diff --git a/static/style.css b/static/style.css
index 65bb418923d92d6e7f7b1fe0d4b418f4e25cca83..5b0c9e0885019e907c2dc768f000f6307e3ece2c 100644
--- a/static/style.css
+++ b/static/style.css
@@ -21,7 +21,7 @@ footer a:hover { color: white; text-decoration: underline; }
-/* -=-=-=-=-=-=-=-= COLOR scheme 2024 =-=-=-=-=-=-=-=- */
+/* -=-=-=-=-=-=-=-= COLOR scheme UZurich 2024 =-=-=-=-=-=-=-=- */
:root {
--dark-blue: rgb(1, 106, 112);
--darker-blue: rgb(1,82,87);
@@ -32,6 +32,8 @@ footer a:hover { color: white; text-decoration: underline; }
--white: rgb(255,255,255);
--white-transp: rgba(255,255,255,0.5);
--brown: rgba(185, 149, 82, 0.5);
+ --dark-brown: rgb(62, 51, 30);
+
}
/* -=-=-=-=-=-=-=-= General styling of the wiki components -=-=-=-=-=-=-=-= */
@@ -66,7 +68,7 @@ a[href^="#ref"] { /* Styling all hyperlinks */
padding: 25px 25px 10px 25px;
}
-.image-model{
+.image-model{ /* Style of all image and graph descriptions without padding */
font-size: 14px;
font-style: italic;
color: var(--dark-blue);
@@ -75,8 +77,6 @@ a[href^="#ref"] { /* Styling all hyperlinks */
-
-
.highlight {/* Box to highlight a section in the text */
background-color: rgb(162,197,121,0.4);
padding: 15px 5px 5px 15px; /* Add some padding for spacing, order is top, right, bottom, left */
@@ -463,11 +463,14 @@ a[href^="#ref"] { /* Styling all hyperlinks */
max-width: 100%; /* Ensure it doesn't exceed container width */
max-height: 100%; /* Ensure it doesn't exceed container height */
position: relative;
- transform: none; /* Ensure no transformations on load */
+ transform: translateX(20px);
transition: none; /* Avoid transitions that alter size or position */
object-fit: contain; /* Ensure aspect ratio is maintained */
+
}
+
+
/* For screens smaller than 1200px */
@media (max-width: 1200px) {
#animation-container {
@@ -478,6 +481,7 @@ a[href^="#ref"] { /* Styling all hyperlinks */
#moving-bacterium {
width: 100%;
height: 100%;
+ transform: translateX(20px); /* Shift the animation 20px to the right */
}
}
@@ -491,6 +495,8 @@ a[href^="#ref"] { /* Styling all hyperlinks */
#moving-bacterium {
width: 100%;
height: 100%;
+ transform: translateX(20px); /* Shift the animation 20px to the right */
+ transform: translateY(-20px);
}
}
@@ -498,18 +504,24 @@ a[href^="#ref"] { /* Styling all hyperlinks */
@media (max-width: 480px) {
#animation-container {
height: 300px;
- margin-top: -80px;
+ margin-top: 50px;
background-size: cover;
background-position: top;
}
+
#moving-bacterium {
width: 500%;
height: 500%;
margin-top: 200px;
- transform: translateY(100px);
+ /* transform: translateY(100px); */
}
}
+
+
+
+
+
/* General Section Animations */
/* Centering the text */
.general-statement-container {
@@ -560,6 +572,19 @@ a[href^="#ref"] { /* Styling all hyperlinks */
transform: translateX(300px); /* Fade out to the right */
}
+.fade-in-behind {
+ color: black;
+ font-size: 5em; /* Bigger text */
+ opacity: 0;
+ transition: opacity 2s ease, transform 2s ease; /* Smooth fade-in and rise */
+ margin-bottom: 50px; /* Adds space between the black and blue text */
+}
+
+.fade-in-behind.visible {
+ opacity: 1;
+ transform: translateY(0); /* Fade in with slight rising effect */
+}
+
/* Add spacing between the text blocks */
@@ -750,7 +775,7 @@ a[href^="#ref"] { /* Styling all hyperlinks */
.progress-box {
height: 5px;
background-color: lightgray;
- width: 32%; /* Each box takes up 1/3 of the space */
+ width: 32%;
transition: background-color 0.5s ease-in-out;
}
diff --git a/wiki/pages/awards.html b/wiki/pages/awards.html
index 45fb35adfae7c124959e8955bd04ca2a381de9e2..696a84a89619cb29370f3c630155f4654e7dfd30 100644
--- a/wiki/pages/awards.html
+++ b/wiki/pages/awards.html
@@ -102,7 +102,7 @@
New Basic Part
</h3>
<p>
- We successfully modified a diguanylate cyclase (DGC) native to Pseudomonas species IsoF to prevent c-di-GMP from binding to the negative allosteric binding, effectively enhancing the enzyme’s activity.
+ We successfully modified a diguanylate cyclase (DGC) native to <i>Pseudomonas species</i> IsoF to prevent c-di-GMP from binding to the negative allosteric binding, effectively enhancing the enzyme’s activity.
Our mutant is a valuable contribution to our project, as this mutation is a novelty not only in our chosen DGC but also in the <i>P. sp.</i> IsoF strain.
Our approach can be applied to other DGCs and understanding the enzyme's inhibitory site has many implications for biofilm-related research.
diff --git a/wiki/pages/description.html b/wiki/pages/description.html
index c5de844a39bf701595ada7e079f21d262ff8b44c..a0e1b600cd2df9ff351744653aaec4c16af243b0 100644
--- a/wiki/pages/description.html
+++ b/wiki/pages/description.html
@@ -111,6 +111,7 @@
<li>The production of c-di-GMP is critical for initiating and regulating the formation of biofilm. It also coordinates the recruitment of more bacteria.</li>
<li>The bacteria form a robust biofilm around the plant roots. This biofilm serves to protect the roots and enhance their resilience against environmental stresses such as drought or overexploited soil.</li>
</ol>
+ Created with Biorender.com.
</p>
</div>
<div class="row mt-0">
diff --git a/wiki/pages/engineering.html b/wiki/pages/engineering.html
index 82740280d06d37a10b6ae3d895ef54223bbe6e68..bcb2892bab68848e9f2fa5ffd41d36351ec40b17 100644
--- a/wiki/pages/engineering.html
+++ b/wiki/pages/engineering.html
@@ -51,13 +51,13 @@
<div class="image-model">
<img src="https://static.igem.wiki/teams/5250/project/engineering/picture-1-updated-min.png" alt="Construct" class="img-fluid" style="width: 90%;display: block; margin-left: auto; margin-right: auto;">
<p style="padding-left:30px; padding-right:30px;">
- <b>Figure 1:</b> This illustration represents our full construct to enhance biofilm formation only when the bacteria are in proximity to plant roots.
+ <b>Figure 1:</b> This illustration represents our full construct to enhance biofilm formation only when the bacteria are in proximity to plant roots. Created with BioRender.com
</p>
</div>
</div>
<div class="row mt-4">
- <h5>Two state/Connection of kill switch to feedback loop</h5>
+ <h5>Two state system: Connection of kill switch to feedback loop</h5>
<p>
By connecting the kill switch, feedback loop and the xylose-sensing module, we created a two-state system, in which the feedback loop acts as a switch.
In the first state, before the plant gets inoculated with our engineered bacteria, neither biofilm production is increased nor the kill switch is active.
@@ -117,7 +117,7 @@
They were induced with the different xylose concentrations and kept for 8 hours at room temperature.
Each strain was tested in triplicate.
The GFP expression was then measured every hour for a total of 15 hours.
- This sensing assay (refer to experiment for more details) failed, there was no increase in GFP when higher xylose concentrations were present.
+ This sensing assay (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">refer to experiment for more details</a>) failed, there was no increase in GFP when higher xylose concentrations were present.
</p>
</div>
@@ -142,7 +142,7 @@
<div class="image-description">
<img src="https://static.igem.wiki/teams/5250/project/engineering/picture-18-xylose-illustration.webp" alt="Xylose Illustration" class="img-fluid" style="width: 100%;">
<p>
- <b>Figure 2:</b> XutR and xylose bind the operator and induce gene expression.
+ <b>Figure 2:</b> XutR and xylose bind the operator and induce gene expression. Created with BioRender.com
</p>
</div>
</div>
@@ -175,7 +175,7 @@
The newly assembled plasmid was transformed into <i>E. coli</i> SY327 and then introduced into <i>P. sp.</i> IsoF using Triparental Conjugation.
</p>
<div class="row mt-4 image-description">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-2-pm-testing-sensing-plasmid-pt12rhyz01.pdf" alt="plasmid map testing sensing plasmid" class="img-fluid " style="width: 50%; display: block; margin-left: auto; margin-right: auto;">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-2-pm-testing-sensing-plasmid-pt12rhyz01-1.png" alt="plasmid map testing sensing plasmid" class="img-fluid " style="width: 50%; display: block; margin-left: auto; margin-right: auto;">
<p style="text-align:center;">
<b>Figure 3:</b> Plasmid map of p12Rhyz01
</p>
@@ -209,11 +209,11 @@
<div class="col-lg-6 col-md-6 col-sm-12 order-1 order-md-2">
<img src="https://static.igem.wiki/teams/5250/project/engineering/picture-19-dgc-illustration.webp" alt="DGC Illustration" class="img-fluid" style="width: 100%;">
<div class="image-model">
- <p><b>Figure 4:</b> DGC Illustration</p>
+ <p><b>Figure 4:</b> DGC Illustration. Created with BioRender.com</p>
</div>
<img src="https://static.igem.wiki/teams/5250/project/engineering/picture-20-pde-illustration.webp" alt="PDE Illustration" class="img-fluid" style="width: 100%;">
<div class="image-model">
- <p><b>Figure 5:</b> PDE Illustration</p>
+ <p><b>Figure 5:</b> PDE Illustration. Created with BioRender.com</p>
</div>
</div>
<div class="col-lg-6 col-md-6 col-sm-12 order-2 order-md-1">
@@ -281,7 +281,7 @@
<div class="image-model">
<img src="https://static.igem.wiki/teams/5250/project/engineering/picture-26-min.png" alt="plasmid map testing sensing plasmid" class="img-fluid " style="width: 50%; display: block; margin-left: auto; margin-right: auto;">
<p style="text-align:center; padding-bottom:20px;">
- <b>Figure 6:</b> Sequence Aligment
+ <b>Figure 6:</b> Sequence Aligment. Created with BioRender.com
</p>
</div>
</div>
@@ -332,9 +332,9 @@
the wild-type WspR of <i>P. aeruginosa</i>, the WspR mutant R242A, the wild-type PisoF_00565 of <i>P. sp. IsoF</i> and our genetically engineered mutants PisoF_00565 R196A and the PisoF_00565 R240A.
All those different sequences, with the right adaptors, were ordered from Twist.
The aim now is to test, which of the different DGCs produce the most c-di-GMP and therefore lead to the highest formation of biofilm components.
- Five different testing plasmids, carrying the five different DGCs, were assembled and transformed into <i>E. coli</i> SY327: pT21Rhyz01, pT21Rhyz02, pT21Rhyz03, pT21Rhyz03, pT21Rhyz04 and pT21Rhyz05 (see Parts List for more details).
+ Five different testing plasmids, carrying the five different DGCs, were assembled and transformed into <i>E. coli</i> SY327: pT21Rhyz01, pT21Rhyz02, pT21Rhyz03, pT21Rhyz03, pT21Rhyz04 and pT21Rhyz05 (<a href="{{ url_for('pages', page='parts') }}" class="hyperlink-under">see Parts List for more details</a>).
Each of those plasmids contain an inducible Rhamnose promoter and one of the five DGC sequences.
- Additionally we performed Triparental conjugation (see experiments) and the five plasmids were transformed into <i>P. sp.</i> IsoF using the helper strain <i>E. coli</i> SY327 pRK2013.
+ Additionally we performed Triparental conjugation (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see experiments</a>) and the five plasmids were transformed into <i>P. sp.</i> IsoF using the helper strain <i>E. coli</i> SY327 pRK2013.
</p>
</div>
</div>
@@ -371,28 +371,28 @@
</p>
<p>
Preliminary tests were conducted to identify the optimal conditions for the assay (refer to experiments for more details).
- After adjusting the protocol based on the preliminary results, the c-di-GMP assay was performed three times (refer to experiments for details).
+ After adjusting the protocol based on the preliminary results, the c-di-GMP assay was performed three times (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see experiments for details</a>).
</p>
<p>
The overnight cultures were adjusted to an OD of 0.03, then induced by adding 125ul of 40% Rhamnose to achieve a final concentration of 1% in a 5ml tube.
This led to the expression of the enzyme.
The cultures were incubated for 5 hours and then washed with NaCl solution to eliminate background interference from the LB medium.
- The absorbance of each overnight culture was measured with a spectrophotometer and adjusted to an optical density (OD) of 0.25 (refer to experiment c-di-GMP assay for more details).
+ The absorbance of each overnight culture was measured with a spectrophotometer and adjusted to an optical density (OD) of 0.25.
A black 96-well plate was set up according to the <a href="{{ url_for('pages', page='experiments') }}#protocol" class="hyperlink-under">c-di-GMP assay protocol</a>.
- As negative controls, we used <i>P. sp.</i> IsoF dCas9 (contains no plasmid but dCas9 is implemented on genome), P. sp. IsoF pBBR1MCS (P. sp. IsoF containing the empty plasmid) and as a positive control we used <i>P. sp.</i> IsoF pBBR1MCS YedQ (constitutively overexpressed DGC).
+ As negative controls, we used <i>P. sp.</i> IsoF dCas9 (contains no plasmid but dCas9 is implemented on genome), <i>P. sp.</i> IsoF pBBR1MCS (<i>P. sp.</i> IsoF containing the empty plasmid) and as a positive control we used <i>P. sp.</i> IsoF pBBR1MCS YedQ (constitutively overexpressed DGC).
Into each well, 50ul of each of the adjusted and diluted cultures, were added. Each strain was tested in triplicate (3 replicates per strain).
The plate was incubated in the dark for 14 hours.
Then the fluorescence was measured with a plate reader, with the first excitation set at 469nm and emission at 501nm, followed by a second measurement with excitation set at 482nm and emission at 505nm.
</p>
<p>
- After the c-di-GMP assay, we performed a biofilm staining assay (refer to experiments for more details).
+ After the c-di-GMP assay, we performed a biofilm staining assay (<a href="{{ url_for('pages', page='experiments') }}#protocol" class="hyperlink-under">see experiments for more details</a>).
A square plate containing 50ml LB medium with agar and 1.25ml of a Congo-Red derived dye (2mg/ml) was prepared and dried.
This dye stains polysaccharides and therefore the biofilm produced by our <i>P. sp.</i> IsoF strains.
The cultures were adjusted to an OD of 1 and 10ul of each adjusted strain were plated onto the prepared plate.
The plate was incubated at 30°C for two days.
</p>
<p>
- Additionally we conducted a swimming motility assay (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">refer to experiments for more details</a>), to assess whether the introduction of a DGC would affect the bacterial motility.
+ Additionally we conducted a swimming motility assay (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see experiments for more details</a>), to assess whether the introduction of a DGC would affect the bacterial motility.
Elevated levels of c-di-GMP are associated with reduced motility, which in turn promotes biofilm formation, since a lower motility is beneficial for forming a robust biofilm<a href="#ref2">2</a>.
</p>
<section style="background-color: var(--bs-gray-100);" class="py-5">
@@ -412,23 +412,23 @@
<!-- Image slides -->
<div class="carousel-inner">
<div class="carousel-item active">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-3-dgc-pisof-00565.pdf" class="d-block w-100" alt="dgc-pisof-00565">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-3-dgc-pisof-00565-1.png" class="d-block w-100" alt="dgc-pisof-00565">
<p class="image-description text-center"><b>Figure 8:</b>Plasmid map of pBBR pT21Rhyz01</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-4-dgc-pisof-00565-r196.pdf" class="d-block w-100" alt="dgc-pisof-00565-r196">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-4-dgc-pisof-00565-r196-1.png" class="d-block w-100" alt="dgc-pisof-00565-r196">
<p class="image-description text-center"><b>Figure 9: </b>Plasmid map of pBBR pT21Rhyz02</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-5-dgc-pisof-00565-r240.pdf" class="d-block w-100" alt="dgc-pisof-00565-r240">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-5-dgc-pisof-00565-r240-1.png" class="d-block w-100" alt="dgc-pisof-00565-r240">
<p class="image-description text-center"><b>Figure 10: </b>Plasmid map of pBBR pT21Rhyz03</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-6-dgc-p-aerug-xutr.pdf" class="d-block w-100" alt="dgc-p-aerug-xutr">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-6-dgc-p-aerug-xutr-1.png" class="d-block w-100" alt="dgc-p-aerug-xutr">
<p class="image-description text-center"><b>Figure 11: </b>Plasmid map of pBBR pT21Rhyz04</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-7-dgc-p-aerug-xutr-r242.pdf" class="d-block w-100" alt="dgc-p-aerug-xutr-r242">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-7-dgc-p-aerug-xutr-r242-1.png" class="d-block w-100" alt="dgc-p-aerug-xutr-r242">
<p class="image-description text-center"><b>Figure 12: </b>Plasmid map of pBBR pT21Rhyz05</p>
</div>
</div>
@@ -460,7 +460,7 @@
</p>
<p>
- Given that the mutated WspR diguanylate cyclase (DGC WspR R242A), native to <i>P. aeruginosa</i>, resulted in the greatest increase in c-di-GMP levels and polysaccharide production (refer to Results for more details, we chose to incorporate this mutated WspR DGC into our final plasmid construct.
+ Given that the mutated WspR diguanylate cyclase (DGC WspR R242A), native to <i>P. aeruginosa</i>, resulted in the greatest increase in c-di-GMP levels and polysaccharide production, we chose to incorporate this mutated WspR DGC into our final plasmid construct.
</p>
<p>
Additionally, we discovered that the origins of replication OriV9 (pBBR322), p15A and pUC are not replicative in <i>P. sp.</i> IsoF.
@@ -479,7 +479,7 @@
<div class="col-lg-6 col-md-6 col-sm-12 order-2 order-md-2">
<img src="https://static.igem.wiki/teams/5250/project/engineering/picture-21-crispri.webp" alt=" CRISPRi llustration" class="img-fluid" style="width: 75%;">
<div class="image-model" style="text-align:center">
- <p><b>Figure 13:</b> CRISPRi Illustration</p>
+ <p><b>Figure 13:</b> CRISPRi Illustration. Created with BioRender.com</p>
</div>
</div>
<div class="col-lg-6 col-md-6 col-sm-12 order-1 order-md-1">
@@ -546,11 +546,11 @@
</div>
<div class="image-model">
<img src="https://static.igem.wiki/teams/5250/project/engineering/picture-22-sgrna.webp" alt="sgRNA" class="img-fluid" style="width: 50%; display: block; margin-left: auto; margin-right: auto;">
- <p style="text-align:center;"><b>Figure 14:</b> Our sgRNA to knockdown PDE PisoF_02645â€</p>
+ <p style="text-align:center;"><b>Figure 14:</b> Our sgRNA to knockdown PDE PisoF_02645. Created with BioRender.com</p>
</div>
<p>
This sequence was then synthesized as a primer by Microsynth.
- Following the CRISPR interference protocol (refer to Experiments for detailed protocol), the sgRNA was cloned into the plasmid using PCR amplification and blunt-end ligation.
+ Following the CRISPR interference protocol (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see experiments detailed protocol</a>), the sgRNA was cloned into the plasmid using PCR amplification and blunt-end ligation.
We performed PCR amplification to insert our sgRNA into the pSCB2-sgRNA-Gm plasmid.
This plasmid already contains the tracr-crRNA sequence, which allows the tracr-crRNA part of our sgRNA to anneal directly to the template plasmid.
The guide RNA sequence, however, is not yet present on the plasmid. Since the guide RNA is physically linked to the tracr-crRNA, the DNA polymerase extends the sequence by adding nucleotides during the PCR reaction, resulting in a plasmid that includes both the guide RNA and the tracr-crRNA.
@@ -559,10 +559,10 @@
</p>
<p>
After purifying the PCR product, we proceeded with ligation and transformed the p1DRhyz04 plasmid into <i>E. coli</i> SY327. We then performed colony PCR and sent the amplified sequence for sequencing to ensure that the correct plasmid was introduced into our <i>E. coli</i> strain.
- Finally, we performed a triparental conjugation (refer to Experiments) to introduce p1DRhyz04 into <i>P. sp.</i> IsoF dCas9.
+ Finally, we performed a triparental conjugation to introduce p1DRhyz04 into <i>P. sp.</i> IsoF dCas9.
</p>
<div class="image-description">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-8-pscb2-p1drhyz04-sgrna.pdf" alt="pscb2-p1drhyz04-sgrna" class="img-fluid" style="width: 50%; display: block; margin-left: auto; margin-right: auto;">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-8-pscb2-p1drhyz04-sgrna-1.png" alt="pscb2-p1drhyz04-sgrna" class="img-fluid" style="width: 50%; display: block; margin-left: auto; margin-right: auto;">
<p style="text-align:center;"><b>Figure 15: </b>Plasmid map of p1DRhyz04</p>
</div>
@@ -572,15 +572,15 @@
<h4>Test</h4>
<p>
Since the gene knockdown is only effective in <i>P. sp.</i> IsoF, we were only able to test our system in <i>P. sp.</i> IsoF dCas9 and could not perform parallel experiments in <i>E. coli</i> SY327.
- To evaluate our gene knockdown, we initially conducted a c-di-GMP assay (refer to experiments for more details), following the same procedure as the assay for our different DGCs and also using the same controls.
+ To evaluate our gene knockdown, we initially conducted a c-di-GMP assay, following the same procedure as the assay for our different DGCs and also using the same controls.
We induced the overnight cultures with 125ul of 40% rhamnose after adjusting them to an OD of 0.02.
Then we washed the cells, let them grow and adjusted them again to an OD of 0.25.
- A black 96-well plate was set up according to the c-di-GMP assay protocol (refer to experiments for more details).
+ A black 96-well plate was set up according to the c-di-GMP assay protocol.
We added 50ul of the adjusted cultures to each well and each strain was tested in triplicate.
The plate was then incubated in the dark for one hour. Then the fluorescence was measured using a plate reader and the first measurement was taken with excitation at 469nm and emission at 501nm, the second measurement with excitation set at 482nm and emission at 505nm.
</p>
<p>
- After the c-di-GMP assay we conducted a biofilm staining assay (refer to experiments for more details), again following the same procedure as the biofilm staining assay for our different DGCs.
+ After the c-di-GMP assay we conducted a biofilm staining assay (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see experiments for more details</a>), again following the same procedure as the biofilm staining assay for our different DGCs.
The overnight culture of each strain was induced with rhamnose and adjusted to an OD of one. 10ul of each adjusted strain was plated onto the prepared dyed plate.
The plate was incubated at 30°C for two days.
The absorbance of each strain was then measured using a fluorescence microscope.
@@ -614,8 +614,8 @@
<div class="row mt-0">
<div class="col-lg-4 col-md-6 col-sm-12 order-1 order-md-2 image-description">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-1.webp" alt="Construct" class="img-fluid" style="width: 100%;">
- <p><b>Figure 16:</b> This illustration represents our full construct to enhance biofilm formation only when the bacteria are in proximity to plant roots.
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-1-updated-min.png" alt="Construct" class="img-fluid" style="width: 100%;">
+ <p><b>Figure 16:</b> This illustration represents our full construct to enhance biofilm formation only when the bacteria are in proximity to plant roots. Created with BioRender.com
</div>
<div class="col-lg-8 col-md-6 col-sm-12 order-2 order-md-1">
<p>
@@ -633,7 +633,7 @@
</div>
<div class="row mt-4">
<p>
- To verify the functionality of this feedback loop and confirm that higher concentrations of T7 RNAP lead to increased gene expression, we designed three level 2 testing plasmids: pT32Rhyz01, pT32Rhyz02 and pT32Rhyz03 (refer to “Parts†for details) using the Golden Gate assembly.
+ To verify the functionality of this feedback loop and confirm that higher concentrations of T7 RNAP lead to increased gene expression, we designed three level 2 testing plasmids: pT32Rhyz01, pT32Rhyz02 and pT32Rhyz03 (<a href="{{ url_for('pages', page='parts') }}" class="hyperlink-under">see "Parts" for more details</a>) using the Golden Gate assembly.
</p>
<p>
The pT32Rhyz01 contains two transcription units (and two linker transcription units). The first one is a constitutive promoter and a T7 RNAP (pT32Rhyz01). The second one is a T7-like promoter and a GFP (pT31Rhyz02).
@@ -664,15 +664,15 @@
<!-- Image slides -->
<div class="carousel-inner">
<div class="carousel-item active">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-9-pt32rhyz01.pdf" class="d-block w-100" alt="pt32rhyz01">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-9-pt32rhyz01-1.png" class="d-block w-100" alt="pt32rhyz01">
<p class="image-description text-center"><b>Figure 17: </b>Plasmid map of pT32Rhyz01</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-10-pt32rhyz02.pdf" class="d-block w-100" alt="pt32rhyz02">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-10-pt32rhyz02-1.png" class="d-block w-100" alt="pt32rhyz02">
<p class="image-description text-center"><b>Figure 18: </b>Plasmid map of pT32Rhyz02</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-11-pt32rhyz03.pdf" class="d-block w-100" alt="pt32rhyz03">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-11-pt32rhyz03-1.png" class="d-block w-100" alt="pt32rhyz03">
<p class="image-description text-center"><b>Figure 19: </b>Plasmid map of pT32Rhyz03</p>
</div>
</div>
@@ -715,19 +715,19 @@
</p>
<p>
Our first goal was to determine the amount of CcdB required to effectively kill the cell.
- Therefore we designed three testing plasmids pT41Rhyz01, pT41Rhyz02 and pT41Rhyz03 (refer to Parts for more details) with Golden Gate Assembly and transformed into <i>E. coli</i> SY327.
+ Therefore we designed three testing plasmids pT41Rhyz01, pT41Rhyz02 and pT41Rhyz03 (<a href="{{ url_for('pages', page='parts') }}" class="hyperlink-under">see "Parts" for more details</a>) with Golden Gate Assembly and transformed into <i>E. coli</i> SY327.
Each of these plasmids contains the toxin gene but with a different ribosome binding site (RBS) strength.
pT41Rhyz01 has the weakest RBS leading to little toxin production, while pT41Rhyz03 has the strongest RBS leading to high toxin production.
The expression of the toxin is controlled by an rhamnose promoter to ensure the toxin is produced only when we induce it with rhamnose.
</p>
<p>
- The first toxin test (refer to experiments for more details) in <i>E. coli</i> SY327 showed that the bacteria does not get killed by the toxin, indicating that <i>E. coli</i> SY327 is resistant to CcdB.
+ The first toxin test (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see experiments for more details</a>) in <i>E. coli</i> SY327 showed that the bacteria does not get killed by the toxin, indicating that <i>E. coli</i> SY327 is resistant to CcdB.
Those three plasmids were then transformed into <i>E. coli</i> DH5alpha and the same toxin test was conducted. Again, the experiment failed and the bacteria weren’t killed.
After in-depth research we found that <i>E. coli</i> SY327 as well as E. coli DH5alpha had a mutation in their gyrase and were therefore resistant to our toxin <a href="#ref6">6</a>.
</p>
<p>
We identified three suitable <i>E. coli</i> strains<a href="#ref6">6</a>: E. coli HB101, <i>E. coli</i> MC1061 and <i>E. coli</i> CSH50.
- We prepared competent cells following the protocol (refer to Protocol for more details) and transformed our plasmids into this new strain.
+ We prepared competent cells following the protocol (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see Protocol for more details</a>) and transformed our plasmids into this new strain.
</p>
<p>
Since these three testing plasmids also contain the pJUMP28-1A backbone, we assumed that they would also not replicate in <i>P. sp.</i> IsoF.
@@ -748,7 +748,7 @@
<div class="row mt-4">
<h3 style="color:black; font-size:20px;">Test</h3>
<p>
- We performed the same toxin assay 1 (refer to Experiments for details) for all different <i>E. coli</i> strains.
+ We performed the same toxin assay 1 (<a href="{{ url_for('pages', page='experiments') }}" class="hyperlink-under">see experiments for more details</a>) for all different <i>E. coli</i> strains.
The toxin assay consists of an OD measurement overnight.
The overnight cultures were adjusted to an OD of 0.01 and induced with different rhamnose concentrations (0%, 1%, 1.5%).
Then they were incubated for four hours.
@@ -777,15 +777,15 @@
<!-- Image slides -->
<div class="carousel-inner">
<div class="carousel-item active">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-12-pt41rhyz01.pdf" class="d-block w-100" alt="pt41rhyz01">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-12-pt41rhyz01-1.png" class="d-block w-100" alt="pt41rhyz01">
<p class="image-description text-center"><b>Figure 20: </b>Plasmid map of pT41Rhyz01</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-13-pt41rhyz02.pdf" class="d-block w-100" alt="pt32rhyz02">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-13-pt41rhyz02-1.png" class="d-block w-100" alt="pt32rhyz02">
<p class="image-description text-center"><b>Figure 21: </b>Plasmid map of pT41Rhyz02</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-14-pt41rhyz03.pdf" class="d-block w-100" alt="pt32rhyz03">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-14-pt41rhyz03-1.png" class="d-block w-100" alt="pt32rhyz03">
<p class="image-description text-center"><b>Figure 22: </b>Plasmid map of pT41Rhyz03</p>
</div>
@@ -822,15 +822,15 @@
<!-- Image slides -->
<div class="carousel-inner">
<div class="carousel-item active">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-15-pbbr1-pt41rhyz01.pdf" class="d-block w-100" alt="pbbr1-pt41rhyz01">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-15-pbbr1-pt41rhyz01-1.png" class="d-block w-100" alt="pbbr1-pt41rhyz01">
<p class="image-description text-center"><b>Figure 23: </b>Plasmid map of pBBR pT41Rhyz01</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-16-pbbr1-pt41rhyz02.pdf" class="d-block w-100" alt="pbbr1-pt41rhyz02">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-16-pbbr1-pt41rhyz02-1.png" class="d-block w-100" alt="pbbr1-pt41rhyz02">
<p class="image-description text-center"><b>Figure 24: </b>Plasmid map of pBBR pT41Rhyz02</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-17-pbbr1-pt41rhyz03.pdf" class="d-block w-100" alt="pbbr1-pt41rhyz03">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-17-pbbr1-pt41rhyz03-1.png" class="d-block w-100" alt="pbbr1-pt41rhyz03">
<p class="image-description text-center"><b>Figure 25: </b>Plasmid map of pBBR pT41Rhyz03 </p>
</div>
@@ -909,11 +909,11 @@
<!-- Image slides -->
<div class="carousel-inner">
<div class="carousel-item active">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-24-p21rhyz02.pdf" class="d-block w-100" alt="p21rhyz02">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-24-p21rhyz02-1.png" class="d-block w-100" alt="p21rhyz02">
<p class="image-description text-center"><b>Figure 26: </b>Plasmid map of p21Rhyz02</p>
</div>
<div class="carousel-item">
- <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-25-p22rhyz02.pdf" class="d-block w-100" alt="p22rhyz02">
+ <img src="https://static.igem.wiki/teams/5250/project/engineering/picture-25-p22rhyz02-1.png" class="d-block w-100" alt="p22rhyz02">
<p class="image-description text-center"><b>Figure 27: </b>Plasmid map of p22Rhyz02</p>
</div>
diff --git a/wiki/pages/home.html b/wiki/pages/home.html
index 6999f0ad4b6798e2eee46c4a223c2cba4c1990d7..0fe535e28065ace7ab9ff777d37f6104aacfd1ac 100644
--- a/wiki/pages/home.html
+++ b/wiki/pages/home.html
@@ -14,18 +14,20 @@
{% block page_content %}
<div class="container">
- <!-- First Section: General Statement (fade-in from left and fade-out on scroll) -->
- <div class="general-statement-container d-flex flex-column justify-content-center align-items-center">
- <div class="general-statement fade-in-left hidden mt-1">
- <h2>Climate Change endangers the safety of global food production.</h2>
- </div>
- <div class="general-statement fade-in-right hidden mt-7">
- <p style="color: var(--dark-blue); font-size:20px; padding-left:100px; padding-right:100px;">
- Increasing risks of drought, heat, and pathogens are rendering large areas of previously arable land unusable
- and transforming them into barren wastelands, unable to recover.
- </h3>
- </div>
- </div>
+ <!-- First Section: General Statement (fade-in from left and fade-out on scroll) -->
+ <div class="general-statement-container d-flex flex-column justify-content-center align-items-center">
+ <div class="general-statement fade-in-left hidden mt-1">
+ <h2>Climate Change endangers the safety of global food production.</h2>
+ </div>
+ <div class="general-statement fade-in-right hidden mt-7">
+ <p style="color: var(--dark-blue); font-size:20px; padding-left:100px; padding-right:100px;">
+ <h1 style="font-size:40px; color:var(--dark-brown); font-weight:bold">
+ Tackling the Problem at its Root.
+ </h1>
+ </p>
+ </div>
+ </div>
+
<!-- Second Section: Circle Pictures with Text (scroll-triggered animation) -->
@@ -113,7 +115,7 @@
</div>
</div>
- <!-- Question 4 -->
+ <!-- Question 4
<div class="quiz-question" data-question="4">
<p class="question-text">What is the extent of crop and livestock production loss caused by drought? <a href="#ref6">6</a></p>
<div class="quiz-answers">
@@ -123,6 +125,7 @@
<button class="quiz-answer" data-correct="false">61%</button>
</div>
</div>
+ -->
</div>
<button id="next-question" class="quiz-nav">→</button>
@@ -163,8 +166,8 @@
<p>
This year's UZurich iGEM Team is a group of 10 students from the University of Zurich.
</p>
- <a href="{{ url_for('pages', page='team') }}" class="hyperlink-button"> Team</a>
- <p>
+ <a href="{{ url_for('pages', page='team') }}" class="hyperlink-button">Team</a>
+ <p style="padding-top:10px">
We designed Pebb, our <b>P</b>lant <b>E</b>nhancing <b>B</b>iofilm <b>B</b>acteria.
Pebb helps us tackle the challenges of climate change in agriculture by forming a biofilm on the roots of plants which protects them from drought and other related stresses.
</p>
@@ -174,17 +177,26 @@
<!-- Fifth Section: Subteam Descriptions (Clickable Boxes) -->
<div class="subteam-container d-flex justify-content-between mt-5">
<div class="subteam-box">
- <h3>WET LAB</h3>
+ <h3>
+ <img src="https://static.igem.wiki/teams/5250/logos/eyedropper.svg" alt="icon" style="width: 28px; height: 22px; margin-right: 8px;">
+ WET LAB
+ </h3>
<p>Our RhyzUp Wet Lab team has been working tirelessly all summer, designing, engineering and testing our genetic circuits to make our dream of a hyper robust biofilm come true.</p>
<a href="{{ url_for('pages', page='results') }}" class="hyperlink-button">Learn more about what they did</a>
</div>
<div class="subteam-box">
- <h3>DRY LAB</h3>
+ <h3>
+ <img src="https://static.igem.wiki/teams/5250/logos/laptop.svg" alt="icon" style="width: 18px; height: 22px; margin-right: 8px;">
+ DRY LAB
+ </h3>
<p>Our RhyzUp Dry Lab team spent countless hours coding models to figure out ways to improve biofilm production and study the effects on our engineered bacteria strain.</p>
<a href="{{ url_for('pages', page='model') }}" class="hyperlink-button">Learn more about what they did</a>
</div>
<div class="subteam-box">
- <h3>HUMAN PRACTICES</h3>
+ <h3>
+ <img src="https://static.igem.wiki/teams/5250/logos/people.svg" alt="icon" style="width: 18px; height: 22px; margin-right: 8px;">
+ HUMAN PRACTICES
+ </h3>
<p>Our RhyzUp Human Practices team talked to farmers, politicians and researchers to find out what the real challenges of drought are and had lots of interesting discussions about the future of agriculture and GMOs.</p>
<a href="{{ url_for('pages', page='human-practices') }}" class="hyperlink-button">Learn more about what they did</a>
</div>
diff --git a/wiki/pages/new-basic-part.html b/wiki/pages/new-basic-part.html
index 1c17eb59f77f05ccc7deeb280d7cc1421183d972..d46883ac8331e316c4ea433ca7ae3f5a89ab666f 100644
--- a/wiki/pages/new-basic-part.html
+++ b/wiki/pages/new-basic-part.html
@@ -33,9 +33,9 @@
This way we could identify the appropriate arginine residues to target and modify them to alanine residues (R196A and R240A).
</p>
<div class="row mt-0 image-model">
- <img src="https://static.igem.wiki/teams/5250/project/new-basic-part/img-1.png"
- alt="Sequence Alignment of WspR wt and WspR mutation R198A to our DGC IsoF wt and DGC IsoF R196A" class="img-fluid d-block mx-auto" style="width: 75%;">
- <p style="text-align:center;"><b>Figure 1:</b> Sequence Alignment of WspR wt and WspR mutation R198A to our DGC IsoF wt and DGC IsoF R196A</p>
+ <img src="https://static.igem.wiki/teams/5250/project/new-basic-part/image-start.png"
+ alt="Sequence Alignment of WspR wt and WspR mutation R198A to our DGC IsoF wt and DGC IsoF R196A" class="img-fluid d-block mx-auto" style="width: 60%;">
+ <p style="text-align:center;"><b>Figure 1:</b> Sequence Alignment of WspR wt and WspR mutation R198A to our DGC IsoF wt and DGC IsoF R196A. Created with BioRender.com</p>
</div>
</div>
</div>
@@ -86,10 +86,12 @@
<p>
When comparing the difference in average c-di-GMP levels between the rhamnose and no rhamnose conditions, we observed a larger difference between our DGC mutation and our control, confirming that this variation is not merely background noise:
</p>
- <p>
- No Plasmid (Rhamnose) - No Plasmid (No Rhamnose): 96.00 RFU <br>
- DGC R196A (Rhamnose) - DGC R196A (No Rhamnose): 240.33 RFU
- </p>
+ <div style="padding-left:20px;">
+ <ul>
+ <li>No Plasmid (Rhamnose) - No Plasmid (No Rhamnose): 96.00 RFU</li>
+ <li>DGC R196A (Rhamnose) - DGC R196A (No Rhamnose): 240.33 RFU</li>
+ </ul>
+ </div>
<p>
<b>This represents a novel approach, as it has to our knowledge, not been attempted before for any DGC native to <i>P. sp.</i> IsoF.
As various DGCs contain the conserved GG(D)EF domain, this makes our approach of c-di-GMP regulation broadly applicable.</b>
diff --git a/wiki/pages/notebook.html b/wiki/pages/notebook.html
index 71dadedca54f1398435732484d3a53f107a8839b..427e1f6b3f6e371653765beecc4fee9c5c390a29 100644
--- a/wiki/pages/notebook.html
+++ b/wiki/pages/notebook.html
@@ -112,7 +112,7 @@
</p>
</div>
<div class="col-lg-6 col-md-6 col-sm-12">
- <img src="https://static.igem.wiki/teams/5250/project/notebook/img-2.jpg" alt="Week 8" class="img-fluid" style="width: 80%; display: block; margin: 0 auto;">
+ <img src="https://static.igem.wiki/teams/5250/project/notebook/img-w2-min.jpg" alt="Week 8" class="img-fluid" style="width: 80%; display: block; margin: 0 auto;">
</div>
</div>
</div>
diff --git a/wiki/pages/safety.html b/wiki/pages/safety.html
index 8ec1b723af2f200629479621f6441bfdeef3852e..1f14f3e649e2615cd696c0b4fc013dd28453ec08 100644
--- a/wiki/pages/safety.html
+++ b/wiki/pages/safety.html
@@ -6,7 +6,7 @@
{% extends "layout.html" %}
-{% set header_background_url = "https://static.igem.wiki/teams/5250/project/headpage-23.webp"%}
+{% set header_background_url = "https://static.igem.wiki/teams/5250/project/safety/headpage-23-min.jpg"%}
{% block page_content %}
@@ -147,20 +147,16 @@
<div class="col">
<h2>Social science research</h2>
<hr>
- </div>
-</div>
-
-<div class="row mt-0">
- <div class="col-lg-3 col-md-3 col-sm-12">
- <div class="contribution-box" style="height: 500px;">
- <p>
+ <p>
Our human subjects research mainly consisted of interviews and in-person teaching.
All our research was done in accordance with relevant laws and regulations.
</p>
- </div>
</div>
- <div class="col-lg-3 col-md-5 col-sm-12">
- <div class="contribution-box" style="height: 500px;">
+</div>
+
+<div class="row mt-0">
+ <div class="col-lg-4 col-md-3 col-sm-12">
+ <div class="contribution-box" style="height: 550px;">
<h3>Written consent</h3>
<p>
We received written, informed consent of all interviewees to record the interviews and use the material appropriately.
@@ -169,8 +165,8 @@
</p>
</div>
</div>
- <div class="col-lg-6 col-md-5 col-sm-12">
- <div class="contribution-box" style="height: 500px;">
+ <div class="col-lg-8 col-md-5 col-sm-12">
+ <div class="contribution-box" style="height: 550px;">
<h3>Political awareness</h3>
<div class="image-description">
<img src="https://static.igem.wiki/teams/5250/project/safety/s-3-min.jpg" alt="Discussion on the topic “designer babies†at our lab workshop for highschool students" class="img-fluid d-block mx-auto" style="width: 50%;">
diff --git a/wiki/pages/sustainability.html b/wiki/pages/sustainability.html
index 6f95cc46df1c2570ef721950b7024c853e88373f..3168c00d3f09bde6fc630edb1f43e47c0b39d408 100644
--- a/wiki/pages/sustainability.html
+++ b/wiki/pages/sustainability.html
@@ -59,7 +59,7 @@
<div class="row mt-4">
<h2>Introduction</h2>
<hr>
- <img src="https://static.igem.wiki/teams/5250/human-practices/sustainability/mindmap1.png" alt="Sustainability Mindmap" class="img-fluid" style="width: 100%;">
+ <img src="https://static.igem.wiki/teams/5250/human-practices/sustainability/mindmap-02.jpg" alt="Sustainability Mindmap" class="img-fluid" style="width: 100%;">
<p>
In order to assess how our project could improve sustainability in agriculture, we first needed to get a good understanding of what makes an agrosystem sustainable and what sustainability challenges exist in agriculture today.
Therefore, on top of a lot of individual research, we also reached out to various stakeholders, including agroecologists, farmers, ethicists, and lawyers, for further insight.