Summary of Study ST002456

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 PR001584. The data can be accessed directly via it's Project DOI: 10.21228/M8Z71C 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.

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Study IDST002456
Study Title1H NMR metabolomics applied to assess the metabolic response of Ruditapes philippinarum clams to sea warming and 17-α-ethinylestradiol exposure
Study Type1H NMR metabolomics to study the effects of warming conditions and exposure to 17-α-ethinylestradiol (EE2) on the polar metabolome of Ruditapes philippinarum clams
Study SummaryIn this study, a comprehensive untargeted 1H NMR metabolomics strategy was applied to measure the metabolic impact of sea warming, in tandem with exposure to EE2, on Ruditapes philippinarum clams. The clams were exposed to five different EE2 concentrations: 0 (control group), 5, 25, 125 and 625 ng/L; either at 17 °C as control temperature or at 21 °C (representing a 4 °C increase, which corresponds to the worst-case warming scenario). The obtained data added important knowledge, unveiling individual metabolic effects of temperature rise and synergetic effects upon EE2 exposure, and paving the way for the definition of new metabolic markers for the monitoring of environmental stressors.
Institute
University of Aveiro
DepartmentCICECO – Aveiro Institute of Materials, Department of Chemistry
LaboratoryMetabolomics Group- CICECO
Last NameRodrigues
First NameJoao A.
AddressUniversity of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
Emailjoao.e.a.rodrigues@gmail.com
Phone00351963481841
Submit Date2023-01-26
Num Groups10
Total Subjects103
Study CommentsThis work was developed within the CICECO-Aveiro Institute of Materials project (UIDB/50011/2020, UIDP/50011/2020 & LA/P/0006/2020) financed by national funds through the FCT/MEC (PIDDAC). We are also grateful to the Portuguese National NMR Network (PTNMR), supported by FCT funds as the NMR spectrometer used is part of PTNMR and partially supported by Infrastructure Project No. 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL, and the FCT through PIDDAC). This work was also financially supported by the project BISPECIAl: BIvalveS under Polluted Environment and ClImate chAnge (POCI-01-0145-FEDER- 028425) funded by FEDER, through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI), and by national funds (OE), through FCT/MCTES. Mónica G. Silva benefited from Research Grant (MSc) (BI/CESAM/0043_2019/POCI-01-0145-FEDER-028425) under the project BISPECIAl: BIvalveS under Polluted Environment and ClImate change PTDC/CTA-AMB/28425/2017 (POCI-01-0145-FEDER-028425).
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2023-10-02
Release Version1
Joao A. Rodrigues Joao A. Rodrigues
https://dx.doi.org/10.21228/M8Z71C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001584
Project DOI:doi: 10.21228/M8Z71C
Project Title:1H NMR metabolomics applied to assess the metabolic response of Ruditapes philippinarum clams to sea warming and 17-α-ethinylestradiol exposure
Project Type:1H NMR metabolomics to study the effects of warming conditions and exposure to 17-α-ethinylestradiol (EE2) on the polar metabolome of Ruditapes philippinarum clams
Project Summary:Hormones correspond to one of the most important classes of PhACs and are usually classified as endocrine-disrupting chemicals (EDCs), due to their ability to alter endocrine system functions, resulting in known adverse health effects on non-target organisms. Among the known EDCs, 17-α-ethinylestradiol (EE2) is characterized by high estrogenic potency, chemical stability, and a tendency to accumulate in aquatic biota. This hormone reaches the environment mainly through human and animal excretion, with conventional WWTP processes not fully managing its removal from treated effluents. Bivalves are excellent model organisms to assess the toxicity of several environmental stressors. Alongside the impacts of pollutants, organisms in coastal ecosystems are also subjected to climate change-related factors, such as temperature rise. Water temperature may increase up to 4 °C by 2100 and this is expected to severely impact several aspects of marine organisms’ biology. In addition, these environmental changes are also likely to affect the sensitivity of organisms to pollutants and, hence, pollutants toxicity. In this study, a comprehensive untargeted 1H NMR metabolomics strategy was applied to measure the metabolic impact of sea warming, in tandem with exposure to EE2, on Ruditapes philippinarum clams. The clams were exposed to different EE2 concentrations, either at 17 °C as control temperature or at 21 °C (representing a 4 °C increase, which corresponds to the worst-case warming scenario). The obtained data added important knowledge, unveiling individual metabolic effects of temperature rise and synergetic effects upon EE2 exposure, and paving the way for the definition of new metabolic markers for the monitoring of environmental stressors.
Institute:University of Aveiro
Department:CICECO – Aveiro Institute of Materials, Department of Chemistry
Laboratory:Metabolomics group
Last Name:Gil
First Name:Ana M.
Address:University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
Email:agil@ua.pt
Phone:+351234370707
Funding Source:This work was developed within the CICECO-Aveiro Institute of Materials project (UIDB/50011/2020, UIDP/50011/2020 & LA/P/0006/2020) financed by national funds through the FCT/MEC (PIDDAC). We are also grateful to the Portuguese National NMR Network (PTNMR), supported by FCT funds as the NMR spectrometer used is part of PTNMR and partially supported by Infrastructure Project No. 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL, and the FCT through PIDDAC). This work was also financially supported by the project BISPECIAl: BIvalveS under Polluted Environment and ClImate chAnge (POCI-01-0145-FEDER- 028425) funded by FEDER, through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI), and by national funds (OE), through FCT/MCTES. Mónica G. Silva benefited from Research Grant (MSc) (BI/CESAM/0043_2019/POCI-01-0145-FEDER-028425) under the project BISPECIAl: BIvalveS under Polluted Environment and ClImate change PTDC/CTA-AMB/28425/2017 (POCI-01-0145-FEDER-028425).

Subject:

Subject ID:SU002545
Subject Type:Invertebrate
Subject Species:Ruditapes philippinarum
Taxonomy ID:129788
Height Or Height Range:length: 3.81 ± 0.42 cm; and width: 3.06 ± 0.51 cm
Gender:Male and female

Factors:

Subject type: Invertebrate; Subject species: Ruditapes philippinarum (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA245718bivalves_17C_C0_08bivalves_17C_C0
SA245719bivalves_17C_C0_10bivalves_17C_C0
SA245720bivalves_17C_C0_11bivalves_17C_C0
SA245721bivalves_17C_C0_07bivalves_17C_C0
SA245722bivalves_17C_C0_01bivalves_17C_C0
SA245723bivalves_17C_C0_09bivalves_17C_C0
SA245724bivalves_17C_C0_06bivalves_17C_C0
SA245725bivalves_17C_C0_02bivalves_17C_C0
SA245726bivalves_17C_C0_04bivalves_17C_C0
SA245727bivalves_17C_C0_03bivalves_17C_C0
SA245728bivalves_17C_C0_05bivalves_17C_C0
SA245729bivalves_17C_C125_04bivalves_17C_C125
SA245730bivalves_17C_C125_03bivalves_17C_C125
SA245731bivalves_17C_C125_01bivalves_17C_C125
SA245732bivalves_17C_C125_05bivalves_17C_C125
SA245733bivalves_17C_C125_02bivalves_17C_C125
SA245734bivalves_17C_C125_10bivalves_17C_C125
SA245735bivalves_17C_C125_11bivalves_17C_C125
SA245736bivalves_17C_C125_06bivalves_17C_C125
SA245737bivalves_17C_C125_09bivalves_17C_C125
SA245738bivalves_17C_C125_07bivalves_17C_C125
SA245739bivalves_17C_C125_08bivalves_17C_C125
SA245740bivalves_17C_C25_10bivalves_17C_C25
SA245741bivalves_17C_C25_09bivalves_17C_C25
SA245742bivalves_17C_C25_08bivalves_17C_C25
SA245743bivalves_17C_C25_12bivalves_17C_C25
SA245744bivalves_17C_C25_11bivalves_17C_C25
SA245745bivalves_17C_C25_03bivalves_17C_C25
SA245746bivalves_17C_C25_02bivalves_17C_C25
SA245747bivalves_17C_C25_07bivalves_17C_C25
SA245748bivalves_17C_C25_04bivalves_17C_C25
SA245749bivalves_17C_C25_01bivalves_17C_C25
SA245750bivalves_17C_C25_05bivalves_17C_C25
SA245751bivalves_17C_C25_06bivalves_17C_C25
SA245752bivalves_17C_C5_03bivalves_17C_C5
SA245753bivalves_17C_C5_04bivalves_17C_C5
SA245754bivalves_17C_C5_02bivalves_17C_C5
SA245755bivalves_17C_C5_05bivalves_17C_C5
SA245756bivalves_17C_C5_01bivalves_17C_C5
SA245757bivalves_17C_C5_07bivalves_17C_C5
SA245758bivalves_17C_C5_06bivalves_17C_C5
SA245759bivalves_17C_C5_10bivalves_17C_C5
SA245760bivalves_17C_C5_11bivalves_17C_C5
SA245761bivalves_17C_C5_09bivalves_17C_C5
SA245762bivalves_17C_C5_08bivalves_17C_C5
SA245763bivalves_17C_C625_08bivalves_17C_C625
SA245764bivalves_17C_C625_09bivalves_17C_C625
SA245765bivalves_17C_C625_11bivalves_17C_C625
SA245766bivalves_17C_C625_10bivalves_17C_C625
SA245767bivalves_17C_C625_07bivalves_17C_C625
SA245768bivalves_17C_C625_06bivalves_17C_C625
SA245769bivalves_17C_C625_01bivalves_17C_C625
SA245770bivalves_17C_C625_03bivalves_17C_C625
SA245771bivalves_17C_C625_02bivalves_17C_C625
SA245772bivalves_17C_C625_04bivalves_17C_C625
SA245773bivalves_17C_C625_05bivalves_17C_C625
SA245774bivalves_21C_C0_07bivalves_21C_C0
SA245775bivalves_21C_C0_08bivalves_21C_C0
SA245776bivalves_21C_C0_09bivalves_21C_C0
SA245777bivalves_21C_C0_06bivalves_21C_C0
SA245778bivalves_21C_C0_10bivalves_21C_C0
SA245779bivalves_21C_C0_05bivalves_21C_C0
SA245780bivalves_21C_C0_01bivalves_21C_C0
SA245781bivalves_21C_C0_02bivalves_21C_C0
SA245782bivalves_21C_C0_03bivalves_21C_C0
SA245783bivalves_21C_C0_04bivalves_21C_C0
SA245784bivalves_21C_C125_03bivalves_21C_C125
SA245785bivalves_21C_C125_01bivalves_21C_C125
SA245786bivalves_21C_C125_04bivalves_21C_C125
SA245787bivalves_21C_C125_02bivalves_21C_C125
SA245788bivalves_21C_C125_06bivalves_21C_C125
SA245789bivalves_21C_C125_05bivalves_21C_C125
SA245790bivalves_21C_C125_08bivalves_21C_C125
SA245791bivalves_21C_C125_09bivalves_21C_C125
SA245792bivalves_21C_C125_07bivalves_21C_C125
SA245793bivalves_21C_C25_07bivalves_21C_C25
SA245794bivalves_21C_C25_08bivalves_21C_C25
SA245795bivalves_21C_C25_06bivalves_21C_C25
SA245796bivalves_21C_C25_09bivalves_21C_C25
SA245797bivalves_21C_C25_02bivalves_21C_C25
SA245798bivalves_21C_C25_05bivalves_21C_C25
SA245799bivalves_21C_C25_03bivalves_21C_C25
SA245800bivalves_21C_C25_01bivalves_21C_C25
SA245801bivalves_21C_C25_04bivalves_21C_C25
SA245802bivalves_21C_C5_04bivalves_21C_C5
SA245803bivalves_21C_C5_02bivalves_21C_C5
SA245804bivalves_21C_C5_01bivalves_21C_C5
SA245805bivalves_21C_C5_05bivalves_21C_C5
SA245806bivalves_21C_C5_03bivalves_21C_C5
SA245807bivalves_21C_C5_06bivalves_21C_C5
SA245808bivalves_21C_C5_09bivalves_21C_C5
SA245809bivalves_21C_C5_10bivalves_21C_C5
SA245810bivalves_21C_C5_07bivalves_21C_C5
SA245811bivalves_21C_C5_08bivalves_21C_C5
SA245812bivalves_21C_C625_07bivalves_21C_C625
SA245813bivalves_21C_C625_08bivalves_21C_C625
SA245814bivalves_21C_C625_09bivalves_21C_C625
SA245815bivalves_21C_C625_06bivalves_21C_C625
SA245816bivalves_21C_C625_03bivalves_21C_C625
SA245817bivalves_21C_C625_01bivalves_21C_C625
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 103

Collection:

Collection ID:CO002538
Collection Summary:Ruditapes philippinarum clams were collected at the Ria de Aveiro, a shallow coastal system located on the Northwest Atlantic coast of Portugal. Individuals of similar size (length: 3.81 ± 0.42 cm; and width: 3.06 ± 0.51 cm) were selected. For depuration and acclimation to laboratory conditions, all clams were maintained in artificial seawater for 10 days (salinity: 30 ± 1, Tropic Marin® SEA SALT, from Tropic Marine Center), under continuous aeration, constant temperature (17 ± 1 ºC) and a natural photoperiod. Artificial seawater was renewed every 2-3 days and clams were fed every 2-3 days with Algamac Protein Plus (150,000 cells/animal/day) after the 3rd day. After depuration, the organisms were subjected to a chronic toxicity test for 28 days, consisting of exposure to five different EE2 concentrations (Sigma-Aldrich, purity ≥ 98%, MW = 296.40 g/mol, 1 mg/L stock solution in ultrapure water): 0 (control group), 5, 25, 125 and 625 ng/L. To assess the effects of a warming scenario on the impacts of EE2, the experiments were carried out at 17 ± 1 °C (control; mean temperature of sampling area during September: 16 - 19 °C) and at 21 ± 1 °C (worst-case climate change scenario, IPCC, 2021). The aquaria were placed in distinct climatic rooms for each temperature. To reach 21 °C, the temperature was raised by 2 °C, every 2–3 days. For each concentration level and temperature, 12 samples were considered: 4 individuals per aquarium and 3 aquaria per treatment. In each aquarium, a total of 3 L of artificial seawater (salinity: 30 ± 1), continuous aeration, and a natural photoperiod were used. The exposure medium for each condition was renewed weekly, after which EE2 concentration levels were re-established. Mortality was checked daily and found to be null. At the end of the 28-day exposure period, the clams were frozen in liquid nitrogen and stored at – 80 ºC.
Collection Protocol Filename:Bivalves_Experimental_Procedure.docx
Sample Type:Tissue
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002557
Treatment Summary:Sea warming and 17-α-ethinylestradiol exposure. After depuration, the organisms were subjected to a chronic toxicity test for 28 days, consisting of exposure to five different EE2 concentrations: 0 (control group), 5, 25, 125 and 625 ng/L. To assess the effects of a warming scenario on the impacts of EE2, the experiments were carried out at 17 ± 1 °C (control; mean temperature of sampling area during September) and at 21 ± 1 °C (worst-case climate change scenario). The aquaria were placed in distinct climatic rooms for each temperature. To reach 21 °C, the temperature was raised by 2 °C, every 2–3 days. For each concentration level and temperature, 12 samples were considered: 4 individuals per aquarium and 3 aquaria per treatment. In each aquarium, a total of 3 L of artificial seawater (salinity: 30 ± 1), continuous aeration, and a natural photoperiod were used. The exposure medium for each condition was renewed weekly, after which EE2 concentration levels were re-established. Mortality was checked daily and found to be null. At the end of the 28-day exposure period, the clams were frozen in liquid nitrogen and stored at – 80 ºC.
Treatment Protocol Filename:Bivalves_Experimental_Procedure.docx
Treatment Compound:Sea warming and 17-α-ethinylestradiol exposure
Treatment Dose:Clams were exposed to five different EE2 concentrations: 0 (control group), 5, 25, 125 and 625 ng/L. To assess the effects of a warming scenario on the impacts of EE2, the experiments were carried out at 17 ± 1 °C (control) and at 21 ± 1 °C (worst-case climate change scenario).

Sample Preparation:

Sampleprep ID:SP002551
Sampleprep Summary:Metabolite extraction was performed using a water/methanol/chloroform method, as described in (Hines, Oladiran, Bignell et al., 2007). Briefly, the clams´ soft tissue (0.15 g per sample) was ground with a pestle and mortar, in liquid nitrogen, and then transferred to a microtube, followed by the addition of cold methanol (600 µL), ultrapure water (128 µL) and chloroform (300 µL). The mixture was vortexed, left in ice for 10 min and centrifuged (2,500 g, 4 °C, 10 min). The top layer was transferred into a microtube to which chloroform (300 µL) and water (300 µL) were added. The mixture was vortexed and centrifuged (2,500 g, 4 °C, 10 min). The upper layer (aqueous) was transferred into vials, dried in a centrifugal vacuum concentrator (UNIVAP 100H) and stored at −80 °C until NMR analysis.
Sampleprep Protocol Filename:Bivalves_Experimental_Procedure.docx
Processing Storage Conditions:-80℃
Extraction Method:Water/methanol/chloroform method, as described in (Hines, Oladiran, Bignell et al., 2007)
Extract Storage:-80℃
Sample Resuspension:The dried polar extracts of clam samples were resuspended in 600 μL of sodium phosphate buffer (0.1 M in D2O, 99.96% D, pH 7.4, containing 0.5 mM sodium salt of 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, TSP-d4, chemical shift referencing). The mixture was vortexed and centrifuged (16,000 g, 10 min, room temperature) and 550 μL were transferred into 5 mm NMR tubes.
Sample Spiking:0.5 mM sodium salt of 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid (TSP-d4), as a chemical shift reference.

Analysis:

Analysis ID:AN004006
Laboratory Name:Metabolomics group
Analysis Type:NMR
Analysis Protocol File:Bivalves_Experimental_Procedure.docx
Software Version:TopSpin 3.2 and Amix 3.9.14
Operator Name:Joao A. Rodrigues
Detector Type:Bruker Avance III 500 MHz spectrometer
Data Format:fid, 1r

NMR:

NMR ID:NM000263
Analysis ID:AN004006
Instrument Name:Bruker AVANCE III 500 spectrometer
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Spectrometer Frequency:500 MHz
NMR Probe:TXI probe
NMR Solvent:D2O
NMR Tube Size:5 mm NMR tubes
Shimming Method:Topshim
Pulse Sequence:noesypr1d
Water Suppression:presat
Pulse Width:90-degree
Receiver Gain:203
Temperature:298 K
Number Of Scans:256
Dummy Scans:8
Acquisition Time:2.34 s
Relaxation Delay:3 s
Spectral Width:7,002.8 Hz
Num Data Points Acquired:32 k
Line Broadening:0.3 Hz
Zero Filling:64 k
Baseline Correction Method:manual
Chemical Shift Ref Std:0 ppm for TSP-d4
NMR Results File:4._Bivalves_results_data.txt UNITS:ppm
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