diff --git a/wiki/pages/home.html b/wiki/pages/home.html
index a43658f534fc620db708554adea468db2d2af7a5..ef89e6e2cc8c995fb30327bee4ee223d864d0b51 100644
--- a/wiki/pages/home.html
+++ b/wiki/pages/home.html
@@ -136,7 +136,7 @@
We engineer <i>Pseudomonas sp.</i> IsoF, a bacteria found in the rhizosphere, to form an enhanced biofilm on plant roots.
This biofilm increases the plant's tolerance to drought, improves the uptake of nutrients and offers protection against pathogens.
</p>
- <a href="{{ url_for('pages', page='description') }}" class="hyperlink-button"> More details in the project description</a>
+ <a href="{{ url_for('pages', page='description') }}" class="hyperlink-button"> More details in the Project Description</a>
</div>
<div class="col-lg-4 col-md-6 col-sm-12">
<img src="https://static.igem.wiki/teams/5250/project-description/igem-drawing-02.png" alt="iGEM drawing" class="img-fluid" style="max-width: 70%; height: auto;">
@@ -168,7 +168,7 @@
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>
+ <a href="{{ url_for('pages', page='results') }}" class="hyperlink-button">Learn more about their results</a>
</div>
<div class="subteam-box">
<h3>
@@ -176,15 +176,15 @@
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>
+ <a href="{{ url_for('pages', page='model') }}" class="hyperlink-button">Learn more about their model</a>
</div>
<div class="subteam-box">
<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>
+ <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 sustainable agriculture and GMOs.</p>
+ <a href="{{ url_for('pages', page='human-practices') }}" class="hyperlink-button">Learn more about their work</a>
</div>
</div>
<div class="row mt-4">
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index 3f3b1114241101f4cbb8650e01ef333620a6cf76..a5fbb16b3828716f2f9f6640d91b4b2cc8c8b27c 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -54,8 +54,8 @@ Holmes M, et al. (2003),", "title": "Pseudomonas putida KT2440 [ppu].", "link":
{"names": "[20] Purtschert-Montenegro, G., Cárcamo-Oyarce G., Pinto-Carbó M., Agnoli K., Bailly A., und Eberl L.",
"title": "„Pseudomonas Putida Mediates Bacterial Killing, Biofilm Invasion and Biocontrol with a Type IVB Secretion
System“. Nature Microbiology 7, Nr. 10 (19. September 2022): 1547–57.", "link": "https://doi.org/10.1038/s41564-022-01209-6"},
-{"names": "[21] ",
-"title": "", "link": ""}
+{"names": "[21] Botero D., Monk J., RodrÃguez Cubillos M. J. , RodrÃguez Cubillos A., Restrepo M., Bernal-Galeano V., Reyes A., González Barrios A., Ø Palsson b., Restrepo S., Bernal A. (2020)",
+"title": "Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level", "link": "https://doi.org/10.3389/fgene.2020.00837"}
] %}
{% extends "layout_TOC.html" %}
@@ -164,7 +164,7 @@ System“. Nature Microbiology 7, Nr. 10 (19. September 2022): 1547–57.", "lin
Since we can write a stoichiometric $m \times n$ matrix $\mathbf{S}$ containing the coefficient for each metabolite and coefficient and $\mathbf{v} \in \mathbb{R}^n$ a vector containing all the fluxes, we get
$$\mathbf{Sv} = 0.$$
The additional assumptions for the bounds of each reaction flux are defined in two vectors $\mathbf{a},\mathbf{b} \in \mathbb{R}^n$. The first one contains all lower bounds and the second all upper bounds. The objective function $f(\mathbf{v})$ is what the FBA optimizes by solving for the flux distribution in the network. The problem solved by the FBA is thus described by
- $$\max_{\mathbf{v} \in \mathbb{R}^n} f(\mathbf{v}), \text{ such that } \mathbf{Sv}=0 \text{ and } a_i \leq v_i \leq b_i \ \forall i \in \{1,...,n\}$$
+ $$\max_{\mathbf{v} \in \mathbb{R}^n} f(\mathbf{v}), \text{ such that } \mathbf{Sv}=0,$$ $$a_i \leq v_i \leq b_i \ \forall i \in \{1,...,n\}$$
</p>
<p>
Let’s consider a simple example to make this concept easier to understand:
@@ -1148,7 +1148,7 @@ System“. Nature Microbiology 7, Nr. 10 (19. September 2022): 1547–57.", "lin
<p>
We focused on the competition test described in the <a href="#section-15" class="hyperlink-under">outlook</a> section.
As a proof of concept, we selected two GEMs of soil bacteria, a gram-positive and a gram-negative strain, that our bacterium would likely compete with in field applications.
- For the gram-positive bacterium, we used <i>Bacillus subtilis</i> str. 168 and used its GEM, iYO844 <a href="#ref18">18</a>, and for the gram-negative bacterium, we chose <i>Xanthomonas phaseoli pv. manihotis </i>, using its GEM, iXpm1556<a href="#ref21">21</a>.
+ For the gram-positive bacterium, we used <i>Bacillus subtilis</i> str. 168 and used its GEM, iYO844<a href="#ref18">18</a>, and for the gram-negative bacterium, we chose <i>Xanthomonas phaseoli pv. manihotis </i>, using its GEM, iXpm1556<a href="#ref21">21</a>.
We adapted both models to our established soil conditions <a href="#section-11" class="hyperlink-under">in stage 3</a> and analyzed their biomass production in the given environment.
Assuming that growth rate is a reasonable proxy for competitiveness - where a bacterium gains a competitive advantage by outgrowing others - we compared their biomass production levels to those of our pre-established <i>P. putida</i> KT2440 model.
</p>
diff --git a/wiki/pages/results.html b/wiki/pages/results.html
index ac354f9cdae84d2e815d03b278f246910f77921c..6fb863addb106d5bcd13780d30530f02308962ea 100644
--- a/wiki/pages/results.html
+++ b/wiki/pages/results.html
@@ -1,8 +1,16 @@
{% set sources = [
- {"names": "[1] Brás T. A., Seixas J., Carvalhais N., Jägermeyr J. (2021).", "title": "Severity of drought and heatwave crop losses tripled over the last five decades in Europe, Environmental Research Letters.", "link": "https://doi.org/10.1088/1748-9326/abf004"},
- {"names": "[2] Ferreira C. S. S., Seifollahi-Aghmiuni S., Destouni G., Ghajarnia N., Kalantari Z. (2022)","title": "Soil degradation in the European Mediterranean region: Processes, status and consequences.", "link": "https://doi.org/10.1016/j.scitotenv.2021.150106"},
- {"names": "[3] FLe Roux FBinesse J, Saulnier D, Mazel D. (2007).", "title": "Construction of a Vibrio splendidus Mutant Lacking the Metalloprotease Gene vsm by Use of a Novel Counterselectable Suicide Vector. Appl Environ Microbiol73", "link": "https://doi.org/10.1128/AEM.02147-06"},
- {"names": "[4] Ferenc, M. (2024).", "title": "Plasmids 101: Common Lab E. coli Strains.", "link": "https://blog.addgene.org/plasmids-101-common-lab-e-coli-strains"}
+ {"names": "[1] Hailing Nie, Yujie Xiao, Jinzhi He, Huizhong Liu, Liang Nie, Wenli Chen and Qiaoyun Huang. (2020).",
+ "title": "Phenotypic-genotypic analysis of GGDEF/EAL/HD-GYP domain-encoding genes in Pseudomonas putida. Environmental Microbiology Reports, (12(1), 38-48).",
+ "link": "https://doi.org/10.1111/1758-2229.12808"},
+ {"names": "[2] Minh-Hoa Dao-Thi, Laurence Van Melderen, Erwin De Genst, Hassan Afif, Lieven Buts, Lode Wyns, Remy Loris. (2005).",
+ "title": "Molecular Basis of Gyrase Poisoning by the Addiction Toxin CcdB, Journal of Molecular Biology (V. 348, I. 5, pg 1091-1102).",
+ "link": "https://doi.org/10.1016/j.jmb.2005.03.049"},
+ {"names": "[3] Le Roux FBinesse J, Saulnier D, Mazel D. (2007).",
+ "title": "Construction of a Vibrio splendidus Mutant Lacking the Metalloprotease Gene vsm by Use of a Novel Counterselectable Suicide Vector. Appl Environ Microbiol73",
+ "link": "https://doi.org/10.1128/AEM.02147-06"},
+ {"names": "[4] Ferenc, M. (2024).",
+ "title": "Plasmids 101: Common Lab E. coli Strains.",
+ "link": "https://blog.addgene.org/plasmids-101-common-lab-e-coli-strains"}
] %}
{% extends "layout_TOC.html" %}