Journal: Life Science Alliance

Article Title: Concomitant gain and loss of function pathomechanisms in C9ORF72 amyotrophic lateral sclerosis

doi: 10.26508/lsa.202000764

Figure Lengend Snippet: (A) Schematic live setup of motor neurons (MNs) in zona microfluidic chambers (MFCs). The central microgroove of channels formed a physical barrier between the distal (left) and proximal (right) site where the somata were seeded. Only axons, not dendrites, could penetrate the microchannels. (B) Multiparametric high-content signatures corresponding to the maximum intensity projections in , D21. Shown is the Z-score deviation of each tracking parameter from the proximal readout of pooled Ctrl lines (in blue). A set of 11 parameters (bottom labels) was deduced for both the Mito- and LysoTracker, distal versus proximal each, as indicated in the header, resulting in 44 parameters in total. The signatures of mutant FUS (in grey) and TDP43 (in green) were taken from our previous publication to facilitate the comparison to C9ORF (in red, pooled lines, for individual lines refer to ). Horizontal grey lines at 5 and −5 indicate significance thresholds. Note the nearly unaltered trafficking in FUS and TDP43 at the proximal readout as opposed to strong negative parameter deviations at the distal site in FUS distinct from the more modest phenotype of TDP43. Conversely, C9ORF exhibited a flat line similar to control lines, consistent with no phenotype at D21 . (C) Hierarchical cluster dendrogram of entire signatures shown in (B). The hierarchical Z-score (ordinate) indicates the deviation of entire signatures from each other and is not to be mistaken with the individual parameter Z-scores in (B). Blue boxed cluster highlights physiological signatures. Note how the phenotypically unremarkable C9ORF (red) clustered with Ctrl (blue) against the deviate TDP43 (green) and more severe FUS mutant (grey). (D) Hierarchical cluster dendogram of partial signatures comprising either only all distal or proximal parameters (Mito- and LysoTracker, respectively) to compare site-specific phenotypes. Note how both Ctrl parts (blue; distal and proximal) clustered closely with the proximal FUS part (grey) on the right into a physiological super cluster boxed in blue because of the close physiological trafficking state, whereas the drastic organelle arrest in the distal FUS part on the far left (grey) was highly distinct to its physiological parts at the proximal site. TDP43 showed some moderate deviation in its proximal part (green) within the physiological super cluster and a clear deviation in its distal part (green), albeit less drastic than FUS (grey). C9ORF was contained in the physiological super cluster with both the distal and proximal parts because of no phenotype at D21.

Article Snippet: We generated a hierarchical cluster dendrogram with KNIME, as described ( ) ( ).

Techniques: Mutagenesis, Comparison, Control

Journal: PeerJ

Article Title: Variability within a clonal population of Erwinia amylovora disclosed by phenotypic analysis

doi: 10.7717/peerj.13695

Figure Lengend Snippet: Phylogenetic tree using four concatenated housekeeping genes ( gapA , gyrB , infB , and rpoD ) with 2,276 bp from seven Portuguese Erwinia amylovora strains (Ea 230, 320, 390, 490, 630, 680, and 820) (blue), available strains of E. amylovora , and closely related of the genus Erwinia . Every strain used to build the dendrogram are available in . Neighbour-joining method (bootstrap: 1,000 replicates) was used to construct the phylogenetic tree on Geneious Prime software, scale bar represents the number of the nucleotide substitutions per site.

Article Snippet: The dendrogram (UPGMA, bootstrap of 1,000) was obtained resorting to RStudio ( ).

Techniques: Construct, Software

Journal: PeerJ

Article Title: Variability within a clonal population of Erwinia amylovora disclosed by phenotypic analysis

doi: 10.7717/peerj.13695

Figure Lengend Snippet: Dendrogram was built from (black) that summarises the biolog pattern for each strain tested.

Article Snippet: The dendrogram (UPGMA, bootstrap of 1,000) was obtained resorting to RStudio ( ).

Techniques:

Journal: PeerJ

Article Title: Variability within a clonal population of Erwinia amylovora disclosed by phenotypic analysis

doi: 10.7717/peerj.13695

Figure Lengend Snippet: Dendrogram was built from (red) that summarises the biolog pattern for each strain tested.

Article Snippet: The dendrogram (UPGMA, bootstrap of 1,000) was obtained resorting to RStudio ( ).

Techniques:

Journal: PeerJ

Article Title: On the origin of mitochondria: a multilayer network approach

doi: 10.7717/peerj.14571

Figure Lengend Snippet: Dissimilarity graph for the networks of the eight included orthologues. Arrows indicate the values of σ th used to obtain the dendrograms in (Cob: 64%; Cox2: 51%; Cox3: 59%; Nad1: 69%; Nad4: 55%; Nad5: 53%; Nad6: 50%; Nad9: 59%) and in of the (Cob: 70%; Cox2: 61%; Cox3: 67%; Nad1: 72%; Nad4: 68%; Nad5: 67%; Nad6: 67%; Nad9: 66%).

Article Snippet: Dendrograms were constructed using Origin version 2015 (OriginLab, Northampton, MA, USA).

Techniques: