Summary of Study ST001900
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001195. The data can be accessed directly via it's Project DOI: 10.21228/M87M55 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001900 |
| Study Title | Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites (part II) |
| Study Type | Study part 2 of 2 (independent experiment 2; replication experiment of Study part 1) |
| Study Summary | Previous reports suggest that the maturation rate of malaria parasites within red blood cells (RBC) is not constant for a given species in vivo. For instance, maturation can be influenced by host nutrient status or circadian rhythm. Here we observed in mice that systemic host inflammation, induced by lipopolysaccharide (LPS) conditioning or ongoing acute malaria infection, slowed the progression of a single cohort of parasites from one generation of RBC to the next. LPS-conditioning and acute infection both triggered substantial changes to the metabolomic composition of plasma in which parasites circulated. This altered plasma directly slowed parasite maturation in a manner that could not be rescued by supplementation, consistent with the presence of inhibitory factors. Single-cell transcriptomic assessment of mixed parasite populations, exposed to a short period of systemic host inflammation in vivo, revealed specific impairment in the transcriptional activity and translational capacity of trophozoites compared to rings or schizonts. Thus, we provide in vivo evidence of transcriptomic and phenotypic plasticity of asexual blood-stage Plasmodium parasites when exposed to systemic host inflammation |
| Institute | QIMR Berghofer Medical Research Institute |
| Department | Cell & Molecular Biology Department |
| Laboratory | Precision & Systems Biomedicine |
| Last Name | Stoll |
| First Name | Thomas |
| Address | 300 Herston Road |
| thomas.stoll@qimrberghofer.edu.au | |
| Phone | +61 7 3845 3992 |
| Submit Date | 2021-08-09 |
| Num Groups | 5 |
| Total Subjects | 30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-26 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003087 | AN003088 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Agilent Zorbax HILIC Plus RRHD (100 x 2.1mm,1.8um,95Å) | Agilent Zorbax HILIC Plus RRHD (100 x 2.1mm,1.8um,95Å) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6545 QTOF | Agilent 6545 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
MS:
| MS ID: | MS002869 |
| Analysis ID: | AN003087 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | MS acquisition: The LC/MS platform consisted of a 1290 Infinity II UHPLC coupled to a 6545 QTOF mass spectrometer via Dual AJS ESI source (Agilent, Santa Clara, USA) and was controlled using MassHunter data acquisition software (v.10.1). Assessment of MS instrument performance and usage of reference ions were also performed as described previously. Full scan MS data (m/z 50-1700) was acquired at a scan rate of 2.5 spectra/sec (equals 3224 transients/spectrum) with the following source conditions: Gas temperature 250°C, gas flow 13 L/min, sheath gas temperature and flow at 400°C and 12 L/min, respectively, nebulizer 30 psi, fragmentor 135, capillary voltage at +4500 V and -4000 V, nozzle voltage was zero. Data processing: Positive and negative mode data was analysed separately. Data files (30 sample files, 6 QC files and 3 tube blank extraction files) were loaded into MassHunter Profinder (v 10 SP1, Agilent) and assigned to sample groups. Spectral feature extraction was performed using the recursive feature extraction method employing default settings with minor adjustments: Peak extraction was restricted to retention time (Rt) range 0-6.5 min, compound binning and alignment tolerances were set to 1% + 0.3 min for Rt and 20 ppm + 2 mDa for mass, integrator Agile 2 was used for peak integration, peak filters were set to at least 2500 counts and features must have satisfied filter conditions in at least 75 % of files in at least one sample group. Feature peak area was exported and data cleaning was performed using an in-house R script compiled of the following steps. Features were deleted if they: had a mean QC/tube blank area ratio of < 10; were absent across all QC samples; and had duplicates present. In addition, samples with a TIC scaling factor more than 50% above or below the median TIC were removed. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002870 |
| Analysis ID: | AN003088 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | MS acquisition: The LC/MS platform consisted of a 1290 Infinity II UHPLC coupled to a 6545 QTOF mass spectrometer via Dual AJS ESI source (Agilent, Santa Clara, USA) and was controlled using MassHunter data acquisition software (v.10.1). Assessment of MS instrument performance and usage of reference ions were also performed as described previously. Full scan MS data (m/z 50-1700) was acquired at a scan rate of 2.5 spectra/sec (equals 3224 transients/spectrum) with the following source conditions: Gas temperature 250°C, gas flow 13 L/min, sheath gas temperature and flow at 400°C and 12 L/min, respectively, nebulizer 30 psi, fragmentor 135, capillary voltage at +4500 V and -4000 V, nozzle voltage was zero. Data processing: Positive and negative mode data was analysed separately. Data files (30 sample files, 6 QC files and 3 tube blank extraction files) were loaded into MassHunter Profinder (v 10 SP1, Agilent) and assigned to sample groups. Spectral feature extraction was performed using the recursive feature extraction method employing default settings with minor adjustments: Peak extraction was restricted to retention time (Rt) range 0-6.5 min, compound binning and alignment tolerances were set to 1% + 0.3 min for Rt and 20 ppm + 2 mDa for mass, integrator Agile 2 was used for peak integration, peak filters were set to at least 2500 counts and features must have satisfied filter conditions in at least 75 % of files in at least one sample group. Feature peak area was exported and data cleaning was performed using an in-house R script compiled of the following steps. Features were deleted if they: had a mean QC/tube blank area ratio of < 10; were absent across all QC samples; and had duplicates present. In addition, samples with a TIC scaling factor more than 50% above or below the median TIC were removed. |
| Ion Mode: | NEGATIVE |
