{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000247","ANALYSIS_ID":"AN000389","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Utilization of a global and targeted metabolomics approach to probe the effects nitric oxide on physiology of the pathogen Staphylococcus aureus","PROJECT_TYPE":"Targeted LCMS Metabolomics","PROJECT_SUMMARY":"Staphylococcus aureus is a significant cause of morbidity and mortality in both settings and the community at-large, and methicillin-resistant S. aureus (MRSA) been recently categorized by the CDC as a significant antibiotic-resistant As such, there exists an on-going critical need to study S. aureus genes that growth and resistance to host immune responses, so that their encoded products eventually be evaluated for potential as novel antimicrobial targets. In this S. aureus nitric-oxide (NO) synthase (saNOS) and NO-reductase (saNOR) have been shown to dramatically affect the physiology of this pathogen. Specifically, nos have displayed decreased virulence in both subcutaneous abscess and sepsis of infection, and our own research has suggested that NO produced via saNOS has negative effect on endogenous reactive oxygen species (ROS) accumulation under conditions promoting aerobic respiration and may regulate metabolism in an unknown fashion. Our research has also demonstrated a role for saNOR in cellular NO levels when exposed to exogenous NO donor and may contribute to metabolism under conditions of nitrosative stress. Therefore, overall of this proposal is that modulation of exogenous and endogenous NO levels (by and saNOS, respectively) represent novel metabolic adaptations that contribute S. aureus survival during infection. To this end, a global untargeted approach will be employed to complete two research aims: Aim 1: Compare the of saNOR on S. aureus metabolism when grown in the presence and absence of NO. Aim 2: Identify the effects of endogenous NO produced by saNOS on S. aureus when grown under conditions promoting aerobic respiration. These proposed will help catalogue the exact metabolic changes that occur as a function of and saNOR, which will help unravel the upstream regulatory circuits and cellular targets of both of these enzymes.","INSTITUTE":"University of Florida","DEPARTMENT":"Microbiology and Cell Science","LABORATORY":"Kelly Rice","LAST_NAME":"Rice","FIRST_NAME":"Kelly","ADDRESS":"Room 1130, 1355 Museum Dr, UF campus, 32611-0700","EMAIL":"kcrice@ufl.edu","PHONE":"352-392-1192","FUNDING_SOURCE":"Southeastern Center for Integrated Metabolomics (SECIM) pilot and feasibility NIH U24 DK097209"},

"STUDY":{"STUDY_TITLE":"Determining the metabolic profile of wildtype and nos mutant Staphylococcus grown in media lacking glucose using targeted LC/MS","STUDY_TYPE":"Single time point","STUDY_SUMMARY":"Whole cells from wildtype, nos mutant, SrrAB mutant, SrrAB nos double mutant, complement strains will be isolated for targeted metabolite analysis. In supernatants (extracellular metabolites) will also be analyzed for their profile.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LAST_NAME":"Rice","FIRST_NAME":"Kelly","ADDRESS":"-","EMAIL":"kcrice@ufl.edu","PHONE":"-","NUM_GROUPS":"7","TOTAL_SUBJECTS":"21"},

"SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Staphylococcus aureus","TAXONOMY_ID":"1280","SPECIES_GROUP":"Microorganism"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"13A",
"Factors":{"Strain":"N/A","Sample type":"Media Only"},
"Additional sample data":{"Sample Type":"Fresh TSB No Dextrose Media","Genus_Or_Species":"N/A","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"13B",
"Factors":{"Strain":"N/A","Sample type":"Media Only"},
"Additional sample data":{"Sample Type":"Fresh TSB No Dextrose Media","Genus_Or_Species":"N/A","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"13C",
"Factors":{"Strain":"N/A","Sample type":"Media Only"},
"Additional sample data":{"Sample Type":"Fresh TSB No Dextrose Media","Genus_Or_Species":"N/A","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"9A",
"Factors":{"Strain":"nos complement","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos complement","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"9B",
"Factors":{"Strain":"nos complement","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos complement","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"9C",
"Factors":{"Strain":"nos complement","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos complement","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"3A",
"Factors":{"Strain":"nos complement","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos complement","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"3B",
"Factors":{"Strain":"nos complement","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos complement","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"3C",
"Factors":{"Strain":"nos complement","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos complement","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"8A",
"Factors":{"Strain":"nos mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"8B",
"Factors":{"Strain":"nos mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"8C",
"Factors":{"Strain":"nos mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"2A",
"Factors":{"Strain":"nos mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"2B",
"Factors":{"Strain":"nos mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"2C",
"Factors":{"Strain":"nos mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"12A",
"Factors":{"Strain":"nos SrrAB mutant nos complement","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant nos complement","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"12B",
"Factors":{"Strain":"nos SrrAB mutant nos complement","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant nos complement","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"12C",
"Factors":{"Strain":"nos SrrAB mutant nos complement","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant nos complement","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"6A",
"Factors":{"Strain":"nos SrrAB mutant nos complement","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant nos complement","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"6B",
"Factors":{"Strain":"nos SrrAB mutant nos complement","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant nos complement","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"6C",
"Factors":{"Strain":"nos SrrAB mutant nos complement","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant nos complement","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"11A",
"Factors":{"Strain":"nos SrrAB mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"11B",
"Factors":{"Strain":"nos SrrAB mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"11C",
"Factors":{"Strain":"nos SrrAB mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"5A",
"Factors":{"Strain":"nos SrrAB mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"5B",
"Factors":{"Strain":"nos SrrAB mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"5C",
"Factors":{"Strain":"nos SrrAB mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus nos SrrAB double mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"10A",
"Factors":{"Strain":"SrrAB mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus SrrAB mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"10B",
"Factors":{"Strain":"SrrAB mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus SrrAB mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"10C",
"Factors":{"Strain":"SrrAB mutant","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus SrrAB mutant","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"4A",
"Factors":{"Strain":"SrrAB mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus SrrAB mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"4B",
"Factors":{"Strain":"SrrAB mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus SrrAB mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"4C",
"Factors":{"Strain":"SrrAB mutant","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus SrrAB mutant","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"7A",
"Factors":{"Strain":"Wildtype","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus Wildtype","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"7B",
"Factors":{"Strain":"Wildtype","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus Wildtype","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"7C",
"Factors":{"Strain":"Wildtype","Sample type":"Supernatant"},
"Additional sample data":{"Sample Type":"Supernatant metabolites in TSB No Dextrose","Genus_Or_Species":"Staphylococcus aureus Wildtype","Volume":"1","Units":"ml"}
},
{
"Subject ID":"-",
"Sample ID":"1A",
"Factors":{"Strain":"Wildtype","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus Wildtype","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"1B",
"Factors":{"Strain":"Wildtype","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus Wildtype","Volume":"N/A","Units":"Cell Pellet"}
},
{
"Subject ID":"-",
"Sample ID":"1C",
"Factors":{"Strain":"Wildtype","Sample type":"Whole Cells"},
"Additional sample data":{"Sample Type":"Dry Cell Pellet","Genus_Or_Species":"Staphylococcus aureus Wildtype","Volume":"N/A","Units":"Cell Pellet"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The wildtype S. aureus, nos mutant, SrrAB mutant, nos SrrAB double mutant, and strains will be grown in 40 ml trytic soy broth lacking dextrose for 4 hours. 4 hours growth, all 40 ml was isolated, centrifuged at 4500 rpms and 4C for 10 and then placed on ice. 1 ml of supernatant was removed in duplicate and saved supernatant. The rest of the supernatant was discarded and pellets were in 2 ml PBS, centrifuged at 4500 rpms for 3 minutes (4C). Supernatant was and samples were again resuspended in 2 ml PBS. These samples were split into 2 1 ml aliquots (for metabolite and protein determination) and frozen with liquid Separate media only samples of Tryptic Soy Broth without dextrose were isolated each day (3 total) Samples were stored at -80C. A total of 39 samples (18 whole 18 supernatant, and 3 media) were isolated.","COLLECTION_PROTOCOL_FILENAME":"Rice_Collections_targeted_20150807.txt"},

"TREATMENT":{"TREATMENT_SUMMARY":"nos mutation, SrrAB mutation, and nos SrrAB double mutant mutations were as well as complementation before growing each strain under the same All strains were grown in Tryptic soy broth without dextrose. No additional and/or variables are included in the experiment.","TREATMENT_PROTOCOL_FILENAME":"Rice_Treatments_targeted_20150807.txt"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Amino acid|Organic acid|NAD|NADH","SAMPLEPREP_PROTOCOL_FILENAME":"SB_AA_Assay.pdf;SB_OA_Assay.pdf;SB_NAD_Assay.pdf;SB_NADH_Assay.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Amino acid|Organic acid|NAD|NADH","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Quantiva QQQ","COLUMN_NAME":"Waters Acquity HSS T3 (100 x 2.1mm, 1.8um)","METHODS_FILENAME":"SB_AA_Assay.pdf;SB_OA_Assay.pdf;SB_NAD_Assay.pdf;SB_NADH_Assay.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Sanford Burnham","DETECTOR_TYPE":"Triple Quadrupole"},

"MS":{"INSTRUMENT_NAME":"Thermo Quantiva QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"NADH(Instrument:Thermo Scientific Quantiva) ATP"},

"MS_METABOLITE_DATA":{
"Units":"nmol/mg protein",

"Data":[{"Metabolite":"ADP","13A":"","13B":"","13C":"","9A":"","9B":"","9C":"","3A":"33.0630","3B":"44.3227","3C":"48.4712","8A":"","8B":"","8C":"","2A":"22.8207","2B":"15.5647","2C":"20.2849","12A":"","12B":"","12C":"","6A":"33.3916","6B":"42.2665","6C":"27.9766","11A":"","11B":"","11C":"","5A":"31.0975","5B":"28.2016","5C":"31.0458","10A":"","10B":"","10C":"","4A":"30.2342","4B":"15.3497","4C":"28.7965","7A":"","7B":"","7C":"","1A":"26.0310","1B":"19.1471","1C":"23.3225"},{"Metabolite":"AMP","13A":"","13B":"","13C":"","9A":"","9B":"","9C":"","3A":"7.8345","3B":"37.4850","3C":"18.8616","8A":"","8B":"","8C":"","2A":"5.4021","2B":"12.5162","2C":"4.3169","12A":"","12B":"","12C":"","6A":"7.9553","6B":"16.2918","6C":"10.9659","11A":"","11B":"","11C":"","5A":"10.8553","5B":"11.7168","5C":"10.9759","10A":"","10B":"","10C":"","4A":"5.8020","4B":"9.5182","4C":"8.3126","7A":"","7B":"","7C":"","1A":"7.5527","1B":"35.9440","1C":"9.4644"},{"Metabolite":"ATP","13A":"","13B":"","13C":"","9A":"","9B":"","9C":"","3A":"59.0992","3B":"37.4789","3C":"66.2267","8A":"","8B":"","8C":"","2A":"37.9747","2B":"11.3462","2C":"33.3250","12A":"","12B":"","12C":"","6A":"69.4979","6B":"69.8353","6C":"46.0852","11A":"","11B":"","11C":"","5A":"39.8965","5B":"31.0911","5C":"42.5207","10A":"","10B":"","10C":"","4A":"61.5765","4B":"15.3722","4C":"46.6690","7A":"","7B":"","7C":"","1A":"44.6990","1B":"8.5451","1C":"38.9800"}],

"Metabolites":[{"Metabolite":"ADP","moverz_quant":"428.0, 136.1","ri":"1.51","ri_type":"UFLORIDA_MS_RI","pubchem_id":"6022","inchi_key":"","kegg_id":"C00008","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"AMP","moverz_quant":"348.1, 136.1","ri":"1.51","ri_type":"UFLORIDA_MS_RI","pubchem_id":"6083","inchi_key":"","kegg_id":"C00020","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"ATP","moverz_quant":"508.1, 136.1","ri":"1.50","ri_type":"UFLORIDA_MS_RI","pubchem_id":"5957","inchi_key":"","kegg_id":"C00002","other_id":"","other_id_type":"UFLORIDA_FEATURE"}]
}

}