| 1. |
- Alexandersson, Elin, et al.
(author)
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Band-selective NMR experiments for suppression of unwanted signals in complex mixtures
- 2020
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In: RSC Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 10, s. 32511-32515
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Journal article (peer-reviewed)abstract
- Band-selective NMR experiments are presented that allow selective suppression of unwanted signals (SUN) from the spectra of complex metabolite mixtures. As a result, spectral overlap and dynamic range problems are substantially reduced and low-intensity signals normally covered by dominant signals can be observed. The usefulness of the experiments is exemplified with selective suppression of sugar signals from the NMR spectra of fruit juice and a plant sample. Other possible applications include blood, milk, and wine samples.
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| 2. |
- Alexandersson, Elin, et al.
(author)
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Extended automated quantification algorithm (AQuA) for targeted 1H NMR metabolomics of highly complex samples: application to plant root exudates
- 2023
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In: Metabolomics. - 1573-3882 .- 1573-3890. ; 20
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Journal article (peer-reviewed)abstract
- Introduction The Automated Quantification Algorithm (AQuA) is a rapid and efficient method for targeted NMR-based metabolomics, currently optimised for blood plasma. AQuA quantifies metabolites from 1D-H-1 NMR spectra based on the height of only one signal per metabolite, which minimises the computational time and workload of the method without compromising the quantification accuracy.Objectives To develop a fast and computationally efficient extension of AQuA for quantification of selected metabolites in highly complex samples, with minimal prior sample preparation. In particular, the method should be capable of handling interferences caused by broad background signals.Methods An automatic baseline correction function was combined with AQuA into an automated workflow, the extended AQuA, for quantification of metabolites in plant root exudate NMR spectra that contained broad background signals and baseline distortions. The approach was evaluated using simulations as well as a spike-in experiment in which known metabolite amounts were added to a complex sample matrix.Results The extended AQuA enables accurate quantification of metabolites in 1D-H-1 NMR spectra with varying complexity. The method is very fast (< 1 s per spectrum) and can be fully automated.Conclusions The extended AQuA is an automated quantification method intended for 1D-H-1 NMR spectra containing broad background signals and baseline distortions. Although the method was developed for plant root exudates, it should be readily applicable to any NMR spectra displaying similar issues as it is purely computational and applied to NMR spectra post-acquisition.
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| 3. |
- Bankefors, Johan, et al.
(author)
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A comparison of the metabolic profile on intact tissue and extracts of muscle and liver of juvenile Atlantic salmon (Salmo salar L.) - Application to a short feeding study
- 2011
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In: Food Chemistry. - : Elsevier BV. - 0308-8146 .- 1873-7072. ; 129, s. 1397-1405
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Journal article (peer-reviewed)abstract
- The metabolite profiles from muscles and livers of Atlantic salmon were investigated using high resolution nuclear magnetic resonance (HR-NMR) spectroscopy of aqueous extracts and magic angle spinning (MAS) NMR spectroscopy of intact tissues. Comparison of the data showed that most small metabolites present in the aqueous extracts were also identified in the Carr-Purcell-Meiboom-Gill (CPMG) MAS NMR spectra of the intact tissues. Not only the total omega-3 fatty acid content, but also the EPA and DHA content, in the muscle and liver tissues could be calculated directly from the diffusion-edited MAS NMR spectra without the need for lipophilic extraction. The effect of replacing a normal fish meal during a period of 3 months with a diet containing 20% zygomycete was also investigated by multivariate analysis of the NMR spectra. Principal component analysis (PCA) was used to study the small metabolites distribution in the aqueous extracts of liver and muscles, and revealed that the feed containing zygomycete could have an influence on the metabolites profiles of juvenile Atlantic salmon. (C) 2011 Elsevier Ltd. All rights reserved.
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| 4. |
- Blasi-Romero, Anna, et al.
(author)
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In Vitro Investigation of Thiol-Functionalized Cellulose Nanofibrils as a Chronic Wound Environment Modulator
- 2021
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In: Polymers. - : MDPI. - 2073-4360. ; 13:2
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Journal article (peer-reviewed)abstract
- There is currently a huge need for new, improved therapeutic approaches for the treatment of chronic wounds. One promising strategy is to develop wound dressings capable of modulating the chronic wound environment (e.g., by controlling the high levels of reactive oxygen species (ROS) and proteases). Here, we selected the thiol-containing amino acid cysteine to endow wood-derived cellulose nanofibrils (CNF) with bioactivity toward the modulation of ROS levels and protease activity. Cysteine was covalently incorporated into CNF and the functionalized material, herein referred as cys-CNF, was characterized in terms of chemical structure, degree of substitution, radical scavenging capacity, and inhibition of protease activity. The stability of the thiol groups was evaluated over time, and an in vitro cytotoxicity study with human dermal fibroblasts was performed to evaluate the safety profile of cys-CNF. Results showed that cys-CNF was able to efficiently control the activity of the metalloprotease collagenase and to inhibit the free radical DPPH (1,1-Diphenyl-2-picrylhydrazyl radical), activities that were correlated with the presence of free thiol groups on the nanofibers. The stability study showed that the reactivity of the thiol groups challenged the bioactivity over time. Nevertheless, preparing the material as an aerogel and storing it in an inert atmosphere were shown to be valid approaches to increase the stability of the thiol groups in cys-CNF. No signs of toxicity were observed on the dermal fibroblasts when exposed to cys-CNF (concentration range 0.1-0.5 mg/mL). The present work highlights cys-CNF as a promising novel material for the development of bioactive wound dressings for the treatment of chronic wounds.
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| 5. |
- Djodjic, Faruk, et al.
(author)
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Soils potentially vulnerable to phosphorus losses : speciation of inorganic and organic phosphorus and estimation of leaching losses
- 2023
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In: Nutrient Cycling in Agroecosystems. - : Springer. - 1385-1314 .- 1573-0867. ; 127, s. 225-245
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Journal article (peer-reviewed)abstract
- Eutrophication is an important threat to aquatic ecosystems world-wide, and reliable identification of areas vulnerable to phosphorus (P) losses from diffuse sources is essential for high efficiency of mitigation measures. In this three-step study we investigated (i) relationships between the agronomic (Olsen-P and P-AL) and environmental soil P tests (P-CaCl2) with molecular techniques (P-31 NMR and XANES) followed by (ii) rainfall simulation experiment on topsoil lysimeters and (iii) comparison to long-term field measurements of water quality. Soil samples were collected from seven sites indicated to be vulnerable to nutrient losses due to underlying geology. High P release correlated to standard agronomic P tests (Olsen P, r = 0.67; and P-AL, r = 0.74) and low P sorption capacity (r = - 0.5). High content of iron-bound P compounds indicated more labile P and higher release of dissolved P (r = 0.67). The leaching experiment showed that three out of four soils with high initial soil P status had both higher P leaching concentrations before fertilization (0.83-7.7 mg P l(-1)) compared to soil with low initial soil P status (0.007-0.23 mg P l(-1)), and higher increase in P concentrations after fertilization. Higher soil P sorption capacity reduced P leaching losses. Finally, long-term monitoring data show no significant trends in P losses in a field with low initial P content and moderate P fertilization rates whereas high and over time increasing P losses were recorded in a field with high initial soil P content and repetitively high P fertilization rates.
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| 6. |
- Eriksson Röhnisch, Hanna, et al.
(author)
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AQuA: An Automated Quantification Algorithm for High-Throughput NMR-Based Metabolomics and Its Application in Human Plasma
- 2018
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In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 90, s. 2095-2102
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Journal article (peer-reviewed)abstract
- A key limiting step for high-throughput NMR-based metabolomics is the lack of rapid and accurate tools for absolute quantification of many metabolites. We developed, implemented, and evaluated an algorithm, AQUA (Automated Quantification Algorithm), for targeted metabolite quantification from complex H-1 NMR spectra. AQUA operates based on spectral data extracted from a library consisting of one standard calibration spectrum for each metabolite. It uses one preselected NMR signal per metabolite for determining absolute concentrations and does so by effectively accounting for interferences caused by other metabolites. AQUA was implemented and evaluated using experimental NMR spectra from human plasma. The accuracy of AQUA was tested and confirmed in comparison with a manual spectral fitting approach using the ChenomX software, in which 61 out of 67 metabolites quantified in 30 human plasma spectra showed a goodness-of-fit (r(2)) close to or exceeding 0.9 between the two approaches. In addition, three quality indicators generated by AQUA, namely, occurrence, interference, and positional deviation, were studied. These quality indicators permit evaluation of the results each time the algorithm is operated. The efficiency was tested and confirmed by implementing AQUA for quantification of 67 metabolites in a large data set comprising 1342 experimental spectra from human plasma, in which the whole computation took less than 1 s.
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| 7. |
- Eriksson Röhnisch, Hanna, et al.
(author)
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Improved Automated Quantification Algorithm (AQuA) and Its Application to NMR-Based Metabolomics of EDTA-Containing Plasma
- 2021
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In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 93, s. 8729-8738
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Journal article (peer-reviewed)abstract
- We have recently presented an Automated Quantification Algorithm (AQuA) and demonstrated its utility for rapid and accurate absolute metabolite quantification in H-1 NMR spectra in which positions and line widths of signals were predicted from a constant metabolite spectral library. The AQuA quantifies based on one preselected signal per metabolite and employs library spectra to model interferences from other metabolite signals. However, for some types of spectra, the interspectral deviations of signal positions and line widths can be pronounced; hence, interferences cannot be modeled using a constant spectral library. We here address this issue and present an improved AQuA that handles interspectral deviations. The improved AQuA monitors and characterizes the appearance of specific signals in each spectrum and automatically adjusts the spectral library to model interferences accordingly. The performance of the improved AQuA was tested on a large data set from plasma samples collected using ethylenediaminetetraacetic acid (EDTA) as an anticoagulant (n = 772). These spectra provided a suitable test system for the improved AQuA since EDTA signals (i) vary in intensity, position, and line width between spectra and (ii) interfere with many signals from plasma metabolites targeted for quantification (n = 54). Without the improvement, ca. 20 out of the 54 metabolites would have been overestimated. This included acetylcarnitine and ornithine, which are considered particularly difficult to quantify with H-1 NMR in EDTA-containing plasma. Furthermore, the improved AQuA performed rapidly (<10 s for all spectra). We believe that the improved AQuA provides a basis for automated quantification in other data sets where specific signals show interspectral deviations.
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| 8. |
- Escalante, Alfredo, 1975, et al.
(author)
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Flexible oxygen barrier films from spruce xylan
- 2012
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In: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617 .- 1879-1344. ; 87:4, s. 2381-2387
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Journal article (peer-reviewed)abstract
- Arabinoglucuronoxylan was extracted from Norway spruce and films prepared by casting from aqueous solution. The sugar analysis and NMR confirmed that the spruce xylan was composed of arabinose, 4-O-methyl-glucuronic acid and xylose in a ratio of 1:2:11 respectively. Substitutions of 4-O-methyl-alpha-D-GlcpA at O-2 and of alpha-L-Araf at O-3 on the xylose backbone were found by NOE analysis. NOE cross-peaks indicated as well that there is at least one free xylose on the main chain present between two substitutions. Whether the distribution of side chains was random or in blocks was uncertain. The average molecular weight of the sample was determined by size exclusion chromatography to be 12,780 g/mol. Arabinoglucoronoxylan casting yielded transparent flexible films with an average stress at break of 55 MPa, strain at break of 2.7% and a Young's Modulus 2735 MPa. Wide-angle X-ray scattering analysis showed that the arabinoglucuronoxylan films were totally amorphous. Addition of sorbitol as plasticizer resulted in less strong but more flexible films (strain at break of 5%). Peaks of crystallinity could be seen in X-ray which corresponds to sorbitol crystallizing in distinct phases. The dynamic mechanical analysis showed that the arabinoglucuronoxylan film softened at a later relative humidity (80% RH) in comparison with plasticized films (60% RH). The films showed low oxygen permeability and thus have a potential application in food packaging.
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| 9. |
- Furevi, Axel, 1992-
(author)
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Structural and Conformational Analysis of Bacterial Polysaccharides using NMR Spectroscopy
- 2022
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Doctoral thesis (other academic/artistic)abstract
- Carbohydrates is one of the three classes of biomolecules found in nature. It is the most common one in comparison to the other two classes, lipids and proteins. However, this simple categorization does not reflect the reality since carbohydrates often are covalently linked to e.g., proteins, so-called glycoproteins where, for example, N-glycans are used as markers of quality control during the process of protein folding. Another example is lipopolysaccharides, which cover the cell surfaces of gram-negative bacteria and which contain both a lipid moiety (Lipid A) and a carbohydrate chain. The outer part of the carbohydrate chain is a polysaccharide, also called O-antigen, as it interacts with the immune system of the host. The polysaccharide has, like a polymer, a repeating unit consisting of 2-7 monosaccharides. The repeating unit varies between different bacteria. Determining the structure of these polysaccharides is important in order to be able to categorize the various strains that exist, but also to be able to develop future glycoconjugate vaccines. This is important as the WHO estimates that antibiotic resistance is expected to be more lethal than cancer by 2050, and therefore a vaccine is needed to slow down this development.Nuclear Magnetic Resonance Spectroscopy (NMR) is a useful analytical tool to analyze these carbohydrates at the atomic level in order to determine their structures.The first part (Paper I-III) of this thesis will summarize the structural determination of three Escherichia coli serogroups with hitherto unknown lipopolysaccharides.The second part (Paper IV) will discuss the structure determination, using NMR spectroscopy, for various mono-, di-, and tri-saccharides that have recently been implemented in the structure-determination program, CASPER. The chapter will also present examples of predictions of complex carbohydrates that CASPER can perform.The third part (Paper V) of the thesis will investigate conformational aspects of the polysaccharides from Shigella flexneri serotypes 7a and 7b using NMR spectroscopy and molecular dynamics simulations.
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| 10. |
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