| 1. |
- Steffen, Karin, 1989-, et al.
(författare)
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Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges
- 2022
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Ingår i: Scientific Reports. - : NATURE RESEARCH. - 2045-2322. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5 % of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.
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| 2. |
- Carlsson, Henrik, 1987-, et al.
(författare)
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Combining the targeted and untargeted screening of environmental contaminants reveals associations between PFAS exposure and vitamin D metabolism in human plasma.
- 2023
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Ingår i: Environmental Science. - : Royal Society of Chemistry. - 2050-7887 .- 2050-7895. ; 25:6, s. 1116-1130
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Tidskriftsartikel (refereegranskat)abstract
- We have developed, validated, and applied a method for the targeted and untargeted screening of environmental contaminants in human plasma using liquid chromatography high-resolution mass spectrometry (LC-HRMS). The method was optimized for several classes of environmental contaminants, including PFASs, OH-PCBs, HBCDs, and bisphenols. One-hundred plasma samples from blood donors (19-75 years, men n = 50, women n = 50, from Uppsala, Sweden) were analyzed. Nineteen targeted compounds were detected across the samples, with 18 being PFASs and the 19th being OH-PCB (4-OH-PCB-187). Ten compounds were positively associated with age (in order of increasing p-values: PFNA, PFOS, PFDA, 4-OH-PCB-187, FOSA, PFUdA, L-PFHpS, PFTrDA, PFDoA, and PFHpA; p-values ranging from 2.5 × 10-5 to 4.67 × 10-2). Three compounds were associated with sex (in order of increasing p-values: L-PFHpS, PFOS, and PFNA; p-values ranging from 1.71 × 10-2 to 3.88 × 10-2), all with higher concentrations in male subjects compared with female subjects. Strong correlations (0.56-0.93) were observed between long-chain PFAS compounds (PFNA, PFOS, PFDA, PFUdA, PFDoA, and PFTrDA). In the non-targeted data analysis, fourteen unknown features correlating with known PFASs were found (correlation coefficients 0.48-0.99). Five endogenous compounds were identified from these features, all correlating strongly with PFHxS (correlation coefficients 0.59-0.71). Three of the identified compounds were vitamin D3 metabolites, and two were diglyceride lipids (DG 24:6;O). The results demonstrate the potential of combining targeted and untargeted approaches to increase the coverage of compounds detected with a single method. This methodology is well suited for exposomics to detect previously unknown associations between environmental contaminants and endogenous compounds that may be important for human health.
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| 3. |
- Erngren, Ida, 1989-
(författare)
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Analytical method development in liquid chromatography- mass spectrometry based metabolomics
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Metabolomics is the analytical field which aims at analyzing all small molecules, metabolites, in a biological system simultaneously. Currently no analytical methods are able to capture the entire metabolome, therefore, the analytical methods are often developed to be as general as possible. However, as research within the metabolomics field is generally driven by biological questions method development is often overlooked. Moreover, method development in metabolomics is very challenging, as evaluation of the methods are difficult since they are not developed for any particular metabolites. Method development is very important though, data quality and accuracy of relative quantitations is paramount if metabolomics is to be used to answer the biological questions at hand.The articles included in the thesis focus around both analytical method development and applications of metabolomics. In the first paper, head and neck cancer cell lines with different sensitivity to ionizing radiation was investigated using LC-MS based metabolomics. A theory on how the radiation resistant (UM-SCC-74B) cell line could alter its metabolism to handle redox status, DNA repair and DNA methylation was formulated. In the second article the sampling of sponge samples (Geodia barretti) was investigated with regard to its effects on detected metabolite profiles and data quality. It was found that freezing the samples directly was the best alternative which allowed for analysis of most metabolite classes. Storing the samples in solvent lead to a substantial extraction of metabolites to the solvent. For metabolomics, the solvents were more useful than the actual sponge samples that had been stored in solvent. In article three the problems caused by high concentrations of inorganic ions in biological samples in HILIC-ESI-MS analyses was described. The inorganic ions can affect relative quantitation and lead to erroneous results and overly complicated datasets inflated by the extra signals caused by cluster formation. To mitigate the problems caused by the inorganic ions a sample preparation method was developed in article four. The method used cation exchange SPE to trap alkali metal ions which, resulted in less ion-suppression, higher signal intensities of relevant metabolites as well as reduced adduct and cluster formation.In conclusion, this thesis have described projects where metabolomics have been applied to answer biological questions as well as analytical method development in LC-MS based metabolomics. Limitations with current methods was described and possible solutions to improve the methods has been presented.
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| 4. |
- Erngren, Ida, 1989-, et al.
(författare)
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Improved sensitivity in hydrophilic interaction liquid chromatography-electrospray-mass spectrometry after removal of sodium and potassium ions from biological samples
- 2021
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Ingår i: Metabolites. - : MDPI. - 2218-1989. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- Inorganic ions, such as sodium and potassium, are present in all biological matrices and are sometimes also added during sample preparation. However, these inorganic ions are known to hamper electrospray ionization -mass spectrometry (ESI-MS) applications, especially in hydrophilic interaction liquid chromatography (HILIC) where they are retained and can be detected as adducts and clusters with mobile phase components or analytes. The retention of inorganic ions leads to co-elution with analytes and as a result ion-suppression, extensive adduct formation and problems with reproducibility. In the presented work, a sample preparation method using cation exchange solid phase extraction (SPE) was developed to trap Na+ and K+ ions from human blood plasma and head and neck cancer cells for the analysis of small cationic, anionic as well as neutral organic analytes. The investigated analytes were small, hydrophilic compounds typically in focus in metabolomics studies. The samples were analyzed using full-scan HILIC-ESI-quadrupole time of flight (QTOF)-MS with an untargeted, screening approach. Method performance was evaluated using multivariate data analysis as well as relative quantifications, spiking of standards to evaluate linearity of response and post-column infusion to study ion-suppression. In blood plasma, the reduction of sodium and potassium ion concentration resulted in improved sensitivity increased signal intensity for 19 out of 28 investigated analytes, improved linearity of response, reduced ion-suppression and reduced cluster formation as well as adduct formation. Thus, the presented method has significant potential to improve data quality in metabolomics studies.
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| 5. |
- Erngren, Ida, 1989-, et al.
(författare)
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The effects of sampling and storage conditions on the metabolite profile of the marine sponge Geodia barretti
- 2021
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Ingår i: Frontiers in Chemistry. - : Frontiers Media S.A.. - 2296-2646. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Geodia barretti is a marine sponge common in the north Atlantic and waters outside of Norway and Sweden. The sampling and subsequent treatment as well as storage of sponges for metabolomics analyses can be performed in different ways, the most commonly used being freezing (directly upon collection or later) or by storage in solvent, commonly ethanol, followed by freeze-drying. In this study we therefore investigated different sampling protocols and their effects on the detected metabolite profiles in LC-MS. Sponges (G. barretti) were collected outside the Swedish west coast and pieces from three sponge specimens were either flash frozen in liquid nitrogen, frozen later after the collection cruise, stored in ethanol or stored in methanol. The storage solvents as well as the actual sponge pieces were analyzed, all samples were analyzed with hydrophilic interaction liquid chromatography (HILIC) as well as reversed phase liquid chromatography with high resolution mass spectrometry (HRMS) in positive and negative ionization mode. The data were evaluated using multivariate data analysis. The highest metabolite intensities were found in the frozen samples (flash frozen and frozen after sampling cruise) as well as in the storage solvents (methanol and ethanol). Metabolites extracted from the sponge pieces that had been stored in solvent were found in very low intensity, since the majority of metabolites were extracted to the solvents to a high degree. The exception being larger peptides and some lipids. The lowest variation between replicates were found in the flash frozen samples. In conclusion, the preferred method for sampling of sponges for metabolomics was found to be immediate freezing in liquid nitrogen. However, freezing the sponge samples after some time proved to be a reliable method as well, albeit with higher variation between the replicates. Thus, the study highlights the importance of saving ethanol extracts after preservation of specimens; these valuable extracts could be further used in studies of natural products, chemosystematics or metabolomics.
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