Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562373 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR10041766_1.fastq.gz | Fastqsanger.gz | |||
| SRR10041766_2.fastq.gz | Fastqsanger.gz | |||
| SRR10041767_1.fastq.gz | Fastqsanger.gz | |||
| SRR10041767_2.fastq.gz | Fastqsanger.gz |
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Project description:Treponema pallidum ssp. pallidum, the causative agent of syphilis, can now be cultured continuously in vitro utilizing a tissue culture system, and the multiplication rates are similar to those obtained in experimental infection of rabbits. In this study, the RNA transcript profiles of the T. pallidum Nichols during in vitro culture and rabbit infection were compared to examine whether gene expression patterns differed in these two environments. To this end, RNA preparations were converted to cDNA and subjected to RNA-seq using high throughput Illumina sequencing; reverse transcriptase quantitative PCR was also performed on selected genes for validation of results. The transcript profiles in the in vivo and in vitro environments were remarkably similar, exhibiting a high degree of concordance overall. However, transcript levels of 94 genes (9%) out of the 1,063 predicted genes in the T. pallidum genome were significantly different during rabbit infection versus in vitro culture, varying by up to 8-fold in the two environments. Genes that exhibited significantly higher transcript levels during rabbit infection included those encoding multiple ribosomal proteins, several prominent membrane proteins, glycolysis-associated enzymes, replication initiator DnaA, rubredoxin, thioredoxin, two putative regulatory proteins, and proteins associated with solute transport. In vitro cultured T. pallidum had higher transcript levels of DNA repair proteins, cofactor synthesis enzymes, and several hypothetical proteins. The overall concordance of the transcript profiles may indicate that these environments are highly similar in terms of their effects on T. pallidum physiology and growth, and may also reflect a relatively low level of transcriptional regulation in this reduced genome organism.
2021-10-12 | GSE185709 | GEO
Project description:Treponema pallidum subspecies pallidum (T. pallidum) infection induces significant immune responses, resulting in tissue damage. Gene expression plays an essential role in regulating the progression of syphilis infection. However, little is known about the regulatory role of miRNAs in the immune response to T. pallidum infection. Here, we analyze the differential expression of miRNAs in peripheral blood mononuclear cells (PBMCs) between secondary syphilis (SS) patients and healthy controls and study the correlation between miRNAs expression and clinical features with bioinformatics.
2020-08-19 | GSE156421 | GEO
Project description:Culture-independent targeted-WGS of the syphilis-causing agent Treponema pallidum directly from clinical samples
| PRJNA322283 | ENA
Project description:Raw data files (RAW and mzML) and Scaffold search engine files corresponding to the whole proteome analyses of the syphilis spirochete, Treponema pallidum ssp. pallidum, strain SS14.
| MSV000095818 | MassIVE
Project description:Background A molecular diagnostic test that could directly evaluate Treponema pallidum subspecies pallidum antigens in urine would greatly facilitate the prompt diagnosis of syphilis. Methods A multi-platform high resolution shotgun proteomics approach was used to investigate the presence of T. pallidum proteins in male urine samples collected from individuals with and without syphilis. Study participants were included in an observational cohort study conducted at the Institute of Tropical Medicine, Antwerp, Belgium from 2014 to 2017. In total, N = 60 individuals were included in this sub-study, including n = 36 with early symptomatic stage (primary/secondary), n = 13 early latent and n = 5 late latent stage and n = 6 controls. Almost all participants were HIV-positive (56/60; 93 %) and identified as men who have sex with men (MSM) (59/60; 98 %). Sixteen (27 %) individuals were serum PCR positive for T. pallidum at the time of diagnosis. Ten pools containing urine from six participants (±1.5 mL per individual) were created based on clinical staging. Urine protein was extracted from the pools by a two-step molecular weight cut-off centrifugal filtration to remove large proteins and non-protein material. Samples were digested, subjected to multi-dimensional liquid chromatographic separation based on hydrophobicity and were analysed with matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and/or liquid chromatography- electrospray ionization quadruple ion mobility time-of-flight high-definition mass spectrometry (LC/ESI-Q-IM-TOF) in data dependent (MALDI-TOF/TOF) and data independent HDMSE (ESI-IM-Q-TOF) acquisition modes. Results In total, 26 peptides corresponding to four unique T. pallidum proteins were uncovered in four different pooled urine samples, from n = 3 symptomatic (primary/secondary stage; PSS) and n = 1 latent stage pool. Peptides from GTPase Obg (Tp0742) were detected in two separate PSS pooled samples. Protein designations are listed as in the currently annotated T. pallidum proteome available at the UniProt database (Proteome ID: UP000014259) which is related to the genome assembly and annotation ID GCA_000410535.2 listed on the European Nucleotide Archive. Eleven peptides from an uncharacterized protein (Tp0369) and 8 peptides from a protein annotated as the Borrelia-like p83/100 protein (Tp0486) were detected in two different PSS pooled samples. A protein annotated as an ABC superfamily transport protein (Tp0804) was uncovered in a latent stage pooled sample. BLAST analyses revealed low peptide sequence similarity with other pathogenic and commensal prokaryotes and human proteins. Conclusions High resolution mass spectrometric analyses of protein extracts from pooled urine samples resulted in the detection of four T. pallidum proteins. This is the first successful account of applying proteomics approaches to detect treponemal antigens in clinical samples. These proteins could represent potential biomarkers for downstream diagnostic applications.
2018-10-18 | PXD009707 | Pride
Project description:Treponema pallidum subsp. pallidum Genome sequencing
| PRJNA271237 | ENA
Project description:Whole cell lysates from hCMEC/d3 brain microvascular endothelial cells grown in medium and heavy SILAC media and exposed to Treponema pallidum or control media for 5 hours. Prior to Mass-spec analysis, each sample was fractionated into 12 fractions via high-pH reversed-phase liquid chromatography, then each fraction was analyzed by liquid chromatography tandem mass spectrometry.
Exposures were repeated with 4 biological replicates, which we define as individual sample wells. In samples 1&2 medium SILAC cells were exposed to Treponema pallidum, and heavy SILAC cells were exposed to control media. In Samples 3&4 medium SILAC cells were exposed to control media, and heavy SILAC cells were exposed to Treponema pallidum. Cells were grown in D4-lysine (37.5 mg/liter) and 13C6-arginine (21.75 mg/liter) for medium isotope-labeled cells, or 13C615N2-lysine (38.5 mg/liter) and 13C615N4-arginine (22.25 mg/liter) for heavy isotope-labeled cells.
2023-06-26 | MSV000092275 | MassIVE
Project description:Treponema pallidum subsp. pallidum strain:Amoy Genome sequencing
| PRJNA315615 | ENA