diff --git a/_episodes/03-horizontalGeneTransfer-TDA.md b/_episodes/03-horizontalGeneTransfer-TDA.md index 8d1a938..662017e 100644 --- a/_episodes/03-horizontalGeneTransfer-TDA.md +++ b/_episodes/03-horizontalGeneTransfer-TDA.md @@ -5,9 +5,9 @@ exercises: 15 questions: - "How can I detect HGT with TDA?" objectives: +- "Understand hierarchical data does not have 1-holes" - "Compute the Hamming matrix for applying Persistent Homology." -- "Construct a median complex to detect 1-holes" -- "Entender que lo árboles jerárquicos no tienen 1-holes" + keypoints: - "Horizontal Gene Transfer (HGT) is a phenomenon where an organism transfers genetic material to another one that is not its descendant." - "1-holes can detect HGT." @@ -21,22 +21,16 @@ HGT is crucial in the rapid spread of antibiotic-resistant genes among bacteria, > ## Know more: Mechanisms of HGT > >You can read more about Horizontal Gene Transfer in this [Wikipedia Article](https://en.wikipedia.org/wiki/Horizontal_gene_transfer). -> > For instance the main mechanisms of HGT are the following: -> > - **Transformation:** Direct uptake of DNA from the environment. +> > For instance, the main mechanisms of HGT are the following: +> > - **Transformation:** Direct DNA uptake from the environment. > > - **Transduction:** Transfer of genes by bacteriophages (viruses that infect bacteria). > > - **Conjugation:** Transfer of genetic material between bacteria through direct contact, usually via a structure known as a pilus. > {: .solution} {: .callout} -Topological data analysis (TDA) allows for identifying complex patterns and structures in large genomic datasets, facilitating the detection -of HGT can be a powerful tool for detecting the horizontal transfer of antibiotic resistance genes. -TDA. - -This approach educates your audience on an important topic in microbiology and public health and introduces them to advanced data analysis techniques that are transforming research in these areas. - -### Applying Topological Data Analysis to HGT Detection - -After introducing the concept of horizontal gene transfer (HGT) and its significance, we delve into how topological data analysis (TDA), and more specifically persistent homology, offers a sophisticated approach for detecting HGT within bacterial populations. +Topological data analysis (TDA), in particular persistent homology, allows for +identifying complex patterns and structures in large genomic datasets, +facilitating the detection of HGT of antibiotic resistance genes. **Understanding Persistent Homology in the Context of HGT:** - In a population experiencing only horizontal gene transfer, persistent homology applied to genomic data reveals a notable pattern: we observe non-empty homology only at $H_0$, indicating the presence of connected components in the barcode diagram. This is expected because HGT tends to link different genomes, thereby increasing connectivity without necessarily creating higher-dimensional holes.