Summary of Study ST001659
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 PR001064. The data can be accessed directly via it's Project DOI: 10.21228/M85H6W 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 | ST001659 |
| Study Title | Identify putative volatile biomarkers of Coccidioides spp. grown in vitro |
| Study Type | Untargeted metabolomics |
| Study Summary | Valley fever (coccidioidomycosis) is an endemic fungal pneumonia of the North and South American deserts. The causative agents of Valley fever are the dimorphic fungi Coccidioides immitis and C. posadasii, which grow as mycelia in the environment and spherules within the lungs of vulnerable hosts. The current diagnostics for Valley fever are severely lacking due to poor sensitivity and invasiveness, contributing to a 23-day median time-to-diagnosis, and therefore new diagnostic tools are needed. We are working toward the development of a breath-based diagnostic for coccidioidomycosis, and in this initial study we characterized the volatile metabolomes (or volatilomes) of in vitro cultures of Coccidioides. Using solid-phase microextraction and comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC–TOFMS), we characterized the VOCs produced by six strains of each species during mycelial or spherule growth. We detected a total of 353 VOCs that were at least two-fold more abundant in a Coccidioides culture versus medium controls and found the volatile metabolome of Coccidioides is more dependent on growth phase (spherule versus mycelia) than on the species. The volatile profiles of C. immitis and C. posadasii have strong similarities, indicating that a single suite of Valley fever breath biomarkers can be developed to detect both species. |
| Institute | Arizona State University |
| Department | School of Life Sciences |
| Laboratory | Bean Laboratory |
| Last Name | Bean |
| First Name | Heather |
| Address | PO Box 874501 Tempe, AZ 85287 |
| Heather.D.Bean@asu.edu | |
| Phone | 4807273395 |
| Submit Date | 2021-01-22 |
| Publications | Lifecycle dominates the volatilome character of the dimorphic fungus Coccidioides spp Emily A. Higgins Keppler, Heather L. Mead, Bridget M. Barker, Heather D. Bean bioRxiv 2021.01.15.426916; doi: https://doi.org/10.1101/2021.01.15.426916 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | smp |
| Analysis Type Detail | GC-MS |
| Release Date | 2021-03-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001064 |
| Project DOI: | doi: 10.21228/M85H6W |
| Project Title: | Volatile Biomarkers for a Valley Fever Breath Test |
| Project Type: | GCxGC-TOFMS metabolomics |
| Project Summary: | Coccidioidomycosis, or valley fever, is prevalent in AZ, with more than 12,000 new human infections diagnosed every year. In highly endemic areas, e.g., Phoenix and Tucson, up to 30% of community-acquired pneumonia may be caused by Valley fever, and cases are on the rise. The current diagnostics for Valley fever are severely lacking due to invasiveness (biopsy) and poor sensitivity (serology), strongly contributing to an unacceptable 23-day median time-to-diagnosis. There is a critical need for sensitive and non-invasive diagnostics for identifying Valley fever lung infections. Our long-term goal is to substantially shorten the time-to-diagnosis for Valley fever through the development of sensitive and specific breath-based diagnostics for coccidioidomycosis lung infections. The overall objective of this application is to identify and validate putative volatile biomarkers of Coccidioides infections via metabolomics analyses of in vitro cultures, mouse model lung infections, and lung specimens from humans with Valley fever. At the completion of the proposed study, we expect to have identified and validated a panel of 10-15 volatile biomarkers for the sensitive and specific detection of valley fever in lung specimens. |
| Institute: | Arizona State University |
| Department: | School of Life Sciences |
| Laboratory: | Bean Laboratory |
| Last Name: | Bean |
| First Name: | Heather |
| Address: | PO Box 874501, Tempe, AZ, 85287, USA |
| Email: | Heather.D.Bean@asu.edu |
| Phone: | 480-727-3395 |
| Funding Source: | Arizona Biomedical Research Centre New Investigator Award to HDB |
Subject:
| Subject ID: | SU001736 |
| Subject Type: | Fungi |
| Subject Species: | Coccidioides posadasii;Coccidioides immitis |
| Taxonomy ID: | 199306;5501 |
Factors:
Subject type: Fungi; Subject species: Coccidioides posadasii;Coccidioides immitis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Culture tempurature | Culture conditions |
|---|---|---|---|
| SA151948 | RMSCC2010 Mycelia_2 | 30°C | normoxia |
| SA151949 | RMSCC3506 Mycelia_2 | 30°C | normoxia |
| SA151950 | RMSCC2010 Mycelia_3 | 30°C | normoxia |
| SA151951 | RMSCC2010 Mycelia_4 | 30°C | normoxia |
| SA151952 | RMSCC3506 Mycelia_3 | 30°C | normoxia |
| SA151953 | RMSCC2009 Mycelia_3 | 30°C | normoxia |
| SA151954 | RMSCC2006 Mycelia_3 | 30°C | normoxia |
| SA151955 | RS Mycelia_1 | 30°C | normoxia |
| SA151956 | RMSCC2009 Mycelia_2 | 30°C | normoxia |
| SA151957 | B3221 Mycelia_2 | 30°C | normoxia |
| SA151958 | RMSCC2009 Mycelia_4 | 30°C | normoxia |
| SA151959 | RMSCC3506 Mycelia_1 | 30°C | normoxia |
| SA151960 | RMSCC2395 Mycelia_3 | 30°C | normoxia |
| SA151961 | RMSCC2395 Mycelia_4 | 30°C | normoxia |
| SA151962 | RMSCC3505 Mycelia_3 | 30°C | normoxia |
| SA151963 | RMSCC3505 Mycelia_2 | 30°C | normoxia |
| SA151964 | RMSCC2395 Mycelia_1 | 30°C | normoxia |
| SA151965 | RMSCC3505 Mycelia_4 | 30°C | normoxia |
| SA151966 | RMSCC2343 Mycelia_1 | 30°C | normoxia |
| SA151967 | RMSCC2343 Mycelia_3 | 30°C | normoxia |
| SA151968 | RMSCC2343 Mycelia_4 | 30°C | normoxia |
| SA151969 | RMSCC2006 Mycelia_2 | 30°C | normoxia |
| SA151970 | RMSCC2006 Mycelia_4 | 30°C | normoxia |
| SA151971 | Silveira Mycelia_2 | 30°C | normoxia |
| SA151972 | Control Mycelia_2 | 30°C | normoxia |
| SA151973 | RS Mycelia_3 | 30°C | normoxia |
| SA151974 | Control Mycelia_4 | 30°C | normoxia |
| SA151975 | Silveira Mycelia_3 | 30°C | normoxia |
| SA151976 | B3222 Mycelia_4 | 30°C | normoxia |
| SA151977 | B3221 Mycelia_3 | 30°C | normoxia |
| SA151978 | B3221 Mycelia_4 | 30°C | normoxia |
| SA151979 | B3222 Mycelia_2 | 30°C | normoxia |
| SA151980 | B3222 Mycelia_3 | 30°C | normoxia |
| SA151981 | Silveira Mycelia_1 | 30°C | normoxia |
| SA151982 | Control Mycelia_3 | 30°C | normoxia |
| SA151983 | GT-166 Mycelia_4 | 30°C | normoxia |
| SA151984 | GT-166 Mycelia_2 | 30°C | normoxia |
| SA151985 | GT-166 Mycelia_3 | 30°C | normoxia |
| SA151986 | RS Mycelia_4 | 30°C | normoxia |
| SA151987 | RS Spherule_1 | 39°C | 10% CO2 |
| SA151988 | RMSCC3506 Spherule_3 | 39°C | 10% CO2 |
| SA151989 | Silveira Spherule_2 | 39°C | 10% CO2 |
| SA151990 | RMSCC2395 Spherule_2 | 39°C | 10% CO2 |
| SA151991 | Silveira Spherule_3 | 39°C | 10% CO2 |
| SA151992 | RMSCC3505 Spherule_1 | 39°C | 10% CO2 |
| SA151993 | RMSCC3506 Spherule_2 | 39°C | 10% CO2 |
| SA151994 | RMSCC3506 Spherule_1 | 39°C | 10% CO2 |
| SA151995 | RS Spherule_2 | 39°C | 10% CO2 |
| SA151996 | RMSCC3505 Spherule_3 | 39°C | 10% CO2 |
| SA151997 | Silveira Spherule_1 | 39°C | 10% CO2 |
| SA151998 | RS Spherule_3 | 39°C | 10% CO2 |
| SA151999 | RMSCC3505 Spherule_2 | 39°C | 10% CO2 |
| SA152000 | RMSCC2010 Spherule_1 | 39°C | 10% CO2 |
| SA152001 | Control Spherule_2 | 39°C | 10% CO2 |
| SA152002 | Control Spherule_1 | 39°C | 10% CO2 |
| SA152003 | Control Spherule_3 | 39°C | 10% CO2 |
| SA152004 | GT-166 Spherule_1 | 39°C | 10% CO2 |
| SA152005 | GT-166 Spherule_2 | 39°C | 10% CO2 |
| SA152006 | B3222 Spherule_3 | 39°C | 10% CO2 |
| SA152007 | B3222 Spherule_2 | 39°C | 10% CO2 |
| SA152008 | B3221 Spherule_1 | 39°C | 10% CO2 |
| SA152009 | B3221 Spherule_2 | 39°C | 10% CO2 |
| SA152010 | B3221 Spherule_3 | 39°C | 10% CO2 |
| SA152011 | B3222 Spherule_1 | 39°C | 10% CO2 |
| SA152012 | GT-166 Spherule_3 | 39°C | 10% CO2 |
| SA152013 | RMSCC2006 Spherule_1 | 39°C | 10% CO2 |
| SA152014 | RMSCC2343 Spherule_1 | 39°C | 10% CO2 |
| SA152015 | RMSCC2010 Spherule_3 | 39°C | 10% CO2 |
| SA152016 | RMSCC2343 Spherule_2 | 39°C | 10% CO2 |
| SA152017 | RMSCC2343 Spherule_3 | 39°C | 10% CO2 |
| SA152018 | RMSCC2395 Spherule _1 | 39°C | 10% CO2 |
| SA152019 | RMSCC2010 Spherule_2 | 39°C | 10% CO2 |
| SA152020 | RMSCC2009 Spherule_3 | 39°C | 10% CO2 |
| SA152021 | RMSCC2006 Spherule_2 | 39°C | 10% CO2 |
| SA152022 | RMSCC2006 Spherule_3 | 39°C | 10% CO2 |
| SA152023 | RMSCC2009 Spherule_1 | 39°C | 10% CO2 |
| SA152024 | RMSCC2009 Spherule_2 | 39°C | 10% CO2 |
| SA152025 | RMSCC2395 Spherule_1 | 39°C | 10% CO2 |
| Showing results 1 to 78 of 78 |
Collection:
| Collection ID: | CO001729 |
| Collection Summary: | All Coccidioides isolates were grown under BSL-3 containment, using conditions that induce mycelial or spherule growth. For mycelial growth, a 50 ml vented falcon tube containing 10 ml of RPMI media (filter sterilized RPMI 1640, 10% fetal bovine serum) was inoculated with a 1 cm x 1 cm 2xGYE agar plug for each strain. These plates were inoculated using 100 µl of glycerol stock, spread across the plate, and cultured for 30°C for two weeks. Control RPMI media was inoculated with a plug from sterile 2xGYE agar media. Each sample, including media control, was prepared in triplicate. Cultures were grown on a shaking incubator at 150 rpm, 30°C for 96 h. For spherule cultures, a 50 ml vented falcon tube containing 10 ml of RPMI media was inoculated to a final concentration of 1.0 x 10^5 arthroconidia/ml in 1xPBS. Arthroconidia were grown and harvested. Strains RMSCC2343 and RMSCC3505 did not produce enough conidia to achieve 1.0 x 10^5 arthroconidia/ml, and were inoculated at 7.0 x 10^4 and 4.0 x 10^4 arthroconidia/ml, respectively. Control media was inoculated with 1 ml of sterile 1xPBS. Cultures were grown on a shaking incubator at 150 rpm, at 39°C in 10% CO2 for 96 h. Mycelial and spherule cultures were spun at 12,000 x g at 4°C for 10 min to pellet the cells. The supernatant was removed and place in a Nanosep MF Centrifugal Devices with Bio-Inert® Membrane 0.2 µm spin filter and centrifuged at 3,200 x g for 4 min. The filtrate was stored at −80°C until volatile metabolomics analysis. The Coccidioides spp. culture filtrates and media blanks were allowed to thaw at 4°C overnight, and then 2 ml were transferred and sealed into sterilized 10 ml GC headspace vials with PTFE/silicone septum screw caps. All samples were stored for up to 12 d at 4°C until analyzed. |
| Sample Type: | Fungi cells |
Treatment:
| Treatment ID: | TR001749 |
| Treatment Summary: | All Coccidioides isolates were grown under BSL-3 containment, using conditions that induce mycelial or spherule growth. See Collection Protocol for details |
Sample Preparation:
| Sampleprep ID: | SP001742 |
| Sampleprep Summary: | Filtrate samples were heated to 50 degrees Celsius with agitation, and volatiles were sampled for 10 minutes using solid-phase microextraction (SPME) and analyzed using comprehensive gas chromatography coupled to time-of-flight mass spectrometry. |
| Sampleprep Protocol Filename: | ehiggins_invitro_GCxGC_methods.docx |
| Extraction Method: | Solid-phase microextraction (SPME) |
Combined analysis:
| Analysis ID | AN002710 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890B |
| Column | Multidimensional configuration |
| MS Type | EI |
| MS instrument type | GC x GC-TOF |
| MS instrument name | Leco Pegasus 4D GCxGC TOF |
| Ion Mode | POSITIVE |
| Units | Peak areas |
Chromatography:
| Chromatography ID: | CH001999 |
| Chromatography Summary: | Samples analyzed using comprehensive two-dimensional gas chromatography (GCxGC). See attached method file. |
| Instrument Name: | Agilent 7890B |
| Column Name: | Multidimensional configuration |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002507 |
| Analysis ID: | AN002710 |
| Instrument Name: | Leco Pegasus 4D GCxGC TOF |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| MS Comments: | see attached MS methods |
| Ion Mode: | POSITIVE |
