add visualisation refinement page

_quarto.yml

@@ -28,7 +28,7 @@ book:
     - loading-tree.qmd
     - itol-visualisation-1.qmd
     - make-a-tree.qmd
-#    - playground.qmd        
+    - tree-refinement.qmd
 #    - summary.qmd
 #    - glossary.qmd
 #    - resources.qmd

_variables.yml

@@ -13,3 +13,5 @@ myplace:
   bm211: "https://classes.myplace.strath.ac.uk/course/view.php?id=21574"
   quiz1: ""
   quiz2: ""
+  quiz3: ""
+  quiz4: ""

index.qmd

@@ -27,6 +27,11 @@ By the end of this workshop, students will be able to:
 The workshop is not formally assessed although, as noted above, all the material contained in the workshop is examinable. [**FILL IN TEXT HERE**]
 
 ::: { .callout-important }
-There are three formative exercises, one for each exercise in the workshop, and they can be found on the workshop [MyPlace page]({{< var myplace.bm211 >}}). You should complete these as part of the workshop.
+There are four formative exercises in this workshop, and they can be found on the workshop [MyPlace page]({{< var myplace.bm211 >}}). You should complete these as part of the workshop.
+
+- [Formative quiz 1]({{< var myplace.quiz1 >}})
+- [Formative quiz 1]({{< var myplace.quiz2 >}})
+- [Formative quiz 1]({{< var myplace.quiz3 >}})
+- [Formative quiz 1]({{< var myplace.quiz4 >}})
 :::
 

itol-visualisation-1.qmd

@@ -183,4 +183,23 @@ Rectangular and unrooted phylograms of the same phylogeny.
 To generate an unrooted tree in `iTol`, select `Unrooted` mode in the `Basic` tab:
 
 ![Use the `Circular` mode to generate an unrooted tree in `iToL`](assets/images/itol-control-panel-unrooted.png){#fig-itol-unrooted width=80%}
+:::
+
+## Summary
+
+::: { .callout-note title="Well Done!"}
+After successfully working through this section you should be able to:
+
+- explain the difference between a phylogram and cladogram
+- generate a rectangular phylogram and a rectangular cladogram using `iToL`
+- describe and interpret the _topology_ of a tree
+- describe and interpret _branch lengths_ of a tree
+- explain how rotation of a tree, and clades within the tree, affects what the tree represents
+- generate slanted cladograms, unrooted trees, and circular trees using `iToL`
+:::
+
+::: { .callout-important }
+**Please complete the workshop by answering the questions below in the formative quiz on MyPlace**
+
+- [MyPlace formative quiz]({{< var myplace.quiz2 >}})
 :::

loading-tree.qmd

@@ -196,7 +196,16 @@ Group 4, (`K`, `L`) does form a clade as `K`, `L` and all descendants from their
 Thus, the answer is **only groups 2 and 4 form clades**.
 :::
 
-## MyPlace Quiz
+## Summary
+
+::: { .callout-note title="Well Done!"}
+After successfully working through this section you should be able to:
+
+- upload a phylogenetic tree into `iToL`
+- explain the meaning of branching events and branch lengths in a phylogenetic tree
+- explain how a phylogenetic tree represents history and ancestry
+- explain the concept of a _clade_ in phylogenetics
+:::
 
 ::: { .callout-important }
 **Please answer the questions below in the formative quiz on MyPlace**

make-a-tree.qmd

@@ -1,4 +1,4 @@
-# Making a Phylogenetic Tree
+# Making a Phylogenetic Tree {#sec-making-a-tree}
 
 ## Introduction
 
@@ -15,7 +15,7 @@ Although the principles and the order of actions taken here are the same as we w
 
 ### Scenario
 
-You are a biomedical researcher interested in the pathogen _Burkholderia pseudomallei_, which causes [melioidosis](https://en.wikipedia.org/wiki/Melioidosis) in humans. Depending on whether you live in a medically well-resourced, or poorly-resourced, area the risk of death from infection varies from 10%-40%. The pathogen itself has the capability to infect a range of human cells and evade the immune system, in part because it produces proteins called _effectors_: these are proteins adapted to interfere with host biology and make the environment more favourable for the bacterium.
+You are a biomedical researcher interested in evolution of the pathogen _Burkholderia pseudomallei_, which causes [melioidosis](https://en.wikipedia.org/wiki/Melioidosis) in humans (@Chewapreecha2017-lx). Depending on whether you live in a medically well-resourced, or poorly-resourced, area the risk of death from infection varies from 10%-40%. The pathogen itself has the capability to infect a range of human cells and evade the immune system, in part because it produces proteins called _effectors_: these are proteins adapted to interfere with host biology and make the environment more favourable for the bacterium.
 
 The protein you are studying, BipC, is such an _effector_ protein. Specifically, it is a _translocator_ protein that makes holes in the host's cells, allowing its own effector proteins to enter and manipulate host biochemistry, and also binds to [actin microfilaments](https://en.wikipedia.org/wiki/Actin), disrupting host cell structure.
 
@@ -343,4 +343,22 @@ You will now use `iTol` to visualise the tree you produced. Use what you have le
 The tree file shown in `iTol` should resemble @fig-itol-simpphy-tree.
 
 ![The tree generated for BipC by `Simple Phylogeny`, visualised in `iTol`](assets/images/itol-simpphy-tree.png){#fig-itol-simpphy-tree width=80%}
+:::
+
+## Summary
+
+::: { .callout-note title="Well Done!"}
+After successfully working through this section you should be able to:
+
+- use UniProt to obtain annotation and functional information about a protein sequence
+- use UniProt to identify and download homologues of a protein sequence
+- generate a protein multiple sequence alignment using `MUSCLE`
+- produce a Neighbour-Joining phylogenetic tree using `Simple Phylogeny`
+- visualise a phylogenetic tree using `iToL`
+:::
+
+::: { .callout-important }
+**Please complete the workshop by answering the questions below in the formative quiz on MyPlace**
+
+- [MyPlace formative quiz]({{< var myplace.quiz3 >}})
 :::

references.bib

@@ -75,3 +75,142 @@ @ARTICLE{Perelman2011-jg
   year      =  2011,
   language  = "en"
 }
+
+@ARTICLE{Chewapreecha2017-lx,
+  title     = "Global and regional dissemination and evolution of Burkholderia
+               pseudomallei",
+  author    = "Chewapreecha, Claire and Holden, Matthew T G and Vehkala, Minna
+               and V{\"a}lim{\"a}ki, Niko and Yang, Zhirong and Harris, Simon R
+               and Mather, Alison E and Tuanyok, Apichai and De Smet, Birgit
+               and Le Hello, Simon and Bizet, Chantal and Mayo, Mark and
+               Wuthiekanun, Vanaporn and Limmathurotsakul, Direk and
+               Phetsouvanh, Rattanaphone and Spratt, Brian G and Corander,
+               Jukka and Keim, Paul and Dougan, Gordon and Dance, David A B and
+               Currie, Bart J and Parkhill, Julian and Peacock, Sharon J",
+  journal   = "Nat. Microbiol.",
+  publisher = "Springer Science and Business Media LLC",
+  volume    =  2,
+  number    =  4,
+  month     =  jan,
+  year      =  2017,
+  copyright = "https://www.springernature.com/gp/researchers/text-and-data-mining",
+  language  = "en"
+}
+
+@ARTICLE{Hall2022-pk,
+  title     = "Expanding the Burkholderia pseudomallei Complex with the
+               Addition of Two Novel Species: Burkholderia mayonis sp. nov. and
+               Burkholderia savannae sp. nov",
+  author    = "Hall, Carina M and Baker, Anthony L and Sahl, Jason W and Mayo,
+               Mark and Scholz, Holger C and Kaestli, Mirjam and Schupp, James
+               and Martz, Madison and Settles, Erik W and Busch, Joseph D and
+               Sidak-Loftis, Lindsay and Thomas, Astrid and Kreutzer, Lisa and
+               Georgi, Enrico and Schweizer, Herbert P and Warner, Jeffrey M
+               and Keim, Paul and Currie, Bart J and Wagner, David M",
+  abstract  = "Distinct Burkholderia strains were isolated from soil samples
+               collected in tropical northern Australia (Northern Territory and
+               the Torres Strait Islands, Queensland). Phylogenetic analysis of
+               16S rRNA and whole genome sequences revealed these strains were
+               distinct from previously described Burkholderia species and
+               assigned them to two novel clades within the B. pseudomallei
+               complex (Bpc). Because average nucleotide identity and digital
+               DNA-DNA hybridization calculations are consistent with these
+               clades representing distinct species, we propose the names
+               Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov.
+               Strains assigned to B. mayonis sp. nov. include type strain
+               BDU6T (=TSD-80; LMG 29941; ASM152374v2) and BDU8. Strains
+               assigned to B. savannae sp. nov. include type strain MSMB266T
+               (=TSD-82; LMG 29940; ASM152444v2), MSMB852, BDU18, and BDU19.
+               Comparative genomics revealed unique coding regions for both
+               putative species, including clusters of orthologous genes
+               associated with phage. Type strains of both B. mayonis sp. nov.
+               and B. savannae sp. nov. yielded biochemical profiles distinct
+               from each other and from other species in the Bpc, and profiles
+               also varied among strains within B. mayonis sp. nov. and B.
+               savannae sp. nov. Matrix-assisted laser desorption ionization
+               time-of-flight (MLST) analysis revealed a B. savannae sp. nov.
+               cluster separate from other species, whereas B. mayonis sp. nov.
+               strains did not form a distinct cluster. Neither B. mayonis sp.
+               nov. nor B. savannae sp. nov. caused mortality in mice when
+               delivered via the subcutaneous route. The addition of B. mayonis
+               sp. nov. and B. savannae sp. nov. results in a total of eight
+               species currently within the Bpc. IMPORTANCE Burkholderia
+               species can be important sources of novel natural products, and
+               new species are of interest to diverse scientific disciplines.
+               Although many Burkholderia species are saprophytic, Burkholderia
+               pseudomallei is the causative agent of the disease melioidosis.
+               Understanding the genomics and virulence of the closest
+               relatives to B. pseudomallei, i.e., the other species within the
+               B. pseudomallei complex (Bpc), is important for identifying
+               robust diagnostic targets specific to B. pseudomallei and for
+               understanding the evolution of virulence in B. pseudomallei. Two
+               proposed novel species, B. mayonis sp. nov. and B. savannae sp.
+               nov., were isolated from soil samples collected from multiple
+               locations in northern Australia. The two proposed species belong
+               to the Bpc but are phylogenetically distinct from all other
+               members of this complex. The addition of B. mayonis sp. nov. and
+               B. savannae sp. nov. results in a total of eight species within
+               this significant complex of bacteria that are available for
+               future studies.",
+  journal   = "Appl. Environ. Microbiol.",
+  publisher = "American Society for Microbiology",
+  volume    =  88,
+  number    =  1,
+  pages     = "e0158321",
+  month     =  jan,
+  year      =  2022,
+  keywords  = "BDU6T; Burkholderia; Burkholderia mayonis sp. nov.; Burkholderia
+               pseudomallei complex; Burkholderia savannae sp. nov.; MSMB266T;
+               novel species",
+  copyright = "https://doi.org/10.1128/ASMCopyrightv2",
+  language  = "en"
+}
+
+@ARTICLE{Janesomboon2021-dd,
+  title     = "Detection and differentiation of Burkholderia species with
+               pathogenic potential in environmental soil samples",
+  author    = "Janesomboon, Sujintana and Muangsombut, Veerachat and Srinon,
+               Varintip and Meethai, Chatruthai and Tharinjaroen, Chayada S and
+               Amornchai, Premjit and Withatanung, Patoo and Chantratita,
+               Narisara and Mayo, Mark and Wuthiekanun, Vanaporn and Currie,
+               Bart J and Stevens, Joanne M and Korbsrisate, Sunee",
+  abstract  = "The Burkholderia pseudomallei phylogenetic cluster includes B.
+               pseudomallei, B. mallei, B. thailandensis, B. oklahomensis, B.
+               humptydooensis and B. singularis. Regarded as the only
+               pathogenic members of this group, B. pseudomallei and B. mallei
+               cause the diseases melioidosis and glanders, respectively.
+               Additionally, variant strains of B. pseudomallei and B.
+               thailandensis exist that include the geographically restricted
+               B. pseudomallei that express a B. mallei-like BimA protein
+               (BPBM), and B. thailandensis that express a B. pseudomallei-like
+               capsular polysaccharide (BTCV). To establish a PCR-based assay
+               for the detection of pathogenic Burkholderia species or their
+               variants, five PCR primers were designed to amplify
+               species-specific sequences within the bimA (Burkholderia
+               intracellular motility A) gene. Our multiplex PCR assay could
+               distinguish pathogenic B. pseudomallei and BPBM from the
+               non-pathogenic B. thailandensis and the BTCV strains. A second
+               singleplex PCR successfully discriminated the BTCV from B.
+               thailandensis. Apart from B. humptydooensis, specificity testing
+               against other Burkholderia spp., as well as other Gram-negative
+               and Gram-positive bacteria produced a negative result. The
+               detection limit of the multiplex PCR in soil samples
+               artificially spiked with known quantities of B. pseudomallei and
+               B. thailandensis were 5 and 6 CFU/g soil, respectively.
+               Furthermore, comparison between standard bacterial culture and
+               the multiplex PCR to detect B. pseudomallei from 34 soil
+               samples, collected from an endemic area of melioidosis, showed
+               high sensitivity and specificity. This robust, sensitive, and
+               specific PCR assay will be a useful tool for epidemiological
+               study of B. pseudomallei and closely related members with
+               pathogenic potential in soil.",
+  journal   = "PLoS One",
+  publisher = "Public Library of Science (PLoS)",
+  volume    =  16,
+  number    =  1,
+  pages     = "e0245175",
+  month     =  jan,
+  year      =  2021,
+  copyright = "http://creativecommons.org/licenses/by/4.0/",
+  language  = "en"
+}