GNPS - Pseudomonas fragi LC-MS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive|MS:1001911
ORGANISM(S): 296|pseudomonas Fragi
SUBMITTER: 
Hosein Mohimani Pieter C Dorrestein
PROVIDER: MSV000086956 | GNPS | Thu Feb 25 13:09:00 GMT 2021
REPOSITORIES: GNPS
Similar Datasets
Project description:Time-course pilot culture of Bacteroides thetaiotaomicron VPI-5482 NCBI:txid818 (Zengler Lab UCSD) in diluted BHI enriched with chemical compounds under anaerobic conditions. Data was acquired in positive ion mode.
2021-03-30 | MSV000087130 | GNPS
Project description:Pilot culture of human gut bacteria on diluted BHI enriched with chemical compounds under anaerobic conditions. Data was acquired in positive ion mode.
2021-02-08 | MSV000086821 | GNPS
Project description:Pseudomonas aeruginosa is one of the most frequent pathogen dominant in complicated urinary tract infections (UTI). To unravel the adaptation strategies of P. aeruginosa to the conditions in the urinary tract and to define the underlying regulatory network an artificial growth system mimicking the conditions in the urinary tract was established. Transcriptome analyses were used to investigate the physiological status of P. aeruginosa under this conditions. We performed comparisons to identify genes induced under artificial urinary tract conditions to unravel the adaptive strategies and the underlying regulatory network used by Pseudomonas aeruginosa during urinary tract infections using Affimetrix GeneChips. Pseudomonas aeruginosa wild type strain PAO1 was grown in an artificial in vitro growth system mimicking the conditions in the urinary tract. Therefore, biofilms were grown on the surface of membrane filters placed on agar plates at 37 °C up to the late logarithmic state under aerobic and anaerobic conditions (incubated in an anaerobic beanch). An artificial urine medium (AUM) simulating the averaged urine of an human adult was used as nutrient souce. 10-fold diluted Luria Bertani (LB)-medium was used as reference medium. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. The biofilms were harveted at this time points and resuspsended in 0.9% (w/v) NaCl. The OD578 of biofilm suspension was 0.8 for all tested conditions. First comparison: Identification of genes induced or repressed under aerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown aerobically for 18 h to the late logarithmic phase in biofilms on AUM with the transcriptome profile of the PAO1 strain, which was grown aerobically for 18 h to the late logarithmic phase in biofilms on 10-fold diluted LB. Second comparison: Identification of genes induced or repressed under anaerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown anaerobically for 2 days up to the late logarithmic phase in biofilms on AUM supplemented with 50 mM nitrate with the transcriptome profile of the PAO1 strain, which was grown anaerobically for 2 days up to the late logarithmic phase in biofilms on 10-fold diluted LB supplemented with 50 mM nitrate.
2013-06-30 | E-GEOD-33160 | biostudies-arrayexpress
Project description:Cultures of human gut bacteria [Bacteroides thetaiotaomicron VPI-5482 NCBI:txid818 | Bacteroides vulgatus ATCC 8482 NCBI:txid435590 | Akkermansia muciniphila ATCC BAA-835 NCBI:txid349741 | Bifidobacterium longum subsp. infantis ATCC 15697 NCBI:txid391904] (Zengler Lab UCSD) on diluted BHI enriched with coffee extract or chemical compounds under anaerobic conditions. 50% MeOH:water extracts analyzed by LC-MS/MS performed in an UltiMate 3000 UPLC system (Thermo Scientific) using a Kinetex 1.7 um C18 reversed phase UHPLC column (50 X 2.1 mm) and Maxis Impact Q-TOF mass spectrometer (Bruker Daltonics) equipped with ESI source. Data was acquired in positive ion mode.
2020-11-13 | MSV000086455 | GNPS
Project description:Cultures of human gut bacteria [Bacteroides thetaiotaomicron VPI-5482 NCBI:txid818 | Bacteroides vulgatus ATCC 8482 NCBI:txid435590 | Akkermansia muciniphila ATCC BAA-835 NCBI:txid349741 | Bifidobacterium longum subsp. infantis ATCC 15697 NCBI:txid391904] (Zengler Lab UCSD) on diluted BHI enriched with reference chemical compounds under anaerobic conditions. 50% MeOH:water extracts analyzed by LC-MS/MS performed in an UltiMate 3000 UPLC system (Thermo Scientific) using a Kinetex 1.7 um C18 reversed phase UHPLC column (50 X 2.1 mm) and Maxis Impact Q-TOF mass spectrometer (Bruker Daltonics) equipped with ESI source. Data was acquired in positive ion mode.
2021-01-07 | MSV000086673 | GNPS
Project description:Cultures of human gut bacteria [Bacteroides thetaiotaomicron VPI-5482 NCBI:txid818 | Bacteroides vulgatus ATCC 8482 NCBI:txid435590 | Akkermansia muciniphila ATCC BAA-835 NCBI:txid349741 | Bifidobacterium longum subsp. infantis ATCC 15697 NCBI:txid391904] (Zengler Lab UCSD) on diluted BHI enriched with coffee extract or chemical compounds under anaerobic conditions. 50% MeOH:water extracts analyzed by LC-MS/MS performed in an UltiMate 3000 UPLC system (Thermo Scientific) using a Kinetex 1.7 um C18 reversed phase UHPLC column (50 X 2.1 mm) and Maxis Impact Q-TOF mass spectrometer (Bruker Daltonics) equipped with ESI source. Data was acquired in negative ion mode.
2020-11-13 | MSV000086456 | GNPS
Project description:We aim to compare global transcriptomic analysis of wt and delta-nrdRmutant in Pseudomonas aeruginosa PAO1 during aerobic and anaerobic conditions.
2016-06-27 | E-MTAB-3006 | biostudies-arrayexpress
Project description:RNAseq of microaerobic and aerobic cultures in LB+KNO3 of the Antarctic bacterium Pseudomonas extremaustralis
2017-11-17 | E-MTAB-5440 | biostudies-arrayexpress
Project description:The anaerobic metabolism of the opportunistic pathogen Pseudomonas aeruginosa is important for growth and survival during persistent infections. The two Fnr-type transcription factors Anr and Dnr regulate different parts of the underlying network. Both are proposed to bind to a non-distinguishable DNA sequence named Anr box. The aim of this study was the identification of genes induced under anaerobic conditions in the P. aeruginosa wild type and identification of genes under control of the Anr or Dnr regulators. We performed three comparisons to identify genes induced under anaerobic denitrifying conditions in the P. aeruginosa wild type strain and genes which are under control of the Anr or Dnr regulators under these anaerobic conditions. Since the anr and dnr mutant strains do not grow under anaerobic denitrifying conditions, we applied anaerobic shift experiments. Pseudomonas aeruginosa was grown in a modified AB minimal medium, containing 25 µM FeSO4, 20 mM glucose and 50 mM NaNO3. The 200 ml aerobic cultures were grown in 1 l Erlenmeyer flasks at 37 oC and 300 rpm. The aerobic culture was grown to an OD578 of 0.3. For the aerobic culture, cells were harvested at this point. For the anaerobic shift experiments 130 ml of the respective aerobic culture were transferred to a 135 ml sealed serum flask. Control experiments verified that oxygen tension decreased within 3 - 5 min below the detection limit of an oxygen electrode. The cells were harvested after incubation for additional 2h under anaerobic conditions. Within these 2h incubation period no growth of the wild type, the anr mutant or the dnr mutant strain was observed. First comparison: Identification of genes induced or repressed under anaerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown under aerobic conditions up to an OD578 of 0.3 with the transcriptome profile of the PAO1 strain, which was first grown under aerobic conditions up to an OD578 of 0.3 and than shifted to anaerobic conditions by transfer to a sealed serum flask and further incubated for two hours under anaerobic conditions. Second comparison: Identification of genes regulated differently in the anr mutant strain PAO6261. Here we compared the transcriptome profile of the P. aeruginosa wild type PAO1 with the transcriptome profile of the P. aeruginosa anr mutant strain PAO6261. Both strains were harvested after 2h incubation under anaerobic conditions. Third comparison: Identification of genes regulated differently in the dnr mutant strain RM536. Here we compared the transcriptome profile of the P. aeruginosa wild type PAO1 with the transcriptome profile of the P. aeruginosa dnr mutant strain RM536. Both strains were harvested after 2h incubation under anaerobic conditions.
2010-07-07 | E-GEOD-17179 | biostudies-arrayexpress
Project description:To assess the role of two redox-sensitive transcriptional regulators, RoxSR and ANR, in Pseudomonas aeruginosa under aerobic conditions, microarray analysis was performed. Transcriptome profiles of roxSR mutant and anr mutant aerobically grown in LB medium were determined by Affymetrix GeneChip at both the exponential phase and early stationary phase and compared to that of the wild type strain.
2009-07-31 | GSE17296 | GEO