and others wrote down lingering questions. Many thanked us for
- giving an educational yet entertaining presentation. The postcard activity
- was crucial because it gave the audience a chance to express their thoughts,
- and it gave us space for improvement.
- </div>
+ <a class="button_education" href="{{ url_for('pages', page='notebook') }}">
+ Click here for more postcards!
+ </a>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/s-21823509.jpg"
- />
+ <b class="heading1" id="educationheading1">
+ COMMUNICATION
+ </b>
- <div class="image_description" id="greencontents">
- Fig. 6 Image drawn by Tianmu Elementary School students.
- </div>
+ <div class="index_container" id="socialmed"></div>
+ <div class="heading2" id="educationheading2">
+ Social Media
+ </div>
- <div class="info_contents_centered">
- Postcards written by Grade 9 students in Wego.
- </div>
- <!-- Slideshow container -->
- <div class="slideshow-container">
- <!-- Full-width images with number and caption text -->
- <div class="mySlides3">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-0-0.jpg"
- style="width: 100%;"
- />
+ <div class="info_contents" id="greencontents">
+ Under pandemic, reaching the community through social media is the most
+ effective and optimal way for safety concerns. To reach a wider range of
+ audience and raise public awareness, we regularly updated bilingual
+ stories, posts, and reels on our
+ <a
+ class="content_link"
+ target="_blank"
+ id="education_link"
+ href="https://www.instagram.com/taipei_wego_igem/"
+ >
+ instagram account
+ </a>
+ . We posted trivial quizzes on a daily-basis which related to our project,
+ facts about eutrophication, and basic knowledge of synthetic biology. By
+ analyzing common misunderstandings shared by our followers, we created
+ reels to specifically explain the causes, effects, and gravity of
+ Eutrophication and further introduce our solution to mitigating the issue.
</div>
- <div class="mySlides3">
- <img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-41.jpg"
- style="width: 100%;"
- />
+ <div class="info_contents" id="greencontents">
+ Moreover, our instagram posts have promoted a variety of scientific
+ knowledge, including synthetic biology, backgrounds of notable scientists,
+ and environment-related holidays. With colorful illustrations and
+ interesting animation, we hope to make the concepts more accessible to the
+ audience. Finally, with a deep comprehension of eutrophication, the public
+ can also use their voice to save the devastated Earth.
</div>
- <div class="mySlides3">
+ <div class="promo">
<img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-23.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="education_image"
+ src="https://static.igem.wiki/teams/4271/wiki/biology.png"
/>
- </div>
-
- <div class="mySlides3">
<img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-15.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="education_image"
+ src="https://static.igem.wiki/teams/4271/wiki/biology-2.png"
/>
</div>
+ <div class="image_description" id="greencontents">
+ Fig. 7 Promotion posters.
+ </div>
- <div class="mySlides3">
+ <div style="height: 50px;"></div>
+ <div class="promo" id="promo_pic">
<img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-10.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/ins1.jpg"
/>
- </div>
- <div class="mySlides3">
<img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-40.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/insta1.jpg"
/>
</div>
- <div class="mySlides3">
+ <div class="promo" id="promo_pic">
<img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-11.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/ins3.jpg"
/>
- </div>
- <div class="mySlides3">
<img
- src="https://static.igem.wiki/teams/4271/wiki/line-album-221005-16.jpg"
- style="width: 100%;"
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/ins4.jpg"
/>
</div>
- <!-- Next and previous buttons -->
- <a class="prev" id="prev3" onclick="plusSlides3(-1)">❮</a>
- <a class="next" id="prev3" onclick="plusSlides3(1)">❯</a>
- </div>
- <br />
-
- <!-- The dots/circles -->
- <div class="dots_slideshow">
- <span class="dot3" onclick="currentSlide3(1)"></span>
- <span class="dot3" onclick="currentSlide3(2)"></span>
- <span class="dot3" onclick="currentSlide3(3)"></span>
- <span class="dot3" onclick="currentSlide3(4)"></span>
- <span class="dot3" onclick="currentSlide3(5)"></span>
- <span class="dot3" onclick="currentSlide3(6)"></span>
- <span class="dot3" onclick="currentSlide3(7)"></span>
- <span class="dot3" onclick="currentSlide3(8)"></span>
- </div>
-
- <a class="button_education" href="{{ url_for('pages', page='notebook') }}">
- Click here for more postcards!
- </a>
+ <div style="height: 50px;"></div>
+ <div class="image_description" id="greencontents">
+ Fig. 8 Educational pop quizzes and posts.
+ </div>
+ <div class="index_container" id="mediaout"></div>
- <b class="heading1" id="educationheading1">
- COMMUNICATION
- </b>
+ <div class="heading2" id="educationheading2">
+ Media Outreach
+ </div>
- <div class="index_container" id="socialmed"></div>
- <div class="heading2" id="educationheading2">
- Social Media
- </div>
+ <b class="heading4">
+ English Version - Taipei Times
+ </b>
+
+ <div class="info_contents" id="greencontents">
+ Taipei Times is the leading English news outlet in Taiwan. We reached out
+ with a letter emphasizing the direness and severity of eutrophication and
+ detailing our proposed solution, and were fortunate enough to be accepted
+ for publication. As it is Taiwan-based, all of the examples and statistics
+ were specific to our homeland. With such a wide-reaching platform, we
+ stressed the importance of taking action. Individual efforts such as
+ buying phosphate-free detergents and supporting pesticide-free agriculture
+ can amount to incredible changes.
+ </div>
- <div class="info_contents" id="greencontents">
- Under pandemic, reaching the community through social media is the most
- effective and optimal way for safety concerns. To reach a wider range of
- audience and raise public awareness, we regularly updated bilingual stories,
- posts, and reels on our
<a
- class="content_link"
+ class="button_education"
target="_blank"
- id="education_link"
- href="https://www.instagram.com/taipei_wego_igem/"
+ href="https://www.taipeitimes.com/News/editorials/archives/2022/08/23/2003783982"
>
- instagram account
+ Click here to read!
</a>
- . We posted trivial quizzes on a daily-basis which related to our project,
- facts about eutrophication, and basic knowledge of synthetic biology. By
- analyzing common misunderstandings shared by our followers, we created reels
- to specifically explain the causes, effects, and gravity of Eutrophication
- and further introduce our solution to mitigating the issue.
- </div>
-
- <div class="info_contents" id="greencontents">
- Moreover, our instagram posts have promoted a variety of scientific
- knowledge, including synthetic biology, backgrounds of notable scientists,
- and environment-related holidays. With colorful illustrations and
- interesting animation, we hope to make the concepts more accessible to the
- audience. Finally, with a deep comprehension of eutrophication, the public
- can also use their voice to save the devastated Earth.
- </div>
-
- <div class="promo">
- <img
- class="constant_height"
- id="education_image"
- src="https://static.igem.wiki/teams/4271/wiki/biology.png"
- />
- <img
- class="constant_height"
- id="education_image"
- src="https://static.igem.wiki/teams/4271/wiki/biology-2.png"
- />
- </div>
- <div class="image_description" id="greencontents">
- Fig. 7 Promotion posters.
- </div>
-
- <div style="height: 50px;"></div>
- <div class="promo" id="promo_pic">
- <img
- class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/ins1.jpg"
- />
- <img
- class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/insta1.jpg"
- />
- </div>
- <div class="promo" id="promo_pic">
- <img
- class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/ins3.jpg"
- />
- <img
- class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/ins4.jpg"
- />
- </div>
-
- <div style="height: 50px;"></div>
- <div class="image_description" id="greencontents">
- Fig. 8 Educational pop quizzes and posts.
- </div>
- <div class="index_container" id="mediaout"></div>
-
- <div class="heading2" id="educationheading2">
- Media Outreach
- </div>
-
- <b class="heading4">
- English Version - Taipei Times
- </b>
-
- <div class="info_contents" id="greencontents">
- Taipei Times is the leading English news outlet in Taiwan. We reached out
- with a letter emphasizing the direness and severity of eutrophication and
- detailing our proposed solution, and were fortunate enough to be accepted
- for publication. As it is Taiwan-based, all of the examples and statistics
- were specific to our homeland. With such a wide-reaching platform, we
- stressed the importance of taking action. Individual efforts such as buying
- phosphate-free detergents and supporting pesticide-free agriculture can
- amount to incredible changes.
- </div>
+ <b class="heading4">
+ Chinese Version
+ </b>
+
+ <div class="info_contents" id="greencontents">
+ Language is one of the biggest hindrances to education. It only made sense
+ to broaden our target audience to include the local community.
+ EutroinVitro started because of a desire to improve our immediate living
+ conditions, and we wanted our actions to reflect that. The final draft is
+ awaiting publication.
+ </div>
- <a
- class="button_education"
- target="_blank"
- href="https://www.taipeitimes.com/News/editorials/archives/2022/08/23/2003783982"
- >
- Click here to read!
- </a>
- <b class="heading4">
- Chinese Version
- </b>
-
- <div class="info_contents" id="greencontents">
- Language is one of the biggest hindrances to education. It only made sense
- to broaden our target audience to include the local community. EutroinVitro
- started because of a desire to improve our immediate living conditions, and
- we wanted our actions to reflect that. The final draft is awaiting
- publication.
+ <a
+ class="button_education"
+ target="_blank"
+ href="https://docs.google.com/document/d/1F3tMdb9U5h3EQ8R7o96vTsjJLrcEWQnu5Yjk_W49pM8/edit?usp=sharing"
+ >
+ Click here to read!
+ </a>
</div>
-
- <a
- class="button_education"
- target="_blank"
- href="https://docs.google.com/document/d/1F3tMdb9U5h3EQ8R7o96vTsjJLrcEWQnu5Yjk_W49pM8/edit?usp=sharing"
- >
- Click here to read!
- </a>
</div>
{% endblock %}
diff --git a/wiki/pages/engineering.html b/wiki/pages/engineering.html
index e35bbba..4359ef5 100644
--- a/wiki/pages/engineering.html
+++ b/wiki/pages/engineering.html
@@ -1,4 +1,5 @@
{% extends "layout.html" %} {% block page_content %}
+<div>
<div class="loadingwrap">
<img
class="loadinggif"
@@ -1032,4 +1033,5 @@
618–627. https://doi.org/10.1111/j.1365-2958.2010.07233.x
</div>
</div>
+</div>
{% endblock %}
diff --git a/wiki/pages/entrepreneurship.html b/wiki/pages/entrepreneurship.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/entrepreneurship.html
+++ b/wiki/pages/entrepreneurship.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/experiments.html b/wiki/pages/experiments.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/experiments.html
+++ b/wiki/pages/experiments.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/hardware.html b/wiki/pages/hardware.html
index 2d1c3b8..2ef61af 100644
--- a/wiki/pages/hardware.html
+++ b/wiki/pages/hardware.html
@@ -1,368 +1,372 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/hardware.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="hardwarepointer" href="#background">Background</a>
- <a class="pointer" id="hardwarepointer" href="#designoverview">
- Design Overview
- </a>
- <a class="pointer" id="hardwarepointer" href="#design">
- Design
- </a>
- <a class="pointer" id="hardwarepointer" href="#price">
- Price Estimation
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
-
- <b class="heading1" id="hardwareheading1">
- Hardware
- </b>
-
- <div class="index_container" id="background"></div>
- <div class="heading2" id="hardwareheading2">
- Background
- </div>
-
- <div class="info_contents" id="greencontents">
- Reservoirs around the world are facing serious pollution: eutrophication.
- Once the water body accumulates excessive amounts of nutrients, algae grow
- rapidly and cover the whole area. This coverage will block aquatic plants
- from light and they cannot photosynthesize oxygen. Moreover, when a large
- amount of algae decomposes, oxygen in the water is consumed. The large and
- abrupt consumption of oxygen will lead to serious environmental problems
- such as fish kill and dead zones.
- </div>
-
- <div class="index_container" id="designoverview"></div>
- <div class="heading2" id="hardwareheading2">
- Design Overview
- </div>
-
- <div class="info_contents" id="greencontents">
- Our team developed an engineered E. coli, TripleP, that can hydrolyze
- paraoxon (PXN), organic phosphate, into inorganic phosphate, and fixate
- inorganic phosphate in the form of polyphosphate. To implement our synbiotic
- solution in the real world, we developed a filtering device hardware
- containing TripleP cells.
- </div>
-
- <div class="index_container" id="design"></div>
- <div class="heading2" id="hardwareheading2">
- Design
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- Artificial Ecological Island
- </em>
-
- <div class="info_contents" id="greencontents">
- To ensure the filters stay around at the water surface, we chose an
- artificial ecological island to support our filters. The island can mitigate
- eutrophication through ecological methods. The aquatic plants on the island,
- such as common Rush, water arum, water chestnut, and hygrophila, absorb
- phosphates and nitrogen in the eutrophic water. The total area of the island
- is 25 square meters, and we further designed 4 solar panels on the island to
- provide the energy required for the additional functions of the device.
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-1.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 1 The artificial ecological island with the solar panels
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- Structure of the Filtering Device Under the Ecological Island
- </em>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-2.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 2 The 3D model of the device
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
- <div class="info_contents" id="greencontents">
- The filtering tubes are connected to the upper part of the device, the
- ecological island with threads. (We chose nylon threads due to its
- prestigious flexibility and stretch.) The engineered bacteria TripleP are
- contained in the filter tubes, which are attached with filter papers on both
- sides. The filter tube would continue to float in the water with the support
- of the outer tube. The function of the engineered bacteria in the filter
- tube would be monitored by the light source, light sensor, and the Arduino
- chip designed in the water-proof container.
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware.png"
+ />
</div>
-
- <em class="info_contents_italics" id="greencontents">
- Filtering tube
- </em>
-
- <div class="info_contents" id="greencontents">
- The filter tube is composed of two filter papers and a transparent acrylic
- tube. The filter papers cover the top and bottom of the tube. Eutrophic
- water will flow through the tube, while the engineered bacteria (TripleP
- cells) absorb the phosphate in the water. The filter papers are composed of
- cellulose acetate, whose hydrophilic property will allow water to pass
- easily, and they have a pore size of 0.45μm. As E. coli has a diameter of
- about 1.0-2.0 micrometers, the holes allow water, and phosphate particles to
- pass but not bacteria. So, when the phosphate concentration in the tube
- decreases, the phosphate outside the tube will diffuse into the tube, and
- TripleP will continue to hydrolyze and uptake phosphate. The TripleP cells
- in the filter tubes will work until they overaccumulate polyphosphate, which
- will be monitored by the Arduino chip.
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
</div>
-
- <em class="info_contents_italics" id="greencontents">
- Engineered Bacteria
- </em>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-3.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 3 The filter tube with bacteria in spheres
- </div>
-
- <div class="heading4" id="hardwareheading2">
- Original Design
- </div>
-
- <div class="info_contents" id="greencontents">
- In our original hardware design, we contained the TripleP cells in the tube
- without other materials. However, bacteria are inclined to adhere to nearby
- surfaces. Therefore, if we let bacteria disperse freely in the tube, they
- would attach to the filter paper and block the diffusion, leading to the
- malfunction of our device.
- </div>
- <div class="heading4" id="hardwareheading2">
- Final Design
- </div>
-
- <div class="info_contents" id="greencontents">
- As a result, we took advice from the HNU_China team during our collaboration
- and decided to use sodium chloride to fix bacteria into spheres. We mix
- sodium alginate solution with a culture medium and add the solution to a
- calcium oxide solution. The spheres can keep their shape for 12 hours, and
- both water and phosphate can pass through the material of the spheres. We'll
- then fix the spheres containing the engineered bacteria in the center of the
- filtering tube by restricting them in an additional permeable sack,
- refraining them from directly contacting and causing damage to the filter
- paper on both sides of the tube. The design would allow water flow to be
- free from bacteria’s biofilm blockade while making it easier for users to
- organize and replace the engineered bacteria in the tube.
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- Caps of the Filtering Tube
- </em>
-
- <div class="info_contents" id="greencontents">
- The caps that cover both ends of the tube are designed to tighten the filter
- papers. They will push the paper against the tube wall such that the water
- will not escape through the space between the filter paper and the tube.
- This design can ensure that the engineered bacteria would not escape from
- the filter and leak into the environment. Furthermore, to protect filter
- papers from being broken by stones and branches in the waterbody, we added
- an additional web to protect the filter paper. We design another cap that
- can cover the filter paper with filter screen made of nylon. The filter
- screen is tightened and fixed between the space of to cap such that it will
- not fall off even under strong impact.
- </div>
-
- <div class="info_contents" id="greencontents">
- Parts of the hardware have been 3D printed as our prototype. For more
- information on the design and 3D printing of our device, please visit our
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="hardwarepointer" href="#background">Background</a>
+ <a class="pointer" id="hardwarepointer" href="#designoverview">
+ Design Overview
+ </a>
+ <a class="pointer" id="hardwarepointer" href="#design">
+ Design
+ </a>
+ <a class="pointer" id="hardwarepointer" href="#price">
+ Price Estimation
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+
+ <b class="heading1" id="hardwareheading1">
+ Hardware
+ </b>
+
+ <div class="index_container" id="background"></div>
+ <div class="heading2" id="hardwareheading2">
+ Background
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Reservoirs around the world are facing serious pollution: eutrophication.
+ Once the water body accumulates excessive amounts of nutrients, algae grow
+ rapidly and cover the whole area. This coverage will block aquatic plants
+ from light and they cannot photosynthesize oxygen. Moreover, when a large
+ amount of algae decomposes, oxygen in the water is consumed. The large and
+ abrupt consumption of oxygen will lead to serious environmental problems
+ such as fish kill and dead zones.
+ </div>
+
+ <div class="index_container" id="designoverview"></div>
+ <div class="heading2" id="hardwareheading2">
+ Design Overview
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Our team developed an engineered E. coli, TripleP, that can hydrolyze
+ paraoxon (PXN), organic phosphate, into inorganic phosphate, and fixate
+ inorganic phosphate in the form of polyphosphate. To implement our
+ synbiotic solution in the real world, we developed a filtering device
+ hardware containing TripleP cells.
+ </div>
+
+ <div class="index_container" id="design"></div>
+ <div class="heading2" id="hardwareheading2">
+ Design
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Artificial Ecological Island
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ To ensure the filters stay around at the water surface, we chose an
+ artificial ecological island to support our filters. The island can
+ mitigate eutrophication through ecological methods. The aquatic plants on
+ the island, such as common Rush, water arum, water chestnut, and
+ hygrophila, absorb phosphates and nitrogen in the eutrophic water. The
+ total area of the island is 25 square meters, and we further designed 4
+ solar panels on the island to provide the energy required for the
+ additional functions of the device.
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-1.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 1 The artificial ecological island with the solar panels
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Structure of the Filtering Device Under the Ecological Island
+ </em>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-2.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 2 The 3D model of the device
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ The filtering tubes are connected to the upper part of the device, the
+ ecological island with threads. (We chose nylon threads due to its
+ prestigious flexibility and stretch.) The engineered bacteria TripleP are
+ contained in the filter tubes, which are attached with filter papers on
+ both sides. The filter tube would continue to float in the water with the
+ support of the outer tube. The function of the engineered bacteria in the
+ filter tube would be monitored by the light source, light sensor, and the
+ Arduino chip designed in the water-proof container.
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Filtering tube
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ The filter tube is composed of two filter papers and a transparent acrylic
+ tube. The filter papers cover the top and bottom of the tube. Eutrophic
+ water will flow through the tube, while the engineered bacteria (TripleP
+ cells) absorb the phosphate in the water. The filter papers are composed
+ of cellulose acetate, whose hydrophilic property will allow water to pass
+ easily, and they have a pore size of 0.45μm. As E. coli has a diameter of
+ about 1.0-2.0 micrometers, the holes allow water, and phosphate particles
+ to pass but not bacteria. So, when the phosphate concentration in the tube
+ decreases, the phosphate outside the tube will diffuse into the tube, and
+ TripleP will continue to hydrolyze and uptake phosphate. The TripleP cells
+ in the filter tubes will work until they overaccumulate polyphosphate,
+ which will be monitored by the Arduino chip.
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Engineered Bacteria
+ </em>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-3.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 3 The filter tube with bacteria in spheres
+ </div>
+
+ <div class="heading4" id="hardwareheading2">
+ Original Design
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ In our original hardware design, we contained the TripleP cells in the
+ tube without other materials. However, bacteria are inclined to adhere to
+ nearby surfaces. Therefore, if we let bacteria disperse freely in the
+ tube, they would attach to the filter paper and block the diffusion,
+ leading to the malfunction of our device.
+ </div>
+ <div class="heading4" id="hardwareheading2">
+ Final Design
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ As a result, we took advice from the HNU_China team during our
+ collaboration and decided to use sodium chloride to fix bacteria into
+ spheres. We mix sodium alginate solution with a culture medium and add the
+ solution to a calcium oxide solution. The spheres can keep their shape for
+ 12 hours, and both water and phosphate can pass through the material of
+ the spheres. We'll then fix the spheres containing the engineered bacteria
+ in the center of the filtering tube by restricting them in an additional
+ permeable sack, refraining them from directly contacting and causing
+ damage to the filter paper on both sides of the tube. The design would
+ allow water flow to be free from bacteria’s biofilm blockade while making
+ it easier for users to organize and replace the engineered bacteria in the
+ tube.
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Caps of the Filtering Tube
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ The caps that cover both ends of the tube are designed to tighten the
+ filter papers. They will push the paper against the tube wall such that
+ the water will not escape through the space between the filter paper and
+ the tube. This design can ensure that the engineered bacteria would not
+ escape from the filter and leak into the environment. Furthermore, to
+ protect filter papers from being broken by stones and branches in the
+ waterbody, we added an additional web to protect the filter paper. We
+ design another cap that can cover the filter paper with filter screen made
+ of nylon. The filter screen is tightened and fixed between the space of to
+ cap such that it will not fall off even under strong impact.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Parts of the hardware have been 3D printed as our prototype. For more
+ information on the design and 3D printing of our device, please visit our
+ <a
+ class="content_link"
+ id="hardwarelink"
+ href="{{ url_for('pages', page='contribution') }}"
+ >
+ Contribution Page
+ </a>
+ for more.
+ </div>
+ <div style="height: 15px;"></div>
<a
class="content_link"
id="hardwarelink"
- href="{{ url_for('pages', page='contribution') }}"
+ target="_blank"
+ href="https://static.igem.wiki/teams/4271/wiki/cap.stl"
>
- Contribution Page
+ Stl. 1
</a>
- for more.
- </div>
- <div style="height: 15px;"></div>
- <a
- class="content_link"
- id="hardwarelink"
- target="_blank"
- href="https://static.igem.wiki/teams/4271/wiki/cap.stl"
- >
- Stl. 1
- </a>
- <a
- class="content_link"
- id="hardwarelink"
- target="_blank"
- href="https://static.igem.wiki/teams/4271/wiki/cap-s-cap.stl"
- >
- Stl. 2
- </a>
-
- <em class="info_contents_italics" id="greencontents">
- Arduino's Chip
- </em>
-
- <div class="info_contents" id="greencontents">
- Arduino Uno is a microcontroller board used in the device. It contains 14
- input/output pins which are ample for the modules used in the project. The
- chip can be programmed and connected to different modules and sensors to
- perform various tasks. In this project, the Arduino chip will monitor the
- filtering status and return information back to the users. The specific
- steps will be explained below: In our device, the Arduino controller is used
- with a laser, light sensors, and a wifi module. The laser will emit light
- into the filter tube continually with an interval of two hours and excite
- mCherry, a fluorescent protein whose production is, based on the biosensor
- plasmid design, would be inhibited by polyphosphate. If the engineered
- bacteria TripleP absorbs inorganic phosphate and fixates it into
- polyphosphate, the production of mCherry would decrease. The light sensor
- connected to the Arduino chip will detect mCherry fluorescence, whose
- information will then be processed by the Arduino chip and sent to users via
- the wifi module. The effectiveness of the bacteria’s filter can hence be
- determined by the continuous monitoring of mCherry. If the software’s
- calculation of the mCherry level has lowered to a minimum, an alert would be
- sent to remind the user of the necessity to replace the filter, thus
- providing a convenient way for the users to ensure the efficiency of the
- device and the safety of the environment. Since the filtering tubes are
- designed under the ecological island, the island itself creates a dark
- environment suitable for the sensor chip to detect the fluorescent protein
- generated by TripleP.
- </div>
-
- <div class="info_contents" id="greencontents">
- For more information about the polyphosphate biosensor design and the
- experimental validation, please visit our
<a
class="content_link"
id="hardwarelink"
- href="{{ url_for('pages', page='engineering') }}"
+ target="_blank"
+ href="https://static.igem.wiki/teams/4271/wiki/cap-s-cap.stl"
>
- Engineering Success Page
+ Stl. 2
</a>
- .
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-4.png"
- />
- <div class="image_description" id="greencontents">
- Fig. 4 The diagram of the Arduino chip and other auxiliary devices
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-5.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 5 The general view of filter tube and the container
- </div>
-
- <div class="index_container" id="price"></div>
- <div class="heading2" id="hardwareheading2">
- Price Estimation
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- Island: 50,000 NTD
- </em>
-
- <div class="info_contents" id="greencontents">
- the composition of an island:
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/table-1-2.png"
- />
- <em class="info_contents_italics" id="greencontents">
- Filter: 850 NTD
- </em>
-
- <div class="info_contents" id="greencontents">
- the composition of a filter tube
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/table-2-2.png"
- />
-
- <em class="info_contents_italics" id="greencontents">
- The Design of Hardware
- </em>
-
- <div class="info_contents" id="greencontents">
- Here's a video and a few pictures about the hardware device.
- </div>
- <div class="video_hardware">
- <iframe
- title="Wego_Taipei: The Hardware (2022) [English]"
- width="100%"
- height="100%"
- src="https://video.igem.org/videos/embed/0fbb07f0-e031-45ec-bcdf-46f9f7abcbc3"
- frameborder="0"
- allowfullscreen=""
- sandbox="allow-same-origin allow-scripts allow-popups"
- ></iframe>
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-l-holes.jpg"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 6 The L-shape holes
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-filter-tube.jpg"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 7 The filter tube without bacteria
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/hardware-device.jpg"
- />
- <div class="image_description" id="greencontents">
- Fig. 8 The device overview
+ <em class="info_contents_italics" id="greencontents">
+ Arduino's Chip
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ Arduino Uno is a microcontroller board used in the device. It contains 14
+ input/output pins which are ample for the modules used in the project. The
+ chip can be programmed and connected to different modules and sensors to
+ perform various tasks. In this project, the Arduino chip will monitor the
+ filtering status and return information back to the users. The specific
+ steps will be explained below: In our device, the Arduino controller is
+ used with a laser, light sensors, and a wifi module. The laser will emit
+ light into the filter tube continually with an interval of two hours and
+ excite mCherry, a fluorescent protein whose production is, based on the
+ biosensor plasmid design, would be inhibited by polyphosphate. If the
+ engineered bacteria TripleP absorbs inorganic phosphate and fixates it
+ into polyphosphate, the production of mCherry would decrease. The light
+ sensor connected to the Arduino chip will detect mCherry fluorescence,
+ whose information will then be processed by the Arduino chip and sent to
+ users via the wifi module. The effectiveness of the bacteria’s filter can
+ hence be determined by the continuous monitoring of mCherry. If the
+ software’s calculation of the mCherry level has lowered to a minimum, an
+ alert would be sent to remind the user of the necessity to replace the
+ filter, thus providing a convenient way for the users to ensure the
+ efficiency of the device and the safety of the environment. Since the
+ filtering tubes are designed under the ecological island, the island
+ itself creates a dark environment suitable for the sensor chip to detect
+ the fluorescent protein generated by TripleP.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ For more information about the polyphosphate biosensor design and the
+ experimental validation, please visit our
+ <a
+ class="content_link"
+ id="hardwarelink"
+ href="{{ url_for('pages', page='engineering') }}"
+ >
+ Engineering Success Page
+ </a>
+ .
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-4.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 4 The diagram of the Arduino chip and other auxiliary devices
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-5.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 5 The general view of filter tube and the container
+ </div>
+
+ <div class="index_container" id="price"></div>
+ <div class="heading2" id="hardwareheading2">
+ Price Estimation
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Island: 50,000 NTD
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ the composition of an island:
+ </div>
+
+ <img
+ id="table6"
+ src="https://static.igem.wiki/teams/4271/wiki/table-1-2.png"
+ />
+ <em class="info_contents_italics" id="greencontents">
+ Filter: 850 NTD
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ the composition of a filter tube
+ </div>
+ <img
+ id="table6"
+ src="https://static.igem.wiki/teams/4271/wiki/table-2-2.png"
+ />
+
+ <em class="info_contents_italics" id="greencontents">
+ The Design of Hardware
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ Here's a video and a few pictures about the hardware device.
+ </div>
+ <div class="video_hardware">
+ <iframe
+ title="Wego_Taipei: The Hardware (2022) [English]"
+ width="100%"
+ height="100%"
+ src="https://video.igem.org/videos/embed/0fbb07f0-e031-45ec-bcdf-46f9f7abcbc3"
+ frameborder="0"
+ allowfullscreen=""
+ sandbox="allow-same-origin allow-scripts allow-popups"
+ ></iframe>
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-l-holes.jpg"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 6 The L-shape holes
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-filter-tube.jpg"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 7 The filter tube without bacteria
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/hardware-device.jpg"
+ />
+ <div class="image_description" id="greencontents">
+ Fig. 8 The device overview
+ </div>
</div>
</div>
{% endblock %}
diff --git a/wiki/pages/human-practices.html b/wiki/pages/human-practices.html
index 96d54d0..d84b454 100644
--- a/wiki/pages/human-practices.html
+++ b/wiki/pages/human-practices.html
@@ -1,568 +1,573 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
+ </div>
+
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src=" https://static.igem.wiki/teams/4271/wiki/ihp.png"
+ />
+ </div>
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
+ </div>
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="ihpheading1" href="#interviews">Interviews</a>
+ <a class="pointer" id="iphpointer" href="#overview">Overview</a>
+ <a class="pointer" id="iphpointer" href="#interviewees">Interviewees</a>
+ <a class="pointer" id="iphpointer" href="#implhard">Hardware</a>
+ <a class="pointer" id="iphpointer" href="#software">Software</a>
+ <a class="pointer" id="iphpointer" href="#educationandcommunication">
+ Education
+ </a>
+ <a class="pointer" id="iphpointer" href="#biosafety">Biosafety</a>
+ <a class="pointer" id="iphpointer" href="#addinfo">
+ Additional Information
+ </a>
+ <a class="pointer" id="ihpheading1" href="#publicsurvey">Public Survey</a>
+ <a class="pointer" id="iphpointer" href="#overview2">Overview</a>
+ <a class="pointer" id="iphpointer" href="#education2">Education</a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+
+ <div class="index_container" id="interviews"></div>
+ <b class="heading1" id="hpheading1">
+ Interviews
+ </b>
+
+ <div class="index_container" id="overview"></div>
+ <div class="heading2" id="hpheading2">
+ Overview
+ </div>
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src=" https://static.igem.wiki/teams/4271/wiki/ihp.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="ihpheading1" href="#interviews">Interviews</a>
- <a class="pointer" id="iphpointer" href="#overview">Overview</a>
- <a class="pointer" id="iphpointer" href="#interviewees">Interviewees</a>
- <a class="pointer" id="iphpointer" href="#implhard">Hardware</a>
- <a class="pointer" id="iphpointer" href="#software">Software</a>
- <a class="pointer" id="iphpointer" href="#educationandcommunication">
- Education
- </a>
- <a class="pointer" id="iphpointer" href="#biosafety">Biosafety</a>
- <a class="pointer" id="iphpointer" href="#addinfo">
- Additional Information
- </a>
- <a class="pointer" id="ihpheading1" href="#publicsurvey">Public Survey</a>
- <a class="pointer" id="iphpointer" href="#overview2">Overview</a>
- <a class="pointer" id="iphpointer" href="#education2">Education</a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
-
- <div class="index_container" id="interviews"></div>
- <b class="heading1" id="hpheading1">
- Interviews
- </b>
-
- <div class="index_container" id="overview"></div>
- <div class="heading2" id="hpheading2">
- Overview
- </div>
+ <div class="info_contents" id="greencontents">
+ Throughout the span of our project, human practices have acted as a source
+ of creativity and guidance, addressing social and academic aspects of our
+ topic and engaging with the world through interviews, surveys, education,
+ and collaboration. As for Integrated Human Practices, our team has sought
+ expert opinions and professional advice, hoping to improve all aspects of
+ our project through discussions and evaluations. By conducting interviews,
+ we had the opportunity to inquire about current governmental policies,
+ solutions to eutrophication, the enforceability of our product, and other
+ comments and suggestions for our project through the perspectives of
+ stakeholders. In addition, post-interview discussions are important to
+ gather information to supplement different parts of our project, ranging
+ from hardware and software to education and biosafety concerns. On the
+ following page, we will dive into the processes and takeaways we gained
+ from integrated human practices.
+ </div>
- <div class="info_contents" id="greencontents">
- Throughout the span of our project, human practices have acted as a source
- of creativity and guidance, addressing social and academic aspects of our
- topic and engaging with the world through interviews, surveys, education,
- and collaboration. As for Integrated Human Practices, our team has sought
- expert opinions and professional advice, hoping to improve all aspects of
- our project through discussions and evaluations. By conducting interviews,
- we had the opportunity to inquire about current governmental policies,
- solutions to eutrophication, the enforceability of our product, and other
- comments and suggestions for our project through the perspectives of
- stakeholders. In addition, post-interview discussions are important to
- gather information to supplement different parts of our project, ranging
- from hardware and software to education and biosafety concerns. On the
- following page, we will dive into the processes and takeaways we gained from
- integrated human practices.
- </div>
+ <div class="index_container" id="interviewees"></div>
+ <div class="heading2" id="hpheading2">
+ Interviewees
+ </div>
- <div class="index_container" id="interviewees"></div>
- <div class="heading2" id="hpheading2">
- Interviewees
- </div>
+ <div class="heading4" id="hpheading2">
+ <b>Doctor Chih-Hung Tsai</b>
+ from the Taiwan Water Resources Protection Union
+ </div>
- <div class="heading4" id="hpheading2">
- <b>Doctor Chih-Hung Tsai</b>
- from the Taiwan Water Resources Protection Union
- </div>
+ <div class="info_contents" id="greencontents">
+ Taiwan Water Resources Protection Union promoted the efforts to combat
+ water pollution and destruction of the environment. In the past decades,
+ they have been fighting for illegal waste water disposal from local
+ factories and agricultural systems. To specifically understand the
+ scenarios of different reservoirs and rivers in Taiwan, our team reached
+ out to the president of the Union Dr. Tsai to further discuss the severity
+ and distribution of eutrophication in the local community. Our
+ conversation also extended to government policies and possible campaigns
+ that can effectively raise public awareness in the younger generation.
+ </div>
- <div class="info_contents" id="greencontents">
- Taiwan Water Resources Protection Union promoted the efforts to combat water
- pollution and destruction of the environment. In the past decades, they have
- been fighting for illegal waste water disposal from local factories and
- agricultural systems. To specifically understand the scenarios of different
- reservoirs and rivers in Taiwan, our team reached out to the president of
- the Union Dr. Tsai to further discuss the severity and distribution of
- eutrophication in the local community. Our conversation also extended to
- government policies and possible campaigns that can effectively raise public
- awareness in the younger generation.
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-09-17-at-11-05-55-am.png"
+ />
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-09-17-at-11-05-55-am.png"
- />
+ <div class="heading4" id="hpheading2">
+ <b>Professor Tsair-Fuh Lin</b>
+ from National Cheng Kung University
+ </div>
- <div class="heading4" id="hpheading2">
- <b>Professor Tsair-Fuh Lin</b>
- from National Cheng Kung University
- </div>
+ <div class="info_contents" id="greencontents">
+ Prof. Lin currently serves as the professor in the Environmental
+ Engineering department at National Cheng Kung University. He has
+ considerable expertise in using chemical and engineering methods to deal
+ with environmental issues. His related research topics include absorption
+ technology, ​​identification and treatment of algae metabolites, site
+ remediation, etc. Aiming at consulting his past research about
+ cynopeptides detection and pre-treatment system for nutrients removal, our
+ team interviewed Prof. Lin with questions ranging from his research
+ interests to biosafety mechanisms of our
+ <a
+ class="content_link"
+ id="ihplink"
+ href="{{ url_for('pages', page='hardware') }}"
+ >
+ hardware
+ </a>
+ .
+ </div>
- <div class="info_contents" id="greencontents">
- Prof. Lin currently serves as the professor in the Environmental Engineering
- department at National Cheng Kung University. He has considerable expertise
- in using chemical and engineering methods to deal with environmental issues.
- His related research topics include absorption technology, ​​identification
- and treatment of algae metabolites, site remediation, etc. Aiming at
- consulting his past research about cynopeptides detection and pre-treatment
- system for nutrients removal, our team interviewed Prof. Lin with questions
- ranging from his research interests to biosafety mechanisms of our
- <a
- class="content_link"
- id="ihplink"
- href="{{ url_for('pages', page='hardware') }}"
- >
- hardware
- </a>
- .
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-09-18-at-6-21-22-pm.png"
+ />
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-09-18-at-6-21-22-pm.png"
- />
+ <div class="heading4" id="hpheading2">
+ <b>Professor Chen-Yao Chen</b>
+ from Tzu-Chi University
+ </div>
- <div class="heading4" id="hpheading2">
- <b>Professor Chen-Yao Chen</b>
- from Tzu-Chi University
- </div>
+ <div class="info_contents" id="greencontents">
+ Prof. Chen currently works in the Life Science Department at Tzu-Chi
+ University. His research interests include microbiology, environmental
+ science, etc. Our interview mainly focused on the feasibility and the
+ potential risk our device would bring after installing an aquatic
+ environment. His expertise in the aquatic environment informed us of the
+ risk of bacteria leakage and the potential methods we could use to
+ optimize our biosafety mechanisms.
+ </div>
+ <div class="heading4" id="hpheading2">
+ <b>Teacher Iching Hung</b>
+ from Tianmu elementary school
+ </div>
- <div class="info_contents" id="greencontents">
- Prof. Chen currently works in the Life Science Department at Tzu-Chi
- University. His research interests include microbiology, environmental
- science, etc. Our interview mainly focused on the feasibility and the
- potential risk our device would bring after installing an aquatic
- environment. His expertise in the aquatic environment informed us of the
- risk of bacteria leakage and the potential methods we could use to optimize
- our biosafety mechanisms.
- </div>
- <div class="heading4" id="hpheading2">
- <b>Teacher Iching Hung</b>
- from Tianmu elementary school
- </div>
+ <div class="info_contents" id="greencontents">
+ Tr. Hung is a teacher at Tianmu elementary school with familiar knowledge
+ of the Taiwanese 108 syllabus. Through our interview we have gained a
+ better understanding of the current curriculum design elementary schools
+ have regarding environmental issues, specifically regarding the aquatic
+ ecosystem.
+ </div>
- <div class="info_contents" id="greencontents">
- Tr. Hung is a teacher at Tianmu elementary school with familiar knowledge of
- the Taiwanese 108 syllabus. Through our interview we have gained a better
- understanding of the current curriculum design elementary schools have
- regarding environmental issues, specifically regarding the aquatic
- ecosystem.
- </div>
+ <div class="index_container" id="implhard"></div>
+ <div class="heading2" id="hpheading2">
+ Implementation - Hardware
+ </div>
- <div class="index_container" id="implhard"></div>
- <div class="heading2" id="hpheading2">
- Implementation - Hardware
- </div>
+ <div class="heading4" id="hpheading2">
+ Prof. Chen
+ </div>
- <div class="heading4" id="hpheading2">
- Prof. Chen
- </div>
+ <div class="info_contents" id="greencontents">
+ Regarding our implementation, Prof. Chen pointed out several concerns
+ about the filter paper we planned to use. The original design was to use a
+ cellulose acetate membrane with a pore size of 0.45 um to prevent bacteria
+ leakage. However, Prof. Chen informed us that E. coli would naturally
+ secrete substances over time, such as biofilm, can help bacteria attach to
+ the abiotic surface, leading to block water inflow and affect the
+ efficiency of our device. More than mere secretions, other organic
+ substances in water bodies may also cover up the outer surface of our
+ filter. He stated that the 0.45 pore sized filter could only filtrate 5
+ liters of normal lake or ocean water before being plugged by substances.
+ </div>
- <div class="info_contents" id="greencontents">
- Regarding our implementation, Prof. Chen pointed out several concerns about
- the filter paper we planned to use. The original design was to use a
- cellulose acetate membrane with a pore size of 0.45 um to prevent bacteria
- leakage. However, Prof. Chen informed us that E. coli would naturally
- secrete substances over time, such as biofilm, can help bacteria attach to
- the abiotic surface, leading to block water inflow and affect the efficiency
- of our device. More than mere secretions, other organic substances in water
- bodies may also cover up the outer surface of our filter. He stated that the
- 0.45 pore sized filter could only filtrate 5 liters of normal lake or ocean
- water before being plugged by substances.
- </div>
+ <div class="info_contents" id="greencontents">
+ In the interview with Prof. Chen, we concluded the two main issues to be
+ addressed about our implementation hardware are the limited pore size for
+ water inflow and the blockage of organic substances on filter paper. After
+ receiving these useful suggestions from Prof. Chen, we reevaluated the
+ device. We decided to address the secretion blockage problem by adding
+ <a
+ class="content_link"
+ id="ihplink"
+ href="{{ url_for('pages', page='implementation') }}"
+ >
+ bacterial houses
+ </a>
+ made in the material of sodium alginate, which allows E. coli to adhere
+ and grow on the surface of the houses, thus preventing secreted substances
+ from covering the filter pores and blocking water infiltration.
+ </div>
- <div class="info_contents" id="greencontents">
- In the interview with Prof. Chen, we concluded the two main issues to be
- addressed about our implementation hardware are the limited pore size for
- water inflow and the blockage of organic substances on filter paper. After
- receiving these useful suggestions from Prof. Chen, we reevaluated the
- device. We decided to address the secretion blockage problem by adding
- <a
- class="content_link"
- id="ihplink"
- href="{{ url_for('pages', page='implementation') }}"
- >
- bacterial houses
- </a>
- made in the material of sodium alginate, which allows E. coli to adhere and
- grow on the surface of the houses, thus preventing secreted substances from
- covering the filter pores and blocking water infiltration.
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-25-30-pm.png"
+ />
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-25-30-pm.png"
- />
+ <div class="image_description" id="greencontents">
+ Fig. 1 An image of our bacterial house design.
+ </div>
+ <div class="heading4" id="hpheading2">
+ Prof. Lin
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 1 An image of our bacterial house design.
- </div>
- <div class="heading4" id="hpheading2">
- Prof. Lin
- </div>
+ <div class="info_contents" id="greencontents">
+ In our interview with Prof. Lin, he specifically suggested solutions to
+ solve the substance blockage problem that inhibits water flow. Prof. Lin
+ stated that we could install an additional appliance that spout water or a
+ brush that would scrub unwanted materials off the surface of the membrane.
+ Other ideas provided were using filter sand or silver coded filter papers
+ to prevent bacteria from growing on the surface.
+ </div>
- <div class="info_contents" id="greencontents">
- In our interview with Prof. Lin, he specifically suggested solutions to
- solve the substance blockage problem that inhibits water flow. Prof. Lin
- stated that we could install an additional appliance that spout water or a
- brush that would scrub unwanted materials off the surface of the membrane.
- Other ideas provided were using filter sand or silver coded filter papers to
- prevent bacteria from growing on the surface.
- </div>
+ <div class="info_contents" id="greencontents">
+ We also consulted Prof. Lin about the sustainability and recycling of
+ resources of our product. Prof. Lin provided an idea about incorporating
+ <a
+ class="content_link"
+ id="ihplink"
+ href="{{ url_for('pages', page='implementation') }}"
+ >
+ aquatic plants on our artificial island
+ </a>
+ which floats on the surface of the water. By growing plants on the island,
+ the root of these plants would be able to simultaneously absorb phosphate
+ thus improving the overall efficiency of phosphate extraction from bodies
+ of water. Therefore, we decided to add aquatic plants such as Common Rush,
+ water arum, water chestnut, and Hygrophila into the design of our hardware
+ island.
+ </div>
- <div class="info_contents" id="greencontents">
- We also consulted Prof. Lin about the sustainability and recycling of
- resources of our product. Prof. Lin provided an idea about incorporating
- <a
- class="content_link"
- id="ihplink"
- href="{{ url_for('pages', page='implementation') }}"
- >
- aquatic plants on our artificial island
- </a>
- which floats on the surface of the water. By growing plants on the island,
- the root of these plants would be able to simultaneously absorb phosphate
- thus improving the overall efficiency of phosphate extraction from bodies of
- water. Therefore, we decided to add aquatic plants such as Common Rush,
- water arum, water chestnut, and Hygrophila into the design of our hardware
- island.
- </div>
+ <div class="info_contents" id="greencontents">
+ Other than the artificial island, Prof. Lin stated that we could use a
+ molecular method, which uses ionic attractions between anion and cations
+ to adhere negatively charged phosphorus to the positively charged exterior
+ at the bottom of our device. This idea has great potential in improving
+ the efficiency of our device, and we are planning on adding it into our
+ future plans and implementing it after further research and design.
+ </div>
- <div class="info_contents" id="greencontents">
- Other than the artificial island, Prof. Lin stated that we could use a
- molecular method, which uses ionic attractions between anion and cations to
- adhere negatively charged phosphorus to the positively charged exterior at
- the bottom of our device. This idea has great potential in improving the
- efficiency of our device, and we are planning on adding it into our future
- plans and implementing it after further research and design.
- </div>
+ <div class="index_container" id="software"></div>
+ <div class="heading2" id="hpheading2">
+ Implementation - Software
+ </div>
- <div class="index_container" id="software"></div>
- <div class="heading2" id="hpheading2">
- Implementation - Software
- </div>
+ <div class="heading4" id="hpheading2">
+ Prof. Lin
+ </div>
- <div class="heading4" id="hpheading2">
- Prof. Lin
- </div>
+ <div class="info_contents" id="greencontents">
+ When discussing about how reservoir water quality are measured, Prof. Lin
+ introduced us to the Carlson Trophic State Index (CTSI), which determines
+ eutrophication quantitatively using the concentration of three water
+ quality parameters – Transparency(SD), Chlorophyll-a(Chl-a), Total
+ Phosphate(TP). Given that the Taiwanese government calculates eutrophic
+ levels solely using CTSI, we thought that it would be helpful to
+ incorporate this measurement into our software application, so users would
+ be easier to understand the specific water quality of the reservoirs. In
+ addition to the three parameters, CTSI also categorizes water quality into
+ three severity classifications, “oligotrophic†indicating low levels of
+ nutrients, “mesotrophic†indicating moderate inheren fertility, and
+ “eutrophic†indicating an overabundance of nutrients. Thus, our software
+ also provides information in such forms to ensure data quality and the
+ variety of information presented to users.
+ </div>
- <div class="info_contents" id="greencontents">
- When discussing about how reservoir water quality are measured, Prof. Lin
- introduced us to the Carlson Trophic State Index (CTSI), which determines
- eutrophication quantitatively using the concentration of three water quality
- parameters – Transparency(SD), Chlorophyll-a(Chl-a), Total Phosphate(TP).
- Given that the Taiwanese government calculates eutrophic levels solely using
- CTSI, we thought that it would be helpful to incorporate this measurement
- into our software application, so users would be easier to understand the
- specific water quality of the reservoirs. In addition to the three
- parameters, CTSI also categorizes water quality into three severity
- classifications, “oligotrophic†indicating low levels of nutrients,
- “mesotrophic†indicating moderate inheren fertility, and “eutrophicâ€
- indicating an overabundance of nutrients. Thus, our software also provides
- information in such forms to ensure data quality and the variety of
- information presented to users.
- </div>
+ <div class="index_container" id="educationandcommunication"></div>
+ <div class="heading2" id="hpheading2">
+ Education & Communication
+ </div>
- <div class="index_container" id="educationandcommunication"></div>
- <div class="heading2" id="hpheading2">
- Education & Communication
- </div>
+ <div class="heading4" id="hpheading2">
+ Dr. Tsai
+ </div>
- <div class="heading4" id="hpheading2">
- Dr. Tsai
- </div>
+ <div class="info_contents" id="greencontents">
+ While diving into his viewpoints on the current solutions and governmental
+ policies on eutrophication, Dr. Tsai emphasized that the best and most
+ effective way of solving an environmental issue, especially one that
+ doesn’t necessarily relate closely to the people’s lives, is to raise
+ public awareness and educate people about the severity of the issue along
+ with the urgent need of support in implementing solutions. Raising public
+ awareness on eutrophication not only inspires people to lessen phosphate
+ use as much as possible but could also influence them to encourage
+ governmental policies on solving this specific problem. Dr. Tsai
+ particularly stressed the necessity of educating the younger generation so
+ they would have an embedded value on environmental issues and ecological
+ preservation. This not only reminds them of the effects of their choices
+ on our environment but could also inspire them to invest more time and
+ effort into environmental research in the future.
+ </div>
- <div class="info_contents" id="greencontents">
- While diving into his viewpoints on the current solutions and governmental
- policies on eutrophication, Dr. Tsai emphasized that the best and most
- effective way of solving an environmental issue, especially one that doesn’t
- necessarily relate closely to the people’s lives, is to raise public
- awareness and educate people about the severity of the issue along with the
- urgent need of support in implementing solutions. Raising public awareness
- on eutrophication not only inspires people to lessen phosphate use as much
- as possible but could also influence them to encourage governmental policies
- on solving this specific problem. Dr. Tsai particularly stressed the
- necessity of educating the younger generation so they would have an embedded
- value on environmental issues and ecological preservation. This not only
- reminds them of the effects of their choices on our environment but could
- also inspire them to invest more time and effort into environmental research
- in the future.
- </div>
+ <div class="info_contents" id="greencontents">
+ In the process of holding lectures and courses about eutrophication in
+ <a
+ class="content_link"
+ id="ihplink"
+ href="{{ url_for('pages', page='education') }}"
+ >
+ local communities
+ </a>
+ we also decided that it would be a great opportunity to know the level of
+ understanding students have about our topic before and after our
+ education. Therefore, we designed
+
+ <a
+ class="content_link"
+ target="_blank"
+ id="ihplink"
+ href="https://forms.gle/duKNDNAKZC7dK9jcA"
+ >
+ survey forms
+ </a>
+ for the students to fill out, which consisted of questions about the
+ causes of eutrophication, the effects of eutrophication, and more
+ knowledge based questions related to our topic. By knowing how much
+ students know about the issue we’re focusing on, we would be able to
+ design more suitable and understandable information while promoting our
+ topic in the future.
+ </div>
- <div class="info_contents" id="greencontents">
- In the process of holding lectures and courses about eutrophication in
- <a
- class="content_link"
- id="ihplink"
- href="{{ url_for('pages', page='education') }}"
- >
- local communities
- </a>
- we also decided that it would be a great opportunity to know the level of
- understanding students have about our topic before and after our education.
- Therefore, we designed
-
- <a
- class="content_link"
- target="_blank"
- id="ihplink"
- href="https://forms.gle/duKNDNAKZC7dK9jcA"
- >
- survey forms
- </a>
- for the students to fill out, which consisted of questions about the causes
- of eutrophication, the effects of eutrophication, and more knowledge based
- questions related to our topic. By knowing how much students know about the
- issue we’re focusing on, we would be able to design more suitable and
- understandable information while promoting our topic in the future.
- </div>
+ <div class="heading4" id="hpheading2">
+ Tr. Hung
+ </div>
- <div class="heading4" id="hpheading2">
- Tr. Hung
- </div>
+ <div class="info_contents" id="greencontents">
+ In our interview with Tr. Hung, we focused on the level of environmental
+ education required and taught in elementary schools. Tr. Hung gave us
+ insights on how the 108 Taiwanese syllabus teaches students about the
+ environment, our ecosystem, and sustainability goals. Tr. Hung suggested
+ that it would be a great idea to teach elementary students about
+ eutrophication in simpler terms, so that even students could understand
+ the seriousness of algae blooms and how the lack of oxygen affects
+ underwater ecology.
+ </div>
- <div class="info_contents" id="greencontents">
- In our interview with Tr. Hung, we focused on the level of environmental
- education required and taught in elementary schools. Tr. Hung gave us
- insights on how the 108 Taiwanese syllabus teaches students about the
- environment, our ecosystem, and sustainability goals. Tr. Hung suggested
- that it would be a great idea to teach elementary students about
- eutrophication in simpler terms, so that even students could understand the
- seriousness of algae blooms and how the lack of oxygen affects underwater
- ecology.
- </div>
+ <div class="info_contents" id="greencontents">
+ After Tr. Hung informed us that environmental courses related to water
+ preservation are specifically taught in fourth and fifth grade, we planned
+ a two hour course to teach fourth grade students the basic ideas of
+ photosynthesis, how oxygen is a necessity for organism survival, and how
+ algae blooms lead to the death of aquatic life. Moreover, we gave them
+ examples of how they also have the power and ability to make a change,
+ such as preventing the use of insecticides, detergent powder, and other
+ products that consist of phosphate as ingredients.
+ </div>
- <div class="info_contents" id="greencontents">
- After Tr. Hung informed us that environmental courses related to water
- preservation are specifically taught in fourth and fifth grade, we planned a
- two hour course to teach fourth grade students the basic ideas of
- photosynthesis, how oxygen is a necessity for organism survival, and how
- algae blooms lead to the death of aquatic life. Moreover, we gave them
- examples of how they also have the power and ability to make a change, such
- as preventing the use of insecticides, detergent powder, and other products
- that consist of phosphate as ingredients.
- </div>
+ <div class="index_container" id="biosafety"></div>
+ <div class="heading2" id="hpheading2">
+ Biosafety
+ </div>
- <div class="index_container" id="biosafety"></div>
- <div class="heading2" id="hpheading2">
- Biosafety
- </div>
+ <div class="heading4" id="hpheading2">
+ Prof. Chen
+ </div>
- <div class="heading4" id="hpheading2">
- Prof. Chen
- </div>
+ <div class="info_contents" id="greencontents">
+ One of the most concerning aspects of our project is biosafety and dealing
+ with the risk of TripleP leakage to the outer aquatic environment. Prof.
+ Chen suggested that despite the fact that we already have filter membranes
+ to restrict bacteria in the filter tube, there are still possibilities of
+ engineered E. coli being leading to ecological unbalance. Due to this
+ concern, we did further research on the mechanism of our bacteria, and
+ discovered that once our E. coli is saturated with phosphate, its growth
+ mechanism would be hindered, thus disabling its functions from affecting
+ the balance within the outside ecosystem. Furthermore, we decided to
+ change our filters more frequently and put in lesser quantities of
+ bacteria to reduce the harm brought to the environment if the filter
+ papers ever break.
+ </div>
- <div class="info_contents" id="greencontents">
- One of the most concerning aspects of our project is biosafety and dealing
- with the risk of TripleP leakage to the outer aquatic environment. Prof.
- Chen suggested that despite the fact that we already have filter membranes
- to restrict bacteria in the filter tube, there are still possibilities of
- engineered E. coli being leading to ecological unbalance. Due to this
- concern, we did further research on the mechanism of our bacteria, and
- discovered that once our E. coli is saturated with phosphate, its growth
- mechanism would be hindered, thus disabling its functions from affecting the
- balance within the outside ecosystem. Furthermore, we decided to change our
- filters more frequently and put in lesser quantities of bacteria to reduce
- the harm brought to the environment if the filter papers ever break.
- </div>
+ <div class="index_container" id="addinfo"></div>
+ <div class="heading2" id="hpheading2">
+ Additional Information
+ </div>
- <div class="index_container" id="addinfo"></div>
- <div class="heading2" id="hpheading2">
- Additional Information
- </div>
+ <em class="info_contents_italics" id="greencontents">
+ Target Users
+ </em>
+
+ <div class="heading4" id="hpheading2">
+ Dr. Tsai and Prof. Lin
+ </div>
+ <div class="info_contents" id="greencontents">
+ While evaluating the environments where our hardware device could achieve
+ maximum efficiency, Dr. Tsai informed us that there are two main types of
+ reservoirs: on-stream and off-stream reservoirs. On-stream reservoirs have
+ a greater tendency to encounter eutrophication problems since they are
+ located at the streambed, where water flow is blocked, so accumulation of
+ nutrients and algae blooms are more likely to happen. Whereas off-stream
+ reservoirs are supplied by pipelines, aqueducts, or adjacent streams and
+ water inflow and outflow that could prevent nutrient accretion. On the
+ other hand, Prof. Lin also provided information that off-stream reservoirs
+ with lower flow rates and small shallow sizes still possess potential
+ risks that cannot be overlooked.
+ </div>
- <em class="info_contents_italics" id="greencontents">
- Target Users
- </em>
+ <div class="info_contents" id="greencontents">
+ With all information provided we learned in the interviews, we decided to
+ utilize our product in on-stream reservoirs in Taiwan, which includes the
+ Zengwen Reservoir, Feicui Reservoir, Shimen Reservoir, Deji Reservoir,
+ etc. However, we would also exert our power and be more concerned about
+ the off-stream reservoirs, which have more severe eutrophication levels.
+ </div>
- <div class="heading4" id="hpheading2">
- Dr. Tsai and Prof. Lin
- </div>
- <div class="info_contents" id="greencontents">
- While evaluating the environments where our hardware device could achieve
- maximum efficiency, Dr. Tsai informed us that there are two main types of
- reservoirs: on-stream and off-stream reservoirs. On-stream reservoirs have a
- greater tendency to encounter eutrophication problems since they are located
- at the streambed, where water flow is blocked, so accumulation of nutrients
- and algae blooms are more likely to happen. Whereas off-stream reservoirs
- are supplied by pipelines, aqueducts, or adjacent streams and water inflow
- and outflow that could prevent nutrient accretion. On the other hand, Prof.
- Lin also provided information that off-stream reservoirs with lower flow
- rates and small shallow sizes still possess potential risks that cannot be
- overlooked.
- </div>
+ <em class="info_contents_italics" id="greencontents">
+ Product Positioning
+ </em>
- <div class="info_contents" id="greencontents">
- With all information provided we learned in the interviews, we decided to
- utilize our product in on-stream reservoirs in Taiwan, which includes the
- Zengwen Reservoir, Feicui Reservoir, Shimen Reservoir, Deji Reservoir, etc.
- However, we would also exert our power and be more concerned about the
- off-stream reservoirs, which have more severe eutrophication levels.
- </div>
+ <div class="heading4" id="hpheading2">
+ Prof. Lin
+ </div>
- <em class="info_contents_italics" id="greencontents">
- Product Positioning
- </em>
+ <div class="info_contents" id="greencontents">
+ During our interview, Prof. Lin told us the importance of evaluating the
+ cost and price of our product, the quantified efficiency, and how these
+ aspects act as strengths or weaknesses compared to other solutions to
+ eutrophication. Prof. Lin suggested us to research on themulti-soil laying
+ (MSL) technology, a current solution to eutrophication implemented by the
+ Taiwanese government, and compare and contrast the qualities of their and
+ our solutions from various aspects. With these evaluations, he said we
+ would be able to place our
+ <a
+ class="content_link"
+ id="ihplink"
+ href="{{ url_for('pages', page='implementation') }}"
+ >
+ product
+ </a>
+ <div class="info_contents" id="greencontents">
+ in the market. Other than positioning our product in the market, we also
+ quantified our cost of 50 thousand NTD per entire device, 850 NTD per
+ specific replaceable filter, and a total cost of 50,0850 NTD.
+ </div>
+ </div>
- <div class="heading4" id="hpheading2">
- Prof. Lin
- </div>
+ <div class="index_container" id="publicsurvey"></div>
+ <b class="heading1" id="hpheading1">
+ Public Survey
+ </b>
+
+ <div class="index_container" id="overview2"></div>
+ <div class="heading2" id="hpheading2">
+ Overview
+ </div>
- <div class="info_contents" id="greencontents">
- During our interview, Prof. Lin told us the importance of evaluating the
- cost and price of our product, the quantified efficiency, and how these
- aspects act as strengths or weaknesses compared to other solutions to
- eutrophication. Prof. Lin suggested us to research on themulti-soil laying
- (MSL) technology, a current solution to eutrophication implemented by the
- Taiwanese government, and compare and contrast the qualities of their and
- our solutions from various aspects. With these evaluations, he said we would
- be able to place our
- <a
- class="content_link"
- id="ihplink"
- href="{{ url_for('pages', page='implementation') }}"
- >
- product
- </a>
<div class="info_contents" id="greencontents">
- in the market. Other than positioning our product in the market, we also
- quantified our cost of 50 thousand NTD per entire device, 850 NTD per
- specific replaceable filter, and a total cost of 50,0850 NTD.
+ To verify the public's knowledge of Eutrophication, we performed a public
+ survey of middle and high school students to compare their understanding
+ of synthetic biology, eutrophication, and biosafety before and after the
+ lectures.
</div>
- </div>
- <div class="index_container" id="publicsurvey"></div>
- <b class="heading1" id="hpheading1margin">
- Public Survey
- </b>
+ <em class="info_contents_italics" id="greencontents">
+ Understanding of eutrophication
+ </em>
- <div class="index_container" id="overview2"></div>
- <div class="heading2" id="hpheading2">
- Overview
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-25-57-pm.png"
+ />
- <div class="info_contents" id="greencontents">
- To verify the public's knowledge of Eutrophication, we performed a public
- survey of middle and high school students to compare their understanding of
- synthetic biology, eutrophication, and biosafety before and after the
- lectures.
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 2 More than half servers successively point out the cause of
+ eutrophication
+ </div>
- <em class="info_contents_italics" id="greencontents">
- Understanding of eutrophication
- </em>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-03-pm.png"
+ />
+
+ <em class="info_contents_italics" id="greencontents">
+ Our Solution
+ </em>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-09-pm.png"
+ />
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-15-pm.png"
+ />
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-20-pm.png"
+ />
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-26-pm.png"
+ />
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-31-pm.png"
+ />
+
+ <em class="info_contents_italics" id="greencontents">
+ Implementation
+ </em>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-36-pm.png"
+ />
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-25-57-pm.png"
- />
+ <div class="info_contents" id="greencontents">
+ As the graph shown above, the results indicate that responses became more
+ diverse when professional language appeared in questions. Regarding this
+ problem, our team recorded short Instagram video clips to explain
+ eutrophication. In the following lectures, we also simplified the
+ explanations and specifically introduced the meaning of each term. The
+ results from later respondents showed a great improvement in answering the
+ questions.
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 2 More than half servers successively point out the cause of
- eutrophication
- </div>
+ <div class="index_container" id="education2"></div>
+ <div class="heading2" id="hpheading2">
+ Education
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-03-pm.png"
- />
-
- <em class="info_contents_italics" id="greencontents">
- Our Solution
- </em>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-09-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-15-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-20-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-26-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-31-pm.png"
- />
-
- <em class="info_contents_italics" id="greencontents">
- Implementation
- </em>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-36-pm.png"
- />
-
- <div class="info_contents" id="greencontents">
- As the graph shown above, the results indicate that responses became more
- diverse when professional language appeared in questions. Regarding this
- problem, our team recorded short Instagram video clips to explain
- eutrophication. In the following lectures, we also simplified the
- explanations and specifically introduced the meaning of each term. The
- results from later respondents showed a great improvement in answering the
- questions.
- </div>
+ <div class="info_contents" id="greencontents">
+ To improve our educational practices in bringing the issue to the public,
+ we investigated feedback from the audience. We also introduced the iGEM
+ competition and specific tasks for each group(wet lab, dry lab, human
+ practice, and wiki) in lectures, hoping to provide useful information to
+ students passionate about biology.
+ </div>
- <div class="index_container" id="education2"></div>
- <div class="heading2" id="hpheading2">
- Education
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-42-pm.png"
+ />
- <div class="info_contents" id="greencontents">
- To improve our educational practices in bringing the issue to the public, we
- investigated feedback from the audience. We also introduced the iGEM
- competition and specific tasks for each group(wet lab, dry lab, human
- practice, and wiki) in lectures, hoping to provide useful information to
- students passionate about biology.
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-05-pm.png"
+ />
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-12-pm.png"
+ />
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-26-42-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-05-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-12-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-21-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-26-pm.png"
- />
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-32-pm.png"
- />
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-21-pm.png"
+ />
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-26-pm.png"
+ />
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/screen-shot-2022-10-05-at-7-27-32-pm.png"
+ />
+ </div>
</div>
{% endblock %}
diff --git a/wiki/pages/implementation.html b/wiki/pages/implementation.html
index d763bb2..3a6c2f4 100644
--- a/wiki/pages/implementation.html
+++ b/wiki/pages/implementation.html
@@ -1,421 +1,428 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/implementation.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="implpointer" href="#targetuser">
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
+ </div>
+
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation.png"
+ />
+ </div>
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
+ </div>
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="implpointer" href="#targetuser">
+ Target Users
+ </a>
+
+ <a class="pointer" id="implpointer" href="#impldesign">
+ Implementation Design
+ </a>
+ <a class="pointer" id="implpointer" href="#regulatingsystem">
+ Regulating System & Biosensor
+ </a>
+
+ <a class="pointer" id="implpointer" href="#hardware">
+ Hardware
+ </a>
+
+ <a class="pointer" id="implpointer" href="#biosafety">
+ Biosafety
+ </a>
+ <a class="pointer" id="implpointer" href="#software">
+ Software
+ </a>
+ <a class="pointer" id="implpointer" href="#future">
+ Future Plan
+ </a>
+ <a class="pointer" id="implpointer" href="#conclusion">
+ Conclusion
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+ <b class="heading1" id="implheading1">
+ Proposed Implementation
+ </b>
+ <div class="index_container" id="targetuser"></div>
+
+ <div class="heading2" id="implheading2">
Target Users
- </a>
-
- <a class="pointer" id="implpointer" href="#impldesign">
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ For the implementation, we aim to develop a device that assists with our
+ synthetic biological solution to eutrophication. Eutrophication has been a
+ significant environmental issue for worldwide aquatic environments.
+ Excessively used fertilizers, detergents, and industrial discharge
+ containing phosphorous flow into water bodies and cause algal bloom. The
+ decomposition of the algae leads to the overproduction of CO2 and
+ increased O2 consumption in the aquatic environment. Animals’ lives are
+ threatened by the lack of O2. The fish kills and dead zones have
+ ultimately resulted in significant ecological and economical losses.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Reservoirs in Taiwan have suffered from eutrophication mainly because of
+ wastewater containing agricultural fertilizers and home-use shampoo with
+ high phosphate concentration that is released into water bodies. In 2021,
+ sixty-five percent of Taiwan’s reservoirs were eutrophic. Therefore, we
+ target the local Taiwanese reservoirs for the implementation of our
+ engineered bacteria.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ We have also taken into consideration that temperatures below 21-degree
+ celsius do not allow engineered bacteria to maintain the function or
+ optimal enzymatic function. Since the temperature of Taiwan's local
+ reservoirs has a temperature ranging from 20 to 30 degrees Celsius, we
+ believe that they are the suitable choice of target for our product. In
+ addition, the device is best suited to achieve purification of eutrophic
+ water bodies in which the major factor exacerbating eutrophication is
+ phosphorus, which is the case for our target reservoirs in Taiwan.
+ </div>
+
+ <div class="index_container" id="impldesign"></div>
+ <div class="heading2" id="implheading2">
Implementation Design
- </a>
- <a class="pointer" id="implpointer" href="#regulatingsystem">
- Regulating System & Biosensor
- </a>
-
- <a class="pointer" id="implpointer" href="#hardware">
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ The goal of the implementation design is to decrease organic and inorganic
+ phosphate levels in the water body. The idea of our device hardware
+ consists of an artificial island with a filtering device containing our
+ engineered E. coli, TripleP cells carrying compatible
+ pACYCDuet::OPH/AsPhoU and polyP sensor, with the ability to hydrolyze
+ organic phosphate and overtly absorb, as well as fixate, inorganic
+ phosphate. The device is attached with filter papers on both ends that
+ allow eutrophic water to flow through while preventing the engineered E.
+ coli from leaking into the environment due to safety issues.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ During the interviews by our human practice team, the advice and concerns
+ from experts and stakeholders contributed to the development of our
+ implementation in regard to our hardware and software designs, biosafety
+ measures, and future goals. For more information on our human practice
+ works, please visit our
+ <a
+ class="content_link"
+ id="impllink"
+ href="{{ url_for('pages', page='human-practices') }}"
+ >
+ Integrated Human Practice Page
+ </a>
+ .
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation1.png"
+ />
+ <div class="image_description" id="greencontents">
+ Fig. 1 Functions of our implementation device
+ </div>
+ <div class="image_description_small" id="greencontents">
+ As the eutrophic water with high phosphate concentration flows through the
+ filtering device, organic phosphate (including paraoxon) and inorganic
+ phosphate diffuse into the filtering device, in which the organic
+ phosphate is hydrolyzed and inorganic phosphate is fixated into
+ polyphosphate in the engineered bacteria TripleP cells. As the phosphate
+ is eliminated, the water flowing out of the device would contain a low
+ concentration of phosphate. The expression mCherry fluorescence from the
+ biosensor construct reflects the accumulation of polyphosphate, which
+ could be detected by the light-sensor, and sent to the chip.
+ </div>
+
+ <div class="index_container" id="regulatingsystem"></div>
+ <div class="heading2" id="implheading2">
+ Bacterial Phosphate Regulating System & Biosensor
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ In light of the issue, we wish to decrease the amount of phosphate in
+ bodies of water to resolve eutrophication. Our bacteria “TripleP†are
+ engineered to degrade organic phosphate and absorb inorganic phosphate
+ from the water bodies. In order to complete our goal, we designed three
+ main target genes subcloned into two plasmids coexisting in the bacteria.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ The first plasmid is subcloned with the organic phosphate hydrolase (OPH)
+ gene, which hydrolyzes organic phosphate pollutants such as paraoxon to
+ lessen its harm to the environment, and the anti-sense PhoU (AsPhoU) gene,
+ which reduces the expression of PhoU and increase the intake of inorganic
+ phosphate. The second plasmid contains the polyphosphate sensor (PolyP
+ sensor), which produces mCherry fluorescent protein for the detection of
+ polyphosphate overaccumulation and, therefore, the need to notify the
+ users to replace the filter.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Further information about the design of OPH and AsPhoU genes, as well as
+ the PolyP sensor cells, can be found on the
+ <a
+ class="content_link"
+ id="impllink"
+ href="{{ url_for('pages', page='engineering') }}"
+ >
+ Engineering Success page
+ </a>
+ .
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Further information about the functions of OPH and AsPhoU genes can be
+ found on the
+ <a
+ class="content_link"
+ href="{{ url_for('pages', page='proof-of-concept') }}"
+ >
+ Proof of Concept page
+ </a>
+ .
+ </div>
+
+ <div class="index_container" id="hardware"></div>
+ <div class="heading2" id="implheading2">
Hardware
- </a>
-
- <a class="pointer" id="implpointer" href="#biosafety">
+ </div>
+ <em class="info_contents_italics" id="greencontents">
+ Nature Integrated Smart Filtering Device
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ The main part of the device is a filtering tube containing the engineered
+ E. coli, TripleP. We used filter papers with a hole size smaller than
+ bacteria, and an acrylic tube to prevent bacteria leakage. While the
+ eutrophic water will enter the filter tube through the filter papers, the
+ engineered bacteria can absorb the external phosphate. As the phosphate
+ concentration within the filter tube declines, the phosphate outside the
+ filter will diffuse inward. However, the rate of phosphate absorbance will
+ fall as the phosphate is fixated in the engineering E. coli. Since
+ polyphosphate would inhibit the expression of mCherry fluorescence
+ proteins, the light intensity of fluorescence proteins could reach a
+ minimum when more phosphate is present in the bacteria. This in turn can
+ be an observable indicator for the user to tell when to change the filter.
+ To observe the minimum of fluorescent proteins we use the Arduino light
+ sensor and wifi module. The chip is programmed to control the light beam
+ and light sensor, transport the fluorescence data to device users, and
+ notify them when the user should change the filter. Every six hours, the
+ light source will beam lights on the filter and excite the fluorescence
+ proteins; then, the light sensor will record the light intensity of the
+ exciting proteins and send it to the chip. As the data collected from the
+ sensor shows a minimum in light intensity, the chip will notify the user
+ to change the filter so the device can continue to filter the eutrophic
+ water at full rate.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Moreover, all of the devices will be attached to a giant artificial island
+ set in the water body by threads, so the device can float in the water. We
+ have also designed solar panels generating energy to propel collecting the
+ energy which the electronics and the chip need. For more information about
+ the hardware design, please visit our
+ <a
+ class="content_link"
+ id="impllink"
+ href="{{ url_for('pages', page='hardware') }}"
+ >
+ Hardware Page
+ </a>
+ .
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ During our interviews, several concerns and advice were raised by the
+ experts and stakeholders that led to the improvements of our device. First
+ of all, we decided to address the secretion blockage problem by adding
+ bacterial houses made of sodium alginate, which allows E. coli to adhere
+ and grow on the surface of the houses, thus preventing secreted substances
+ from covering the filter pores and blocking water infiltration. Secondly,
+ aquatic plants will be planted on the artificial islands to improve the
+ phosphorus extraction efficiency of our device since the roots of plants
+ are able to simultaneously absorb phosphorus in bodies of water.
+ </div>
+
+ <div class="index_container" id="biosafety"></div>
+ <div class="heading2" id="implheading2">
Biosafety
- </a>
- <a class="pointer" id="implpointer" href="#software">
+ </div>
+ <div class="info_contents" id="greencontents">
+ The designs of our implementation hardware and software have taken
+ biosafety into consideration. Instead of adopting the more common
+ biosafety design, such as the kill switch, we provide three ways to
+ prevent the problems, including a bacteria filter, taking advantage of
+ bacteria’s natural growth inhibition, and engineering an alerting
+ biosensor. To ensure that the engineered bacteria in the filtering device
+ will not be accidentally released into the environment, we attached
+ filtering paper with a pore size smaller than the bacteria on both sides
+ of the tube. In the event of an unexpected bacteria leakage, the over
+ absorbance and fixation of polyphosphate would also inhibit the growth of
+ bacteria, which lessens the threat it might cause to the environment. In
+ addition, the detection of fluorescence from the expression of the mCherry
+ biosensor and the alert that would then be sent to the user, which
+ decreases the risk of the release of phosphate back into the environment
+ after bacteria death and lysis.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Our approaches ensure the comprehensive biosafety of our implementation
+ design without causing any decrease in bacteria function’s efficiency as a
+ leaky expression of a kill switch gene might. Please visit our
+ <a
+ class="content_link"
+ id="impllink"
+ href="{{ url_for('pages', page='safety') }}"
+ >
+ Safety Page
+ </a>
+ for more information on the safety and security of our implementation
+ design.
+ </div>
+
+ <div class="index_container" id="software"></div>
+ <div class="heading2" id="implheading2">
Software
- </a>
- <a class="pointer" id="implpointer" href="#future">
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Eutrophication Management App
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ Concerning the software implementation of our project, our intention is to
+ elaborate on the topic of eutrophication and raise public awareness of
+ this worldwide aquatic issue. Our software features the calculation of
+ nitrogen and phosphorus in a body of water to determine the status of
+ eutrophication. Moreover, we also construct a Taiwan map for the user to
+ tap on the annotated reservoir, and the system will return sets of
+ information manifesting the extent that the reservoirs are influenced by
+ eutrophication. Please visit our
+ <a
+ class="content_link"
+ id="impllink"
+ href="{{ url_for('pages', page='software') }}"
+ >
+ Software Page
+ </a>
+ for more information on software design.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Our interviews have also contributed to the improvements in our software.
+ Specifically, we incorporated the Carlson Trophic State Index (CTSI), as
+ advised by experts, into the software application to help users gain a
+ better understanding of the precise water quality of the reservoir being
+ tested. To be specific, by adding the three parameters of
+ Transparency(SD), Chlorophyll-a(Chl-a), and Total Phosphate(TP) along with
+ the three classifications of eutrophication levels: oligotrophic,
+ mesotrophic, and eutrophic, our software ensures data quality and the
+ variety of information presented to users.
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-1.jpg"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 2 Calculation of the Severity of Eutrophication
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-2.jpg"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 3 Taiwanese Reservoir Map of Current Eutrophication Status
+ </div>
+
+ <div class="index_container" id="future"></div>
+ <div class="heading2" id="implheading2">
Future Plan
- </a>
- <a class="pointer" id="implpointer" href="#conclusion">
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ To allow our hardware device to reach the highest effectiveness, we plan
+ to design physical and chemical methods for our device to be able to
+ measure the level of eutrophication, especially the concentration of
+ phosphorus. With our improved design, the filtering device could be
+ deployed at specific locations to improve the efficiency of phosphate
+ elimination.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ To bring our implementation to a bigger scale with the advice we received
+ from the human practice works, we are planning to further prevent the
+ membrane blockage problem by applying additional appliances that would
+ spout water and wash or a brush that would scrub unwanted materials off
+ the surface of the membrane. Another idea would be to use filter sand or
+ silver-coded filter papers to prevent bacteria from growing on the
+ surfaces. Going for an even greater leap, we learned that molecular
+ methods could be incorporated into our implementation. Through ionic
+ attractions between anion and cations, negatively charged phosphorus would
+ adhere to the positively charged exterior at the bottom of our device.
+ This idea has great potential in improving the efficiency of our product;
+ therefore, we are planning on incorporating it into our future plans and
+ implementing it after further research and redesign.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ For the software, we hope to achieve the connection between the hardware
+ device and the user’s mobile device through the wifi module of the Arduino
+ chip in the future. The users could then receive notifications from the
+ hardware's monitoring of the bacteria's condition.
+ </div>
+ <div class="index_container" id="conclusion"></div>
+
+ <div class="heading2" id="implheading2">
Conclusion
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="implheading1">
- Proposed Implementation
- </b>
- <div class="index_container" id="targetuser"></div>
-
- <div class="heading2" id="implheading2">
- Target Users
- </div>
-
- <div class="info_contents" id="greencontents">
- For the implementation, we aim to develop a device that assists with our
- synthetic biological solution to eutrophication. Eutrophication has been a
- significant environmental issue for worldwide aquatic environments.
- Excessively used fertilizers, detergents, and industrial discharge
- containing phosphorous flow into water bodies and cause algal bloom. The
- decomposition of the algae leads to the overproduction of CO2 and increased
- O2 consumption in the aquatic environment. Animals’ lives are threatened by
- the lack of O2. The fish kills and dead zones have ultimately resulted in
- significant ecological and economical losses.
- </div>
-
- <div class="info_contents" id="greencontents">
- Reservoirs in Taiwan have suffered from eutrophication mainly because of
- wastewater containing agricultural fertilizers and home-use shampoo with
- high phosphate concentration that is released into water bodies. In 2021,
- sixty-five percent of Taiwan’s reservoirs were eutrophic. Therefore, we
- target the local Taiwanese reservoirs for the implementation of our
- engineered bacteria.
- </div>
-
- <div class="info_contents" id="greencontents">
- We have also taken into consideration that temperatures below 21-degree
- celsius do not allow engineered bacteria to maintain the function or optimal
- enzymatic function. Since the temperature of Taiwan's local reservoirs has a
- temperature ranging from 20 to 30 degrees Celsius, we believe that they are
- the suitable choice of target for our product. In addition, the device is
- best suited to achieve purification of eutrophic water bodies in which the
- major factor exacerbating eutrophication is phosphorus, which is the case
- for our target reservoirs in Taiwan.
- </div>
-
- <div class="index_container" id="impldesign"></div>
- <div class="heading2" id="implheading2">
- Implementation Design
- </div>
-
- <div class="info_contents" id="greencontents">
- The goal of the implementation design is to decrease organic and inorganic
- phosphate levels in the water body. The idea of our device hardware consists
- of an artificial island with a filtering device containing our engineered E.
- coli, TripleP cells carrying compatible pACYCDuet::OPH/AsPhoU and polyP
- sensor, with the ability to hydrolyze organic phosphate and overtly absorb,
- as well as fixate, inorganic phosphate. The device is attached with filter
- papers on both ends that allow eutrophic water to flow through while
- preventing the engineered E. coli from leaking into the environment due to
- safety issues.
- </div>
-
- <div class="info_contents" id="greencontents">
- During the interviews by our human practice team, the advice and concerns
- from experts and stakeholders contributed to the development of our
- implementation in regard to our hardware and software designs, biosafety
- measures, and future goals. For more information on our human practice
- works, please visit our
- <a
- class="content_link"
- id="impllink"
- href="{{ url_for('pages', page='human-practices') }}"
- >
- Integrated Human Practice Page
- </a>
- .
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/implementation1.png"
- />
- <div class="image_description" id="greencontents">
- Fig. 1 Functions of our implementation device
- </div>
- <div class="image_description_small" id="greencontents">
- As the eutrophic water with high phosphate concentration flows through the
- filtering device, organic phosphate (including paraoxon) and inorganic
- phosphate diffuse into the filtering device, in which the organic phosphate
- is hydrolyzed and inorganic phosphate is fixated into polyphosphate in the
- engineered bacteria TripleP cells. As the phosphate is eliminated, the water
- flowing out of the device would contain a low concentration of phosphate.
- The expression mCherry fluorescence from the biosensor construct reflects
- the accumulation of polyphosphate, which could be detected by the
- light-sensor, and sent to the chip.
- </div>
-
- <div class="index_container" id="regulatingsystem"></div>
- <div class="heading2" id="implheading2">
- Bacterial Phosphate Regulating System & Biosensor
- </div>
-
- <div class="info_contents" id="greencontents">
- In light of the issue, we wish to decrease the amount of phosphate in bodies
- of water to resolve eutrophication. Our bacteria “TripleP†are engineered to
- degrade organic phosphate and absorb inorganic phosphate from the water
- bodies. In order to complete our goal, we designed three main target genes
- subcloned into two plasmids coexisting in the bacteria.
- </div>
-
- <div class="info_contents" id="greencontents">
- The first plasmid is subcloned with the organic phosphate hydrolase (OPH)
- gene, which hydrolyzes organic phosphate pollutants such as paraoxon to
- lessen its harm to the environment, and the anti-sense PhoU (AsPhoU) gene,
- which reduces the expression of PhoU and increase the intake of inorganic
- phosphate. The second plasmid contains the polyphosphate sensor (PolyP
- sensor), which produces mCherry fluorescent protein for the detection of
- polyphosphate overaccumulation and, therefore, the need to notify the users
- to replace the filter.
- </div>
-
- <div class="info_contents" id="greencontents">
- Further information about the design of OPH and AsPhoU genes, as well as the
- PolyP sensor cells, can be found on the
- <a
- class="content_link"
- id="impllink"
- href="{{ url_for('pages', page='engineering') }}"
- >
- Engineering Success page
- </a>
- .
- </div>
-
- <div class="info_contents" id="greencontents">
- Further information about the functions of OPH and AsPhoU genes can be found
- on the
- <a
- class="content_link"
- href="{{ url_for('pages', page='proof-of-concept') }}"
- >
- Proof of Concept page
- </a>
- .
- </div>
-
- <div class="index_container" id="hardware"></div>
- <div class="heading2" id="implheading2">
- Hardware
- </div>
- <em class="info_contents_italics" id="greencontents">
- Nature Integrated Smart Filtering Device
- </em>
-
- <div class="info_contents" id="greencontents">
- The main part of the device is a filtering tube containing the engineered E.
- coli, TripleP. We used filter papers with a hole size smaller than bacteria,
- and an acrylic tube to prevent bacteria leakage. While the eutrophic water
- will enter the filter tube through the filter papers, the engineered
- bacteria can absorb the external phosphate. As the phosphate concentration
- within the filter tube declines, the phosphate outside the filter will
- diffuse inward. However, the rate of phosphate absorbance will fall as the
- phosphate is fixated in the engineering E. coli. Since polyphosphate would
- inhibit the expression of mCherry fluorescence proteins, the light intensity
- of fluorescence proteins could reach a minimum when more phosphate is
- present in the bacteria. This in turn can be an observable indicator for the
- user to tell when to change the filter. To observe the minimum of
- fluorescent proteins we use the Arduino light sensor and wifi module. The
- chip is programmed to control the light beam and light sensor, transport the
- fluorescence data to device users, and notify them when the user should
- change the filter. Every six hours, the light source will beam lights on the
- filter and excite the fluorescence proteins; then, the light sensor will
- record the light intensity of the exciting proteins and send it to the chip.
- As the data collected from the sensor shows a minimum in light intensity,
- the chip will notify the user to change the filter so the device can
- continue to filter the eutrophic water at full rate.
- </div>
-
- <div class="info_contents" id="greencontents">
- Moreover, all of the devices will be attached to a giant artificial island
- set in the water body by threads, so the device can float in the water. We
- have also designed solar panels generating energy to propel collecting the
- energy which the electronics and the chip need. For more information about
- the hardware design, please visit our
- <a
- class="content_link"
- id="impllink"
- href="{{ url_for('pages', page='hardware') }}"
- >
- Hardware Page
- </a>
- .
- </div>
-
- <div class="info_contents" id="greencontents">
- During our interviews, several concerns and advice were raised by the
- experts and stakeholders that led to the improvements of our device. First
- of all, we decided to address the secretion blockage problem by adding
- bacterial houses made of sodium alginate, which allows E. coli to adhere and
- grow on the surface of the houses, thus preventing secreted substances from
- covering the filter pores and blocking water infiltration. Secondly, aquatic
- plants will be planted on the artificial islands to improve the phosphorus
- extraction efficiency of our device since the roots of plants are able to
- simultaneously absorb phosphorus in bodies of water.
- </div>
-
- <div class="index_container" id="biosafety"></div>
- <div class="heading2" id="implheading2">
- Biosafety
- </div>
- <div class="info_contents" id="greencontents">
- The designs of our implementation hardware and software have taken biosafety
- into consideration. Instead of adopting the more common biosafety design,
- such as the kill switch, we provide three ways to prevent the problems,
- including a bacteria filter, taking advantage of bacteria’s natural growth
- inhibition, and engineering an alerting biosensor. To ensure that the
- engineered bacteria in the filtering device will not be accidentally
- released into the environment, we attached filtering paper with a pore size
- smaller than the bacteria on both sides of the tube. In the event of an
- unexpected bacteria leakage, the over absorbance and fixation of
- polyphosphate would also inhibit the growth of bacteria, which lessens the
- threat it might cause to the environment. In addition, the detection of
- fluorescence from the expression of the mCherry biosensor and the alert that
- would then be sent to the user, which decreases the risk of the release of
- phosphate back into the environment after bacteria death and lysis.
- </div>
-
- <div class="info_contents" id="greencontents">
- Our approaches ensure the comprehensive biosafety of our implementation
- design without causing any decrease in bacteria function’s efficiency as a
- leaky expression of a kill switch gene might. Please visit our
- <a
- class="content_link"
- id="impllink"
- href="{{ url_for('pages', page='safety') }}"
- >
- Safety Page
- </a>
- for more information on the safety and security of our implementation
- design.
- </div>
-
- <div class="index_container" id="software"></div>
- <div class="heading2" id="implheading2">
- Software
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- Eutrophication Management App
- </em>
-
- <div class="info_contents" id="greencontents">
- Concerning the software implementation of our project, our intention is to
- elaborate on the topic of eutrophication and raise public awareness of this
- worldwide aquatic issue. Our software features the calculation of nitrogen
- and phosphorus in a body of water to determine the status of eutrophication.
- Moreover, we also construct a Taiwan map for the user to tap on the
- annotated reservoir, and the system will return sets of information
- manifesting the extent that the reservoirs are influenced by eutrophication.
- Please visit our
- <a
- class="content_link"
- id="impllink"
- href="{{ url_for('pages', page='software') }}"
- >
- Software Page
- </a>
- for more information on software design.
- </div>
-
- <div class="info_contents" id="greencontents">
- Our interviews have also contributed to the improvements in our software.
- Specifically, we incorporated the Carlson Trophic State Index (CTSI), as
- advised by experts, into the software application to help users gain a
- better understanding of the precise water quality of the reservoir being
- tested. To be specific, by adding the three parameters of Transparency(SD),
- Chlorophyll-a(Chl-a), and Total Phosphate(TP) along with the three
- classifications of eutrophication levels: oligotrophic, mesotrophic, and
- eutrophic, our software ensures data quality and the variety of information
- presented to users.
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-1.jpg"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 2 Calculation of the Severity of Eutrophication
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-2.jpg"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 3 Taiwanese Reservoir Map of Current Eutrophication Status
- </div>
-
- <div class="index_container" id="future"></div>
- <div class="heading2" id="implheading2">
- Future Plan
- </div>
-
- <div class="info_contents" id="greencontents">
- To allow our hardware device to reach the highest effectiveness, we plan to
- design physical and chemical methods for our device to be able to measure
- the level of eutrophication, especially the concentration of phosphorus.
- With our improved design, the filtering device could be deployed at specific
- locations to improve the efficiency of phosphate elimination.
- </div>
-
- <div class="info_contents" id="greencontents">
- To bring our implementation to a bigger scale with the advice we received
- from the human practice works, we are planning to further prevent the
- membrane blockage problem by applying additional appliances that would spout
- water and wash or a brush that would scrub unwanted materials off the
- surface of the membrane. Another idea would be to use filter sand or
- silver-coded filter papers to prevent bacteria from growing on the surfaces.
- Going for an even greater leap, we learned that molecular methods could be
- incorporated into our implementation. Through ionic attractions between
- anion and cations, negatively charged phosphorus would adhere to the
- positively charged exterior at the bottom of our device. This idea has great
- potential in improving the efficiency of our product; therefore, we are
- planning on incorporating it into our future plans and implementing it after
- further research and redesign.
- </div>
-
- <div class="info_contents" id="greencontents">
- For the software, we hope to achieve the connection between the hardware
- device and the user’s mobile device through the wifi module of the Arduino
- chip in the future. The users could then receive notifications from the
- hardware's monitoring of the bacteria's condition.
- </div>
- <div class="index_container" id="conclusion"></div>
-
- <div class="heading2" id="implheading2">
- Conclusion
- </div>
-
- <div class="info_contents" id="greencontents">
- Our implementation provides an alternative to the current solutions to
- eutrophication, such as MSL. While MSL is only suited for smaller water
- bodies, such as ponds, or sewers before the effluent enters water bodies,
- our device could be implemented in larger water bodies including reservoirs.
- </div>
-
- <div class="info_contents" id="greencontents">
- In the future, we hoped to expand the implementation of the device from a
- local to a global level and alleviate eutrophication worldwide. We will
- continue to consult experts’ advice, as well as other stakeholders’
- opinions, and improve the design of our device further.
- </div>
-
- <div class="info_contents_centered" id="implcentered">
- Eutrophication, we have the solution.
- </div>
-
- <div class="workscited" id="greencontents">References</div>
-
- <div class="info_contents" id="greencontents">
- 牟麗娥ã€æ¸¸ç‡å¦‚ã€å¼µåšé›…。〈å°ç£ä¸»è¦æ°´åº«ï¦Œï¦Žæ°´è³ªè®ŠåŒ–特徵〉，第96é 。行政院環境ä¿è·ç½²ã€æ¸…è¯ç§‘技檢驗股份有é™å…¬å¸ã€‚
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Our implementation provides an alternative to the current solutions to
+ eutrophication, such as MSL. While MSL is only suited for smaller water
+ bodies, such as ponds, or sewers before the effluent enters water bodies,
+ our device could be implemented in larger water bodies including
+ reservoirs.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ In the future, we hoped to expand the implementation of the device from a
+ local to a global level and alleviate eutrophication worldwide. We will
+ continue to consult experts’ advice, as well as other stakeholders’
+ opinions, and improve the design of our device further.
+ </div>
+
+ <div class="info_contents_centered" id="implcentered">
+ Eutrophication, we have the solution.
+ </div>
+
+ <div class="workscited" id="greencontents">References</div>
+
+ <div class="info_contents" id="greencontents">
+ 牟麗娥ã€æ¸¸ç‡å¦‚ã€å¼µåšé›…。〈å°ç£ä¸»è¦æ°´åº«ï¦Œï¦Žæ°´è³ªè®ŠåŒ–特徵〉，第96é 。行政院環境ä¿è·ç½²ã€æ¸…è¯ç§‘技檢驗股份有é™å…¬å¸ã€‚
+ </div>
</div>
</div>
{% endblock %}
diff --git a/wiki/pages/improve.html b/wiki/pages/improve.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/improve.html
+++ b/wiki/pages/improve.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/inclusivity.html b/wiki/pages/inclusivity.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/inclusivity.html
+++ b/wiki/pages/inclusivity.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/measurement.html b/wiki/pages/measurement.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/measurement.html
+++ b/wiki/pages/measurement.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index 7a8dcfe..1ae3df7 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -1,715 +1,722 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
+ </div>
+
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/banners.png"
+ />
+ </div>
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
+ </div>
+ <aside class="aside" id="model_aside">
+ <br />
+ <div>
+ <a class="pointer" id="modelpointerhead" href="#introduction">
+ Introduction
+ </a>
+ <a class="pointer" id="modelpointerhead" href="#preliminary">
+ Preliminary Work
+ </a>
+ <a class="pointer" id="modelpointerhead" href="#modelestablishment">
+ Model
+ </a>
+ <a class="pointer" id="modelpointer" href="#assumptions">
+ Assumptions
+ </a>
+ <a class="pointer" id="modelpointer" href="#improved">Improved Model</a>
+ <a class="pointer" id="modelpointer" href="#intialcondition">
+ Simulation & Fitting
+ </a>
+ <a class="pointer" id="modelpointer" href="#flaws">
+ Flaws & Solutions
+ </a>
+ <a class="pointer" id="modelpointerhead" href="#discussion">Discussion</a>
+
+ <a class="pointer" id="modelpointer" href="#applicability">
+ Applicability
+ </a>
+ <a class="pointer" id="modelpointer" href="#limits">
+ Future Improvement
+ </a>
+ <div style="height: 15px;"></div>
+ <a class="pointer" id="modeltable" href="#table4head">
+ Table for species
+ </a>
+ <a class="pointer" id="modeltable" href="#table5head">
+ Table for constants
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/banners.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside" id="model_aside">
- <br />
- <div>
- <a class="pointer" id="modelpointerhead" href="#introduction">
+ <div class="index_container" id="introduction"></div>
+ <b class="heading1" id="modelheading1">
Introduction
- </a>
- <a class="pointer" id="modelpointerhead" href="#preliminary">
- Preliminary Work
- </a>
- <a class="pointer" id="modelpointerhead" href="#modelestablishment">
- Model
- </a>
- <a class="pointer" id="modelpointer" href="#assumptions">
- Assumptions
- </a>
- <a class="pointer" id="modelpointer" href="#improved">Improved Model</a>
- <a class="pointer" id="modelpointer" href="#intialcondition">
- Simulation & Fitting
- </a>
- <a class="pointer" id="modelpointer" href="#flaws">
- Flaws & Solutions
- </a>
- <a class="pointer" id="modelpointerhead" href="#discussion">Discussion</a>
-
- <a class="pointer" id="modelpointer" href="#applicability">
- Applicability
- </a>
- <a class="pointer" id="modelpointer" href="#limits">
- Future Improvement
- </a>
- <div style="height: 15px;"></div>
- <a class="pointer" id="modeltable" href="#table4head">
- Table for species
- </a>
- <a class="pointer" id="modeltable" href="#table5head">
- Table for constants
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
-
- <div class="index_container" id="introduction"></div>
- <b class="heading1" id="modelheading1">
- Introduction
- </b>
-
- <div class="heading2" id="modelheading2">
- Overview
- </div>
+ </b>
- <div class="info_contents" id="greencontents">
- Regarding the
- <a
- class="content_link"
- href="{{ url_for('pages', page='proof-of-concept') }}"
- >
- paraoxon (PXN) hydrolysis experiment
- </a>
- , we sought to build a model that can explain our result. First, we aimed to
- quantify the ability of our target protein organophosphate hydrolase (OPH_P)
- to hydrolyze PXN into p-nitrophenol (pNP) by fitting our model with the data
- from the experiments. We also sought to construct a model that is
- approachable for future high school iGEM teams by forming our model on
- simple yet useful foundations -- the Law of mass action and Enzyme kinetics.
- In addition, we proposed that the transportation of chemicals across the
- membrane is essential for simulating the in vivo system. Then, we sought the
- optimal condition, more specifically the optimal concentration of
- isopropyl-β-D-1- thiogalactopyranoside (IPTG), since a high concentration of
- IPTG exacerbates the expression of our target protein.
- </div>
-
- <div class="index_container" id="review"></div>
- <div class="heading2" id="modelheading2">
- Brief Lac Operon Review
- </div>
+ <div class="heading2" id="modelheading2">
+ Overview
+ </div>
- <div class="info_contents" id="greencontents">
- According to the work by Griffiths et al. (1999), a literature review of the
- mechanism of the lac operon, repressor (rep) protein blocks, not the binding
- of RNA polymerase (RP), but its movement. In other words, RP would still
- bind to the promoter even when the operator (lac O) is occupied by the
- repressor and vice versa. That is, the repressor and RP will not interfere
- with each other upon binding. IPTG would either bind to the repressor in the
- cytosol or bind to the repressor on the DNA. Bound to IPTG, the repressor's
- affinity to DNA decreases and thus allows RP to transcribe the message RNA
- (mRNA) encoding OPH (denoted as OPH_mRNA).
- </div>
+ <div class="info_contents" id="greencontents">
+ Regarding the
+ <a
+ class="content_link"
+ href="{{ url_for('pages', page='proof-of-concept') }}"
+ >
+ paraoxon (PXN) hydrolysis experiment
+ </a>
+ , we sought to build a model that can explain our result. First, we aimed
+ to quantify the ability of our target protein organophosphate hydrolase
+ (OPH_P) to hydrolyze PXN into p-nitrophenol (pNP) by fitting our model
+ with the data from the experiments. We also sought to construct a model
+ that is approachable for future high school iGEM teams by forming our
+ model on simple yet useful foundations -- the Law of mass action and
+ Enzyme kinetics. In addition, we proposed that the transportation of
+ chemicals across the membrane is essential for simulating the in vivo
+ system. Then, we sought the optimal condition, more specifically the
+ optimal concentration of isopropyl-β-D-1- thiogalactopyranoside (IPTG),
+ since a high concentration of IPTG exacerbates the expression of our
+ target protein.
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/lac-operon-illustration.png"
- />
+ <div class="index_container" id="review"></div>
+ <div class="heading2" id="modelheading2">
+ Brief Lac Operon Review
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 1 Regulation of the lac operon (Griffiths et al.,1999, Fig. 14-5)
- </div>
+ <div class="info_contents" id="greencontents">
+ According to the work by Griffiths et al. (1999), a literature review of
+ the mechanism of the lac operon, repressor (rep) protein blocks, not the
+ binding of RNA polymerase (RP), but its movement. In other words, RP would
+ still bind to the promoter even when the operator (lac O) is occupied by
+ the repressor and vice versa. That is, the repressor and RP will not
+ interfere with each other upon binding. IPTG would either bind to the
+ repressor in the cytosol or bind to the repressor on the DNA. Bound to
+ IPTG, the repressor's affinity to DNA decreases and thus allows RP to
+ transcribe the message RNA (mRNA) encoding OPH (denoted as OPH_mRNA).
+ </div>
- <div class="index_container" id="preliminary"></div>
- <b class="heading1" id="modelheading1">
- Preliminary Work
- </b>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/lac-operon-illustration.png"
+ />
- <div class="index_container" id="dnaevaluation"></div>
- <div class="heading2" id="modelheading2">
- DNA Module
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 1 Regulation of the lac operon (Griffiths et al.,1999, Fig. 14-5)
+ </div>
- <div class="info_contents" id="greencontents">
- According to lac operon kinetics provided by Montalva-Medel et al. (2021),
- we observed that their approach to model lac operon using a boolean model.
- However, we sought that the ordinary differential equation (ODE) system
- defined by the Law of mass action would be suitable for our study. To model
- this mechanism, we categorized the plasmids in our engineered Escherichia
- coli into 6 types and identified five important reactions between these
- categories as provided below in Tables 1 and 2, respectively. The components
- involved in these reactions include repressor (rep) and RNA polymerase (RP)
- in the cytoplasm (fr_rep &fr_RP), IPTG, and the complex of IPTG and rep
- (C_I_rep).
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/dna-types-full-description-removebg-preview.png"
- />
+ <div class="index_container" id="preliminary"></div>
+ <b class="heading1" id="modelheading1">
+ Preliminary Work
+ </b>
- <div class="image_description" id="greencontents">
- Table 1: Types of DNA
- </div>
+ <div class="index_container" id="dnaevaluation"></div>
+ <div class="heading2" id="modelheading2">
+ DNA Module
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/table-2-reactions.png"
- />
+ <div class="info_contents" id="greencontents">
+ According to lac operon kinetics provided by Montalva-Medel et al. (2021),
+ we observed that their approach to model lac operon using a boolean model.
+ However, we sought that the ordinary differential equation (ODE) system
+ defined by the Law of mass action would be suitable for our study. To
+ model this mechanism, we categorized the plasmids in our engineered
+ Escherichia coli into 6 types and identified five important reactions
+ between these categories as provided below in Tables 1 and 2,
+ respectively. The components involved in these reactions include repressor
+ (rep) and RNA polymerase (RP) in the cytoplasm (fr_rep &fr_RP), IPTG, and
+ the complex of IPTG and rep (C_I_rep).
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/dna-types-full-description-removebg-preview.png"
+ />
- <div class="image_description" id="greencontents">
- Table 2: Reaction
- </div>
+ <div class="image_description" id="greencontents">
+ Table 1: Types of DNA
+ </div>
- <div class="info_contents" id="greencontents">
- To summarize above, we described the relationship between different types of
- DNA in a simple interaction diagram.
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/table-2-reactions.png"
+ />
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/dna-interaction.png"
- />
+ <div class="image_description" id="greencontents">
+ Table 2: Reaction
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 2 Interactions of DNA
- </div>
+ <div class="info_contents" id="greencontents">
+ To summarize above, we described the relationship between different types
+ of DNA in a simple interaction diagram.
+ </div>
- <div class="heading2" id="modelheading2">
- Module Evaluations
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/dna-interaction.png"
+ />
- <div class="info_contents" id="greencontents">
- Reviewing the study, which took the same approach as ours, done by Dunaway
- et al. (1980), we found that the rate reaction (RR) constants of the
- repressor are very high. The binding and decomposing rate constants for
- fr_rep to lac O are 7200000 hr^-1μM^-1 and 144 hr^-1, respectively, while
- those for C_I_rep are 7200000 hr^-1μM^-1 and 144000 hr^-1, respectively.
- Plugging in these numbers, we stimulated the balance states for different
- IPTG concentrations, specifically 15.625 μM vs. 2000 μM, using the initial
- conditions that we will explain below (see Table 6 for a summary).
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 2 Interactions of DNA
+ </div>
- <img
- class="constant_height"
- id="enlarged_constant_height_doubled"
- src="https://static.igem.wiki/teams/4271/wiki/iptg-15-vs-2000-v3.png"
- />
+ <div class="heading2" id="modelheading2">
+ Module Evaluations
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 3
- <br />
- Left: DNA under 15.625/2000 μM IPTG
- <br />
- Right: Extract DNA_nrep_RP (using logX axis)
- </div>
+ <div class="info_contents" id="greencontents">
+ Reviewing the study, which took the same approach as ours, done by Dunaway
+ et al. (1980), we found that the rate reaction (RR) constants of the
+ repressor are very high. The binding and decomposing rate constants for
+ fr_rep to lac O are 7200000 hr^-1μM^-1 and 144 hr^-1, respectively, while
+ those for C_I_rep are 7200000 hr^-1μM^-1 and 144000 hr^-1, respectively.
+ Plugging in these numbers, we stimulated the balance states for different
+ IPTG concentrations, specifically 15.625 μM vs. 2000 μM, using the initial
+ conditions that we will explain below (see Table 6 for a summary).
+ </div>
- <div class="info_contents" id="greencontents">
- From this simulation plotted in log X scale, we extracted DNA_nrep_RP
- specifically because this species was the one that can transcribe OPH_mRNA
- which translates OPH. Yet, the simulation deviated from our experimental
- data. From Table 3, we can see that, under 15.625 μM IPTG, the production of
- pNP is disproportional compared with that under 2000 μM IPTG, suggesting
- that the PXN hydrolysis process is far from completion. This delay in
- hydrolyzation suggests two possibilities. First, there are much fewer
- plasmids that can express OPH under 15.625 μM than under μM IPTG resulting
- in much less OPH to hydrolyze the PXN. Secondly, there should be an
- observable delay for DNA_nrep_RP to peak up and reach an equilibrium state
- such that the OPH concentration increases slowly. Yet, from the simulation
- above, the concentration of DNA_nrep_RP under 15.625 μM IPTG is only 4.68
- times lower than that under 2000 μM IPTG. This difference can not account
- for the discrepancy between the pNP production under these two conditions.
- This leaves us with the possibility that there is a significant delay for
- plasmids to reach their equilibrium states. However, the simulation above
- shows a delay time, the interval marked between two vertical dotted lines in
- the right chart of Fig. 3, that is insignificant (only a 0.006-hour
- difference). Therefore, it implied that there were interactions in our
- system that we had not considered.
- </div>
+ <img
+ class="constant_height"
+ id="enlarged_constant_height_doubled"
+ src="https://static.igem.wiki/teams/4271/wiki/iptg-15-vs-2000-v3.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 3
+ <br />
+ Left: DNA under 15.625/2000 μM IPTG
+ <br />
+ Right: Extract DNA_nrep_RP (using logX axis)
+ </div>
- <img
- class="constant_height"
- id="table3"
- src="https://static.igem.wiki/teams/4271/wiki/figure-3.png"
- />
+ <div class="info_contents" id="greencontents">
+ From this simulation plotted in log X scale, we extracted DNA_nrep_RP
+ specifically because this species was the one that can transcribe OPH_mRNA
+ which translates OPH. Yet, the simulation deviated from our experimental
+ data. From Table 3, we can see that, under 15.625 μM IPTG, the production
+ of pNP is disproportional compared with that under 2000 μM IPTG,
+ suggesting that the PXN hydrolysis process is far from completion. This
+ delay in hydrolyzation suggests two possibilities. First, there are much
+ fewer plasmids that can express OPH under 15.625 μM than under μM IPTG
+ resulting in much less OPH to hydrolyze the PXN. Secondly, there should be
+ an observable delay for DNA_nrep_RP to peak up and reach an equilibrium
+ state such that the OPH concentration increases slowly. Yet, from the
+ simulation above, the concentration of DNA_nrep_RP under 15.625 μM IPTG is
+ only 4.68 times lower than that under 2000 μM IPTG. This difference can
+ not account for the discrepancy between the pNP production under these two
+ conditions. This leaves us with the possibility that there is a
+ significant delay for plasmids to reach their equilibrium states. However,
+ the simulation above shows a delay time, the interval marked between two
+ vertical dotted lines in the right chart of Fig. 3, that is insignificant
+ (only a 0.006-hour difference). Therefore, it implied that there were
+ interactions in our system that we had not considered.
+ </div>
- <div class="image_description" id="greencontents">
- Table 3: pNP concentration at 6 hr under 15.625/2000 μM IPTG and 500μM PXN
- </div>
- <div class="info_contents" id="greencontents">
- We attributed the transportation of IPTG across the E. coli membrane to the
- delay of the equilibrium state. Thus, we added the reaction of IPTG
- transportation across the membrane. Furthermore, we incorporated the
- transportation of PXN and pNP for compliance. This improvement divided IPTG
- into IPTG inside the bacteria (IPTG_in) and IPTG outside the bacteria
- (IPTG_ex). This division also holds true for PXN and pNP resulting in
- PXN_in, PXN_ex, and pNP_in, pNP_ex.
- </div>
+ <img
+ class="constant_height"
+ id="table3"
+ src="https://static.igem.wiki/teams/4271/wiki/figure-3.png"
+ />
- <div class="index_container" id="modelestablishment"></div>
- <b class="heading1" id="modelheading1">
- Establishment of the Model
- </b>
+ <div class="image_description" id="greencontents">
+ Table 3: pNP concentration at 6 hr under 15.625/2000 μM IPTG and 500μM PXN
+ </div>
+ <div class="info_contents" id="greencontents">
+ We attributed the transportation of IPTG across the E. coli membrane to
+ the delay of the equilibrium state. Thus, we added the reaction of IPTG
+ transportation across the membrane. Furthermore, we incorporated the
+ transportation of PXN and pNP for compliance. This improvement divided
+ IPTG into IPTG inside the bacteria (IPTG_in) and IPTG outside the bacteria
+ (IPTG_ex). This division also holds true for PXN and pNP resulting in
+ PXN_in, PXN_ex, and pNP_in, pNP_ex.
+ </div>
- <div class="index_container" id="assumptions"></div>
- <div class="heading2" id="modelheading2">
- Assumptions
- </div>
+ <div class="index_container" id="modelestablishment"></div>
+ <b class="heading1" id="modelheading1">
+ Establishment of the Model
+ </b>
- <div class="info_contents" id="greencontents">
- Here we made several assumptions to construct our model. First, the liquid
- within the eppendorf is uniform, therefore the concentration changes of
- PXN_ex, pNP_ex, and IPTG_ex caused by each bacteria are the same in the
- whole eppendorf. Second, each bacteria is synchronized to perform the same
- reactions under a given time, for example, plasmids in the bacteria reach
- the equilibrium state simultaneously. Finally, the number of bacteria is
- enough to divide up the space in the eppendorf such that each bacteria
- encounters the substance in the space that has a volume equivalent to the
- volume of a bacteria. Therefore, while a molecule transports into a
- bacteria, the concentration changes of this species inside the bacteria and
- the space with which it is interacting are the same. These assumptions
- simplified our model so that we can model the status of our experiment by
- simulating the interactions of a bacteria that can reflect the situation of
- the whole eppendorf.
- </div>
+ <div class="index_container" id="assumptions"></div>
+ <div class="heading2" id="modelheading2">
+ Assumptions
+ </div>
- <div class="index_container" id="improved"></div>
- <div class="heading2" id="modelheading2">
- Improved Model
- </div>
+ <div class="info_contents" id="greencontents">
+ Here we made several assumptions to construct our model. First, the liquid
+ within the eppendorf is uniform, therefore the concentration changes of
+ PXN_ex, pNP_ex, and IPTG_ex caused by each bacteria are the same in the
+ whole eppendorf. Second, each bacteria is synchronized to perform the same
+ reactions under a given time, for example, plasmids in the bacteria reach
+ the equilibrium state simultaneously. Finally, the number of bacteria is
+ enough to divide up the space in the eppendorf such that each bacteria
+ encounters the substance in the space that has a volume equivalent to the
+ volume of a bacteria. Therefore, while a molecule transports into a
+ bacteria, the concentration changes of this species inside the bacteria
+ and the space with which it is interacting are the same. These assumptions
+ simplified our model so that we can model the status of our experiment by
+ simulating the interactions of a bacteria that can reflect the situation
+ of the whole eppendorf.
+ </div>
- <div class="info_contents" id="greencontents">
- Upon the completion of our DNA module, we obtained the important product of
- transcription -- mRNA encoding OPH. The two major reactions left are the
- translation of mRNA and the hydrolysis of PXN. To model the translation, we
- approximated it to enzyme kinetics in which the enzyme is the ribosome
- (fr_R), the substrate is the OPH_mRNA, the intermediate complex is the
- complex of mRNA and ribosome (C_mRNA_R), and the product is the OPH_P. The
- main difference between our model and enzyme kinetics is that the mRNA will
- not turn into the OPH_P but retain itself after the reactions. In this
- model, we assumed that the concentration of tRNA is consistent throughout
- the whole duration, therefore our translation rate constant (kTL) includes
- the constant concentration of tRNA.
- </div>
+ <div class="index_container" id="improved"></div>
+ <div class="heading2" id="modelheading2">
+ Improved Model
+ </div>
- <img
- class="model_image"
- src="https://static.igem.wiki/teams/4271/wiki/translation.png"
- />
+ <div class="info_contents" id="greencontents">
+ Upon the completion of our DNA module, we obtained the important product
+ of transcription -- mRNA encoding OPH. The two major reactions left are
+ the translation of mRNA and the hydrolysis of PXN. To model the
+ translation, we approximated it to enzyme kinetics in which the enzyme is
+ the ribosome (fr_R), the substrate is the OPH_mRNA, the intermediate
+ complex is the complex of mRNA and ribosome (C_mRNA_R), and the product is
+ the OPH_P. The main difference between our model and enzyme kinetics is
+ that the mRNA will not turn into the OPH_P but retain itself after the
+ reactions. In this model, we assumed that the concentration of tRNA is
+ consistent throughout the whole duration, therefore our translation rate
+ constant (kTL) includes the constant concentration of tRNA.
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 4 Translation
- </div>
+ <img
+ class="model_image"
+ src="https://static.igem.wiki/teams/4271/wiki/translation.png"
+ />
- <div class="info_contents" id="greencontents">
- The remaining part of the reactions was modeled by standard enzyme kinetics
- with a single intermediate complex (C_OPH_PXN).
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 4 Translation
+ </div>
- <img
- class="model_image"
- src="https://static.igem.wiki/teams/4271/wiki/hydrolysis.png"
- />
+ <div class="info_contents" id="greencontents">
+ The remaining part of the reactions was modeled by standard enzyme
+ kinetics with a single intermediate complex (C_OPH_PXN).
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 5: Hydrolysis
- </div>
+ <img
+ class="model_image"
+ src="https://static.igem.wiki/teams/4271/wiki/hydrolysis.png"
+ />
- <div class="info_contents" id="greencontents">
- To construct our model, we used the MATLAB SimBiology Model Builder to
- create the visible diagram for our model. Each circle represents a reaction
- with straight lines linking every reactant involved in the reaction and
- arrows pointing to the products. The two small arrows on top of the circle
- indicate that the reaction is reversible. Since the pNP concentration is our
- primary target to observe, we needed a species that can reflect the
- concentration of the total pNP. Therefore, we added the Monitor_pNP with an
- algebraic rule that gives its value according to the summation of pNP_in and
- pNP_ex. There are 20 species interacting, one monitor species, and 25 RR
- constants. 12 of these constants can be found in the literature review, and
- the values for the other three constants (kTX, kTL, and kdmRNA) are
- estimated with the assumption that all of these values are proportional to
- the length of the sequences. Thus, our model was composed of 20 differential
- equations. Due to the recently published nature of the OPH we used, there
- are limited resources regarding this variant of OPH. According to our
- literature review, there was no research that provides quantitative analysis
- of the reactions of OPH, such as its hydrolysis. Therefore we contributed to
- this OPH part by fitting our experimental data with our model to estimate
- the RR constants of this OPH quantitatively.
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 5: Hydrolysis
+ </div>
- <img
- class="constant_height"
- id="enlarged_constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/model-overview.png"
- />
+ <div class="info_contents" id="greencontents">
+ To construct our model, we used the MATLAB SimBiology Model Builder to
+ create the visible diagram for our model. Each circle represents a
+ reaction with straight lines linking every reactant involved in the
+ reaction and arrows pointing to the products. The two small arrows on top
+ of the circle indicate that the reaction is reversible. Since the pNP
+ concentration is our primary target to observe, we needed a species that
+ can reflect the concentration of the total pNP. Therefore, we added the
+ Monitor_pNP with an algebraic rule that gives its value according to the
+ summation of pNP_in and pNP_ex. There are 20 species interacting, one
+ monitor species, and 25 RR constants. 12 of these constants can be found
+ in the literature review, and the values for the other three constants
+ (kTX, kTL, and kdmRNA) are estimated with the assumption that all of these
+ values are proportional to the length of the sequences. Thus, our model
+ was composed of 20 differential equations. Due to the recently published
+ nature of the OPH we used, there are limited resources regarding this
+ variant of OPH. According to our literature review, there was no research
+ that provides quantitative analysis of the reactions of OPH, such as its
+ hydrolysis. Therefore we contributed to this OPH part by fitting our
+ experimental data with our model to estimate the RR constants of this OPH
+ quantitatively.
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 6 Model overview
- </div>
+ <img
+ class="constant_height"
+ id="enlarged_constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/model-overview.png"
+ />
- <div class="index_container" id="table4head"></div>
- <img
- class="constant_height"
- id="table4"
- src="https://static.igem.wiki/teams/4271/wiki/figure-4.png"
- />
+ <div class="image_description" id="greencontents">
+ Fig. 6 Model overview
+ </div>
- <div class="image_description" id="greencontents">
- Table 4: Species Review
- </div>
+ <div class="index_container" id="table4head"></div>
+ <img
+ class="constant_height"
+ id="table4"
+ src="https://static.igem.wiki/teams/4271/wiki/figure-4.png"
+ />
- <div class="index_container" id="table5head"></div>
- <img
- class="constant_height"
- id="table4"
- src="https://static.igem.wiki/teams/4271/wiki/figure-5.png"
- />
+ <div class="image_description" id="greencontents">
+ Table 4: Species Review
+ </div>
- <div class="image_description" id="greencontents">
- Table 5: Reaction Constants Review & Value
- </div>
+ <div class="index_container" id="table5head"></div>
+ <img
+ class="constant_height"
+ id="table4"
+ src="https://static.igem.wiki/teams/4271/wiki/figure-5.png"
+ />
- <div class="index_container" id="intialcondition"></div>
- <b class="heading1" id="modelheading1">
- Simulation & Fitting
- </b>
- <div class="index_container" id="intialcondition"></div>
- <div class="heading2" id="modelheading2">
- Initial Conditions
- </div>
+ <div class="image_description" id="greencontents">
+ Table 5: Reaction Constants Review & Value
+ </div>
- <div class="info_contents" id="greencontents">
- We used a pET expression vector in our engineered bacteria; thus our
- plasmids have a copy number between 15~20 (Morgan, 2020). In our model, we
- picked 20 to be our copy number which is equivalent to the number of
- available DNA to transcribe mRNA. Furthermore, according to Kubitschek and
- Friske (1986), one molecule in E. coli roughly equals 1nM, thus 20 plasmids
- equate to 0.02 μM. We further set our model to start without any complex;
- that is, the 20 plasmids are in the state of DNA_nrep_nRP which give the
- initial concentration of this species -- 0.02 μM. The initial concentration
- of fr_rep, fr_RP, and fr_r are 0.05, 3, and 73 respectively (Bintu et al.,
- 2005; Muller-Hill, 1996, p.134; Bremer & Dennis, 2008). The table below
- provides a summary of the initial condition for our model simulation. IPTG
- and PXN are set according to the experimental conditions.
- </div>
+ <div class="index_container" id="intialcondition"></div>
+ <b class="heading1" id="modelheading1">
+ Simulation & Fitting
+ </b>
+ <div class="index_container" id="intialcondition"></div>
+ <div class="heading2" id="modelheading2">
+ Initial Conditions
+ </div>
- <img
- class="constant_height"
- id="table6"
- src="https://static.igem.wiki/teams/4271/wiki/figure-6.png"
- />
+ <div class="info_contents" id="greencontents">
+ We used a pET expression vector in our engineered bacteria; thus our
+ plasmids have a copy number between 15~20 (Morgan, 2020). In our model, we
+ picked 20 to be our copy number which is equivalent to the number of
+ available DNA to transcribe mRNA. Furthermore, according to Kubitschek and
+ Friske (1986), one molecule in E. coli roughly equals 1nM, thus 20
+ plasmids equate to 0.02 μM. We further set our model to start without any
+ complex; that is, the 20 plasmids are in the state of DNA_nrep_nRP which
+ give the initial concentration of this species -- 0.02 μM. The initial
+ concentration of fr_rep, fr_RP, and fr_r are 0.05, 3, and 73 respectively
+ (Bintu et al., 2005; Muller-Hill, 1996, p.134; Bremer & Dennis, 2008). The
+ table below provides a summary of the initial condition for our model
+ simulation. IPTG and PXN are set according to the experimental conditions.
+ </div>
- <div class="image_description" id="greencontents">
- Table 6: General Initial conditions
- </div>
- <div class="heading2" id="modelheading2">
- Guessed Values
- </div>
+ <img
+ class="constant_height"
+ id="table6"
+ src="https://static.igem.wiki/teams/4271/wiki/figure-6.png"
+ />
- <div class="info_contents" id="greencontents">
- To test the accuracy of our model, we first arbitrarily yet reasonably
- assigned value for the constants that are not previously tested. We used the
- MATLAB SimBiology Model Analyzer to simulate. Since our model contains
- reaction constants, such as kRD_f, with high values, our model is stiff.
- Thus, we used the built-in differential equation solver ode23t and set the
- absolute tolerance to 10^-9. Using the guesses and initial conditions
- provided below in the table, we had the curves for each species throughout
- the hydrolysis process. Among all the elements, we were particularly
- interested in PXN_ex, PXN_in, OPH_P, C_OPH_PXN, and Moniter_pNP, so we
- plotted these specifically in Fig. 7 to have an overview of the hydrolysis
- process. This graph makes a reasonable prediction of the enzymes’ behaviors
- thus we continue to analyze those guesses and estimations of the reaction
- constants by fitting the model to our experimental data.
- </div>
- <div class="safety_image_wrap">
- <div class="model_wrap">
- <img
- class="constant_height"
- id="enlarged_constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/table-7.png"
- />
-
- <div class="image_description" id="greencontents">
- Table 7: Simulation setting
- </div>
+ <div class="image_description" id="greencontents">
+ Table 6: General Initial conditions
+ </div>
+ <div class="heading2" id="modelheading2">
+ Guessed Values
</div>
- <div class="model_wrap">
- <img
- class="constant_height"
- id="enlarged_constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/simulation-1.png"
- />
- <div class="image_description" id="greencontents">
- Fig. 7 Simulation Curves
+ <div class="info_contents" id="greencontents">
+ To test the accuracy of our model, we first arbitrarily yet reasonably
+ assigned value for the constants that are not previously tested. We used
+ the MATLAB SimBiology Model Analyzer to simulate. Since our model contains
+ reaction constants, such as kRD_f, with high values, our model is stiff.
+ Thus, we used the built-in differential equation solver ode23t and set the
+ absolute tolerance to 10^-9. Using the guesses and initial conditions
+ provided below in the table, we had the curves for each species throughout
+ the hydrolysis process. Among all the elements, we were particularly
+ interested in PXN_ex, PXN_in, OPH_P, C_OPH_PXN, and Moniter_pNP, so we
+ plotted these specifically in Fig. 7 to have an overview of the hydrolysis
+ process. This graph makes a reasonable prediction of the enzymes’
+ behaviors thus we continue to analyze those guesses and estimations of the
+ reaction constants by fitting the model to our experimental data.
+ </div>
+ <div class="safety_image_wrap">
+ <div class="model_wrap">
+ <img
+ class="constant_height"
+ id="enlarged_constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/table-7.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Table 7: Simulation setting
+ </div>
+ </div>
+ <div class="model_wrap">
+ <img
+ class="constant_height"
+ id="enlarged_constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/simulation-1.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 7 Simulation Curves
+ </div>
</div>
</div>
- </div>
- <div class="heading2" id="modelheading2">
- Fitting
- </div>
+ <div class="heading2" id="modelheading2">
+ Fitting
+ </div>
- <div class="info_contents" id="greencontents">
- To perform the quantitative analysis of the OPH protein, we fit our model
- with the data collected from the experiments under 500 μM PXN and various
- concentrations of IPTG from 15.625~2000 μM, a total number of 8 sets of data
- as shown in the table below. We only fit the rate constants that we
- estimated and those without references, using the initial guesses provided
- above in Table 7.
- </div>
- <img
- class="constant_height"
- id="table8"
- src="https://static.igem.wiki/teams/4271/wiki/figure-8.png"
- />
-
- <div class="image_description" id="greencontents">
- Table 8: IDs and Concentrations
- </div>
+ <div class="info_contents" id="greencontents">
+ To perform the quantitative analysis of the OPH protein, we fit our model
+ with the data collected from the experiments under 500 μM PXN and various
+ concentrations of IPTG from 15.625~2000 μM, a total number of 8 sets of
+ data as shown in the table below. We only fit the rate constants that we
+ estimated and those without references, using the initial guesses provided
+ above in Table 7.
+ </div>
+ <img
+ class="constant_height"
+ id="table8"
+ src="https://static.igem.wiki/teams/4271/wiki/figure-8.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Table 8: IDs and Concentrations
+ </div>
- <div class="index_container" id="flaws"></div>
- <div class="heading2" id="modelheading2">
- Identified Flaws & Solution
- </div>
+ <div class="index_container" id="flaws"></div>
+ <div class="heading2" id="modelheading2">
+ Identified Flaws & Solution
+ </div>
- <div class="info_contents" id="greencontents">
- Using these guesses we yielded an array of estimated constants, yet we
- encountered a problem that several constants converge to be negative.
- However, this can not be true since none of the reactions in our system is
- zeroth-order, the only case in which the RR constant can be negative.
- Reviewing the differential equations we implemented for simulation, we found
- out that those observations were reasonable, rather than systematic error,
- during the fitting process. In quest of a fit value, the algorithm only
- searches a range of values around the initial guess and ends at the
- combination that creates the combination of the constants. This caused a
- problem we identified as the Equivalent Parameters Problem. By name, it
- means that there are multiple constants that have the same effect on the
- curves; while the algorithm computes the curve, they will take these
- parameters equally without considering their chemical significance,
- resulting in unrealistic estimations of the RR constants. For example, the
- estimation we reached using our initial guesses results in a negative
- kIPTG_out.
- </div>
+ <div class="info_contents" id="greencontents">
+ Using these guesses we yielded an array of estimated constants, yet we
+ encountered a problem that several constants converge to be negative.
+ However, this can not be true since none of the reactions in our system is
+ zeroth-order, the only case in which the RR constant can be negative.
+ Reviewing the differential equations we implemented for simulation, we
+ found out that those observations were reasonable, rather than systematic
+ error, during the fitting process. In quest of a fit value, the algorithm
+ only searches a range of values around the initial guess and ends at the
+ combination that creates the combination of the constants. This caused a
+ problem we identified as the Equivalent Parameters Problem. By name, it
+ means that there are multiple constants that have the same effect on the
+ curves; while the algorithm computes the curve, they will take these
+ parameters equally without considering their chemical significance,
+ resulting in unrealistic estimations of the RR constants. For example, the
+ estimation we reached using our initial guesses results in a negative
+ kIPTG_out.
+ </div>
- <img
- class="model_image"
- id="model_image_sp"
- src="https://static.igem.wiki/teams/4271/wiki/equation-1.png"
- />
+ <img
+ class="model_image"
+ id="model_image_sp"
+ src="https://static.igem.wiki/teams/4271/wiki/equation-1.png"
+ />
- <div class="image_description" id="greencontents">
- Fig. 8 Differential Equation
- </div>
- <div class="info_contents" id="greencontents">
- From the equation above, we can see that kIPTG_in and kIPTG_out are
- mathematically equivalent. Therefore, the negative kIPTG_out, in fact, acts
- as kIPTG_in but is proportional to IPTG_in instead of IPTG_ex, which means
- it contributes to the influx of IPTG into the cell. We denoted this kind of
- combination of RR constants that have the same mathematical effect as the
- equivalent set. Therefore, by heightening the value of the counterpart in
- the equivalence set, we can adjust the one with a negative value to a
- reasonable number. We devised this method to deal with the negative RR
- constant estimation systematically rather than randomly testing some other
- RR constants that only indirectly affect the one we intended to change.
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 8 Differential Equation
+ </div>
+ <div class="info_contents" id="greencontents">
+ From the equation above, we can see that kIPTG_in and kIPTG_out are
+ mathematically equivalent. Therefore, the negative kIPTG_out, in fact,
+ acts as kIPTG_in but is proportional to IPTG_in instead of IPTG_ex, which
+ means it contributes to the influx of IPTG into the cell. We denoted this
+ kind of combination of RR constants that have the same mathematical effect
+ as the equivalent set. Therefore, by heightening the value of the
+ counterpart in the equivalence set, we can adjust the one with a negative
+ value to a reasonable number. We devised this method to deal with the
+ negative RR constant estimation systematically rather than randomly
+ testing some other RR constants that only indirectly affect the one we
+ intended to change.
+ </div>
- <div class="info_contents" id="greencontents">
- Despite this systematic method and continuous effort, kPXN_out still
- remained negative, just below zero. This might be because the method we
- acquired to deal with the Equivalent Parameters Problem had its limitations.
- We were aware that a constant could be part of multiple equivalence sets,
- therefore, we can not change a RR constant unlimitedly to an unrealistically
- high value this would either make other RR constants become negative to
- balance the effect caused by the augmentation of one value, or would
- collapse the whole algorithm such that it could not converge to a tolerable
- estimation. Taking one more glance at our model, we saw that the OPH_P
- consistently hydrolyzes the PXN inside the bacterium; this suggests that the
- dynamic equilibrium between the PXN inside and outside the membrane is not
- reached, given that PXN_in is quickly bound to OPH_P. While the PXN indeed
- transports across the membrane outward, the presence of OPH_P that binds
- with PXN and hydrolyzes it into pNP makes our model difficult to estimate
- kPXN_out merely by the pNP data we collected. Thus, to take PXN influx
- outnumbering the outflux into consideration, we decided to set kPXN_out to 0
- for our stimulation and left it undetermined for the future improvement of
- both our experiments and model.
- </div>
+ <div class="info_contents" id="greencontents">
+ Despite this systematic method and continuous effort, kPXN_out still
+ remained negative, just below zero. This might be because the method we
+ acquired to deal with the Equivalent Parameters Problem had its
+ limitations. We were aware that a constant could be part of multiple
+ equivalence sets, therefore, we can not change a RR constant unlimitedly
+ to an unrealistically high value this would either make other RR constants
+ become negative to balance the effect caused by the augmentation of one
+ value, or would collapse the whole algorithm such that it could not
+ converge to a tolerable estimation. Taking one more glance at our model,
+ we saw that the OPH_P consistently hydrolyzes the PXN inside the
+ bacterium; this suggests that the dynamic equilibrium between the PXN
+ inside and outside the membrane is not reached, given that PXN_in is
+ quickly bound to OPH_P. While the PXN indeed transports across the
+ membrane outward, the presence of OPH_P that binds with PXN and hydrolyzes
+ it into pNP makes our model difficult to estimate kPXN_out merely by the
+ pNP data we collected. Thus, to take PXN influx outnumbering the outflux
+ into consideration, we decided to set kPXN_out to 0 for our stimulation
+ and left it undetermined for the future improvement of both our
+ experiments and model.
+ </div>
- <div class="index_container" id="discussion"></div>
- <b class="heading1" id="modelheading1">
- Discussion
- </b>
+ <div class="index_container" id="discussion"></div>
+ <b class="heading1" id="modelheading1">
+ Discussion
+ </b>
- <div class="index_container" id="results"></div>
- <div class="heading2" id="modelheading2">
- Results
- </div>
+ <div class="index_container" id="results"></div>
+ <div class="heading2" id="modelheading2">
+ Results
+ </div>
- <div class="info_contents" id="greencontents">
- The removal of kPXN_out from our fitting provides a shift in the value of
- estimated RR constants previously unseen in our fitting so far. Repeating
- the method several times we obtained a set of estimations as shown in the
- table below.
- </div>
+ <div class="info_contents" id="greencontents">
+ The removal of kPXN_out from our fitting provides a shift in the value of
+ estimated RR constants previously unseen in our fitting so far. Repeating
+ the method several times we obtained a set of estimations as shown in the
+ table below.
+ </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/table-9.png"
- />
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/table-9.png"
+ />
- <div class="image_description" id="greencontents">
- Table 9: Fit Results
- <br />
- (0* see the previous section for more information)
- </div>
+ <div class="image_description" id="greencontents">
+ Table 9: Fit Results
+ <br />
+ (0* see the previous section for more information)
+ </div>
- <div class="heading2" id="modelheading2">
- Verification
- </div>
+ <div class="heading2" id="modelheading2">
+ Verification
+ </div>
- <div class="info_contents" id="greencontents">
- The enlargement of these RR constants made the curve turn more sharply than
- the previous simulation (see Fig. 7) did. We used these values to simulate
- the production of pNP under another experimental condition (100 μM IPTG and
- 500 μM PXN). The curve was plotted with the experimental data to see if the
- simulation can predict the experiment. As shown in Fig. 9 below, the
- simulation curve made a good estimation for the experiment; thus it suggests
- our fit results are a reasonable estimation.
- </div>
+ <div class="info_contents" id="greencontents">
+ The enlargement of these RR constants made the curve turn more sharply
+ than the previous simulation (see Fig. 7) did. We used these values to
+ simulate the production of pNP under another experimental condition (100
+ μM IPTG and 500 μM PXN). The curve was plotted with the experimental data
+ to see if the simulation can predict the experiment. As shown in Fig. 9
+ below, the simulation curve made a good estimation for the experiment;
+ thus it suggests our fit results are a reasonable estimation.
+ </div>
- <img
- class="constant_height"
- id="enlarged_constant_height_doubled"
- src="https://static.igem.wiki/teams/4271/wiki/final-proof.png"
- />
+ <img
+ class="constant_height"
+ id="enlarged_constant_height_doubled"
+ src="https://static.igem.wiki/teams/4271/wiki/final-proof.png"
+ />
- <div class="image_description" id="greencontents">
- Fig. 9 Simulation vs Experimental Data
- </div>
+ <div class="image_description" id="greencontents">
+ Fig. 9 Simulation vs Experimental Data
+ </div>
- <div class="index_container" id="applicability"></div>
- <div class="heading2" id="modelheading2">
- Applicability and Implication
- </div>
+ <div class="index_container" id="applicability"></div>
+ <div class="heading2" id="modelheading2">
+ Applicability and Implication
+ </div>
- <div class="info_contents" id="greencontents">
- The fitting results showed that our assumption for three RR constants (kTX,
- kTL, and kdmRNA) that their values are proportional to the length of the
- sequences of the target protein is reasonable. Their proposed values are
- consistent with our initial estimations. Besides confirming our assumption,
- the values of kOPH_PXN_f, kOPH_PXN_r, khydro, and kdOPH we obtained via
- fitting are our contributions to
- <a
- class="content_link"
- target="_blank"
- href="https://www.ncbi.nlm.nih.gov/nucleotide/MG874846.1?report=genbank&log$=nuclalign&blast_rank=2&RID=FZDNC8GZ01R"
- >
- this specific variant of engineered OPH
- </a>
- . Furthermore, besides kPXN_out we can not determine with our fitting due to
- the limited experimental data and the fact that PXN influx occurs more
- readily than outflux, we successfully determine the other five RR constants
- for transportation of IPTG, PXN, and pNP across the cell membrane. The data
- we obtained shows that these are rather slow reactions compared to other
- reactions happening simultaneously in the cell. Thus, this also proved our
- idea of adding transportation into our model to account for an in vivo
- experiment.
- </div>
+ <div class="info_contents" id="greencontents">
+ The fitting results showed that our assumption for three RR constants
+ (kTX, kTL, and kdmRNA) that their values are proportional to the length of
+ the sequences of the target protein is reasonable. Their proposed values
+ are consistent with our initial estimations. Besides confirming our
+ assumption, the values of kOPH_PXN_f, kOPH_PXN_r, khydro, and kdOPH we
+ obtained via fitting are our contributions to
+ <a
+ class="content_link"
+ target="_blank"
+ href="https://www.ncbi.nlm.nih.gov/nucleotide/MG874846.1?report=genbank&log$=nuclalign&blast_rank=2&RID=FZDNC8GZ01R"
+ >
+ this specific variant of engineered OPH
+ </a>
+ . Furthermore, besides kPXN_out we can not determine with our fitting due
+ to the limited experimental data and the fact that PXN influx occurs more
+ readily than outflux, we successfully determine the other five RR
+ constants for transportation of IPTG, PXN, and pNP across the cell
+ membrane. The data we obtained shows that these are rather slow reactions
+ compared to other reactions happening simultaneously in the cell. Thus,
+ this also proved our idea of adding transportation into our model to
+ account for an in vivo experiment.
+ </div>
- <div class="info_contents" id="greencontents">
- With such a detailed model, we believe that our model has wide
- applicability. The DNA module we devised can be applied to all the inducible
- operons, such as gal operon and L-arabinose, just to name a few, by changing
- the RR constant values (Sanganeria & Bordoni, 2021). Also, this model only
- models the PXN hydrolysis experiment, yet since we design it to be as a
- module, this model is extended to simulate our future experiments such as
- the poly-P sensor, or the mCherry fluorescent protein. Our model is designed
- based on fundamental reactions we learned in high school, yet we have shown
- its ability to describe a complex system. This approach can be followed by
- future iGEM teams to develop a simple yet accurate model. Finally, the
- systematic method we used to deal with the Equivalent Parameters Problem can
- also assist future teams in their fitting process.
- </div>
+ <div class="info_contents" id="greencontents">
+ With such a detailed model, we believe that our model has wide
+ applicability. The DNA module we devised can be applied to all the
+ inducible operons, such as gal operon and L-arabinose, just to name a few,
+ by changing the RR constant values (Sanganeria & Bordoni, 2021). Also,
+ this model only models the PXN hydrolysis experiment, yet since we design
+ it to be as a module, this model is extended to simulate our future
+ experiments such as the poly-P sensor, or the mCherry fluorescent protein.
+ Our model is designed based on fundamental reactions we learned in high
+ school, yet we have shown its ability to describe a complex system. This
+ approach can be followed by future iGEM teams to develop a simple yet
+ accurate model. Finally, the systematic method we used to deal with the
+ Equivalent Parameters Problem can also assist future teams in their
+ fitting process.
+ </div>
- <div class="index_container" id="limits"></div>
- <div class="heading2" id="modelheading2">
- Limitation and Future Improvement
- </div>
+ <div class="index_container" id="limits"></div>
+ <div class="heading2" id="modelheading2">
+ Limitation and Future Improvement
+ </div>
- <div class="info_contents" id="greencontents">
- One thing that we were aware of is that due to our limited experimental
- data, there exist multiple estimations for the RR constant that can fit the
- data almost perfectly. Therefore, an improvement we can make to receive a
- more accurate value for the RR constants is to have a greater database that
- allows us to evaluate the fitness of our model with a higher standard.
- Furthermore, IPTG is known to suppress the expression of protein when its
- concentration exceeds a certain concentration. Since the reason for such
- suppression is still obscure, we did not include this biochemical
- interaction in our model. Even though in our fitting process, we saw peaks
- of kTX and kTL under 250 μM IPTG which is the optimal condition we
- identified via experiments, the differences of these RR constants between
- this concentration and others are not significant enough for us to determine
- whether this is caused by the suppression of high IPTG concentration or
- simply the instability of our stiff model. Therefore, we hope to add more
- reactions to our model that can account for such suppression; thus, we will
- be able to find out the optimal concentration of IPTG. Last but not least,
- we also hope to factor in the influence of the toxicity of PXN at high
- concentrations on the expression of protein and bacterial division. By
- having such consideration, we will be capable of simulating the experiment
- more accurately and even simulate the environment in which our bacteria are
- implemented.
- </div>
+ <div class="info_contents" id="greencontents">
+ One thing that we were aware of is that due to our limited experimental
+ data, there exist multiple estimations for the RR constant that can fit
+ the data almost perfectly. Therefore, an improvement we can make to
+ receive a more accurate value for the RR constants is to have a greater
+ database that allows us to evaluate the fitness of our model with a higher
+ standard. Furthermore, IPTG is known to suppress the expression of protein
+ when its concentration exceeds a certain concentration. Since the reason
+ for such suppression is still obscure, we did not include this biochemical
+ interaction in our model. Even though in our fitting process, we saw peaks
+ of kTX and kTL under 250 μM IPTG which is the optimal condition we
+ identified via experiments, the differences of these RR constants between
+ this concentration and others are not significant enough for us to
+ determine whether this is caused by the suppression of high IPTG
+ concentration or simply the instability of our stiff model. Therefore, we
+ hope to add more reactions to our model that can account for such
+ suppression; thus, we will be able to find out the optimal concentration
+ of IPTG. Last but not least, we also hope to factor in the influence of
+ the toxicity of PXN at high concentrations on the expression of protein
+ and bacterial division. By having such consideration, we will be capable
+ of simulating the experiment more accurately and even simulate the
+ environment in which our bacteria are implemented.
+ </div>
- <div class="workscited" id="greencontents">References</div>
- <div class="info_contents" id="greencontents">
- Bintu, L., Buchler, N.E., Garcia, H.G., Gerland, U., Hwa, T., Kondev, J.,
- Kuhlman, T., & Philips, R. (2005). Transcriptional regulation by the
- numbers: applications. Current Opinion in Genetics & Development, 15(2),
- 125-135. https://doi.org/10.1016/j.gde.2005.02.006.
- </div>
- <div class="info_contents" id="greencontents">
- Bremer, H., & Dennis, P. P. (2008). Modulation of chemical composition and
- other parameters of the cell at different exponential growth rates. EcoSal
- Plus, 3(1). https://doi.org/10.1128/ecosal.5.2.3.
- </div>
- <div class="info_contents" id="greencontents">
- Dunaway, M., Olson, J. S., Rosenberg, J. M., Kallai, O. B., Dickerson, R.
- E., & Matthews, K. S. (1980). Kinetic studies of inducer binding to lac
- repressor operator complex. The Journal of Biological Chemistry, 255. (10),
- 3. https://doi.org/10.1016/s0021-9258(19)70435-9.
- </div>
- <div class="info_contents" id="greencontents">
- Dvorak, P., Chrast, L., Nikel, P. I., Fedr, R., Soucek, K., Sedlackova, M.,
- Chaloupkova, R., de Lorenzo, V., Prokop, Z., & Damborsky, J. (2015).
- Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3)
- carrying a synthetic metabolic pathway. Microbial Cell Factories, 14(1).
- https://doi.org/10.1186/s12934-015-0393-3.
- </div>
- <div class="info_contents" id="greencontents">
- Griffiths, A. J. F., Gelbart, W. M., Miller, J. H., Lewontin, R. C. (1999).
- Modern Genetic Analysis. W. H. Freeman and Company.
- </div>
- <div class="info_contents" id="greencontents">
- Kubitschek, H. E., & Friske, J. A. (1986). Determination of bacterial cell
- volume with the Coulter Counter. Journal of Bacteriology, 168(3), 1466–1467.
- https://doi.org/10.1128/jb.168.3.1466-1467.1986.
- </div>
- <div class="info_contents" id="greencontents">
- Montalva-Medel M, Ledger T, Ruz GA, Goles E. Lac Operon Boolean Models:
- Dynamical Robustness and Alternative Improvements. Mathematics. 2021;
- 9(6):600. https://doi.org/10.3390/math9060600
- </div>
- <div class="info_contents" id="greencontents">
- Morgan, K. (2020, November 10). Plasmids 101: Origin of replication. Addgene
- blog. Retrieved September 28, 2022, from
- https://blog.addgene.org/plasmid-101-origin- of-replication.
- </div>
- <div class="info_contents" id="greencontents">
- Muller-Hill B. (1996) The Lac Operon: A Short History of a Genetic Paradigm.
- Berlin: Walter de Gruyter.
- </div>
- <div class="info_contents" id="greencontents">
- Sanganeria, T., & Bordoni, B. (2021, October 12). Genetics, Inducible
- Operon. National Library of Medicine. Retrieved October 2, 2022.
+ <div class="workscited" id="greencontents">References</div>
+ <div class="info_contents" id="greencontents">
+ Bintu, L., Buchler, N.E., Garcia, H.G., Gerland, U., Hwa, T., Kondev, J.,
+ Kuhlman, T., & Philips, R. (2005). Transcriptional regulation by the
+ numbers: applications. Current Opinion in Genetics & Development, 15(2),
+ 125-135. https://doi.org/10.1016/j.gde.2005.02.006.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Bremer, H., & Dennis, P. P. (2008). Modulation of chemical composition and
+ other parameters of the cell at different exponential growth rates. EcoSal
+ Plus, 3(1). https://doi.org/10.1128/ecosal.5.2.3.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Dunaway, M., Olson, J. S., Rosenberg, J. M., Kallai, O. B., Dickerson, R.
+ E., & Matthews, K. S. (1980). Kinetic studies of inducer binding to lac
+ repressor operator complex. The Journal of Biological Chemistry, 255.
+ (10), 3. https://doi.org/10.1016/s0021-9258(19)70435-9.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Dvorak, P., Chrast, L., Nikel, P. I., Fedr, R., Soucek, K., Sedlackova,
+ M., Chaloupkova, R., de Lorenzo, V., Prokop, Z., & Damborsky, J. (2015).
+ Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3)
+ carrying a synthetic metabolic pathway. Microbial Cell Factories, 14(1).
+ https://doi.org/10.1186/s12934-015-0393-3.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Griffiths, A. J. F., Gelbart, W. M., Miller, J. H., Lewontin, R. C.
+ (1999). Modern Genetic Analysis. W. H. Freeman and Company.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Kubitschek, H. E., & Friske, J. A. (1986). Determination of bacterial cell
+ volume with the Coulter Counter. Journal of Bacteriology, 168(3),
+ 1466–1467. https://doi.org/10.1128/jb.168.3.1466-1467.1986.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Montalva-Medel M, Ledger T, Ruz GA, Goles E. Lac Operon Boolean Models:
+ Dynamical Robustness and Alternative Improvements. Mathematics. 2021;
+ 9(6):600. https://doi.org/10.3390/math9060600
+ </div>
+ <div class="info_contents" id="greencontents">
+ Morgan, K. (2020, November 10). Plasmids 101: Origin of replication.
+ Addgene blog. Retrieved September 28, 2022, from
+ https://blog.addgene.org/plasmid-101-origin- of-replication.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Muller-Hill B. (1996) The Lac Operon: A Short History of a Genetic
+ Paradigm. Berlin: Walter de Gruyter.
+ </div>
+ <div class="info_contents" id="greencontents">
+ Sanganeria, T., & Bordoni, B. (2021, October 12). Genetics, Inducible
+ Operon. National Library of Medicine. Retrieved October 2, 2022.
+ </div>
</div>
</div>
{% endblock %}
diff --git a/wiki/pages/part-collection.html b/wiki/pages/part-collection.html
index f347dd1..720bce1 100644
--- a/wiki/pages/part-collection.html
+++ b/wiki/pages/part-collection.html
@@ -29,22 +29,7 @@
Overview
</a>
<a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- The first section of the part collection (BBa_K4271000 ~ BBa_K4271003,
- BBa_K4271015, BBa_K4271016) is designed for the phosphate elimination
- functions, the increase of hydrolysis and absorbance of organic phosphate,
- in bacterial cells. The parts in the second section of the collection
- (BBa_K4271004 ~ BBa_K4271011, BBa_K4271018, BBa_K4271019) are designed for
- the construction of biosensors that could help monitor the functions of
- the parts in the first section. This is a comprehensive collection that
- includes both the parts with functions and the parts that assist the
- measurement of the said functions. This combination not only provides
- methods for phosphate elimination in different fields of application but
- also allows future users to more easily replicate experiments that could
- monitor the effectiveness of their constructs designed with these parts.
- Our part collection also included the integration of ideas from our
- partnership with another iGEM team, particularly in the use of a
- degradation tag (BBa_M0052) to improve the experimental results of
- biosensors.
+ Parts for Eutrophic Water Purification (OPH and AsPhoU)
</a>
<a class="pointer" href="#basicparts">Basic Parts</a>
@@ -75,19 +60,19 @@
</b>
<div class="info_contents" id="greencontents">
The first section of the part collection (BBa_K4271000 ~ BBa_K4271003,
- BBa_K4271015) can be used for the increase of hydrolysis and absorbance of
- organic phosphate in bacterial cells.The parts in the second section of the
- collection (BBa_K4271004 ~ BBa_K4271014, BBa_K4271016) are used for the
- construction of biosensors for the monitoring of the functions of the parts
- in the first section. This is a comprehensive collection that includes both
- the parts with phosphate hydrolysis & absorbance functions and the parts
- that construct the biosensors monitoring the said functions. This
- combination not only provides methods for phosphate elimination in different
- fields of application, but also allows future users to more easily replicate
- experiments that could monitor the effectiveness of their constructs
- designed with these parts. Our part collection also included the integration
- of ideas from our partnership with another iGEM team, particularly in the
- use of a degradation tag
+ BBa_K4271015, BBa_K4271016) is designed for the phosphate elimination
+ functions, the increase of hydrolysis and absorbance of organic phosphate,
+ in bacterial cells. The parts in the second section of the collection
+ (BBa_K4271004 ~ BBa_K4271011, BBa_K4271018, BBa_K4271019) are designed for
+ the construction of biosensors that could help monitor the functions of the
+ parts in the first section. This is a comprehensive collection that includes
+ both the parts with functions and the parts that assist the measurement of
+ the said functions. This combination not only provides methods for phosphate
+ elimination in different fields of application but also allows future users
+ to more easily replicate experiments that could monitor the effectiveness of
+ their constructs designed with these parts. Our part collection also
+ included the integration of ideas from our partnership with another iGEM
+ team, particularly in the use of a degradation tag
<a
class="content_link"
id="partlink"
@@ -96,7 +81,7 @@
>
(BBa_M0052)
</a>
- to improve experimental results of biosensors.
+ to improve the experimental results of biosensors.
</div>
<div class="index_container" id="eutrohpicwater"></div>
<b class="heading1" id="partsheading1">
@@ -189,7 +174,7 @@
<div class="chart_contents" id="greencontents">
<img
class="chart_part_image"
- src="https://static.igem.wiki/teams/4271/wiki/pelb-signal-peptide.png"
+ src="https://static.igem.wiki/teams/4271/wiki/asphou-rbs.png"
/>
</div>
</div>
diff --git a/wiki/pages/partnership.html b/wiki/pages/partnership.html
index e56893c..810b7df 100644
--- a/wiki/pages/partnership.html
+++ b/wiki/pages/partnership.html
@@ -1,204 +1,208 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/partnership.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partnerpointer" href="#meetup">
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
+ </div>
+
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/partnership.png"
+ />
+ </div>
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
+ </div>
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="partnerpointer" href="#meetup">
+ Virtual Meet-up
+ </a>
+
+ <a class="pointer" id="partnerpointer" href="#expcollab">
+ Experimental Collaborations
+ </a>
+ <a class="pointer" id="partnerpointer" href="#implcollab">
+ Implementation Collaborations
+ </a>
+ <a class="pointer" id="partnerpointer" href="#podcast">
+ Podcast: E. Color!
+ </a>
+
+ <a class="pointer" id="partnerpointer" href="#final">
+ Finalization
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+
+ <b class="heading1" id="partnershipheading1">
+ Our partnership begins…
+ </b>
+
+ <div class="info_contents" id="greencontents">
+ Our team has begun a strong partnership with team NYCU_Taipei. Through
+ months of communication and planning, we created a bond that propels both
+ teams to progress more efficiently and effectively.
+ </div>
+ <div class="index_container" id="meetup"></div>
+
+ <div class="heading2" id="partnershipheading2">
Virtual Meet-up
- </a>
-
- <a class="pointer" id="partnerpointer" href="#expcollab">
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Since both of our teams would like to exchange our project ideas, we
+ scheduled a virtual meet-up of which we got inspired and decided to have a
+ long-term partnership.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Our first collaboration came into place when both teams presented their
+ project. Team NYCU_Taipei shared their project about SsrA degradation tags
+ to reduce the half-life of fluorescent proteins. Further, we extended
+ in-depth discussions about using fluorescence sensors as tags to increase
+ accuracy in indicating essential time points within the bacterial growth
+ curve. Through the questions they asked, we learned the underlying
+ problems and potential methods to improve the efficacy of the polyP
+ sensors. Aiming to gain more insights and communication, both teams agreed
+ to collaborate on the experimental aspect. We hope our partnership will
+ help both teams to yield better perceptions to solve our target issues.
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/partnership1.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 1 Team NYCU_Taipei was presenting their project: E. Color!
+ </div>
+
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/partnership2.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 2 The photo we took at the end of the meet-up.
+ </div>
+ <div class="index_container" id="expcollab"></div>
+
+ <div class="heading2" id="partnershipheading2">
Experimental Collaborations
- </a>
- <a class="pointer" id="partnerpointer" href="#implcollab">
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ After a series of communication and task delegations, team NYCU_Taipei and
+ our team started our collaboration on experiments in July. Both teams
+ benefitted from the discussion by adopting ideas of experiments and design
+ contributed by each other to one’s project.
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Phase I
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ Team NYCU_Taipei shared the idea of using the SsrA tag (degradation tag)
+ to improve the efficiency expression of fluorescence protein in polyP
+ sensor plasmids; therefore, our team re-designed and generated the polyP
+ sensor version II, flanking the gene sequence of mCherry fluorescent
+ protein with a C-terminal SsrA tag. For more information on the design and
+ engineering of the polyP sensor, please visit the polyP sensor section of
+ the
+ <a
+ class="content_link"
+ id="partnershiplink"
+ href="{{ url_for('pages', page='engineering') }}"
+ >
+ Engineering Success page
+ </a>
+ .
+ </div>
+
+ <em class="info_contents_italics" id="greencontents">
+ Phase II
+ </em>
+
+ <div class="info_contents" id="greencontents">
+ Our team designed and built an AsPhoU vector using a plasmid-compatible
+ vector used by team NYCU_Taipei. By transforming our vector into the
+ engineered bacteria generated by the NYCU_Taipei team, they could test the
+ application of their bacteria. The phase-sensitive fluorescent proteins
+ produced by the bacteria could assist in demonstrating the activity of
+ AsPhoU on the bacteria's growth, therefore, proving the real-life
+ application value of the NYCU_Taipei project in research fields.
+ </div>
+ <div class="index_container" id="implcollab"></div>
+
+ <div class="heading2" id="partnershipheading2">
Implementation Collaborations
- </a>
- <a class="pointer" id="partnerpointer" href="#podcast">
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ Our team and team NYCU_Taipei collaborated on the design of our
+ implementation devices. As both teams used the sensing and analysis of
+ fluorescent signals, we discussed the technical aspect for the design of
+ Arduino chips. Moreover, we exchanged ideas on the design of filtering
+ devices, including the material and pore size that could help reach the
+ highest efficiency and lowest biosafety risks.
+ </div>
+ <div class="index_container" id="podcast"></div>
+
+ <div class="heading2" id="partnershipheading2">
Podcast: E. Color!
- </a>
-
- <a class="pointer" id="partnerpointer" href="#final">
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ As both teams valued the importance of raising public awareness, our team
+ invited Team NTCU_Taipei to record an episode on our human practice
+ project, the podcast channel Eutro in Vitro. This episode was named after
+ their project, E. Color! The term “Color†comes from their approach to
+ expressing the E. Coli population, using fluorescent proteins with
+ different colors to make E.Coli observed easily. Our conversation began
+ with their goal to improve the present growth status measurement of E.
+ coli, extending to environmental and clinical applications. In this
+ collaboration, we hope to let more people notice their efforts and spread
+ public awareness through our podcast channel.
+ </div>
+
+ <img
+ class="constant_width"
+ src="https://static.igem.wiki/teams/4271/wiki/partnership3.png"
+ />
+
+ <div class="image_description" id="greencontents">
+ Fig. 3 Podcast episode: E. Color!
+ </div>
+ <div class="index_container" id="final"></div>
+
+ <div class="heading2" id="partnershipheading2">
Finalization
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
-
- <b class="heading1" id="partnershipheading1">
- Our partnership begins…
- </b>
-
- <div class="info_contents" id="greencontents">
- Our team has begun a strong partnership with team NYCU_Taipei. Through
- months of communication and planning, we created a bond that propels both
- teams to progress more efficiently and effectively.
- </div>
- <div class="index_container" id="meetup"></div>
-
- <div class="heading2" id="partnershipheading2">
- Virtual Meet-up
- </div>
-
- <div class="info_contents" id="greencontents">
- Since both of our teams would like to exchange our project ideas, we
- scheduled a virtual meet-up of which we got inspired and decided to have a
- long-term partnership.
- </div>
-
- <div class="info_contents" id="greencontents">
- Our first collaboration came into place when both teams presented their
- project. Team NYCU_Taipei shared their project about SsrA degradation tags
- to reduce the half-life of fluorescent proteins. Further, we extended
- in-depth discussions about using fluorescence sensors as tags to increase
- accuracy in indicating essential time points within the bacterial growth
- curve. Through the questions they asked, we learned the underlying problems
- and potential methods to improve the efficacy of the polyP sensors. Aiming
- to gain more insights and communication, both teams agreed to collaborate on
- the experimental aspect. We hope our partnership will help both teams to
- yield better perceptions to solve our target issues.
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/partnership1.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 1 Team NYCU_Taipei was presenting their project: E. Color!
- </div>
-
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/partnership2.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 2 The photo we took at the end of the meet-up.
- </div>
- <div class="index_container" id="expcollab"></div>
-
- <div class="heading2" id="partnershipheading2">
- Experimental Collaborations
- </div>
-
- <div class="info_contents" id="greencontents">
- After a series of communication and task delegations, team NYCU_Taipei and
- our team started our collaboration on experiments in July. Both teams
- benefitted from the discussion by adopting ideas of experiments and design
- contributed by each other to one’s project.
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- Phase I
- </em>
-
- <div class="info_contents" id="greencontents">
- Team NYCU_Taipei shared the idea of using the SsrA tag (degradation tag) to
- improve the efficiency expression of fluorescence protein in polyP sensor
- plasmids; therefore, our team re-designed and generated the polyP sensor
- version II, flanking the gene sequence of mCherry fluorescent protein with a
- C-terminal SsrA tag. For more information on the design and engineering of
- the polyP sensor, please visit the polyP sensor section of the
- <a
- class="content_link"
- id="partnershiplink"
- href="{{ url_for('pages', page='engineering') }}"
- >
- Engineering Success page
- </a>
- .
- </div>
-
- <em class="info_contents_italics" id="greencontents">
- Phase II
- </em>
-
- <div class="info_contents" id="greencontents">
- Our team designed and built an AsPhoU vector using a plasmid-compatible
- vector used by team NYCU_Taipei. By transforming our vector into the
- engineered bacteria generated by the NYCU_Taipei team, they could test the
- application of their bacteria. The phase-sensitive fluorescent proteins
- produced by the bacteria could assist in demonstrating the activity of
- AsPhoU on the bacteria's growth, therefore, proving the real-life
- application value of the NYCU_Taipei project in research fields.
- </div>
- <div class="index_container" id="implcollab"></div>
-
- <div class="heading2" id="partnershipheading2">
- Implementation Collaborations
- </div>
-
- <div class="info_contents" id="greencontents">
- Our team and team NYCU_Taipei collaborated on the design of our
- implementation devices. As both teams used the sensing and analysis of
- fluorescent signals, we discussed the technical aspect for the design of
- Arduino chips. Moreover, we exchanged ideas on the design of filtering
- devices, including the material and pore size that could help reach the
- highest efficiency and lowest biosafety risks.
- </div>
- <div class="index_container" id="podcast"></div>
-
- <div class="heading2" id="partnershipheading2">
- Podcast: E. Color!
- </div>
-
- <div class="info_contents" id="greencontents">
- As both teams valued the importance of raising public awareness, our team
- invited Team NTCU_Taipei to record an episode on our human practice project,
- the podcast channel Eutro in Vitro. This episode was named after their
- project, E. Color! The term “Color†comes from their approach to expressing
- the E. Coli population, using fluorescent proteins with different colors to
- make E.Coli observed easily. Our conversation began with their goal to
- improve the present growth status measurement of E. coli, extending to
- environmental and clinical applications. In this collaboration, we hope to
- let more people notice their efforts and spread public awareness through our
- podcast channel.
- </div>
-
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/partnership3.png"
- />
-
- <div class="image_description" id="greencontents">
- Fig. 3 Podcast episode: E. Color!
- </div>
- <div class="index_container" id="final"></div>
-
- <div class="heading2" id="partnershipheading2">
- Finalization
- </div>
-
- <div class="info_contents" id="greencontents">
- In the last stage of our partnership, we held calls and in-person meetings
- to go through our collaborations in wet lab and human practice. We also
- focused on the discussions about the future goals and the market position of
- our projects. Finally, we confirmed the details in the partnership criteria
- of the competition.
+ </div>
+
+ <div class="info_contents" id="greencontents">
+ In the last stage of our partnership, we held calls and in-person meetings
+ to go through our collaborations in wet lab and human practice. We also
+ focused on the discussions about the future goals and the market position
+ of our projects. Finally, we confirmed the details in the partnership
+ criteria of the competition.
+ </div>
</div>
</div>
{% endblock %}
diff --git a/wiki/pages/parts.html b/wiki/pages/parts.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/parts.html
+++ b/wiki/pages/parts.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/plant.html b/wiki/pages/plant.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/plant.html
+++ b/wiki/pages/plant.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/proof-of-concept.html b/wiki/pages/proof-of-concept.html
index 8281a39..5344030 100644
--- a/wiki/pages/proof-of-concept.html
+++ b/wiki/pages/proof-of-concept.html
@@ -1,71 +1,79 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/proof-of-concept.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
+ </div>
-<aside class="aside" id="proof">
- <br />
- <div>
- <a class="pointer" id="proofheaderpointer" href="#paraxon"> Paraoxon Hydrolysis</a>
-
- <a class="pointer" id="proofpointer" href="#design">Biosensor Design</a>
- <a class="pointer" id="proofpointer" href="#function">
- Biosensor Function
- </a>
- <a class="pointer" id="proofpointer" href="#methods">
- Experimental Methods
- </a>
- <a class="pointer" id="proofpointer" href="#results">
- Experimental Results
- </a>
- <a class="pointer" id="proofheaderpointer" href="#inorganic"> Inorganic Phosphate </a>
-
- <a class="pointer" id="proofpointer" href="#phosphate">Bacterial System</a>
-
-
- <a class="pointer" id="proofpointer" href="#theoretical">
- Function of AsPhoU
- </a>
- <a class="pointer" id="proofpointer" href="#preliminary">
- Preliminary Experiment
- </a>
- <a class="pointer" id="proofpointer" href="#malachite">
- Malachite Green
- </a>
- <a class="pointer" id="proofheaderpointer" href="#polyphosphate"> Polyphosphate</a>
-
- <a class="pointer" id="proofpointer" href="#kit"> Function of Assay Kit</a>
-
- <a class="pointer" id="proofpointer" href="#future">
- Future Plan
- </a>
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/proof-of-concept.png"
+ />
</div>
- <br />
-</aside>
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
+ </div>
+
+ <aside class="aside" id="proof">
+ <br />
+ <div>
+ <a class="pointer" id="proofheaderpointer" href="#paraxon">
+ Paraoxon Hydrolysis
+ </a>
+
+ <a class="pointer" id="proofpointer" href="#design">Biosensor Design</a>
+ <a class="pointer" id="proofpointer" href="#function">
+ Biosensor Function
+ </a>
+ <a class="pointer" id="proofpointer" href="#methods">
+ Experimental Methods
+ </a>
+ <a class="pointer" id="proofpointer" href="#results">
+ Experimental Results
+ </a>
+ <a class="pointer" id="proofheaderpointer" href="#inorganic">
+ Inorganic Phosphate
+ </a>
+
+ <a class="pointer" id="proofpointer" href="#phosphate">
+ Bacterial System
+ </a>
+
+ <a class="pointer" id="proofpointer" href="#theoretical">
+ Function of AsPhoU
+ </a>
+ <a class="pointer" id="proofpointer" href="#preliminary">
+ Preliminary Experiment
+ </a>
+ <a class="pointer" id="proofpointer" href="#malachite">
+ Malachite Green
+ </a>
+ <a class="pointer" id="proofheaderpointer" href="#polyphosphate">
+ Polyphosphate
+ </a>
+
+ <a class="pointer" id="proofpointer" href="#kit">Function of Assay Kit</a>
+
+ <a class="pointer" id="proofpointer" href="#future">
+ Future Plan
+ </a>
+ </div>
+ <br />
+ </aside>
<div class="herowrap" id="experimentalcontents">
<div id="progress-bar"></div>
-
+
<div class="index_container" id="paraxon"></div>
<b class="heading1" id="greenheading1">
The Paraoxon Hydrolysis Detection Experiment
@@ -335,8 +343,7 @@
<img
class="constant_height"
id="lower_height"
- src="https://static.igem.wiki/teams/4271/wiki/pnp-bacteria-standard-curve-6hr.png
-"
+ src="https://static.igem.wiki/teams/4271/wiki/pnp-bacteria-standard-curve-6hr.png"
/>
<div class="image_description" id="greencontents">
Fig. 4 Standard Curve (410 absorbances v.s. pNP concentration)
@@ -828,7 +835,7 @@
Fig. 4 Phosphate content per CFU versus different experimental sets
</div>
<div class="index_container" id="polyphosphate"></div>
-
+
<b class="heading1" id="greenheading1">
Polyphosphate (PolyP) Detection Experiments
</b>
@@ -944,5 +951,5 @@
(1998): 1277-86. doi:10.1128/JB.180.5.1277-1286.1998
</div>
</div>
- {% endblock %}
</div>
+{% endblock %}
diff --git a/wiki/pages/results.html b/wiki/pages/results.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/results.html
+++ b/wiki/pages/results.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
diff --git a/wiki/pages/safety.html b/wiki/pages/safety.html
index dbe5069..721ed7e 100644
--- a/wiki/pages/safety.html
+++ b/wiki/pages/safety.html
@@ -1,223 +1,226 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/safety.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="safetypointer" href="#biosafety">Biosafety</a>
- <a class="pointer" id="safetypointer" href="#laboratory">
- Laboratory Safety
- </a>
- <a class="pointer" id="safetypointer" href="#hp">
- Human Practice Safety
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="safetyheading1">
- Safety
- </b>
- <div class="index_container" id="biosafety"></div>
- <div class="heading2" id="safetyheading2">Biosafety</div>
-
- <div class="info_contents" id="greencontents">
- Our project aims to design an enclosed filtering device containing
- engineered bacteria with an enhanced ability to reduce phosphate in water
- bodies. We have fully considered the risks of our product’s implementation
- and ensured the biosafety in vivo and in the environment.
- </div>
- <em class="info_contents_italics" id="greencontents">
- In vivo Biosafety
- </em>
- <div class="info_contents" id="greencontents">
- To decrease phosphate levels in bodies of water, we engineered the both DH5α
- and BL21 (DE3) competent E. coli. It is not considered hazardous by the 2012
- OSHA Hazard Communication Standard.
- </div>
- <em class="info_contents_italics" id="greencontents">
- Environmental Biosafety
- </em>
- <div class="info_contents" id="greencontents">
- To prevent accidentally leaking bacteria into the environment and increasing
- the risk of environmental hazards, we introduce a biosafety system different
- from the commonly used kill switch. The system includes the following three
- designs:
- </div>
- <ol type="1">
- <li class="info_contents_list" id="greencontents">
- Bacteria Filter for Leakage Prevention
- <div class="info_contents" id="greencontents">
- Having been taken into consideration that the average diameter of an E.
- coli is about 1 to 2 micrometers, filters on both sides of the device
- use filter paper with a pore size of 0.45 micrometers to prevent the
- leakage of the engineered bacteria into the natural environment. For
- further information on the design of the implementation device, please
- visit our
- <a
- class="content_link"
- id="safety_link"
- href="{{ url_for('pages', page='hardware') }}"
- >
- Hardware page
- </a>
- .
- </div>
- </li>
-
- <li class="info_contents_list" id="greencontents">
- Bacteria Natural Growth Inhibition by Polyphosphate Accumulation
- <div class="info_contents" id="greencontents">
- Without any killing mechanism, engineered bacteria would naturally grow
- and reproduce in the filtering device. However, after bacteria can
- absorb more than 20mM of phosphate, their growth cycle would be
- disturbed (Rao). As the bacteria in the device are engineered to over
- absorb and fixate phosphate and the overaccumulation of polyphosphate
- results in natural growth inhibition, environmental hazards could be
- naturally inhibited. Even if the filter paper was accidentally broken by
- any natural object, the concern regarding pollution by bacteria leakage
- is little because the bacteria’s growth and reproduction would be
- naturally inhibited in less than 24 hours.
- </div>
- </li>
- <li class="info_contents_list" id="greencontents">
- Monitoring Polyphosphate Accumulation Biosensor
- <div class="info_contents" id="greencontents">
- The design of the polyP sensor plasmid includes genes encoding for
- polyphosphate-sensitive sigma factor and mCherry fluorescent protein.
- Expression of mCherry decreases followed by polyphosphate accumulation
- in the bacteria. As the hardware detects reduced fluorescence levels to
- the minimum, an alert is sent through the software to notify the users
- to replace the filter in time, thus avoiding the lysis of the bacteria
- cells after bacteria death releasing phosphate and other genetic
- materials into the environment. For more information on the design and
- engineering of the polyP sensor, please visit our
- <a
- class="content_link"
- id="safety_link"
- href="{{ url_for('pages', page='engineering') }}"
- >
- Engineering Success page
- </a>
- . For more information on the light-sensing chips of the hardware and
- alarm system of the software, please visit the
- <a
- class="content_link"
- id="safety_link"
- href="{{ url_for('pages', page='hardware') }}"
- >
- Hardware page
- </a>
- and the
- <a
- class="content_link"
- id="safety_link"
- href="{{ url_for('pages', page='software') }}"
- >
- Software page
- </a>
- , respectively.
- </div>
- </li>
- </ol>
- <div class="info_contents" id="greencontents">
- Our project introduces a combination system to solve the problem. What’s
- more, we consider this system to compete with the other systems broadly
- adapted in iGEM. For example, many iGEM teams today select kill switch
- systems to reach environmental biosafety. A normal kill switch could
- experience leaky expression or malfunction of the gene, causing over-killing
- or under-killing of the engineered bacteria. In addition, expressing the
- kill switch is a waste of energy for the engineered bacteria. The mechanism
- of a kill switch causes the bacteria to produce poison and antidote (iGEM
- Pasteur_Paris) at all times just to stay alive. A lot of energy and
- materials would be consumed during the production process, which lowers the
- efficiency of bacteria functions. However, by limiting the bacteria inside
- the hardware container, naturally inhibiting bacteria growth, and expressing
- biosensors, our biosafety system allows us to ensure biosafety while
- maintaining the efficiency of the bacteria functions. Accordingly, we hold
- that our system is a potential system, and we recommend the former iGEMer
- could take it into consideration and make more exploration.
- </div>
- <div class="index_container" id="laboratory"></div>
- <div class="heading2" id="safetyheading2">Laboratory Safety</div>
- <div class="info_contents" id="greencontents">
- All lab members wear gloves, lab coats, and safety goggles at all times. The
- lab is also equipped with emergency showers, eye washes, ventilators, fire
- blankets, and first aid kits. Dangerous experiments, if any, will be
- performed under supervision. The lab is classified as P1 (Protection level),
- where no substances that cause adverse effects on the human body will be
- used. This team follows the safety protocol provided by iGEM, as well as the
- National Yang-Ming University's Center of Environmental Protection and
- Safety and Health guidelines (
- <u>https://ces.nycu.edu.tw/files/11-1151-89-1.php</u>
- ,
- <u>https://ces.nycu.edu.tw/files/11-1151-2320.php</u>
- ).
- </div>
- <div class="safety_image_wrap">
+<div>
+ <div class="loadingwrap">
<img
- class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/lab.jpg"
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
/>
<img
- class="constant_height"
- id="safetyimage"
- src="https://static.igem.wiki/teams/4271/wiki/lab-2.jpg"
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
/>
</div>
- <div class="index_container" id="hp"></div>
- <div class="heading2" id="safetyheading2">Human Practice Safety</div>
- <div class="info_contents" id="greencontents">
- During interviews and collaborations, participants must have their
- vaccination or exception on record. All participants are required to have an
- increased level of COVID-19 testing, masking, and quarantine procedures. If
- the confirmed cases surge, we will use virtual events to replace in-person
- meetings to prevent the spread of pandemics.
- </div>
- <div class="workscited" id="greencontents">References</div>
- <div class="info_contents" id="greencontents">
- Correlates of smallest sizes for microorganisms - NCBI bookshelf. (n.d.).
- Retrieved September 17, 2022, from
- https://www.ncbi.nlm.nih.gov/books/NBK224751/
- </div>
- <div class="info_contents" id="greencontents">
- How safe is safe enough: Towards best pratices of synthetic biology.
- OpenWetWare. (n.d.). Retrieved September 22, 2022, from
- https://openwetware.org/wiki/
- How_safe_is_safe_enough:_towards_best_pratices_of_synthetic_biology
+
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/safety.png"
+ />
</div>
- <div class="info_contents" id="greencontents">
- Rao, N. N., Liu, S., & Kornberg, A. (1998, April). Inorganic polyphosphate
- in escherichia coli: The phosphate regulon and the stringent response.
- Journal of bacteriology. Retrieved September 17, 2022, from
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC107147/\
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
</div>
- <div class="info_contents" id="greencontents">
- Team:pasteur Paris/kill. (n.d.). Retrieved September 25, 2022, from
- https://2018.igem.org/Team:Pasteur_Paris/Kill
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="safetypointer" href="#biosafety">Biosafety</a>
+ <a class="pointer" id="safetypointer" href="#laboratory">
+ Laboratory Safety
+ </a>
+ <a class="pointer" id="safetypointer" href="#hp">
+ Human Practice Safety
+ </a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+ <b class="heading1" id="safetyheading1">
+ Safety
+ </b>
+ <div class="index_container" id="biosafety"></div>
+ <div class="heading2" id="safetyheading2">Biosafety</div>
+
+ <div class="info_contents" id="greencontents">
+ Our project aims to design an enclosed filtering device containing
+ engineered bacteria with an enhanced ability to reduce phosphate in water
+ bodies. We have fully considered the risks of our product’s implementation
+ and ensured the biosafety in vivo and in the environment.
+ </div>
+ <em class="info_contents_italics" id="greencontents">
+ In vivo Biosafety
+ </em>
+ <div class="info_contents" id="greencontents">
+ To decrease phosphate levels in bodies of water, we engineered the both
+ DH5α and BL21 (DE3) competent E. coli. It is not considered hazardous by
+ the 2012 OSHA Hazard Communication Standard.
+ </div>
+ <em class="info_contents_italics" id="greencontents">
+ Environmental Biosafety
+ </em>
+ <div class="info_contents" id="greencontents">
+ To prevent accidentally leaking bacteria into the environment and
+ increasing the risk of environmental hazards, we introduce a biosafety
+ system different from the commonly used kill switch. The system includes
+ the following three designs:
+ </div>
+ <ol type="1">
+ <li class="info_contents_list" id="greencontents">
+ Bacteria Filter for Leakage Prevention
+ <div class="info_contents" id="greencontents">
+ Having been taken into consideration that the average diameter of an
+ E. coli is about 1 to 2 micrometers, filters on both sides of the
+ device use filter paper with a pore size of 0.45 micrometers to
+ prevent the leakage of the engineered bacteria into the natural
+ environment. For further information on the design of the
+ implementation device, please visit our
+ <a
+ class="content_link"
+ id="safety_link"
+ href="{{ url_for('pages', page='hardware') }}"
+ >
+ Hardware page
+ </a>
+ .
+ </div>
+ </li>
+
+ <li class="info_contents_list" id="greencontents">
+ Bacteria Natural Growth Inhibition by Polyphosphate Accumulation
+ <div class="info_contents" id="greencontents">
+ Without any killing mechanism, engineered bacteria would naturally
+ grow and reproduce in the filtering device. However, after bacteria
+ can absorb more than 20mM of phosphate, their growth cycle would be
+ disturbed (Rao). As the bacteria in the device are engineered to over
+ absorb and fixate phosphate and the overaccumulation of polyphosphate
+ results in natural growth inhibition, environmental hazards could be
+ naturally inhibited. Even if the filter paper was accidentally broken
+ by any natural object, the concern regarding pollution by bacteria
+ leakage is little because the bacteria’s growth and reproduction would
+ be naturally inhibited in less than 24 hours.
+ </div>
+ </li>
+ <li class="info_contents_list" id="greencontents">
+ Monitoring Polyphosphate Accumulation Biosensor
+ <div class="info_contents" id="greencontents">
+ The design of the polyP sensor plasmid includes genes encoding for
+ polyphosphate-sensitive sigma factor and mCherry fluorescent protein.
+ Expression of mCherry decreases followed by polyphosphate accumulation
+ in the bacteria. As the hardware detects reduced fluorescence levels
+ to the minimum, an alert is sent through the software to notify the
+ users to replace the filter in time, thus avoiding the lysis of the
+ bacteria cells after bacteria death releasing phosphate and other
+ genetic materials into the environment. For more information on the
+ design and engineering of the polyP sensor, please visit our
+ <a
+ class="content_link"
+ id="safety_link"
+ href="{{ url_for('pages', page='engineering') }}"
+ >
+ Engineering Success page
+ </a>
+ . For more information on the light-sensing chips of the hardware and
+ alarm system of the software, please visit the
+ <a
+ class="content_link"
+ id="safety_link"
+ href="{{ url_for('pages', page='hardware') }}"
+ >
+ Hardware page
+ </a>
+ and the
+ <a
+ class="content_link"
+ id="safety_link"
+ href="{{ url_for('pages', page='software') }}"
+ >
+ Software page
+ </a>
+ , respectively.
+ </div>
+ </li>
+ </ol>
+ <div class="info_contents" id="greencontents">
+ Our project introduces a combination system to solve the problem. What’s
+ more, we consider this system to compete with the other systems broadly
+ adapted in iGEM. For example, many iGEM teams today select kill switch
+ systems to reach environmental biosafety. A normal kill switch could
+ experience leaky expression or malfunction of the gene, causing
+ over-killing or under-killing of the engineered bacteria. In addition,
+ expressing the kill switch is a waste of energy for the engineered
+ bacteria. The mechanism of a kill switch causes the bacteria to produce
+ poison and antidote (iGEM Pasteur_Paris) at all times just to stay alive.
+ A lot of energy and materials would be consumed during the production
+ process, which lowers the efficiency of bacteria functions. However, by
+ limiting the bacteria inside the hardware container, naturally inhibiting
+ bacteria growth, and expressing biosensors, our biosafety system allows us
+ to ensure biosafety while maintaining the efficiency of the bacteria
+ functions. Accordingly, we hold that our system is a potential system, and
+ we recommend the former iGEMer could take it into consideration and make
+ more exploration.
+ </div>
+ <div class="index_container" id="laboratory"></div>
+ <div class="heading2" id="safetyheading2">Laboratory Safety</div>
+ <div class="info_contents" id="greencontents">
+ All lab members wear gloves, lab coats, and safety goggles at all times.
+ The lab is also equipped with emergency showers, eye washes, ventilators,
+ fire blankets, and first aid kits. Dangerous experiments, if any, will be
+ performed under supervision. The lab is classified as P1 (Protection
+ level), where no substances that cause adverse effects on the human body
+ will be used. This team follows the safety protocol provided by iGEM, as
+ well as the National Yang-Ming University's Center of Environmental
+ Protection and Safety and Health guidelines (
+ <u>https://ces.nycu.edu.tw/files/11-1151-89-1.php</u>
+ ,
+ <u>https://ces.nycu.edu.tw/files/11-1151-2320.php</u>
+ ).
+ </div>
+ <div class="safety_image_wrap">
+ <img
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/lab.jpg"
+ />
+ <img
+ class="constant_height"
+ id="safetyimage"
+ src="https://static.igem.wiki/teams/4271/wiki/lab-2.jpg"
+ />
+ </div>
+ <div class="index_container" id="hp"></div>
+ <div class="heading2" id="safetyheading2">Human Practice Safety</div>
+ <div class="info_contents" id="greencontents">
+ During interviews and collaborations, participants must have their
+ vaccination or exception on record. All participants are required to have
+ an increased level of COVID-19 testing, masking, and quarantine
+ procedures. If the confirmed cases surge, we will use virtual events to
+ replace in-person meetings to prevent the spread of pandemics.
+ </div>
+ <div class="workscited" id="greencontents">References</div>
+ <div class="info_contents" id="greencontents">
+ Correlates of smallest sizes for microorganisms - NCBI bookshelf. (n.d.).
+ Retrieved September 17, 2022, from
+ https://www.ncbi.nlm.nih.gov/books/NBK224751/
+ </div>
+ <div class="info_contents" id="greencontents">
+ How safe is safe enough: Towards best pratices of synthetic biology.
+ OpenWetWare. (n.d.). Retrieved September 22, 2022, from
+ https://openwetware.org/wiki/
+ How_safe_is_safe_enough:_towards_best_pratices_of_synthetic_biology
+ </div>
+ <div class="info_contents" id="greencontents">
+ Rao, N. N., Liu, S., & Kornberg, A. (1998, April). Inorganic polyphosphate
+ in escherichia coli: The phosphate regulon and the stringent response.
+ Journal of bacteriology. Retrieved September 17, 2022, from
+ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC107147/\
+ </div>
+ <div class="info_contents" id="greencontents">
+ Team:pasteur Paris/kill. (n.d.). Retrieved September 25, 2022, from
+ https://2018.igem.org/Team:Pasteur_Paris/Kill
+ </div>
</div>
</div>
{% endblock %}
diff --git a/wiki/pages/software.html b/wiki/pages/software.html
index 029fcb3..2cfe63f 100644
--- a/wiki/pages/software.html
+++ b/wiki/pages/software.html
@@ -1,132 +1,140 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img class="bannerimg" src="https://static.igem.wiki/teams/4271/wiki/6.png" />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="softwarepointer" href="#overview">Overview</a>
- <a class="pointer" id="softwarepointer" href="#feature1">Feature 1</a>
- <a class="pointer" id="softwarepointer" href="#feature2">Feature 2</a>
- <a class="pointer" id="softwarepointer" href="#futureplan">Future Plan</a>
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="softwareheading1">
- Software
- </b>
- <div class="index_container" id="overview"></div>
- <div class="heading2" id="softwareheading2">
- Overview
+ <div class="bannerwrap">
+ <img
+ class="bannerimg"
+ src="https://static.igem.wiki/teams/4271/wiki/6.png"
+ />
</div>
-
- <div class="info_contents" id="greencontents">
- Our team has designed a Eutrophication Management App in order to elaborate
- on the topic of eutrophication and raise public awareness of this worldwide
- aquatic issue. We utilized Xcode and Swift with the connection to Firebase
- Console Authentication to build the application. In this page, we will
- examine two major features, the calculation of the severity of
- eutrophication and the status of eutrophication in Taiwanese reservoirs.
+ <div class="scrolltotop" onclick="scrollToTop()">
+ <img
+ class="backtotop"
+ src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
+ />
</div>
- <div class="index_container" id="feature1"></div>
+ <aside class="aside">
+ <br />
+ <div>
+ <a class="pointer" id="softwarepointer" href="#overview">Overview</a>
+ <a class="pointer" id="softwarepointer" href="#feature1">Feature 1</a>
+ <a class="pointer" id="softwarepointer" href="#feature2">Feature 2</a>
+ <a class="pointer" id="softwarepointer" href="#futureplan">Future Plan</a>
+ </div>
+ <br />
+ </aside>
+ <div class="herowrap" id="experimentalcontents">
+ <div id="progress-bar"></div>
+ <b class="heading1" id="softwareheading1">
+ Software
+ </b>
+ <div class="index_container" id="overview"></div>
- <div class="heading2" id="softwareheading2">
- Feature 1: Calculation of the Severity of Eutrophication
- </div>
+ <div class="heading2" id="softwareheading2">
+ Overview
+ </div>
- <div class="info_contents" id="greencontents">
- Our team determines different water qualities based on their respective
- concentrations of phosphorus and nitrogen. We referred to the Vollenweider
- index (Fig. 1) and calculated the most applicable range of water qualities
- (Fig. 2). The standard is divided into three categories: oligotrophic,
- mesotrophic, and eutrophic from the spectrum of lowest to the highest
- concentration. We built a user interface where the user can input the
- concentration rate of nitrogen and phosphorus. Subsequently, the system will
- calculate the scale of eutrophication and return it to the user. This will
- certainly give the audience a better understanding of the water quality and
- concepts of eutrophication.
- </div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-1.jpg"
- />
+ <div class="info_contents" id="greencontents">
+ Our team has designed a Eutrophication Management App in order to
+ elaborate on the topic of eutrophication and raise public awareness of
+ this worldwide aquatic issue. We utilized Xcode and Swift with the
+ connection to Firebase Console Authentication to build the application. In
+ this page, we will examine two major features, the calculation of the
+ severity of eutrophication and the status of eutrophication in Taiwanese
+ reservoirs.
+ </div>
+ <div class="index_container" id="feature1"></div>
- <div class="image_description" id="greencontents">
- Fig. 1 References to the Vollenweider index (Shourian et al., 2016) Fig. 1
- When the user input certain values regarding the concentration of phosphorus
- and nitrogen, the system will return the index of eutrophication
- (mesotrophic, oligotrophic, eutrophication, or no eutrophic conditions)
- </div>
- <div class="index_container" id="feature2"></div>
+ <div class="heading2" id="softwareheading2">
+ Feature 1: Calculation of the Severity of Eutrophication
+ </div>
- <div class="heading2" id="softwareheading2">
- Feature 2: Taiwanese Reservoir Map of Current Eutrophication Status
- </div>
+ <div class="info_contents" id="greencontents">
+ Our team determines different water qualities based on their respective
+ concentrations of phosphorus and nitrogen. We referred to the Vollenweider
+ index (Fig. 1) and calculated the most applicable range of water qualities
+ (Fig. 2). The standard is divided into three categories: oligotrophic,
+ mesotrophic, and eutrophic from the spectrum of lowest to the highest
+ concentration. We built a user interface where the user can input the
+ concentration rate of nitrogen and phosphorus. Subsequently, the system
+ will calculate the scale of eutrophication and return it to the user. This
+ will certainly give the audience a better understanding of the water
+ quality and concepts of eutrophication.
+ </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-1.jpg"
+ />
- <div class="info_contents" id="greencontents">
- We constructed a user interface with a Taiwan map and annotated the major
- reservoirs on the map. When the user taps on the annotated reservoir, the
- software will provide information about the basic information and eutrophic
- status of the certain reservoir. In the same token, we operated the scale of
- eutrophication based on the aforementioned standard. By viewing different
- reservoirs, the audience can clearly understand the current eutrophication
- status in Taiwan.
- </div>
- <div class="index_container" id="futureplan"></div>
+ <div class="image_description" id="greencontents">
+ Fig. 1 References to the Vollenweider index (Shourian et al., 2016) Fig. 1
+ When the user input certain values regarding the concentration of
+ phosphorus and nitrogen, the system will return the index of
+ eutrophication (mesotrophic, oligotrophic, eutrophication, or no eutrophic
+ conditions)
+ </div>
+ <div class="index_container" id="feature2"></div>
- <img
- class="constant_height"
- src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-2.jpg"
- />
+ <div class="heading2" id="softwareheading2">
+ Feature 2: Taiwanese Reservoir Map of Current Eutrophication Status
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 2 A particular reservoir’s background and status of eutrophication are
- displayed when the user clicks on a major reservoir on the map.
- </div>
- <div class="heading2" id="softwareheading2">
- Future Plan: The Implementation of Arduino Chip
- </div>
+ <div class="info_contents" id="greencontents">
+ We constructed a user interface with a Taiwan map and annotated the major
+ reservoirs on the map. When the user taps on the annotated reservoir, the
+ software will provide information about the basic information and
+ eutrophic status of the certain reservoir. In the same token, we operated
+ the scale of eutrophication based on the aforementioned standard. By
+ viewing different reservoirs, the audience can clearly understand the
+ current eutrophication status in Taiwan.
+ </div>
+ <div class="index_container" id="futureplan"></div>
- <div class="info_contents" id="greencontents">
- For the future enhancement of the software, we hope to append a third
- feature to connect with the Arduino chip. By operating different conditions
- of the chips and implementing modules to connect with the application, the
- users can change the filters when they receive the message from the sensor
- of GFP and mCherry. The users can also monitor the conditions of the chip at
- any time, operating the experiment with a more precise procedure.
- </div>
+ <img
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation-soft-2.jpg"
+ />
- <img class="constant_height" src=" " />
+ <div class="image_description" id="greencontents">
+ Fig. 2 A particular reservoir’s background and status of eutrophication
+ are displayed when the user clicks on a major reservoir on the map.
+ </div>
+ <div class="heading2" id="softwareheading2">
+ Future Plan: The Implementation of Arduino Chip
+ </div>
- <div class="image_description" id="greencontents">
- Fig. 3 References to the Vollenweider index (Shourian et al., 2016)
- </div>
- <div class="workscited" id="greencontents">References</div>
+ <div class="info_contents" id="greencontents">
+ For the future enhancement of the software, we hope to append a third
+ feature to connect with the Arduino chip. By operating different
+ conditions of the chips and implementing modules to connect with the
+ application, the users can change the filters when they receive the
+ message from the sensor of GFP and mCherry. The users can also monitor the
+ conditions of the chip at any time, operating the experiment with a more
+ precise procedure.
+ </div>
+ [missing imagelink]
+ <img class="constant_height" src=" " />
+
+ <div class="image_description" id="greencontents">
+ Fig. 3 References to the Vollenweider index (Shourian et al., 2016)
+ </div>
+ <div class="workscited" id="greencontents">References</div>
- <div class="info_contents" id="greencontents">
- Shourian, Mojtaba & Moridi, Ali & Kaveh, Mohammad. (2016). Modeling of
- eutrophication and strategies for improvement of water quality in
- reservoirs. Water Science and Technology. 74. 10.2166/wst.2016.322.
+ <div class="info_contents" id="greencontents">
+ Shourian, Mojtaba & Moridi, Ali & Kaveh, Mohammad. (2016). Modeling of
+ eutrophication and strategies for improvement of water quality in
+ reservoirs. Water Science and Technology. 74. 10.2166/wst.2016.322.
+ </div>
</div>
</div>
{% endblock %}
diff --git a/wiki/pages/sustainable.html b/wiki/pages/sustainable.html
index 3c85209..03c84e0 100644
--- a/wiki/pages/sustainable.html
+++ b/wiki/pages/sustainable.html
@@ -1,78 +1,14 @@
{% extends "layout.html" %} {% block page_content %}
-<div class="loadingwrap">
- <img
- class="loadinggif"
- src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
- />
- <img
- class="loadingwords"
- src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
- />
-</div>
-
-<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
-</div>
-<div class="scrolltotop" onclick="scrollToTop()">
- <img
- class="backtotop"
- src="https://static.igem.wiki/teams/4271/wiki/logo2-0.png"
- />
-</div>
-<aside class="aside">
- <br />
- <div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
- </a>
-
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
- </a>
-
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
- </a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
- </a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
- </a>
- <a class="pointer" href="#composite">
- Composite Parts
- </a>
- </div>
- <br />
-</aside>
-<div class="herowrap" id="experimentalcontents">
- <div id="progress-bar"></div>
- <b class="heading1" id="partsheading1">
- Heading 1
- </b>
- <div class="heading2" id="partsheading2">
- Heading 2
- </div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
- <div class="info_contents" id="greencontents">
- Contents
- </div>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
-
- <div class="image_description" id="greencontents">
- Image description
+<div>
+ <div class="loadingwrap">
+ <img
+ class="loadinggif"
+ src="https://static.igem.wiki/teams/4271/wiki/logo.gif"
+ />
+ <img
+ class="loadingwords"
+ src="https://static.igem.wiki/teams/4271/wiki/loading2-0.gif"
+ />
</div>
-
- <!-- image -->
</div>
{% endblock %}
--
GitLab