Update background.md

docs/project/background.md

@@ -67,13 +67,13 @@ Now, imagine if we could link the replication of a phage to the activity of our
 
 Fortunately, scientists figured out how to do this back in 2011 creating the Phage-Assisted Continuous Evolution (PACE) approach and sparing us the need to reinvent the wheel [^pace_paper]. They used the fact that M13 phage needs a specific protein, pIII, to infect bacteria. Phages without pIII replicate poorly, while those that produce more pIII generate more infectious particles. This created an opportunity: by coupling the activity of our biomolecule to pIII production, phages carrying more active biomolecule variants would produce more pIII and, as a result, replicate more efficiently.
 
-The key to this system is linking the activity of the biomolecule to the expression of a gene coding for pIII. This challenge, central to synthetic biology, has been successfully addressed for a range of biomolecular functions, including DNA, RNA, and protein binding, as well as enzyme activity [^reporter_paper1] [^reporter_paper2]. To achieve this, we use an accessory plasmid (AP), which carries a regulatory circuit that ties the biomolecule’s activity to the expression of pIII. This plasmid is placed in the host bacteria, allowing for controlled expression of pIII based on the biomolecule's performance. At the same time, we introduce the gene encoding the biomolecule of interest into the genome of the phage, which we call a selection phage (SP). To ensure that only phages with active biomolecules can propagate, we remove the native gene for pIII from the phage genome. This means the phage can only replicate if the biomolecule inside the phage activates the regulatory circuit in the host cell, leading to pIII production. This clever setup ensures that only phages carrying functional or improved biomolecule variants can replicate and propagate, effectively driving the selection process.
+The key to this system is linking the activity of the biomolecule to the expression of a gene coding for pIII (Figure 4). This challenge, central to synthetic biology, has been successfully addressed for a range of biomolecular functions, including DNA, RNA, and protein binding, as well as enzyme activity [^reporter_paper1] [^reporter_paper2]. To achieve this, we use an accessory plasmid (AP), which carries a regulatory circuit that ties the biomolecule’s activity to the expression of pIII. This plasmid is placed in the host bacteria, allowing for controlled expression of pIII based on the biomolecule's performance. At the same time, we introduce the gene encoding the biomolecule of interest into the genome of the phage, which we call a selection phage (SP). To ensure that only phages with active biomolecules can propagate, we remove the native gene for pIII from the phage genome. This means the phage can only replicate if the biomolecule inside the phage activates the regulatory circuit in the host cell, leading to pIII production. This clever setup ensures that only phages carrying functional or improved biomolecule variants can replicate and propagate, effectively driving the selection process.
 
 To make this a self-sustaining evolution system, a few more adjustments are needed. We provide the phages with a steady supply of fresh bacteria in a "lagoon" - a chamber where bacteria and phages grow. This ensures that newly generated phages always have hosts to infect. Simultaneously, we flush out old bacteria and phages, ensuring that only those phages that replicate quickly enough can survive. In this setup, better-performing variants will thrive and outcompete others, driving evolution forward. To speed up this process, a special mutation plasmid (MP) is introduced into the bacteria. This plasmid increases the already high mutation rate of the phages, significantly accelerating the pace of evolution and allowing researchers to quickly refine biomolecules. Over time, phages with beneficial mutations accumulate and become dominant in the population. These mutations can then be identified by sequencing the phages. Finally, one often uses orthogonal methods to confirm the activity of the evolved biomolecule.
 
 <figure markdown>
 ![Figure_pace](https://idec-teams.github.io/2024_Evolution_Suisse/img/PACE_related_schematics/onlypace.png)
-<figcaption> Figure X: A schematic representation of the Phage-Assisted Continuous Evolution (PACE) system. Once a phage infects the cell (1), its genome (SP) enters it and the biomolecule that is being evolved is expressed (2). Through a genetic circuit on AP that links the biomolecule activity to _gIII_ expression, the protein pIII, required for phage propagation is expressed (3). In parallel, the phage genome is being replicated (4), with mutations occuring at a higher pace due to the presence of MP. Finally, the newly generated phage genome, structural proteins and pIII assemble into new phage particles. The resulting phages then go on to infect new cells. Should the variant be inactive, pIII is not produced, resulting in non-infectious phages from that cell. New cells are continuously pumped into the lagoon, while old cells and phages are pumped out.
+<figcaption> Figure 4: A schematic representation of the Phage-Assisted Continuous Evolution (PACE) system. Once a phage infects the cell (1), its genome (SP) enters it and the biomolecule that is being evolved is expressed (2). Through a genetic circuit on AP that links the biomolecule activity to _gIII_ expression, the protein pIII, required for phage propagation is expressed (3). In parallel, the phage genome is being replicated (4), with mutations occuring at a higher pace due to the presence of MP. Finally, the newly generated phage genome, structural proteins and pIII assemble into new phage particles. The resulting phages then go on to infect new cells. Should the variant be inactive, pIII is not produced, resulting in non-infectious phages from that cell. New cells are continuously pumped into the lagoon, while old cells and phages are pumped out.
 </figcaption>
 </figure>