{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001384","ANALYSIS_ID":"AN002310","VERSION":"1","CREATED_ON":"May 26, 2020, 10:06 am"},

"PROJECT":{"PROJECT_TITLE":"Plasmodium falciparum increased time in circulation underlies persistent asymptomatic infection in the dry season","PROJECT_SUMMARY":"The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquitoes to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the host or compromising host survival is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. Parasites isolated during the dry season are transcriptionally distinct from those of subjects with febrile malaria in the transmission season, reflecting longer circulation within each replicative cycle, of parasitized erythrocytes without adhering to the vascular endothelium. Low parasite levels during the dry season are not due to impaired replication, but rather increased splenic clearance of longer-circulating infected erythrocytes. We propose that P. falciparum virulence in areas of seasonal malaria transmission is regulated so that the parasite decreases its endothelial binding capacity, allowing increased splenic clearance and enabling several months of subclinical parasite persistence.","INSTITUTE":"Penn State","LAST_NAME":"Llinas","FIRST_NAME":"Manuel","ADDRESS":"W126 Millennium Science Complex, University Park, PENNSYLVANIA, 16802, USA","EMAIL":"manuel@psu.edu","PHONE":"(814) 867-3527"},

"STUDY":{"STUDY_TITLE":"Plasmodium falciparum increased time in circulation underlies persistent asymptomatic infection in the dry season","STUDY_SUMMARY":"The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquitoes to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the host or compromising host survival is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. Parasites isolated during the dry season are transcriptionally distinct from those of subjects with febrile malaria in the transmission season, reflecting longer circulation within each replicative cycle, of parasitized erythrocytes without adhering to the vascular endothelium. Low parasite levels during the dry season are not due to impaired replication, but rather increased splenic clearance of longer-circulating infected erythrocytes. We propose that P. falciparum virulence in areas of seasonal malaria transmission is regulated so that the parasite decreases its endothelial binding capacity, allowing increased splenic clearance and enabling several months of subclinical parasite persistence.","INSTITUTE":"Penn State","LAST_NAME":"Llinas","FIRST_NAME":"Manuel","ADDRESS":"W126 Millennium Science Complex, University Park, PENNSYLVANIA, 16802, USA","EMAIL":"manuel@psu.edu","PHONE":"(814) 867-3527"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"a244",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a244"}
},
{
"Subject ID":"-",
"Sample ID":"a308",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a308"}
},
{
"Subject ID":"-",
"Sample ID":"a320",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a320"}
},
{
"Subject ID":"-",
"Sample ID":"a325",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a325"}
},
{
"Subject ID":"-",
"Sample ID":"a326",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a326"}
},
{
"Subject ID":"-",
"Sample ID":"a334",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a334"}
},
{
"Subject ID":"-",
"Sample ID":"a351",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a351"}
},
{
"Subject ID":"-",
"Sample ID":"a355",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a355"}
},
{
"Subject ID":"-",
"Sample ID":"a357",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a357"}
},
{
"Subject ID":"-",
"Sample ID":"a373",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a373"}
},
{
"Subject ID":"-",
"Sample ID":"a388",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a388"}
},
{
"Subject ID":"-",
"Sample ID":"a448",
"Factors":{"Genotype":"May"},
"Additional sample data":{"RAW_FILE_NAME":"a448"}
},
{
"Subject ID":"-",
"Sample ID":"b161",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b161"}
},
{
"Subject ID":"-",
"Sample ID":"b170",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b170"}
},
{
"Subject ID":"-",
"Sample ID":"b224",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b224"}
},
{
"Subject ID":"-",
"Sample ID":"b262",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b262"}
},
{
"Subject ID":"-",
"Sample ID":"b322",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b322"}
},
{
"Subject ID":"-",
"Sample ID":"b332",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b332"}
},
{
"Subject ID":"-",
"Sample ID":"b371",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b371"}
},
{
"Subject ID":"-",
"Sample ID":"b385",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b385"}
},
{
"Subject ID":"-",
"Sample ID":"b391",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b391"}
},
{
"Subject ID":"-",
"Sample ID":"b400",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b400"}
},
{
"Subject ID":"-",
"Sample ID":"b443",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b443"}
},
{
"Subject ID":"-",
"Sample ID":"b459",
"Factors":{"Genotype":"MAL"},
"Additional sample data":{"RAW_FILE_NAME":"b459"}
},
{
"Subject ID":"-",
"Sample ID":"poola1",
"Factors":{"Genotype":"May Pool"},
"Additional sample data":{"RAW_FILE_NAME":"poola1"}
},
{
"Subject ID":"-",
"Sample ID":"poola2",
"Factors":{"Genotype":"May Pool"},
"Additional sample data":{"RAW_FILE_NAME":"poola2"}
},
{
"Subject ID":"-",
"Sample ID":"poola3",
"Factors":{"Genotype":"May Pool"},
"Additional sample data":{"RAW_FILE_NAME":"poola3"}
},
{
"Subject ID":"-",
"Sample ID":"poolb1",
"Factors":{"Genotype":"MAL Pool"},
"Additional sample data":{"RAW_FILE_NAME":"poolb1"}
},
{
"Subject ID":"-",
"Sample ID":"poolb2",
"Factors":{"Genotype":"MAL Pool"},
"Additional sample data":{"RAW_FILE_NAME":"poolb2"}
},
{
"Subject ID":"-",
"Sample ID":"poolb3",
"Factors":{"Genotype":"MAL Pool"},
"Additional sample data":{"RAW_FILE_NAME":"poolb3"}
},
{
"Subject ID":"-",
"Sample ID":"qc1",
"Factors":{"Genotype":"Pool"},
"Additional sample data":{"RAW_FILE_NAME":"qc1"}
},
{
"Subject ID":"-",
"Sample ID":"qc2",
"Factors":{"Genotype":"Pool"},
"Additional sample data":{"RAW_FILE_NAME":"qc2"}
},
{
"Subject ID":"-",
"Sample ID":"qc3",
"Factors":{"Genotype":"Pool"},
"Additional sample data":{"RAW_FILE_NAME":"qc3"}
},
{
"Subject ID":"-",
"Sample ID":"blank1",
"Factors":{"Genotype":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"blank1"}
},
{
"Subject ID":"-",
"Sample ID":"blank2",
"Factors":{"Genotype":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"blank2"}
},
{
"Subject ID":"-",
"Sample ID":"blank3",
"Factors":{"Genotype":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"blank3"}
},
{
"Subject ID":"-",
"Sample ID":"blank4",
"Factors":{"Genotype":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"blank4"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"2 mL venous blood was drawn of RDT+ individuals tested at the end of the dry season (May 2012) cross-sectional, and at the first malaria episode of the ensuing transmission season, into EDTA tubes (Vacutainer K3EDTA Tubes, BD) and processed directly at the field site. Plasma (used for metabolomic analysis) was separated by centrifugation and immediately frozen in liquid N2. Buffy coat was discarded and the RBC pellet was further removed of leucocytes in a two-step procedure; first by density gradient on Lymphoprep solution (Fresenius Kabi), followed by Plasmodipur (EuroProxima) filtration.","SAMPLE_TYPE":"Blood (plasma)"},

"TREATMENT":{"TREATMENT_SUMMARY":"None, samples were collected at 2 natural timepoints. RDT+ individuals tested at the end of the dry season (May 2012) cross-sectional, and at the first malaria episode of the ensuing transmission season."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Each plasma sample was split into two independent samples for metabolite extraction. For hydrophilic metabolites, 50µL of plasma was extracted by the addition of 9X volumes of ice cold methanol. Samples were briefly vortexed before centrifuging for 10 minutes to remove precipitated protein. The clarified supernatants were dried under nitrogen gas and resuspended in 100µL (1:2 dilution final). For hydrophobic metabolites, 25µL of plasma was extracted by the addition of 3X volumes of isopropanol. Samples were briefly vortexed and allowed to sit at room temperature for 10 minutes. Samples were then placed at -20 °C to precipitate overnight. Precipitated samples were centrifuged for 20 minutes and the clarified supernatant was diluted to 50% water in a glass LCMS sample vial (1:6 dilution final). Sample groups were pooled to create a group QA and all samples were pooled to create a batch QC, which were injected periodically throughout each run."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Shimadzu Prominence 20 UFLCXR","COLUMN_NAME":"Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex 5600 TripleTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"IDA MS2 method. Ammonium formate and formic acid were added to the positive ESI solvents. Data processing performed using MS-DIAL and annotated using the in silico library. Blank subtraction and analysis was performed in excel.","MS_RESULTS_FILE":"ST001384_AN002310_Results.txt UNITS:Area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}