fix: added few things for sys evolution

_lines/systems_evolution.md

@@ -3,17 +3,29 @@ title: Evolution of biological systems
 description: Systemic root inference of orthologous groups
 ---
 
-# An algorithm to infer the evolutionary root of orthologous groups
+# An algorithm to systemically infer the evolutionary root of orthologous groups
 
-The development of sequencing technologies in the past two decades allowed the study of the phylogenetic relationship of several model organisms. An interesting question relies on the mechanisms behind how new genes arise and how they interact and evolve together to build the intricate network of genes observed in the organism's biochemical pathways. Gene duplication is highlighted as a crucial event in genome evolution, offering a prime source for genetic material and allowing evolutionary forces to generate novelty. In the [Dalmolin et al, 2011](https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-6-22) paper, the importance of duplication events in the evolutionary history of orthologous groups is assessed by the ratio of components to the number of organisms with items from the group. The study extends to analyze Eukaryotic Clusters of Orthologous Groups (KOG) in STRING, evaluating the evolutionary plasticity and conservation of groups based on component distribution across eukaryotic genomes, proposing an equation for plasticity, and identifying correlations between evolutionary distance and plasticity. The algorithm used in this paper to infer the evolutionary root of orthologous groups, based on a phylogenetic tree from eukaryotes, is implemented as an R/Bioconductor package called [geneplast](https://www.bioconductor.org/packages/release/bioc/html/geneplast.html).
+The development of sequencing technologies in the past two decades allowed the study of the phylogenetic relationship of several model organisms. An interesting question relies on the mechanisms behind how new genes arise and how they interact and evolve together to build the intricate network of genes observed in the organism's biochemical pathways. A strategy is proposed in [Castro et al, 2008](https://doi.org/10.1093/nar/gkn636) and in [Dalmolin et al, 2011](https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-6-22) papers, and it envolves two main steps. First, a consensus phylogeny for eukaryotes is constructed. The second step involves reconstructing the evolutionary scenario for each set of orthologous genes. This step aims to find the most parsimonious mapping of orthologs on the species tree, determining the earliest ortholog for each orthologous group associated with a given gene. The algorithm is implemented as an R/Bioconductor package called [geneplast](https://www.bioconductor.org/packages/release/bioc/html/geneplast.html).
 
 {%
   include figure.html
   caption="From the geneplast vignette, we show the evolutionary rooting scenarios . Red circles indicate the evolutionary roots that best explain the observed orthologs in the species tree."
   image="images/lines/evo1.png"
 %}
 
-# This approach was used to unravel the evolution of biochemical systems, such as human synapses
+# This approach was used to unravel the evolution of biochemical systems, such as... 
+
+## Human apoptosis and genome-stability 
+
+In the [Castro et al., 2008](https://doi.org/10.1093/nar/gkn636), we estimated the evolutionary root for the apoptosis and the genome-stability genes and we found that many cancer genes are located in the earlier, more plastic and less essential region. 
+
+{%
+  include figure.html
+  caption="From Castro et al., 2008. Human apoptosis and genome-stability gene network."
+  image="images/lines/evo5.jpeg"
+%}
+
+## Human synapses
 
 In the [Viscardi et al. 2020](https://doi.org/10.1093/molbev/msaa252) paper, we aimed to reconstruct the evolutionary history of the human neurotransmission gene network by analyzing genes in major neurotransmitter systems. The findings suggest that the emergence of receptor families, particularly ionotropic receptors, at the Human–Cnidaria Last Common Ancestor played a crucial role in the evolution of synapses, even before their establishment in Ctenophores.
 
@@ -23,7 +35,17 @@ In the [Viscardi et al. 2020](https://doi.org/10.1093/molbev/msaa252) paper, we
   image="images/lines/evo2.jpeg"
 %}
 
-# And essential genes
+## The reactive oxygen species system in *Arabidopsis thaliana*
+
+In the [Oliveira et a., 2019](https://www.nature.com/articles/s41598-019-52299-y) paper, we used orthologous groups information from 238 eukaryotes to perform an evolutionary analysis of genes related to reactive oxygen species (ROS) in *Arabidopsis thaliana*. We found two interconnected clusters of ROS genes: one formed by SOD-related, Thiol-redox, peroxidases, and other oxido-reductase; and the other formed entirely by class III peroxidases. Each cluster emerged in different periods of evolution: the cluster formed by SOD-related, Thiol-redox, peroxidases, and other oxido-reductase emerged before opisthokonta-plant divergence; the cluster composed by class III peroxidases emerged after opisthokonta-plant divergence and therefore contained the most recent network components. According to our results, class III peroxidases are in expansion throughout plant evolution, with new orthologs emerging in each evaluated plant clade divergence.
+
+{%
+  include figure.html
+  caption="From Oliveira et al., 2019. *Arabidopsis thaliana* redox protein-protein interaction network."
+  image="images/lines/evo4.jpg"
+%}
+
+## Essential genes in eukaryotes
 
 In [De Souza et al, 2021](https://doi.org/10.1007/s10142-021-00794-9) paper, essential genes from five model eukaryotes were analyzed to determine if they differ in age from non-essential genes. The study compared network properties and investigated the biological functions of essential genes in each species, revealing that essential genes are rooted in different evolutionary periods. Despite varying origins, essential genes tend to be older and more connected than other genes across all evaluated model species.