italics.html

wiki/pages/plant.html

@@ -9,7 +9,7 @@
 <h2>Key Achievement</h2>
 
 <ul>
-  <li>We successfully <a class="igem" href="#accessible"><strong>developed a novel plant transformation protocol for bambara groundnut</strong></a> , a non-model crop from Africa.</li>
+  <li>We successfully <a class="igem" href="#accessible"><strong>developed a novel plant transformation protocol for bambara groundnut</strong></a>, a non-model crop from Africa.</li>
   
   <li>We tackled one of the key problems of plant synthetic biology: We worked towards broadening the species range, which
     can be transformed by establishing new tools for engineering <i>Agrobacterium</i>.</li>
@@ -224,23 +224,23 @@
 </div>
 
 
-<h3 id="broadening">Broadening the species range, which can be transformed by establishing new tools for engineering Agrobacterium</h3>
+<h3 id="broadening">Broadening the species range, which can be transformed by establishing new tools for engineering <i>Agrobacterium</i></h3>
 
 <p>
   We aim to overcome the obstacles that hinder iGEM teams when initiating their projects with local plant species,
   including the scarcity of transformation protocols for non-model species and the absence of essential tools for
-  engineering Agrobacterium. To tackle the second and the third challenges above we sought to <strong>improve plant transformation
+  engineering <i>Agrobacterium</i>. To tackle the second and the third challenges above we sought to <strong>improve plant transformation
   efficiency for non-model plant species</strong>.
 </p>
 
 <p>
-  Agrobacterium is the workhorse for the transformation of plants. However its <strong>natural
+  <i>Agrobacterium</i> is the workhorse for the transformation of plants. However its <strong>natural
   host range is limited</strong>, and further improvements are needed to allow for a more broad range of plant species which can be transformed. Still the tools to rewire the regulation of the plant transformation machinery are lacking.
-  That is why we set out to develop the basic synthetic biology tools to fine tune gene expression in Agrobacterium. 
+  That is why we set out to develop the basic synthetic biology tools to fine tune gene expression in <i>Agrobacterium</i>. 
 </p>
 
 <p>
-  First we tested the <strong>gene expression tools of the iGEM community for their functionality in Agrobacterium</strong> and could show
+  First we tested the <strong>gene expression tools of the iGEM community for their functionality in <i>Agrobacterium</i></strong> and could show
   significant differences when comparing to the results in E. coli.
 </p>
 
@@ -250,12 +250,12 @@
     src="https://static.igem.wiki/teams/4729/wiki/composite-part/andersoncompare.png" 
     alt="small description of the image"
   />
-  <figcaption>Figure 5: Comparison of the relative anderson promotor strength between Agrobacterium and E. coli t</figcaption>
+  <figcaption>Figure 5: Comparison of the relative anderson promotor strength between <i>Agrobacterium<i/> and <i>E. coli</i> t</figcaption>
 </figure>
 
 <p>
   These findings underscore the importance of characterizing fundamental components when establishing an organism as a
-  synthetic biology platform. Our work uncovers a new dimension of Anderson promotors in Agrobacterium, igniting novel
+  synthetic biology platform. Our work uncovers a new dimension of Anderson promotors in <i>Agrobacterium</i>, igniting novel
   possibilities and solidifying our commitment to advancing plant transformation. Our findings demonstrate that
   well-established components can adapt effectively to new environments, providing opportunities for future plant
   engineers.
@@ -263,8 +263,8 @@
 
 <p>
   In order to control the virulence during the plant transformation procedure dynamically, we then moved on and
-  characterized inducible promoter systems for Agrobacterium. We selected 9 promoters from the “Marionette Collection”,
-  which contains a number of inducible systems highly optimized (in E. coli) for high dynamic range and low leakyness
+  characterized inducible promoter systems for <i>Agrobacterium</i>. We selected 9 promoters from the “Marionette Collection”,
+  which contains a number of inducible systems highly optimized (in <i>E. coli</i>) for high dynamic range and low leakyness
   (Meyer et al., 2019). Additionally, Ptrc and Ptau were also included (Mostafavi et al., 2014; Stukenberg et al., 2021).
   Another consideration made when selecting the promoter systems to characterize was to include ones that use non-phenolic
   compounds as inducers (Ptau, IPTG, Pbetl, and Pbad), in the hope of minimizing cross talk with the native VirA/VirG two
@@ -277,7 +277,7 @@
     src="https://static.igem.wiki/teams/4729/wiki/results/comparing-all-inducible-promoters.png" 
     alt="Measurement results of inducible promotor in A rhizogenes ARqua1"
   />
-  <figcaption>Figure 6: Measurement results of inducible promotor in A rhizogenes ARqua1.</figcaption>
+  <figcaption>Figure 6: Measurement results of inducible promotor in <i>A.rhizogenes</i> ARqua1.</figcaption>
 </figure>
 
 <p>
@@ -290,7 +290,7 @@
 </p>
 
 <p>
-  Having developed these gene expression tools for Agrobacterium, <strong>we aspired to harness them to control the intricate
+  Having developed these gene expression tools for <i>Agrobacterium</i>, <strong>we aspired to harness them to control the intricate
   plant transformation mechanisms of the bacterium</strong>. For that we went through 4 rounds of the DBTL cycle for our "Best
   composite part".
 </p>
@@ -305,8 +305,8 @@
 </p>
 
 <p>
-  For this protocol, we used the established model organism Arabidopsis thaliana to optimize the speed for generating
-  valid transformation efficiency. Arabidopsis possesses several key attributes such as the short cultivation time proved
+  For this protocol, we used the established model organism <i>Arabidopsis thaliana</i> to optimize the speed for generating
+  valid transformation efficiency. <i>Arabidopsis</i> possesses several key attributes such as the short cultivation time proved
   to be advantageous for prototyping transformation protocols with speed and precision.
 </p>
 
@@ -322,7 +322,7 @@
 <p>
   In total <strong>just 8 days are necessary from germination to obtain the first results of transformation efficiency</strong>. Another 7
   days later the final results were gathered completing the evaluation of the transformation efficiency. Thus, this method
-  is particularly suitable for upcoming iGEM teams to take further steps in A. rhizogenes mediated transformation. This
+  is particularly suitable for upcoming iGEM teams to take further steps in <i>A. rhizogenes</i> mediated transformation. This
   protocol has been benchmarked by us with two different reporter constructs, demonstrating the versatility of this
   approach.
 </p>
@@ -339,10 +339,10 @@
   To improve accessibility of our methods for future teams, we decided to come up with a method not relying on
   fluorescence microscopy. As we did research to find an alternative, we found a publication about a reporter for proteins
   which are converting tyrosine to betalain, called <strong>pRUBY</strong> (He et al., 2020). After cloning and transforming the plasmid
-  35S:RUBY into A. rhizogenes, we were excited to find that with this adaptation we could significantly <strong>speed up the
+  35S:RUBY into <i>A. rhizogenes</i>, we were excited to find that with this adaptation we could significantly <strong>speed up the
   evaluation with the microscope</strong>, reducing the stress on the plants. In fact, RUBY can be seen very well with the naked
   eye, which makes it suitable for protocols that do not require a microscope at all. This allowed us to make the work
-  with A. rhizogenes <strong>more accessible and attractive for upcoming iGEM teams</strong>.
+  with <i>A. rhizogenes</i> <strong>more accessible and attractive for upcoming iGEM teams</strong>.
 </p>
 
 <figure>
@@ -351,7 +351,7 @@
     src="https://static.igem.wiki/teams/4729/wiki/plant-synbio/positive-plant-on-plate.jpg" 
     alt="small description of the image"
   />
-  <figcaption>Figure 8: A. thaliana on plate 3 days after transformation with Agrobacterium rhizogenes ARqua1.</figcaption>
+  <figcaption>Figure 8: <i>A. thaliana</i>) on plate 3 days after transformation with <i>Agrobacterium</i> rhizogenes ARqua1.</figcaption>
 </figure>
 
 <p>
@@ -364,7 +364,7 @@
     src="https://static.igem.wiki/teams/4729/wiki/plant-synbio/ruby-and-hairy-ugly-root-1.jpg" 
     alt="small description of the image"
   />
-  <figcaption>Figure 9: A. thaliana on plate 10 days after transformation with Agrobacterium rhizogenes ARqua1.</figcaption>
+  <figcaption>Figure 9: <i>A. thaliana</i> on plate 10 days after transformation with <i>Agrobacterium rhizogenes</i> ARqua1.</figcaption>
 </figure>
 
 <p>
@@ -500,7 +500,7 @@
     src="https://static.igem.wiki/teams/4729/wiki/plant-synbio/old-plant-with-many-ruby-roots.jpg" 
     alt="small description of the image"
   />
-  <figcaption>Figure 10: A. thaliana on plate 4 weeks after transformation with Agrobacterium rhizogenes ARqua1.</figcaption>
+  <figcaption>Figure 10: <i>A. thaliana</i> on plate 4 weeks after transformation with <i>Agrobacterium rhizogenes</i> ARqua1.</figcaption>
 </figure>
 
 <p>
@@ -515,12 +515,12 @@
 
 <p>
   Most of the world's vital agricultural crops belong to the monocots, making them important candidates for
-  Agrobacterium-mediated transformation. Sadly, Agrobacterium-mediated transformation is particularly critical for
+  <i>Agrobacterium</i>-mediated transformation. Sadly, <i>Agrobacterium</i>-mediated transformation is particularly critical for
   monocots because monocots are not a natural host for the pathogen. Nevertheless, we were determined to achieve the
   transformation of monocots, and our focus turned to foxtail millet (Setaria viridis), an emerging model organism in
-  plant physiology (Brutnell et al., 2010). Leveraging the success of our concise A. thaliana protocol, we sought to
-  extend our efforts to transform Setaria using this approach. Therefore, we adapted our A. thaliana protocol to transform
-  35 germinated Setaria plants using Agrobacterium rhizogenes ARqua1, enhanced virulence with vanillin due to the absence
+  plant physiology (Brutnell et al., 2010). Leveraging the success of our concise <i>A. thaliana protocol</i>, we sought to
+  extend our efforts to transform <i>Setaria</i> using this approach. Therefore, we adapted our <i>A. thaliana</i> protocol to transform
+  35 germinated <i>Setaria</i> plants using <i>Agrobacterium rhizogenes</i> ARqua1, enhanced virulence with vanillin due to the absence
   of naturally occurring phenolic compounds in monocots.
 </p>
 
@@ -530,7 +530,7 @@
     src="https://static.igem.wiki/teams/4729/wiki/plant-synbio/pd18.jpg" 
     alt="small description of the image"
   />
-  <figcaption>Figure 11:Foxtail millet during transformation process with Agrobacterium rhizogenes.</figcaption>
+  <figcaption>Figure 11:Foxtail millet during transformation process with <i>Agrobacterium rhizogenes</i>.</figcaption>
 </figure>
 
 <p>
@@ -544,13 +544,13 @@
     src="https://static.igem.wiki/teams/4729/wiki/plant-synbio/pd16.jpg" 
     alt="small description of the image"
   />
-  <figcaption>Figure 12:Foxtail millet 3 days after transformation with Agrobacterium rhizogenes.</figcaption>
+  <figcaption>Figure 12:Foxtail millet 3 days after transformation with <i>Agrobacterium rhizogenes</i>.</figcaption>
 </figure>
 
 <p>
   In addition to our monocot efforts, we also got the chance to work with oak trees as a chassis, which are propagated in
   sterile culture at our university.
-  Quercus robur is an important forestry species, producing long-lasting and durable timber. Also it is a particularly
+  <i>Quercus robur</i> is an important forestry species, producing long-lasting and durable timber. Also it is a particularly
   important tree in forest ecosystems, as it supports one of the highest biodiversity of insect herbivores (Kennedy &
   Southwood, 1984). Forests worldwide are already suffering from drought stress due to climate change. Accordingly,
   adaptation of tree species to the changing climate is also a pressing issue of today.
@@ -575,7 +575,7 @@
     src="https://static.igem.wiki/teams/4729/wiki/plant-synbio/whatsapp-bild-2023-10-10-um-15-35-25-ebd695a7.jpg" 
     alt="small description of the image"
   />
-  <figcaption>Figure 13: Oak plantlets in test tubes 2 weeks after transformation with Agrobacterium rhizogenes.</figcaption>
+  <figcaption>Figure 13: Oak plantlets in test tubes 2 weeks after transformation with <i>Agrobacterium rhizogenes</i>.</figcaption>
 </figure>
 
 <p>
@@ -597,11 +597,11 @@
 <h3>Outlook and Conclusion</h3>
 
 <p>
-  Building on our refined CDB protocol, future iGEM teams now have a stepping stone to explore Agrobacterium-mediated
+  Building on our refined CDB protocol, future iGEM teams now have a stepping stone to explore <i>Agrobacterium</i>-mediated
   transformation of non-model organisms, <strong>without the constraints of sterile environments and high-cost equipment</strong>. Our
   groundwork, which includes the detailed <strong>characterization of inducible promoters that stimulate virulence genes and their
-  in-plant testing</strong>, paves the way for a more precise targeting of virulence. Our efficient A. thaliana protocol invites
-  upcoming iGEM teams to delve deeper into the genetic intricacies of both Agrobacterium and plant hosts. Through the
+  in-plant testing</strong>, paves the way for a more precise targeting of virulence. Our efficient <i>A. thaliana</i> protocol invites
+  upcoming iGEM teams to delve deeper into the genetic intricacies of both <i>Agrobacterium</i> and plant hosts. Through the
   comprehensive suite of protocols, tools, and resources we've assembled, our vision is to empower subsequent teams,
   facilitating them to root new plant-centric projects in iGEM that resonate with the unique challenges and opportunities
   of their local ecosystems.
@@ -609,7 +609,7 @@
 
 <p>
   Looking ahead, our team is enthusiastic about <strong>refining the inducer concentration</strong>, a step that promises to fine-tune the
-  plant transformation mechanisms in Agrobacterium using our inducible promoter constructs. Such advancements might reveal
+  plant transformation mechanisms in <i>Agrobacterium</i> using our inducible promoter constructs. Such advancements might reveal
   the optimal inducer concentration for gene activation. In addition, we're eager to <strong>broaden the species applicability</strong> of
   our CDB protocol, leveraging the inherent potential of plants to sprout shoot tissue from transgenic roots. This
   approach might revolutionize the regeneration of transgenic plants, sidestepping the complexities of traditional tissue