Dataset Information

Viscum album mother tinctures metabolome

ABSTRACT: Samples: The plants were harvested from 5 different host threes: Abies alba, Malus domestica, Pinis sylvestris, Quercus sp., Ulmus carpinifolia. Samples were harvested in summer and winter seasons.V. album MT was prepared from fresh plant material according to previous methodology described by our group (Anvisa, 2011; Holandino et al., 2020). The fresh material was fragmented into parts smaller than 5 cm and submitted to an ethanolic maceration process for 21 days at room temperature shaking twice a day. The final alcoholic content ranged from 40 to 50% v/v. The mother tinctures were coded according to the respective host tree and the harvest season, as following: Viscum album subsp. abietis from Abies alba in summer (A-17) or winter (A-18), Viscum album subsp. album from Malus domestica in summer (M-17) or winter (M-18), Viscum album subsp. album from Quercus sp. in summer (Q-17) or winter (Q-18), Viscum album subsp. album from Ulmus carpinifolia in summer (U-17) or winter (U-18), Viscum album subsp. austriacum from Pinus sylvestris in summer (P-17) or winter (P-18). 2) Viscum album mother tinctures analysis by liquid chromatography coupled to high-resolution mass spectrometry: Initially, 1.0 g of mother tincture was weighed and transferred to a 5 mL volumetric flask where a solution 9:1 acetonitrile/water with 0.1% v/v formic acid was added. After homogenization, the solution was centrifuged at 7,056 g for 15 minutes and then 200 microliters of each supernatant were removed for analysis in a DionexUltiMate 3000 liquid Chromatography coupled to a hybrid Quadrupole-Orbitrap high-resolution mass spectrometer (Thermo Q-Exactive Plus) equipped with an electrospray ionization source (ESI). Pooled quality control samples (QC) containing 10 microliters of each MT were also prepared. Chromatography separation was performed in a reversed-phase column (Hypersil Gold C18, 100 mm x 2.1 mm x 3.0 micrometers; Thermo Fisher Scientific). Water with 0.1% v/v of formic acid (A) and acetonitrile with 0.1% v/v of formic acid (B) were used as the mobile phases in an elution gradient of: (i) 0-1 min, 10% B; (ii) 1-16 min, 10-95% B; iii) 16-18 min, 95% B; (iv) 18-18.1 min, 95-10% B; (v) 18.1-22 min 10% B. The flow rate was 0.350 microliters/min and the injection volume 5 microliters. Mass spectra were acquired simultaneously in negative and positive ionization modes in the m/z range of 100-1000 at a resolution of 35k (FWHM) followed by sequential mass spectrometry (MS/MS) experiments ddMS2 top 3 (where the 3 most intense ions of each scan were fragmented automatically). The mass spectrometry conditions were the following: spray voltage 3.9 kV for ESI (+) or 3.6kV for ESI (-), ion transfer capillary 300 C, sheath, and auxiliary gases 45 and 15 arbitrary units, respectively. Data were analyzed by the Xcalibur 2.0.7 program (Thermo Scientific, Bremen, Germany) (Holandino et al., 2020).

INSTRUMENT(S): LTQ Orbitrap, Q Exactive Plus

ORGANISM(S): Viscum Album Subsp. Austriacum (ncbitaxon:104254) Viscum Album Subsp. Abietis (ncbitaxon:104252) Viscum Album Subsp. Album (ncbitaxon:104253)

SUBMITTER: Michelle Nonato de Oliveira Melo

PROVIDER: MSV000090351 | MassIVE |

REPOSITORIES: MassIVE

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Samples: The plants were harvested from 5 different host threes: Abies alba, Malus domestica, Pinis sylvestris, Quercus sp., Ulmus carpinifolia. Samples were harvested in summer and winter seasons.V. album MT was prepared from fresh plant material according to previous methodology described by our group (Anvisa, 2011; Holandino et al., 2020). The fresh material was fragmented into parts smaller than 5 cm and submitted to an ethanolic maceration process for 21 days at room temperature shaking twice a day. The final alcoholic content ranged from 40 to 50% v/v. The mother tinctures were coded according to the respective host tree and the harvest season, as following: Viscum album subsp. abietis from Abies alba in summer (A-17) or winter (A-18), Viscum album subsp. album from Malus domestica in summer (M-17) or winter (M-18), Viscum album subsp. album from Quercus sp. in summer (Q-17) or winter (Q-18), Viscum album subsp. album from Ulmus carpinifolia in summer (U-17) or winter (U-18), Viscum album subsp. austriacum from Pinus sylvestris in summer (P-17) or winter (P-18). 2) Viscum album mother tinctures analysis by liquid chromatography coupled to high-resolution mass spectrometry: Initially, 1.0 g of mother tincture was weighed and transferred to a 5 mL volumetric flask where a solution 9:1 acetonitrile/water with 0.1% v/v formic acid was added. After homogenization, the solution was centrifuged at 7,056 g for 15 minutes and then 200 microliters of each supernatant were removed for analysis in a DionexUltiMate 3000 liquid Chromatography coupled to a hybrid Quadrupole-Orbitrap high-resolution mass spectrometer (Thermo Q-Exactive Plus) equipped with an electrospray ionization source (ESI). Pooled quality control samples (QC) containing 10 microliters of each MT were also prepared. Chromatography separation was performed in a reversed-phase column (Hypersil Gold C18, 100 mm x 2.1 mm x 3.0 micrometers; Thermo Fisher Scientific). Water with 0.1% v/v of formic acid (A) and acetonitrile with 0.1% v/v of formic acid (B) were used as the mobile phases in an elution gradient of: (i) 0-1 min, 10% B; (ii) 1-16 min, 10-95% B; iii) 16-18 min, 95% B; (iv) 18-18.1 min, 95-10% B; (v) 18.1-22 min 10% B. The flow rate was 0.350 microliters/min and the injection volume 5 microliters. Mass spectra were acquired simultaneously in negative and positive ionization modes in the m/z range of 100-1000 at a resolution of 35k (FWHM) followed by sequential mass spectrometry (MS/MS) experiments ddMS2 top 3 (where the 3 most intense ions of each scan were fragmented automatically). The mass spectrometry conditions were the following: spray voltage 3.9 kV for ESI (+) or 3.6kV for ESI (-), ion transfer capillary 300 C, sheath, and auxiliary gases 45 and 15 arbitrary units, respectively. Data were analyzed by the Xcalibur 2.0.7 program (Thermo Scientific, Bremen, Germany) (Holandino et al., 2020).

Project description:We combined heritability analysis of larval development rate with a global expression analysis of this phenotype to investigate genotype by environment interactions across three ecologically relevant temperatures in the Glanville fritillary butterfly (Melitaea cinxia). We focused upon the development of final instar caterpillars which is greatly affected by temperature, and during this stage the caterpillars build up most of the resources for adult life. Second generation, lab reared larvae, initially collected from the Åland metapopulation, were reared in standard lab condition until 6th larval instar. At the beginning of the final (7th) instar stage the larvae were separated into of three temperature conditions: Cold treatment (temperature profile: 8°C 18:00-9:59, 14°C 10:00-11:59, 20°C 12:00-15:59 and 14°C 16:00-17:59) Standard treatment (temperature profile: 15°C 17:00-6:59, 18°C 7:00-8:59, 22°C 9:00-10:59 and 26°C 11:00-16:59) Hot treatment (temperature profile: 8°C 20:00-7:59, 15°C 8:00-9:59, 35°C 10:00-17:59 and 15°C 18:00-19:59) The temperature profiles mimic the diurnal thermal variation of the natural habitat (Åland islands) of samples. Cold treatment mimics a cool and cloudy summer, Standard represents an average temperature profile in the Åland islands and Hot treatment mimics an exceptionally hot and sunny summer, with cold night-time temperatures. The experiment contained several larval families (full-sib) of which three were selected for gene expression analysis. Samples were snap-frozen in liquid nitrogen during mid-development (after 6, 5 and 4 days, for Cold, Standard and Hot respectively). Additional larvae from the same treatments were assayed for survival and growth. Gene expression was analyzed using a mixed model approach to identify genes with potential heritable expression variation (variation among families), genes with plastic expression responses (treatment induced changes) and genes with treatment dependent expression that varies among families (family by treatment interactions).

Project description:Serum samples were randomized and extracted using a modified version of the previously-published Folch procedure, as applied recently [20]. The maternal samples were analysed as one batch and the cord blood samples as a second batch. In short, 10 µL of 0.9% NaCl and, 120 µL of CHCl3: MeOH (2:1, v/v) containing the internal standards (c = 2.5 µg/mL) was added to 10 µL of each serum sample. The standard solution contained the following compounds: 1,2-diheptadecanoyl-sn-glycero-3-phosphoethanolamine (PE(17:0/17:0)), N-heptadecanoyl-D-erythro-sphingosylphosphorylcholine (SM(d18:1/17:0)), N-heptadecanoyl-D-erythro-sphingosine (Cer(d18:1/17:0)), 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine (PC(17:0/17:0)), 1-heptadecanoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(17:0)) and 1-palmitoyl-d31-2-oleoyl-sn-glycero-3-phosphocholine (PC(16:0/d31/18:1)), were purchased from Avanti Polar Lipids, Inc. (Alabaster, AL, USA), and, triheptadecanoylglycerol (TG(17:0/17:0/17:0)) was purchased from Larodan AB (Solna, Sweden). The samples were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min). 60 µL from the lower layer of each sample was then transferred to a glass vial with an insert and 60 µL of CHCl3: MeOH (2:1, v/v) was added to each sample. The samples were stored at -80 °C until analysis. Calibration curves using 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(16:0e/18:1(9Z))), 1-(1Z-octadecenyl)-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(18:0p/18:1(9Z))), 1-stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:0)), 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:1)), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)), 1-(1Z-octadecenyl)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PC(18:0p/22:6)) and 1-stearoyl-2-linoleoyl-sn-glycerol (DG(18:0/18:2)), 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (LPE(18:1)), N-(9Z-octadecenoyl)-sphinganine (Cer(d18:0/18:1(9Z))), 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)) from Avanti Polar Lipids, 1-Palmitoyl-2-Hydroxy-sn-Glycero-3-Phosphatidylcholine (LPC(16:0)), 1,2,3 trihexadecanoalglycerol (TG(16:0/16:0/16:0)), 1,2,3-trioctadecanoylglycerol (TG(18:0/18:0/18:)) and 3β-hydroxy-5-cholestene-3-stearate (ChoE(18:0)), 3β-Hydroxy-5-cholestene-3-linoleate (ChoE(18:2)) from Larodan, were prepared to the following concentration levels: 100, 500, 1000, 1500, 2000 and 2500 ng/mL (in CHCl3:MeOH, 2:1, v/v) including 1250 ng/mL of each internal standard. The samples were analyzed by ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS). Briefly, the UHPLC system used in this work was a 1290 Infinity II system from Agilent Technologies (Santa Clara, CA, USA). The system was equipped with a multi sampler (maintained at 10 °C), a quaternary solvent manager and a column thermostat (maintained at 50 °C). Injection volume was 1 µL and the separations were performed on an ACQUITY UPLC® BEH C18 column (2.1 mm × 100 mm, particle size 1.7 µm) by Waters (Milford, MA, USA). The mass spectrometer coupled to the UHPLC was a 6545 QTOF from Agilent Technologies interfaced with a dual jet stream electrospray (Ddual ESI) ion source. All analyses were performed in positive ion mode and MassHunter B.06.01 (Agilent Technologies) was used for all data acquisition. Quality control was performed throughout the dataset by including blanks, pure standard samples, extracted standard samples and control serum samples, including in-house serum and a pooled QC with an aliquot of each sample was collected and pooled and used as quality control sample. Relative standard deviations (% RSDs) for identified lipids in the control serum samples (n = 13) and in the pooled serum samples (n = 54) were on average 22.4% and 17.5%, respectively.

Project description:<p>The sample to be tested was fully ground into powder in the grinder, 50 mg of the sample was freeze-dried, 1000 μL of the extraction solution containing the inner target was added (methanol:acetonitrile:water, 2:2:1, v/v/v, internal standard concentration 20 mg/L) and vortex mixed for 30 s; then add the steel ball to the 45 Hz grinder for 10 min, ultrasonic 10 min; the sample to be tested is obtained after filtration. When detecting metabolites, metabolite determination was performed based on the LC-MS system, which mainly consists of Waters Acquity I-Class PLUS ultra-high performance liquid tandem and Waters Xevo G2-XS QTof high-resolution mass spectrometer. Meanwhile, the Waters Acquity UPLC HSS T3 column (1.8 um 2.1 x 100 mm) was used as the chromatographic column. Positive and negative ion modes were used to determine the metabolites. Mobile phase A: 0.1% formic acid aqueous solution; Mobile phase B: 0.1% acetonitrile formate. The mobile phase conditions of liquid chromatography were as follows: the flow rate was 400 μL/min, 0.0 min: 98% flow A, 2% flow B; 0.25 min: 98% flow A, 2% flow B, 10.0 min: 2% flow A, 98% flow B; 13.0 min: 2% flow A, 98% flow B; 13.1 min: 98% flow A, 2% flow B; 15.0 min: 98% flow A, 2% flow B. MSe mode controlled by acquisition software (MassLynx v4.2, Waters) was used for primary and secondary mass spectrum data acquisition. ESI ion source parameters are as follows: Capillary voltage, 2500 V (positive ion mode) or -2000 V (negative ion mode); Cone hole voltage, 30 V; Ion source temperature, 100 °C; Desolvent temperature, 500 °C; Air flow rate, 50 L/h; Desolvent gas flow rate, 800 L/h; Plastic-nucleus ratio (m/z) collection range 50-1200 m/z. In the qualitative and quantitative analysis of metabolites, the original data collected by MassLynx v4.2 were processed by the Progenesis QI software for peak extraction, peak alignment, and other data, and the metabolites were identified based on the Progenesis QI software online METLIN database. Then, based on the results of the total score, MS2 score, and mass error (ppm), the metabolites were qualitatively determined.</p>

Project description:Bacteria was grown at 30C in 3 different conditions, i.e. SYN (syngas and minimal medium- ATCC no 1789), AC (0.3% acetate in minimal medium- ATCC no 1789) and TSB (tryptic soy broth). After harvesting by centrifugation, O. carboxidovorans pellets (1g) were lysed in 100 mM Tris-Cl pH 8.0, 2% Triton X-100, 2.6 mg/ml sodium azide, 8 mM PMSF by sonication on ice (4 pulses of 15 s duration each). For each condition of growth 4 samples (1g pellets) were separately treated (i.e. lysed and processed further). The supernatants were treated with 50% cold TCA, and the precipitated protein washed with acetone. The pellets were resuspended in solubilization buffer (7M urea, 20 mM tris-Cl, pH 8.0, 5 mM EDTA, 5 mM MgCl2, 4% CHAPS), and protein concentration was determined using the Plus One 2-D Quant Kit (Amersham) following the manufacturers instructions. Protein samples from each treatment were stored at -80 C. One hundred micrograms of each protein sample was resuspended in 0.1 M ammonium bicarbonate, 5% HPLC grade ACN, reduced in 5 mM DTT (65 C, 5 min), alkylated in 10 mM iodoacetamide (30 C, 30 min), and then trypsin digested until there was no visible pellet (1:50 w/w 37 C, 16 h). Peptides were desalted using a peptide microtrap (Michrom BioResources, Auburn, CA) and eluted using a 0.1% TFA, 95% ACN solution. Desalted peptides were dried in a vacuum centrifuge and resuspended in 20 ?l of 0.1% formic acid. Peptides were separated by strong cation exchange (SCX) liquid chromatography (LC) followed by reverse phase (RP) LC coupled directly in line with electrospray ionization (ESI) tandem mass spectrometry (MS/MS). 2DLC ESI MS/MS was done exactly as described (1). All searches were done using TurboSEQUEST (Bioworks Browser 3.2; Thermo Electron). Mass spectra and tandem mass spectra were searched against all annotated proteins from the strain OM5 including all the annotated plasmid-encoded proteins. Cysteine carbamidomethylation and methionine oxidation (single and double) were included in the search strategy. We used the reverse database functionality in Bioworks 3.2 and searched MS2 data against a reversed OM5 database using identical search criteria.

Dataset Information

Viscum album mother tinctures metabolome

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets