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MB Sample ID: SA331979
| Local Sample ID: | R_cont_3 |
| Subject ID: | SU003179 |
| Subject Type: | Plant |
| Subject Species: | Amaranthus caudatus L. |
| Taxonomy ID: | 3567 |
| Gender: | Not applicable |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003179 |
| Subject Type: | Plant |
| Subject Species: | Amaranthus caudatus L. |
| Taxonomy ID: | 3567 |
| Gender: | Not applicable |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| R_cont_3 | SA331979 | FL039271 | Roots | Plant_organs |
| R_cont_3 | SA331979 | FL039271 | Control | Treatment |
Collection:
| Collection ID: | CO003172 |
| Collection Summary: | Amaranthus caudatus L., variety Karwa dauta plants were used in the study. After two weeks culturing in the hydroponic system (nutrient solution (in mmol/L) was as follows: Ca(NO3)2·4H2O - 3.81; KNO3 - 6.44; MgSO4·7H2O - 0.81; KH2PO4 - 1.83; NH4NO3 - 0.87; Fe-EDTA - 0.09; H3BO3 - 0.047; MnSO4·5H2O - 0.007; ZnSO4·7H2O - 0.0007; CuSO4·5H2O - 0.0008; (NH4)2MoO4 - 0.0005), the vessels with six-week-old plants (experimental group) were subjected to Zn2+ stress for one week which was accomplished by supplementation of 300 µmol/L ZnSO4·7H2O in the nutrient solution. Control plants remained untreated. Roots, young and mature leaves of seven-week-old Zn-treated and control plants were collected separately. Approximately 10 and 20 mg of ground dry leaf and root material, respectively, were extracted with 1 mL methanol. After vortexing (3000 g, 30 s) and centrifugation (12000 g, 4 °C, 10 min) of the suspensions, the resulted supernatants were collected. The plant material residues were additionally supplemented with 0.1 mL of deionized water. After a following vortex and centrifugation cycle, the obtained supernatants were combined with the first portions. The total extract volume was 1090 μL. Aliquots (30 μL) of the resulted aq. methanolic extracts were freeze-dried under reduced pressure with Labconco CentriVap centrifugal concentrator. The residues were sequentially derivatized with methoxyamine hydrochloride in pyridine, and N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) according to the established procedure (Leonova et al., 2020, http://dx.doi.org/10.3390/ijms21020567) |
| Sample Type: | Plant leaves and roots |
Treatment:
| Treatment ID: | TR003188 |
| Treatment Summary: | Amaranthus caudatus L., variety Karwa dauta plants were used in the study. After two weeks culturing in the hydroponic system (nutrient solution (in mmol/L) was as follows: Ca(NO3)2·4H2O - 3.81; KNO3 - 6.44; MgSO4·7H2O - 0.81; KH2PO4 - 1.83; NH4NO3 - 0.87; Fe-EDTA - 0.09; H3BO3 - 0.047; MnSO4·5H2O - 0.007; ZnSO4·7H2O - 0.0007; CuSO4·5H2O - 0.0008; (NH4)2MoO4 - 0.0005), the vessels with six-week-old plants (experimental group) were subjected to Zn2+ stress for one week which was accomplished by supplementation of 300 µmol/L ZnSO4·7H2O in the nutrient solution. Control plants remained untreated. Roots, young and mature leaves of seven-week-old Zn-treated and control plants were collected separately. |
| Treatment Protocol Comments: | 6 sample groups: LY_cont - young leaves of control plants; LY_Zn - young leaves of Zn-treated plants; LM_cont - mature leaves of control plants; LM_Zn - mature leaves of Zn-treated plants; R_cont - roots of control plants; R_Zn - roots of Zn-treated plants. |
| Treatment: | Heavy metal stress |
| Treatment Compound: | ZnSO4·7H2O |
| Treatment Route: | supplementation in the nutrient solution |
| Treatment Dose: | 300 µmol/L |
| Treatment Doseduration: | 1 week |
| Plant Plot Design: | total 27 plants in nine vessels |
| Plant Light Period: | 16 : 8 day/night regimen |
| Plant Humidity: | 70-75% relative humidity |
| Plant Temp: | day/night temperatures of 24/18° C |
| Plant Watering Regime: | plant were culturing in the hydroponic system |
| Plant Nutritional Regime: | nutrient solution in mmol/L as follows: Ca(NO3)2·4H2O - 3.81; KNO3 - 6.44; MgSO4·7H2O - 0.81; KH2PO4 - 1.83; NH4NO3 - 0.87; Fe-EDTA - 0.09; H3BO3 - 0.047; MnSO4·5H2O - 0.007; ZnSO4·7H2O - 0.0007; CuSO4·5H2O - 0.0008; (NH4)2MoO4 - 0.0005 |
| Plant Growth Stage: | vegetative stage |
Sample Preparation:
| Sampleprep ID: | SP003185 |
| Sampleprep Summary: | Approximately 10 and 20 mg of ground dry leaf and root material, respectively, were extracted with 1 mL methanol. After vortexing (3000 g, 30 s) and centrifugation (12000 g, 4 °C, 10 min) of the suspensions, the resulted supernatants were collected. The plant material residues were additionally supplemented with 0.1 mL of deionized water. After a following vortex and centrifugation cycle, the obtained supernatants were combined with the first portions. The total extract volume was 1090 μL. Aliquots (30 μL) of the resulted aq. methanolic extracts were freeze-dried under reduced pressure with Labconco CentriVap centrifugal concentrator. The residues were sequentially derivatized with methoxyamine hydrochloride in pyridine, and N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) according to the established procedure (Leonova et al., 2020, http://dx.doi.org/10.3390/ijms21020567). |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | -20℃ |
Combined analysis:
| Analysis ID | AN005019 | AN005020 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | GC | GC |
| Chromatography system | Shimadzu GC-2010 | Shimadzu GC-2010 |
| Column | Phenomenex ZB-5MS (30 m × 0.25 mm, 0.25 μm) | Phenomenex ZB-5MS (30 m × 0.25 mm, 0.25 μm) |
| MS Type | EI | EI |
| MS instrument type | Single quadrupole | Single quadrupole |
| MS instrument name | Shimadzu QP2010 Plus | Shimadzu QP2010 Plus |
| Ion Mode | POSITIVE | POSITIVE |
| Units | peak areas | μmol/g DW |
Chromatography:
| Chromatography ID: | CH003792 |
| Chromatography Summary: | The samples (1μL) were injected with CTC GC PAL Liquid Injector (Shimadzu Deutschland GmbH, Duisburg, Germany) into GC2010 gas chromatograph coupled online to a quadrupole mass selective detector Shimadzu GCMS QP201 operating under the instrumental settings summarized in PR_2.pdf |
| Instrument Name: | Shimadzu GC-2010 |
| Column Name: | Phenomenex ZB-5MS (30 m × 0.25 mm, 0.25 μm) |
| Column Temperature: | 1 min at 40°C, ramp 15°C/min to 70°C, 1 min at 70°C, ramp 6°C/min to 320°C, 12 min at 320°C |
| Flow Gradient: | - |
| Flow Rate: | 1 mL/min |
| Injection Temperature: | 250 |
| Sample Injection: | 1μm |
| Solvent A: | - |
| Solvent B: | - |
| Analytical Time: | 5.5-55 min |
| Chromatography Type: | GC |
| Solvent C: | - |
MS:
| MS ID: | MS004758 |
| Analysis ID: | AN005019 |
| Instrument Name: | Shimadzu QP2010 Plus |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | Targeted GC-MS analysis The samples (1μL) were injected with CTC GC PAL Liquid Injector (Shimadzu Deutschland GmbH, Duisburg, Germany) into GC2010 gas chromatograph coupled online to a quadrupole mass selective detector Shimadzu GCMS QP201. The GC-MS instrumental settings are summarized in PR_2.pdf. The quality of the acquired chromatograms was assessed by verification of the baseline regularity, background MS noise, the symmetry, width and height of chromatographic peaks. To obtain qualitative information about the Zn-related dynamics of individual metabolites, the chromatograms were processed by AMDIS software (www.amdis.net/) to accomplish deconvolution of mass spectra, peak picking, calculation of Kovach retention indices (RI) and annotation of analytes. The analytes annotated in the experimental samples were quantified by integration of the corresponding extracted ion chromatograms (XIC, m/z ± 0.5 Da) for representative intense signals at specific retention times. This analyte quantification procedure was accomplished with XcaliburTM (version 2.0.7), LCquanTM (version 2.5.6, TermoFisher Scientific Inc., Bremen, Germany) and MSDial (http://prime.psc.riken.jp/compms/msdial/main.html) softwares which perform alignment of chromatograms by retention times of analytes and the integration of analyte peak areas. Metabolite identification and targeted absolute quantitative analysis relied on external standardization with 29 authentic standards (oxalic acid, malonic acid, succinic acid, tartaric acid, malic acid, aconitic acid, citric acid, fumaric acid, benzoic acid, ascorbic acid, erythronic acid, glycerol, arabinose, glucose, galactose, myo-inositol, sucrose, urea, Ala, Trp, Ile, Leu, Asn, Asp, Glu, Pro, Val, Ser, Thr) prepared as a total mix serially diluted in the range from 0.2 pmol/μL to 200 pmol/μL. Among these, only 21 compounds were confirmed in leaves and roots of control and Zn2+-treated A. caudatus plants (Result table). |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 240 |
| Ionization: | EI |
| Ionization Energy: | 70eV |
| MS ID: | MS004759 |
| Analysis ID: | AN005020 |
| Instrument Name: | Shimadzu QP2010 Plus |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | Untargeted GC-MS analysis The samples (1μL) were injected with CTC GC PAL Liquid Injector (Shimadzu Deutschland GmbH, Duisburg, Germany) into GC2010 gas chromatograph coupled online to a quadrupole mass selective detector Shimadzu GCMS QP201 operating under the settings summarized in PR_2.pdf. The quality of the acquired chromatograms was assessed by verification of the baseline regularity, background MS noise, the symmetry, width and height of chromatographic peaks. The chromatograms were processed by AMDIS software (www.amdis.net/) to accomplish deconvolution of mass spectra, peak picking, calculation of Kovach retention indices (RI) and annotation of analytes. The further analysis relied on the untargeted approach, i.e. unbiased TIC-based identification of all signals with the signal to noise ratio (S/N) ≥ 3 and relative quantification via direct comparison of individual analyte abundances, derived as integral areas of corresponding peaks in extracted ion chromatograms built for characteristic signals (XIC, m/z ± 0.5 Da) in EI mass spectra. For this, the trimethylsilyl (TMS) and methyl oxime (MEOX)-TMS derivatives underlying all detected individual chromatographic peaks were annotated by retention indexes (calculated by retention time of C8–C20 alkanes, and EI-MS data - the results of spectral similarity search against available EI-MS spectral libraries such as NIST (https://webbook.nist.gov/chemistry/), GMD (http://gmd.mpimp-golm.mpg.de/), HMDB (https://hmdb.ca/), RIKEN Center for Sustainable Resource Science (http://prime.psc.riken.jp/Metabolomics Software/MS-DIAL/) and in-house spectral library. The quantitation results (i.e. integrated peak areas detected in each sample) were organized into a digital matrix, normalized to the dry weights of the samples, filtered to exclude the features not detected in ≥ 20% of the samples, and processed by statistical methods using the Metaboanalyst 5.0 (https://www.metaboanalyst.ca/). |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 240 |
| Ionization: | EI |
| Ionization Energy: | 70eV |
