From 84423db2167805f8ce03448f8392f5bbcb77b27b Mon Sep 17 00:00:00 2001
From: Ruby Chang <ruby931109@gmail.com>
Date: Fri, 7 Oct 2022 09:47:13 +0800
Subject: [PATCH] modified: static/style.css modified:
wiki/pages/implementation.html modified: wiki/pages/software.html
---
static/style.css | 3 +
wiki/pages/implementation.html | 344 ++++++++++++++++++++++++++++++---
wiki/pages/software.html | 105 ++++++----
3 files changed, 388 insertions(+), 64 deletions(-)
diff --git a/static/style.css b/static/style.css
index 34a3fb7..0d2b82d 100644
--- a/static/style.css
+++ b/static/style.css
@@ -1666,6 +1666,9 @@ html {
text-transform: uppercase;
color: #e8a353;
}
+#implcentered {
+ margin-top: 100px;
+}
.info_contents_list {
font-size: 19px;
margin-top: 35px;
diff --git a/wiki/pages/implementation.html b/wiki/pages/implementation.html
index 3c85209..d4754ea 100644
--- a/wiki/pages/implementation.html
+++ b/wiki/pages/implementation.html
@@ -13,7 +13,7 @@
<div class="bannerwrap">
<img
class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation.png"
/>
</div>
<div class="scrolltotop" onclick="scrollToTop()">
@@ -25,26 +25,26 @@
<aside class="aside">
<br />
<div>
- <a class="pointer" id="partheadpointer" href="#eutrohpicwater">
- Parts for Eutrophic Water Purification (OPH and AsPhoU)
+ <a class="pointer" href="#targetuser">
+ Target Users
</a>
- <a class="pointer" href="#basicparts">Basic Parts</a>
- <a class="pointer" href="#compositeparts">
- Composite Parts
+ <a class="pointer" href="#impldesign">Implementation Design</a>
+ <a class="pointer" href="#regulatingsystem">
+ Regulating System & Biosensor
</a>
- <a class="pointer" id="partheadpointer" href="#biosensors">
- Parts for Biosensors (pNP sensor & polyP sensor)
+ <a class="pointer" href="#biosafety">
+ Biosafety
</a>
- <a class="pointer" href="#basicpartspnp">
- Basic Parts (pNP sensor)
+ <a class="pointer" href="#software">
+ Software
</a>
- <a class="pointer" href="#basicpartspolyp">
- Basic Parts (polyP sensor)
+ <a class="pointer" href="#future">
+ Future Plan
</a>
- <a class="pointer" href="#composite">
- Composite Parts
+ <a class="pointer" href="#conclusion">
+ Conclusion
</a>
</div>
<br />
@@ -52,27 +52,321 @@
<div class="herowrap" id="experimentalcontents">
<div id="progress-bar"></div>
<b class="heading1" id="partsheading1">
- Heading 1
+ Proposed Implementation
</b>
+ <div class="index_container" id="targetuser"></div>
+
<div class="heading2" id="partsheading2">
- Heading 2
+ Target Users
</div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
+
+ <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="partsheading2">
+ Implementation Design
+ </div>
+
<div class="info_contents" id="greencontents">
- Contents
+ 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"
+ href="{{ url_for('pages', page='human-practices') }}"
+ >
+ Integrated Human Practice Page
+ </a>
+ .
</div>
- <!-- image -->
+
<img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
+ class="constant_height"
+ src="https://static.igem.wiki/teams/4271/wiki/implementation1.png"
/>
+ <div class="image_description" id="greencontents">
+ Fig. 1
+ </div>
+ <div class="index_container" id="regulatingsystem"></div>
+ <div class="heading2" id="partsheading2">
+ 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" 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>
+
+ <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 the 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 reache 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" 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="partsheading2">
+ 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" 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="partsheading2">
+ 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" 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>
+
+ [URL NOT YET PROVIDED]
+ <img class="constant_height" src="" />
<div class="image_description" id="greencontents">
- Image description
+ Fig. 2 Calculation of the Severity of Eutrophication & Taiwanese Reservoir
+ Map of Current Eutrophication Status
+ </div>
+
+ <div class="index_container" id="future"></div>
+ <div class="heading2" id="partsheading2">
+ Future Plan
</div>
- <!-- image -->
+ <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="partsheading2">
+ 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">
+ 1.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>
{% endblock %}
diff --git a/wiki/pages/software.html b/wiki/pages/software.html
index 3c85209..5ae4a79 100644
--- a/wiki/pages/software.html
+++ b/wiki/pages/software.html
@@ -11,10 +11,7 @@
</div>
<div class="bannerwrap">
- <img
- class="bannerimg"
- src="https://static.igem.wiki/teams/4271/wiki/part-collection.png"
- />
+ <img class="bannerimg" src="https://static.igem.wiki/teams/4271/wiki/6.png" />
</div>
<div class="scrolltotop" onclick="scrollToTop()">
<img
@@ -25,54 +22,84 @@
<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>
+ <a class="pointer" href="#overview">Overview</a>
+ <a class="pointer" href="#feature1">Feature 1</a>
+ <a class="pointer" href="#feature2">Feature 2</a>
+ <a class="pointer" href="#futureplan">Future Plan</a>
</div>
<br />
</aside>
<div class="herowrap" id="experimentalcontents">
<div id="progress-bar"></div>
<b class="heading1" id="partsheading1">
- Heading 1
+ Software
</b>
+ <div class="index_container" id="overview"></div>
+
<div class="heading2" id="partsheading2">
- Heading 2
+ Overview
</div>
- <em class="info_contents_italics" id="greencontents">
- Heading 3
- </em>
+
<div class="info_contents" id="greencontents">
- Contents
+ 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>
- <!-- image -->
- <img
- class="constant_width"
- src="https://static.igem.wiki/teams/4271/wiki/linear-map-of-sensor-plasmid.png"
- />
+ <div class="index_container" id="feature1"></div>
- <div class="image_description" id="greencontents">
- Image description
+ <div class="heading2" id="partsheading2">
+ Feature 1: Calculation of the Severity of Eutrophication
+ </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 (Figure 1) and calculated the most applicable range of water qualities
+ (Figure 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>
+ <div class="index_container" id="feature2"></div>
+
+ <div class="heading2" id="partsheading2">
+ Feature 2: Taiwanese Reservoir Map of Current Eutrophication Status
+ </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="heading2" id="partsheading2">
+ Future Plan: The Implementation of Arduino Chip
+ </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>
- <!-- image -->
+ <img class="constant_height" src=" " />
+
+ <div class="image_description" id="greencontents">
+ Fig. 1 References to the Vollenweider index
+ </div>
</div>
{% endblock %}
--
GitLab