0000000000005595
AUTHOR
Jan Oppelt
MOESM8 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 8. The phylogenetic trees of the tp0136 and tp0548 genes. The phylogenetic trees were constructed using the Maximum Likelihood method based on the Tamura–Nei model. The bar scale represents the number of substitutions per site. The analysis involved 14 TPA nucleotide sequences including eight derived from the Chinese samples: SHC-0, SHD-R, SHE-V, SHG-I2, B3, C3, K3, and Q3. The T. pallidum subsp. pertenue Fribourg-Blanc sequence [1] was used as an outgroup. There were totals of 1547 and 1317 positions in the final dataset for tp0136 and tp0548 genes, respectively. For both genes, two separate clusters were identified: one cluster of Nichols-like TPA strains (TPA Lineage 1), …
MOESM2 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 2. Mapping statistics of input read pairs mapped to the reference genomes. Sequencing reads derived from the Chinese strain SRA data were mapped to the Treponema pallidum subsp. pallidum (TPA) SS14 and Nichols reference genomes [6] and to the rabbit genome (Statistics was calculated from post-processed mappings; repetitive and homologous sequences and PCR duplicated reads were excluded from the statistics).
MOESM6 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 6. Analysis of indels (deletions/insertions) between SS14-like and Nichols-like TPA strains. The Nichols genome (CP004010.2) [6] was used as a reference for the comparison of TPA strains.
Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery
Spinocerebellar ataxia type-1 (SCA1) is caused by an abnormally expanded polyglutamine (polyQ) tract in ataxin-1. These expansions are responsible for protein misfolding and self-assembly into intranuclear inclusion bodies (IIBs) that are somehow linked to neuronal death. However, owing to lack of a suitable cellular model, the downstream consequences of IIB formation are yet to be resolved. Here, we describe a nuclear protein aggregation model of pathogenic human ataxin-1 and characterize IIB effects. Using an inducible Sleeping Beauty transposon system, we overexpressed the ATXN1(Q82) gene in human mesenchymal stem cells that are resistant to the early cytotoxic effects caused by the expr…
MOESM7 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 7. Alignment of tprD/tprD2 alleles. tprD and tprD2 alleles were downloaded from the NCBI GenBank database for each reference Nichols and SS14 TPA strain, CP004010.2 and CP004011.1 [6], respectively. While the Nichols reference genome harbors identical copies of tprC and tprD genes, the SS14 reference genome carries the tprD2 allele, which is not identical to the tprC gene and differs from the tprD allele by roughly 320 nucleotides. As shown in the alignment, we were able to identify the tprD2 allele (in positions 800–1791 according to the SS14 tprD2 allele) among the sequencing reads from the Chinese SRA data. The alignment was performed using SeqMan software (DNASTAR, Madis…
Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
[Objective]: Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identifed. Recently, Sun et al. (Oncotarget 2016. https://doi. org/10.18632/oncotarget.10154) described a new “phylogenetic group” (called Lineage 2) among Chinese TPA strains. This lineage exhibited a “mosaic genomic structure” of Nichols-like and SS14-like lineages.
MOESM3 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 3. Genome coverage statistics for individual Chinese strains. Sequencing reads derived from the Chinese strains SRA data were mapped to the TPA SS14 and Nichols reference genomes [6]. The number of bases with a coverage depth of 1 or more, number of bases with more than 10× coverage depth and average/median coverage depth are shown. Statistics were calculated from previously post-processed mappings; repetitive and homologous regions and PCR duplicated reads were excluded from statistical analysis.
MOESM5 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 5. Number of SNVs from whole genome alignments produced by NUCmer. Only SNVs detected in all analyzed genomes (i.e., positions with the “N” base in any of the compared genomes were not considered) were used in the analysis. Genes tp0433 (arp), tp0470, and tp0897 (tprK) were excluded from analyses. Chinese strains are shown in bold.
MOESM1 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 1. Data analysis and methods used in the reanalysis of Chinese Treponema pallidum samples.
MOESM4 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 4. A Genome coverage statistics—number of non-covered bases for individual Chinese strains. SS14 genome (CP004011.1) [6] was used as a reference for mapping; coordinates according to the CP004011.1. The list includes all positions without any coverage by mapped reads. B Genome covearge statistics—number of zero covered bases for individual Chinese strains. Nichols genome (CP004010.2) [6] was used as a reference for mapping; coordinates according to the CP004010.2. The list includes all positions without any coverage by mapped reads.
MOESM9 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 9. Genomic SNVs used for phylogenetic analysis. List of SNVs used for construction of phylogenetic trees. Only SNVs detected in all analyzed genomes (i.e., positions with the “N” base in any of the compared genomes were not considered) were used in the analysis. Genes tp0433 (arp), tp0470, and tp0897 (tprK) were excluded from analyses. Altogether, 2444 unique SNV positions were identified when the TPE Fribourg-Blanc genome sequence was used as an outgroup. Coordinates (positions) and gene annotations according to the SS14 genome (CP04011.1); “NA” = not annotated (IGR, intergenic region); “.” = deletion.