| 1. |
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| 2. |
- McGivney, Eric, et al.
(författare)
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Rapid Physicochemical Changes in Microplastic Induced by Biofilm Formation
- 2020
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Ingår i: Frontiers in Bioengineering and Biotechnology. - : Frontiers Media SA. - 2296-4185. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Risk assessment of microplastic (MP) pollution requires understanding biodegradation processes and related changes in polymer properties. In the environment, there are two-way interactions between the MP properties and biofilm communities: (i) microorganisms may prefer some surfaces, and (ii) MP surface properties change during the colonization and weathering. In a 2-week experiment, we studied these interactions using three model plastic beads (polyethylene [PE], polypropylene [PP], and polystyrene [PS]) exposed to ambient bacterioplankton assemblage from the Baltic Sea; the control beads were exposed to bacteria-free water. For each polymer, the physicochemical properties (compression, crystallinity, surface chemistry, hydrophobicity, and surface topography) were compared before and after exposure under controlled laboratory conditions. Furthermore, we characterized the bacterial communities on the MP surfaces using 16S rRNA gene sequencing and correlated community diversity to the physicochemical properties of the MP. Significant changes in PE crystallinity, PP stiffness, and PS maximum compression were observed as a result of exposure to bacteria. Moreover, there were significant correlations between bacterial diversity and some physicochemical characteristics (crystallinity, stiffness, and surface roughness). These changes coincided with variation in the relative abundance of unique OTUs, mostly related to the PE samples having significantly higher contribution of Sphingobium, Novosphingobium, and uncultured Planctomycetaceae compared to the other test materials, whereas PP and PS samples had significantly higher abundance of Sphingobacteriales and Alphaproteobacteria, indicating possible involvement of these taxa in the initial biodegradation steps. Our findings demonstrate measurable signs of MP weathering under short-term exposure to environmentally relevant microbial communities at conditions resembling those in the water column. A systematic approach for the characterization of the biodegrading capacity in different systems will improve the risk assessment of plastic litter in aquatic environments.
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| 3. |
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| 4. |
- Ogonowski, Martin, et al.
(författare)
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Microplastic Intake, Its Biotic Drivers, and Hydrophobic Organic Contaminant Levels in the Baltic Herring
- 2019
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Ingår i: Frontiers in Environmental Science. - : Frontiers Media SA. - 2296-665X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- It is commonly accepted that microplastic (MP) ingestion can lead to lower food intake and bioaccumulation of hydrophobic organic contaminants (HOCs) in aquatic organisms. However, causal links between MP and contaminant levels in biota are poorly understood and in situ data are very limited. Here, we investigated whether HOC concentrations in herring muscle tissue (Clupea harengus membras) are related to MP ingestion using fish caught along the West coast of the Baltic Sea. The MP occurrence exhibited a large geographic variability, with MP found in 22.3% of the fish examined, and the population average being 0.9 MP ind(-1). However, when only individuals containing MP were considered, the average MP burden was 3.9 MP ind(-1). We also found that MP burden decreased with reproductive stage of the fish but increased with its body size. To predict MP abundance in fish guts, we constructed a mass-balance model using literature data on MP in the water column and physiological rates on ingestion and gut evacuation for clupeids of a similar size. The model output was in agreement with the observed values, thus supporting the validity of the results. Contaminant concentrations in the muscle tissue varied substantially across the study area but were unrelated to the MP levels in fish, suggesting a lack of direct links between the levels of HOCs and MP ingestion. Thus, despite their ubiquity, MP are unlikely to have a measurable impact on food intake or the total body burden of hydrophobic contaminants in Baltic herring.
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| 5. |
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| 6. |
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| 7. |
- Abelein, Axel, et al.
(författare)
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Ionic Strength Modulation of the Free Energy Landscape of A beta(40) Peptide Fibril Formation
- 2016
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 138:21, s. 6893-6902
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Tidskriftsartikel (refereegranskat)abstract
- Protein misfolding and formation of cross-beta structured amyloid fibrils are linked to, many neurodegenerative disorders. Although recently developed,quantitative approaches have started to reveal the molecular nature of self-assembly and fibril formation of proteins and peptides, it is yet unclear how these self-organization events are precisely modulated by microenvironmental factors, which are known to strongly affect the macroscopic aggregation properties. Here, we characterize the explicit effect of ionic strength on the microscopic aggregation rates of amyloid beta peptide (A beta 40) self-association, implicated in Alzheimer's disease. We found that physiological ionic strength accelerates A beta 40 aggregation kinetics by promoting surface-catalyzed secondary nucleation reactions. This promoted catalytic effect can be assigned to shielding of electrostatic repulsion between Monomers on the fibril surface or between the fibril surface itself and monomeric peptides. Furthermore, we observe the formation of two different beta-structured states with =similar but distinct spectroscopic features, which can be assigned to an off-pathway immature state (F-beta*) and a mature stable State (F-beta), where salt favors formation of the F-beta fibril morphology. Addition of salt to preformed F-beta* accelerates transition to F-beta, underlining the dynamic nature of A beta 40 fibrils in solution. On the basis of,these results we suggest a model where salt decreases the free-energy barrier for A beta 40 folding to the F-beta state, favoring the buildup of the mature fibril morphology while omitting competing, energetically less favorable structural states.
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| 8. |
- Andersson, Julia, et al.
(författare)
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Protonation and hydrogen bonding of Ca2+ site residues in the E2P phosphoenzyme intermediate of sarcoplasmic reticulum Ca2+-ATPase studied by a combination of infrared spectroscopy and electrostatic calculations.
- 2008
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Ingår i: Biophys J. - 1542-0086. ; 94:2, s. 600-11
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Tidskriftsartikel (refereegranskat)abstract
- Protonation of the Ca(2+) ligands of the SR Ca(2+)-ATPase (SERCA1a) was studied by a combination of rapid scan FTIR spectroscopy and electrostatic calculations. With FTIR spectroscopy, we investigated the pH dependence of C=O bands of the Ca(2+)-free phosphoenzyme (E2P) and obtained direct experimental evidence for the protonation of carboxyl groups upon Ca(2+) release. At least three of the infrared signals from protonated carboxyl groups of E2P are pH dependent with pK(a) values near 8.3: a band at 1758 cm(-1) characteristic of nonhydrogen-bonded carbonyl groups, a shoulder at 1720 cm(-1), and part of a band at 1710 cm(-1), both characteristic of hydrogen-bonded carbonyl groups. The bands are thus assigned to H(+) binding residues, some of which are involved in H(+) countertransport. At pH 9, bands at 1743 and 1710 cm(-1) remain which we do not attribute to Ca(2+)/H(+) exchange. We also obtained evidence for a pH-dependent conformational change in beta-sheet or turn structures of the ATPase. With MCCE on the E2P analog E2(TG+MgF(4)(2-)), we assigned infrared bands to specific residues and analyzed whether or not the carbonyl groups of the acidic Ca(2+) ligands are hydrogen bonded. The carbonyl groups of Glu(771), Asp(800), and Glu(908) were found to be hydrogen bonded and will thus contribute to the lower wave number bands. The carbonyl group of some side-chain conformations of Asp(800) is left without a hydrogen-bonding partner; they will therefore contribute to the higher wave number band.
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| 9. |
- Arbesu Valdivia, Alejandro, et al.
(författare)
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Characterization of recombinant antibodies for cancer therapy by infrared spectroscopy
- 2013
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Ingår i: Biologicals (Print). - : Elsevier BV. - 1045-1056 .- 1095-8320. ; 41:2, s. 104-110
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Tidskriftsartikel (refereegranskat)abstract
- Fourier transform infrared (FTIR) spectroscopy was used to study the structure of the recombinant antibodies 1E10, anti-CD20 and hR3, which are used as anti-cancer therapeutic drugs. We tested their sensitivity against different conditions and treatments such as pH, temperature, freeze-thaw cycles and drying, which are relevant for the practical usefulness of the drugs. All antibodies were stable against moderate temperature increases (up to 50 degrees C) and pH changes (range 5-9). 1E10 was sensitive to extreme pH values (pH 3 and 12), whereas hR3 was most sensitive to temperature (at and above 60 degrees C). We did not observe any significant changes upon freeze-thaw and drying treatments. The secondary structure content of all three antibodies was estimated to be similar to that of IgG with similar to 64% beta-sheet, 0% alpha-helix and similar to 36% other structure. (C) 2012 The International Alliance for Biological Standardization.
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| 10. |
- Ariöz, Candan, 1983-, et al.
(författare)
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Anionic Lipid Binding to the Foreign Protein MGS Provides a Tight Coupling between Phospholipid Synthesis and Protein Overexpression in Escherichia coli
- 2013
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 52:33, s. 5533-5544
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Tidskriftsartikel (refereegranskat)abstract
- Certain membrane proteins involved in lipid synthesis can induce formation of new intracellular membranes in Escherichia coli, i.e., intracellular vesicles. Among those, the foreign monotopic glycosyltransferase MGS from Acholeplasma laidlawii triggers such massive lipid synthesis when overexpressed. To examine the mechanism behind the increased lipid synthesis, we investigated the lipid binding properties of MGS in vivo together with the correlation between lipid synthesis and MGS overexpression levels. A good correlation between produced lipid quantities and overexpressed MGS protein was observed when standard LB medium was supplemented with four different lipid precursors that have significant roles in the lipid biosynthesis pathway. Interestingly, this correlation was highest concerning anionic lipid production and at the same time dependent on the selective binding of anionic lipid molecules by MGS. A selective interaction with anionic lipids was also observed in vitro by P-31 NMR binding studies using bicelles prepared with E. coli lipids. The results clearly demonstrate that the discriminative withdrawal of anionic lipids, especially phosphatidylglycerol, from the membrane through MGS binding triggers an in vivo signal for cells to create a feed-forward stimulation of lipid synthesis in E. coil. By this mechanism, cells can produce more membrane surface in order to accommodate excessively produced MGS molecules, which results in an interdependent cycle of lipid and MGS protein synthesis.
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| 11. |
- Ariöz, Candan, 1983-, et al.
(författare)
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Heterologous overexpression of a monotopic glucosyltransferase (MGS) induces fatty acid remodeling in Escherichia coli membranes :
- 2014
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Ingår i: Biochimica et Biophysica Acta - Biomembranes. - : Elsevier BV. - 0005-2736 .- 1879-2642. ; 1838:7, s. 1862-1870
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Tidskriftsartikel (refereegranskat)abstract
- The membrane protein monoglucosyldiacylglycerol synthase (MGS) from Acholeplasma laidlawii is responsible for the creation of intracellular membranes when overexpressed in Escherichia coli (E. coli). The present study investigates time dependent changes in composition and properties of E. coli membranes during 22 h of MGS induction. The lipid/protein ratio increased by 38% in MGS-expressing cells compared to control cells. Time-dependent screening of lipids during this period indicated differences in fatty acid modeling. (1) Unsaturation levels remained constant for MGS cells (~ 62%) but significantly decreased in control cells (from 61% to 36%). (2) Cyclopropanated fatty acid content was lower in MGS producing cells while control cells had an increased cyclopropanation activity. Among all lipids, phosphatidylethanolamine (PE) was detected to be the most affected species in terms of cyclopropanation. Higher levels of unsaturation, lowered cyclopropanation levels and decreased transcription of the gene for cyclopropane fatty acid synthase (CFA) all indicate the tendency of the MGS protein to force E. coli membranes to alter its usual fatty acid composition.
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| 12. |
- Arndt, Tina, et al.
(författare)
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Engineered Spider Silk Proteins for Biomimetic Spinning of Fibers with Toughness Equal to Dragline Silks
- 2022
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Ingår i: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 32:23
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Tidskriftsartikel (refereegranskat)abstract
- Spider silk is the toughest fiber found in nature, and bulk production of artificial spider silk that matches its mechanical properties remains elusive. Development of miniature spider silk proteins (mini-spidroins) has made large-scale fiber production economically feasible, but the fibers’ mechanical properties are inferior to native silk. The spider silk fiber's tensile strength is conferred by poly-alanine stretches that are zipped together by tight side chain packing in β-sheet crystals. Spidroins are secreted so they must be void of long stretches of hydrophobic residues, since such segments get inserted into the endoplasmic reticulum membrane. At the same time, hydrophobic residues have high β-strand propensity and can mediate tight inter-β-sheet interactions, features that are attractive for generation of strong artificial silks. Protein production in prokaryotes can circumvent biological laws that spiders, being eukaryotic organisms, must obey, and the authors thus design mini-spidroins that are predicted to more avidly form stronger β-sheets than the wildtype protein. Biomimetic spinning of the engineered mini-spidroins indeed results in fibers with increased tensile strength and two fiber types display toughness equal to native dragline silks. Bioreactor expression and purification result in a protein yield of ≈9 g L−1 which is in line with requirements for economically feasible bulk scale production.
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| 13. |
- Arndt, Tina, et al.
(författare)
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Spidroin N-terminal domain forms amyloid-like fibril based hydrogels and provides a protein immobilization platform
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Recombinant spider silk proteins (spidroins) have multiple potential applications in development of novel biomaterials, but their multimodal and aggregation-prone nature have complicated production and straightforward applications. Here, we report that recombinant miniature spidroins, and importantly also the N-terminal domain (NT) on its own, rapidly form self-supporting and transparent hydrogels at 37 °C. The gelation is caused by NT α-helix to β-sheet conversion and formation of amyloid-like fibrils, and fusion proteins composed of NT and green fluorescent protein or purine nucleoside phosphorylase form hydrogels with intact functions of the fusion moieties. Our findings demonstrate that recombinant NT and fusion proteins give high expression yields and bestow attractive properties to hydrogels, e.g., transparency, cross-linker free gelation and straightforward immobilization of active proteins at high density.
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| 14. |
- Baldassarre, Maurizio, et al.
(författare)
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Amyloid beta-peptides 1-40 and 1-42 form oligomers with mixed beta-sheets
- 2017
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 8:12, s. 8247-8254
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Tidskriftsartikel (refereegranskat)abstract
- Two main amyloid-beta peptides of different length (A beta(40) and A beta(42)) are involved in Alzheimer's disease. Their relative abundance is decisive for the severity of the disease and mixed oligomers may contribute to the toxic species. However, little is know about the extent of mixing. To study whether A beta(40) and A beta(42) co-aggregate, we used Fourier transform infrared spectroscopy in combination with C-13-labeling and spectrum calculation and focused on the amide I vibration, which is sensitive to backbone structure. Mixtures of monomeric labeled A beta(40) and unlabeled A beta(42) (and vice versa) were co-incubated for similar to 20 min and their infrared spectrum recorded. The position of the main C-13-amide I' band shifted to higher wavenumbers with increasing admixture of C-12-peptide due to the presence of C-12-amides in the vicinity of C-13-amides. The results indicate that A beta(40) and A beta(42) form mixed oligomers with a largely random distribution of A beta(40) and A beta(42) strands in their beta-sheets. The structures of the mixed oligomers are intermediate between those of the pure oligomers. There is no indication that one of the peptides forces the backbone structure of its oligomers on the other peptide when they are mixed as monomers. We also demonstrate that isotope-edited infrared spectroscopy can distinguish aggregation modulators that integrate into the backbone structure of their interaction partner from those that do not. As an example for the latter case, the pro-inflammatory calcium binding protein S100A9 is shown not to incorporate into the b-sheets of A beta(42).
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| 15. |
- Baldassarre, Maurizio, et al.
(författare)
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Pushing the detection limit of infrared spectroscopy for structural analysis of dilute protein samples.
- 2014
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Ingår i: The Analyst. - : Royal Society of Chemistry (RSC). - 0003-2654 .- 1364-5528. ; 139:21, s. 5393-5399
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Tidskriftsartikel (refereegranskat)abstract
- Fourier-transform infrared spectroscopy is a powerful and versatile tool to investigate the structure and dynamics of proteins in solution. The intrinsically low extinction coefficient of the amide I mode, the main structure-related oscillator, together with the high infrared absorptivity of aqueous media, requires that proteins are studied at high concentrations (>10 mg L(-1)). This may represent a challenge in the study of aggregation-prone proteins and peptides, and questions the significance of structural data obtained for proteins physiologically existing at much lower concentrations. Here we describe the development of a simple experimental approach that increases the detection limit of protein structure analysis by infrared spectroscopy. Our approach relies on custom-made filters to isolate the amide I region (1700-1600 cm(-1)) from irrelevant spectral regions. The sensitivity of the instrument is then increased by background attenuation, an approach consisting in the use of a neutral density filter, such as a non-scattering metal grid, to attentuate the intensity of the background spectrum. When the filters and grid are combined, a 2.4-fold improvement in the noise level can be obtained. We have successfully tested this approach using a highly diluted solution of pyruvate kinase in deuterated medium (0.2% w/v), and found that it provides spectra of a quality comparable to those recorded with a 10-fold higher protein concentration.
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| 16. |
- Baldassarre, Maurizio, et al.
(författare)
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Simultaneous acquisition of infrared, fluorescence and light scattering spectra of proteins : direct evidence for pre-fibrillar species in amyloid fibril formation
- 2016
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Ingår i: The Analyst. - : Royal Society of Chemistry (RSC). - 0003-2654 .- 1364-5528. ; 141:3, s. 963-973
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Tidskriftsartikel (refereegranskat)abstract
- Different spectroscopic approaches are often used to probe specific aspects of amyloid fibril formation but are usually performed separately and under different conditions. This makes it problematic to relate different aspects of the aggregation process when these are monitored by different methods. We report on a multispectral approach for simultaneous acquisition of infrared, fluorescence and light scattering spectra of proteins undergoing aggregation. We have applied our approach to study beta-lactoglobulin, a milk protein known to form amyloid fibrils under well-established conditions. Our real-time multispectral measurements show that unfolding of this protein is followed by formation of early aggregates consisting of intermolecular beta-sheets with a typical infrared absorption at similar to 1619 cm(-1) in (H2O)-H-2. These aggregates, which lead to an increase in the light scattering signal, do not bind the amyloid-specific fluorophore ThT and therefore consist of oligomers or protofibrils. Fibril growth is then observed as a sigmoidal increase in ThT fluorescence. After similar to 25 h, a plateau is observed in the intensities of ThT emission and of the band at 1619 cm(-1), indicating that no new fibrils are forming. However, a second phase in the light scattering signal taking place after similar to 25 h suggests that the fibrils are assembling into larger structures, known as mature fibrils. This is associated with an upshift of the main beta-sheet band in the infrared spectrum. TEM analyses confirmed the existence of thick fibrils comprising 3-5 filaments.
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| 17. |
- Baldassarre, Maurizio, et al.
(författare)
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Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra
- 2015
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Ingår i: Molecules. - : MDPI AG. - 1431-5157 .- 1420-3049. ; 20:7, s. 12599-12622
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Tidskriftsartikel (refereegranskat)abstract
- Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spectra are fitted simultaneously. Our approach, which we name co-fitting, leads to a more reliable modelling of the experimental data because it uses more spectral information than the standard approach of fitting only the absorption spectrum. It also avoids that the fitting routine becomes trapped in local minima. We have tested the proposed approach using infrared absorption spectra of three mixed α/β proteins with different degrees of spectral overlap in the amide I region: ribonuclease A, pyruvate kinase, and aconitase.
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| 18. |
- Baldassarre, Maurizio, et al.
(författare)
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The carbonate/bicarbonate system as a pH indicator for infrared spectroscopy
- 2014
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Ingår i: The Analyst. - : Royal Society of Chemistry (RSC). - 0003-2654 .- 1364-5528. ; 139:9, s. 2167-2176
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Tidskriftsartikel (refereegranskat)abstract
- Caged compounds capable of inducing large pH-jumps upon UV illumination have represented a breakthrough in time-resolved infrared spectroscopy of acidification-triggered phenomena, but their use is hampered by the inability to control the initial pH as well as to measure the final pH in mu L volumes. We have developed an experimental approach that accurately measures the initial and final pH values in pH-jump experiments. Our approach exploits the concomitant presence of two or more inorganic ions, such as carbonate and bicarbonate, that are added to the sample at a known concentration. The difference spectrum obtained in the infrared measurement is fitted to isolate the bands arising from the appearance or disappearance of either protonation state, and is then compared to a synthetic library of difference spectra generated using both qualitative (band position and width, extinction coefficient, pK) and quantitative (concentration, pathlength) parameters of the reporter ions. We have tested this approach in UV-photolysis experiments of 1-(2-nitrophenyl)ethyl sulfate in the presence of different concentrations of Na2CO3 and successfully used the infrared absorption of the carbonate and the bicarbonate ions to determine the initial and final pH values before and after the pH-jump, respectively.
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| 19. |
- Baronio, Cesare Michele, 1987-
(författare)
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Computational infrared spectroscopy : Calculation of the amide I absorption of proteins
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Infrared spectroscopy is an important technique that allows to retrieve structural information from the analysis of absorption spectra. The main application of infrared spectroscopy within life science is the study of the amide I band, which is correlated with protein backbone conformation and, consequently, with the secondary structure of proteins. However, band assignment and interpretation of the infrared spectra is not straightforward.Therefore, several simulation methods were developed to guide the interpretation of experimental amide I spectra. In this thesis, one of these methods is a normal mode analysis, which is based on the evaluation of the intrinsic vibration of the amide groups and the interactions between them. The calculation considers several effects: transition dipole coupling, nearest neighbor interaction, the local environment effect and the effect of hydrogen bond. From the normal mode analysis, it is possible to obtain the simulated infrared spectrum and the contribution of each amide group to a specific spectral range of the spectrum.The aim of this thesis and of the included publications is to explain this approach, to improve it and to show its potential. Results from simulations were compared with experimental data for different proteins of interest: amyloid-β oligomers and β-helix proteins. Simulated and experimental infrared spectra showed similar bands. Simulations also provided additional conclusions: they confirmed the random mixing of amyloid-β peptides in oligomers; they suggested that amyloid-β peptides contribute at least two strands in the structure of the oligomers; they revealed that the high wavenumber band, typical of antiparallel β-sheets, can be caused by other secondary structures, but not by parallel β-sheets. In addition, to verify and to improve the accuracy of this approach, simulation results were also put in a direct comparison with results from density functional theory calculations. From this comparison, a new optimal set of parameters for the calculations is suggested.
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| 20. |
- Baronio, Cesare M., et al.
(författare)
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Insight into the internal structure of amyloid-β oligomers by isotope-edited Fourier transform infrared spectroscopy
- 2019
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 21:16, s. 8587-8597
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Tidskriftsartikel (refereegranskat)abstract
- The internal structure of amyloid-β (Aβ) oligomers was investigated with isotope-edited Fourier transform infrared spectroscopy. Homo-oligomers of Aβ(40) and Aβ(42) were prepared from unlabeled and C-13, N-15-labeled monomeric Aβ and from mixtures of these. For the unlabeled peptides, two main bands were observed in (H2O)-H-2 at 1685 and 1622 cm(-1) for Aβ(40) and at 1685 and 1626 cm(-1) for Aβ(42). These band positions indicate that the number of strands per sheet is at least four. The obtained experimental amide I spectra were simulated using a number of structural models (antiparallel β-sheets, β-barrels and a dodecamer structure). According to experiments and calculations, the main C-13-band shifts down at increasing molar ratio of labeled peptides. This shift occurs when vibrational coupling becomes possible between C-13-amide groups in close-by strands. It is small, when intervening C-12-strands increase the distance between C-13-strands; it is large, when many neighboring strands are labeled. The shift depends on the internal structure of the peptides within the oligomers, i.e. on the building block that each peptide molecule contributes to the β-sheets of the oligomers. The shift is largest, when individual peptides contribute just a single strand surrounded by strands from other peptide molecules. It is smaller when each molecule forms two or three adjacent strands. As indicated by a comparison between experiment and computation, the number of adjacent β-strands per peptide molecule is two for Aβ(40) oligomers and two or more for Aβ(42) oligomers. Our results are well explained by regular, antiparallel β-sheets or β-barrels.
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| 21. |
- Baronio, Cesare M., 1987-, et al.
(författare)
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Refining protein amide I spectrum simulations with simple yet effective electrostatic models for local wavenumbers and dipole derivative magnitudes
- 2024
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 26:2, s. 1166-1181
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures – α-helices, parallel and antiparallel β-sheets – with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the CO bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment.
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| 22. |
- Baronio, Cesare M., et al.
(författare)
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The amide I spectrum of parallel β-sheet proteins
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The amide I absorption of the polypeptide backbone has long been used to analyze the secondary structure of proteins. This approach has gained additional attention in the context of amyloid diseases where a particular focus is on the distinction between parallel and antiparallel β-sheets because these structures often discriminate between pre-fibrillar structures and fibrils. Some earlier infrared spectra with typical features of antiparallel β-sheets were interpreted as arising from the parallel β-sheets of fibrils. Therefore, the ability of infrared spectroscopy to distinguish between both types of β-sheets is debated. While it is established that regular, antiparallel β-sheets give rise to a high wavenumber band near 1690 cm-1, it is less clear whether or not this band may also occur for parallel β-sheets. Here we present and analyze the amide I spectra of two β-helix proteins, SV2 and Pent. The overall shape of the proteins is that of a cuboid which has parallel β-sheets on its four sides, which are connected by bends. The main features of their amide I spectrum are a band at 1665, and two bands between 1645 and 1628 cm-1. Both proteins exhibit also a weak component band near 1690 cm-1. Calculations of the amide I spectrum indicate that the absorption at high wavenumbers is not caused by the parallel β-sheets but by the bends between the β-strands. We therefore suggest to modify the interpretation of the amide I spectrum as follows: a high wavenumber band near 1690 cm-1 may be caused by other structures than antiparallel β-sheets. However, when the spectrum consists of only two distinct bands, one near 1690 cm-1 and one near 1630 cm-1, then an assignment to antiparallel β-sheets is consistent with the literature.
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| 23. |
- Baronio, Cesare M., et al.
(författare)
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The Amide I Spectrum of Proteins—Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations
- 2020
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:9, s. 1703-1714
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Tidskriftsartikel (refereegranskat)abstract
- The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: α-helices, antiparallel β-sheets, and parallel β-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.
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| 24. |
- Barth, Andreas
(författare)
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Infrared spectroscopy of proteins
- 2007
-
Ingår i: Biochim Biophys Acta: Bioenergetics. - 0006-3002. ; 1767:9, s. 1073-101
-
Forskningsöversikt (populärvet., debatt m.m.)abstract
- This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.
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| 25. |
- Barth, Andreas
(författare)
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Infrared Spectroscopy - Past and Present
- 2009
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Ingår i: Biological and Biomedical Infrared Spectroscopy. - Amsterdam : IOS Press BV. ; , s. 1-52
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Bokkapitel (populärvet., debatt m.m.)abstract
- History of infrared spectroscopy as well as current technology and applications are reviewed.
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| 26. |
- Barth, Andreas
(författare)
-
Quantifying bond distortions in transient enzyme species by a combination of density functional theory calculations and time-resolved infrared difference spectroscopy. Implications for the mechanism of dephosphorylation of the sarcoplasmic reticulum Ca2+-ATPase (SERCA1a)
- 2015
-
Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1847:10, s. 1036-1043
-
Tidskriftsartikel (refereegranskat)abstract
- The sarcoplasmic Ca2+-ATPase (SERCA1a) forms two phosphoenzyme intermediates during Ca2+ pumping. The second intermediate E2P hydrolyzes rapidly, which is essential for the rapid removal of Ca2+ from the cytosol of muscle cells. The present work studies whether a weakening of the scissile P-O bond in the E2P ground state facilitates dephosphorylation. To this end, the experimentally known vibrational spectrum of the E2P phosphate group was calculated with density functional theory (DFT) using structural models at two levels of structural complexity: (i) Models of acetyl phosphate in simple environments and (ii) similar to 150 atom models of the catalytic site. It was found that the enzyme environment distorts the structure of the phosphate group: one of the terminal P-O bonds is shorter in the catalytic site indicating weaker interactions than in water. However, the bond that bridges phosphate and Asp351 is unaffected. This indicates that the scissile P-O bond is not weakened by the enzyme environment of E2P. A second finding was that the catalytic site of the E2P state in aqueous solution appears to adopt a structure as in the crystals with BeF3-, where the ATPase is in a non-reactive conformation. The reactant state of the dephosphorylation reaction differs from the E2P ground state: Glu183 faces Asp351 and positions the attacking water molecule. This state has a 0.04 angstrom longer, and thus weaker, bridging P-O bond. The reactant state is not detected in our experiments, indicating that its energy is at least 1 kcal/mol higher than that of the E2P ground state.
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| 27. |
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| 28. |
- Barth, Andreas
(författare)
-
Structural dynamics of the Ca2+-ATPase studied by time-resolved infrared spectroscopy
- 2008
-
Ingår i: Spectroscopy. ; 22, s. 63-82
-
Forskningsöversikt (populärvet., debatt m.m.)abstract
- Protonation of acidic residues in the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA 1a) was studied by multiconformation continuum electrostatic calculations in the Ca(2+)-bound state Ca(2)E1, in the Ca(2+)-free state E2(TG) with bound thapsigargin, and in the E2P (ADP-insensitive phosphoenzyme) analog state with MgF(4)(2-) E2(TG+MgF(4)(2-)). Around physiological pH, all acidic Ca(2+) ligands (Glu(309), Glu(771), Asp(800), and Glu(908)) were unprotonated in Ca(2)E1; in E2(TG) and E2(TG+MgF(4)(2-)) Glu(771), Asp(800), and Glu(908) were protonated. Glu(771) and Glu(908) had calculated pK(a) values larger than 14 in E2(TG) and E2(TG+MgF(4)(2-)), whereas Asp(800) titrated with calculated pK(a) values near 7.5. Glu(309) had very different pK(a) values in the Ca(2+)-free states: 8.4 in E2(TG+MgF(4)(2-)) and 4.7 in E2(TG) because of a different local backbone conformation. This indicates that Glu(309) can switch between a high and a low pK(a) mode, depending on the local backbone conformation. Protonated Glu(309) occupied predominantly two main, very differently orientated side-chain conformations in E2(TG+MgF(4)(2-)): one oriented inward toward the other Ca(2+) ligands and one oriented outward toward a protein channel that seems to be in contact with the cytoplasm. Upon deprotonation, Glu(309) adopted completely the outwardly orientated side-chain conformation. The contact of Glu(309) with the cytoplasm in E2(TG+MgF(4)(2-)) makes this residue unlikely to bind lumenal protons. Instead it might serve as a proton shuttle between Ca(2+)-binding site I and the cytoplasm. Glu(771), Asp(800), and Glu(908) are proposed to take part in proton countertransport.
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| 29. |
- Barth, Andreas
(författare)
-
The study of protein reactions by reaction-induced infrared difference spectroscopy
- 2009
-
Ingår i: Biological and Biomedical Infrared Spectroscopy. - Amsterdam : IOS Press BV. ; , s. 53-78
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Reaction-induced infrared difference spectroscopy of proteins is reviewed. This technique enables detailed characterization of enzyme function on the level of single bonds of proteins, cofactors or substrates. Discussed are methods to initiate protein reactions in the infrared samples, general aspects of spectra interpretation, measurements of enzyme activity and studies of protein function at the example of the Ca2+ pump.
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| 30. |
- Barth, Andreas
(författare)
-
Two sides of the same coin : How enzymes distort substrates and vice versa. An infrared spectroscopic view on pyruvate kinase and Ca2+-ATPase
- 2016
-
Ingår i: Biomedical Spectroscopy and Imaging. - 2212-8794. ; 5:2, s. 101-114
-
Tidskriftsartikel (refereegranskat)abstract
- This review summarises our infrared spectroscopy and density functional theory studies on the mutual interactions between enzymes and their substrates. We investigated phosphoenolpyruvate bound to pyruvate kinase (EC 2.7.1.40, M1 isozyme), ATP bound to the Ca2+-ATPase (SERCA1a), and the aspartylphosphate moiety of the Ca2+-ATPase phosphoenzyme E2P. Conformational changes of the enzymes and distortions of substrate structure are discussed. In all cases, the infrared absorption of the substrate in the enzyme environment could be identified by a combination of reaction-induced difference spectroscopy and isotopic labelling. The experimentally-determined vibrational frequencies were interpreted in structural terms using experimental correlations or modelling of the active site in density functional theory calculations. For none of the three systems, a weakening of the bond that is cleaved in the following enzymatic reaction could be detected in the ground state of the enzyme-substrate complex. However, for the dephosphorylation reaction of the Ca2+-ATPase phosphoenzyme E2P, a high energy intermediate, not detected in experiments, is the reactant state according to density functional theory calculations.
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| 31. |
- Barth, Cornelia Anne, et al.
(författare)
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Retrospective observational study of characteristics of persons with amputations accessing International Committee of the Red Cross (ICRC) rehabilitation centres in five conflict and postconflict countries
- 2021
-
Ingår i: BMJ Open. - : BMJ. - 2044-6055. ; 11:12
-
Tidskriftsartikel (refereegranskat)abstract
- Objectives Limb amputation incidence is particularly high in fragile contexts due to conflict, accidents and poorly managed diabetes. The study aim was to analyse (1) demographic and amputation characteristics of persons with any type of acquired amputation (PwA) and (2) time between amputation and first access to rehabilitation in five conflict and postconflict countries. Design A retrospective, observational study analysing differences in demographic and clinical factors and time to access rehabilitation between users with traumatic and non-traumatic amputations. Setting Five countries with the highest numbers of PwA in the global International Committee of the Red Cross database (Afghanistan, Cambodia, Iraq, Myanmar, Sudan). Cleaned and merged data from 2009 to 2018 were aggregated by sex; age at amputation and registration; cause, combination and anatomical level of amputation(s); living environment. Participants All PwA newly attending rehabilitation. Results Data for 28 446 individuals were included (4329 (15.2%) female). Most were traumatic amputations (73.4%, 208 90); of these, 48.6% (138 01) were conflict related. Average age at traumatic amputation for men and women was 26.9 and 24.1 years, respectively; for non-traumatic amputation it was 49.1 years and 45.9 years, respectively. Sex differences in age were statistically significant for traumatic and non-traumatic causes (p<0.001, p=0.003). Delay between amputation and rehabilitation was on average 8.2 years for those with traumatic amputation, significantly higher than an average 3 years for those with non-traumatic amputation (p<0.001). Conclusions Young age for traumatic and non-traumatic amputations indicates the devastating impact of war and fragile health systems on a society. Long delays between amputation and rehabilitation reveal the mismatch of needs and resources. For rehabilitation service providers in fragile settings, it is an enormous task to manage the diversity of PwA of various causes, age, sex and additional conditions. Improved collaboration between primary healthcare, surgical and rehabilitation services, a prioritisation of rehabilitation and increased resource provision are recommended to ensure adequate access to comprehensive rehabilitation care for PwA.
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| 32. |
- Barth, Cornelia Anne, et al.
(författare)
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Ways to improve surgical outcomes in low- and middle-income countries
- 2022
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Ingår i: Bulletin of the World Health Organization. - : WHO Press. - 0042-9686 .- 1564-0604. ; 100:11, s. 726-732
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Tidskriftsartikel (refereegranskat)abstract
- Global surgery initiatives such as the Lancet Commission on Global Surgery have highlighted the need for increased investment to enhance surgical capacity in low- and middle-income countries. A neglected issue, however, is surgery-related rehabilitation, which is known to optimize functional outcomes after surgery. Increased investment to enhance surgical capacity therefore needs to be complemented by promotion of rehabilitation interventions. We make the case for strengthening surgery-related rehabilitation in lower-resource countries, outlining the challenges but also potential solutions and policy directions. Proposed solutions include greater leadership and awareness, augmented by recent global efforts around the World Health Organization's Rehabilitation 2030 initiative, and professionalization of the rehabilitation workforce. More research on rehabilitation is needed in low- and middle-income countries, along with support for system approaches, notably on strengthening and integrating rehabilitation within the health systems. Finally, we outline a set of policy implications and recommendations, aligned to the components of the national surgical plan proposed by the Lancet Commission: infrastructure, workforce, service delivery, financing, and information management. Collaboration and sustained efforts to embed rehabilitation within national surgical plans is key to optimize health outcomes for patients with surgical conditions and ensure progress towards sustainable development goal 3: health and well-being for all.
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| 33. |
- Barth, Cornelia, et al.
(författare)
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Users of rehabilitation services in 14 countries and territories affected by conflict, 1988–2018
- 2020
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Ingår i: Bulletin of the World Health Organization. - Geneva, Switzerland : World Health Organization. - 0042-9686 .- 1564-0604. ; 98, s. 599-614
-
Tidskriftsartikel (refereegranskat)abstract
- Objective To analyse the demographic and clinical characteristics of people attending physical rehabilitation centres run or supported by the International Committee of the Red Cross in countries and territories affected by conflict.Methods Of 150 such rehabilitation centres worldwide, 38 use an electronic patient management system. We invited all 38 centres to participate. We extracted de-identified data from 1988 to 2018 and categorized them by sex, age, country or territory and reason for using rehabilitation services.Findings Thirty-one of the 38 rehabilitation centres in 14 countries and territories participated. We included data for 287 274 individuals. Of people using rehabilitation services, 61.6% (176 949/287 274) were in Afghanistan, followed by 15.7% (44 959/287 274) in Cambodia. Seven places had over 9000 service users each (Afghanistan, Cambodia, Gaza Strip, Iraq, Myanmar, Somalia and Sudan). Overall, 72.6% (208 515/287 274) of service users were male. In eight countries, more than half of the users were of working age (18–59 years). Amputation was the most common reason for using rehabilitation services; 33.3% (95 574/287 274) of users were people with amputations, followed by 13.7% (39 446/287 274) with cerebral palsy. The male predominance was greater in the population aged 18–34 years (83.1%; 71 441/85 997) and in people with amputations (88.6%; 84 717/95 574) but was evident across all places, age groups and health conditions.Conclusion The considerably lower attendance of females at the rehabilitation centres highlights the need to understand the factors that affect the accessibility and acceptability of rehabilitation for women and girls in conflict settings.
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| 34. |
- Barth, Maren S., et al.
(författare)
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Emergency exit layout planning using optimization and agent-based simulation
- 2024
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Ingår i: Computational Management Science. - : SPRINGER HEIDELBERG. - 1619-697X .- 1619-6988. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Evacuation preparedness includes ensuring proper infrastructure, resources and planning for moving people from a dangerous area to safety. This is especially important and challenging during mass gatherings, such as large concerts. In this paper, we present the Emergency Exit Layout Problem (EELP) which is the problem of locating a given number of emergency exits and deciding their width such that the time it takes to evacuate the crowd from an arena is minimized. The EELP takes into account the geography of the arena and its surroundings, as well as the number of pedestrians in the crowd and the distribution of these within the arena. The EELP is formulated as a two-stage stochastic mixed integer linear program to handle the uncertainty related to the location of the possible incidents and the distribution of the pedestrians. Two cases are studied, a large concert planned at the Leangen trotting track in Trondheim and a smaller indoor arena. For each case, the EELP is solved for different scenarios, and the suggested layouts are evaluated using an agent-based simulation model. In particular, the potential of incorporating detailed assessment regarding the location and probability of specific incidents and the distribution of pedestrians are investigated. The computational study shows that making a more detailed risk assessment has little effect on the large concert, but a significant impact on the location of the emergency exits for the smaller indoor case. The results also indicate that it is more important to consider the location and probability of specific incidents rather than the pedestrian distribution.
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| 35. |
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| 36. |
- Berntsson, Elina, et al.
(författare)
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Characterization of Uranyl (UO22+) Ion Binding to Amyloid Beta (Aβ) Peptides : Effects on Aβ Structure and Aggregation
- 2023
-
Ingår i: ACS Chemical Neuroscience. - 1948-7193. ; 14:15, s. 2618-2633
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Tidskriftsartikel (refereegranskat)abstract
- Uranium (U) is naturally present in ambient air, water, and soil, and depleted uranium (DU) is released into the environment via industrial and military activities. While the radiological damage from U is rather well understood, less is known about the chemical damage mechanisms, which dominate in DU. Heavy metal exposure is associated with numerous health conditions, including Alzheimer’s disease (AD), the most prevalent age-related cause of dementia. The pathological hallmark of AD is the deposition of amyloid plaques, consisting mainly of amyloid-β (Aβ) peptides aggregated into amyloid fibrils in the brain. However, the toxic species in AD are likely oligomeric Aβ aggregates. Exposure to heavy metals such as Cd, Hg, Mn, and Pb is known to increase Aβ production, and these metals bind to Aβ peptides and modulate their aggregation. The possible effects of U in AD pathology have been sparsely studied. Here, we use biophysical techniques to study in vitro interactions between Aβ peptides and uranyl ions, UO22+, of DU. We show for the first time that uranyl ions bind to Aβ peptides with affinities in the micromolar range, induce structural changes in Aβ monomers and oligomers, and inhibit Aβ fibrillization. This suggests a possible link between AD and U exposure, which could be further explored by cell, animal, and epidemiological studies. General toxic mechanisms of uranyl ions could be modulation of protein folding, misfolding, and aggregation.
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| 37. |
- Berntsson, Elina, et al.
(författare)
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Lithium ions display weak interaction with amyloid-beta (Aβ) peptides and have minor effects on their aggregation
- 2021
-
Ingår i: Acta Biochimica Polonica. - : Polskie Towarzystwo Biochemiczne (Polish Biochemical Society). - 0001-527X .- 1734-154X. ; 68:2, s. 169-179
-
Tidskriftsartikel (refereegranskat)abstract
- Alzheimer’s disease (AD) is an incurable disease and the main cause of age-related dementia worldwide, despite decades of research. Treatment of AD with lithium (Li) has shown promising results, but the underlying mechanism is unclear. The pathological hallmark of AD brains is deposition of amyloid plaques, consisting mainly of amyloid-β (Aβ) peptides aggregated into amyloid fibrils. The plaques contain also metal ions of e.g. Cu, Fe, and Zn, and such ions are known to interact with Aβ peptides and modulate their aggregation and toxicity. The interactions between Aβ peptides and Li+ions have however not been well investigated. Here, we use a range of biophysical techniques to characterize in vitro interactions between Aβ peptides and Li+ions. We show that Li+ions display weak and non-specific interactions with Aβ peptides, and have minor effects on Aβ aggregation. These results indicate that possible beneficial effects of Li on AD pathology are not likely caused by direct interactions between Aβ peptides and Li+ions.
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| 38. |
- Berntsson, Elina, et al.
(författare)
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Residue-specific binding of Ni(II) ions influences the structure and aggregation of amyloid beta (Aβ) peptides
- 2023
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Alzheimer's disease (AD) is the most common cause of dementia worldwide. AD brains display deposits of insoluble amyloid plaques consisting mainly of aggregated amyloid-β (Aβ) peptides, and Aβ oligomers are likely a toxic species in AD pathology. AD patients display altered metal homeostasis, and AD plaques show elevated concentrations of metals such as Cu, Fe, and Zn. Yet, the metal chemistry in AD pathology remains unclear. Ni(II) ions are known to interact with Aβ peptides, but the nature and effects of such interactions are unknown. Here, we use numerous biophysical methods-mainly spectroscopy and imaging techniques-to characterize Aβ/Ni(II) interactions in vitro, for different Aβ variants: Aβ(1-40), Aβ(1-40)(H6A, H13A, H14A), Aβ(4-40), and Aβ(1-42). We show for the first time that Ni(II) ions display specific binding to the N-terminal segment of full-length Aβ monomers. Equimolar amounts of Ni(II) ions retard Aβ aggregation and direct it towards non-structured aggregates. The His6, His13, and His14 residues are implicated as binding ligands, and the Ni(II)·Aβ binding affinity is in the low µM range. The redox-active Ni(II) ions induce formation of dityrosine cross-links via redox chemistry, thereby creating covalent Aβ dimers. In aqueous buffer Ni(II) ions promote formation of beta sheet structure in Aβ monomers, while in a membrane-mimicking environment (SDS micelles) coil-coil helix interactions appear to be induced. For SDS-stabilized Aβ oligomers, Ni(II) ions direct the oligomers towards larger sizes and more diverse (heterogeneous) populations. All of these structural rearrangements may be relevant for the Aβ aggregation processes that are involved in AD brain pathology.
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| 39. |
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| 40. |
- Carissimi, Guzmán, et al.
(författare)
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Direct Quantification of Drug Loading Content in Polymeric Nanoparticles by Infrared Spectroscopy
- 2020
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Ingår i: Pharmaceutics. - : MDPI AG. - 1999-4923. ; 12:10
-
Tidskriftsartikel (refereegranskat)abstract
- Nanotechnology has enabled the development of novel therapeutic strategies such as targeted nanodrug delivery systems, control and stimulus-responsive release mechanisms, and the production of theranostic agents. As a prerequisite for the use of nanoparticles as drug delivery systems, the amount of loaded drug must be precisely quantified, a task for which two approaches are currently used. However, both approaches suffer from the inefficiencies of drug extraction and of the solid-liquid separation process, as well as from dilution errors. This work describes a new, reliable, and simple method for direct drug quantification in polymeric nanoparticles using attenuated total reflection Fourier transform infrared spectroscopy, which can be adapted for a wide variety of drug delivery systems. Silk fibroin nanoparticles and naringenin were used as model polymeric nanoparticle carrier and drug, respectively. The specificity, linearity, detection limit, precision, and accuracy of the spectroscopic approach were determined in order to validate the method. A good linear relation was observed within 0.00 to 7.89% of naringenin relative mass with an R-2 of 0.973. The accuracy was determined by the spike and recovery method. The results showed an average 104% recovery. The limit of detection and limit of quantification of the drug loading content were determined to be 0.3 and 1.0%, respectively. The method's robustness is demonstrated by the notable similarities between the calibrations carried out using two different equipment setups at two different institutions.
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| 41. |
- Carissimi, Guzmán, et al.
(författare)
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On the Secondary Structure of Silk Fibroin Nanoparticles Obtained Using Ionic Liquids : An Infrared Spectroscopy Study
- 2020
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Ingår i: Polymers. - : MDPI AG. - 2073-4360. ; 12:6
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Tidskriftsartikel (refereegranskat)abstract
- Silk fibroin from Bombyx mori caterpillar is an outstanding biocompatible polymer for the production of biomaterials. Its impressive combination of strength, flexibility, and degradability are related to the protein’s secondary structure, which may be altered during the manufacture of the biomaterial. The present study looks at the silk fibroin secondary structure during nanoparticle production using ionic liquids and high-power ultrasound using novel infrared spectroscopic approaches. The infrared spectrum of silk fibroin fibers shows that they are composed of 58% β-sheet, 9% turns, and 33% irregular and/or turn-like structures. When fibroin was dissolved in ionic liquids, its amide I band resembled that of soluble silk and no β-sheet absorption was detected. Silk fibroin nanoparticles regenerated from the ionic liquid solution exhibited an amide I band that resembled that of the silk fibers but had a reduced β-sheet content and a corresponding higher content of turns, suggesting an incomplete turn-to-sheet transition during the regeneration process. Both the analysis of the experimental infrared spectrum and spectrum calculations suggest a particular type of β-sheet structure that was involved in this deficiency, whereas the two other types of β-sheet structure found in silk fibroin fibers were readily formed.
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| 42. |
- Carlson, Johan E., et al.
(författare)
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Estimation of dielectric properties of crude oils based on IR spectroscopy
- 2014
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : Elsevier BV. - 0169-7439 .- 1873-3239. ; 139, s. 1-5
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Tidskriftsartikel (refereegranskat)abstract
- Dielectric properties of crude oils play an important role in characterization and quality control. Measuring permittivity accurately over a wide range of frequencies is, however, a time-consuming task and existing measurement methods are not easily adapted for real-time diagnostics. IR spectroscopy, on the other hand, provides rapid measurements of fundamental molecular properties.In this paper we show that by using multivariate calibration tools such as PLS regression, it is possible to extract dielectric properties of crude oils directly from IR spectra, in addition to conventional interpretation of the spectra, hence reducing the need for direct electrical measurements. Results on 16 different oil samples show that the dielectric parameters obtained with the proposed method agree well with those obtained using direct permittivity measurements. The PLS regression method has also been extended with Monte-Carlo simulation capabilities to account for uncertainties in the data
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| 43. |
- Corrie, John E T, et al.
(författare)
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Studies of decarboxylation in photolysis of alpha-carboxy-2-nitrobenzyl (CNB) caged compounds.
- 2008
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Ingår i: Photochem Photobiol Sci. - 1474-905X. ; 7:1, s. 84-97
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Tidskriftsartikel (refereegranskat)abstract
- Photolysis of alpha-carboxy-2-nitrobenzyl (CNB) caged compounds, studied here by time-resolved IR and UV spectroscopy, involves at least two pathways. In one, a conventional 2-nitrobenzyl type rearrangement takes place to release the photoprotected species via rapid decay of an aci-nitro intermediate. The alpha-carboxylate moiety of the CNB group is retained and the final by-product from this pathway is 2-nitrosophenylglyoxylate. Direct measurements of product formation confirmed that release via this pathway is faster for CNB-caged compounds than for related caged compounds without an alpha-carboxylate substituent and a rationale for the faster release rate is proposed. In a second pathway, photodecarboxylation of the starting material occurs: this pathway leads only to a slow, minor release of the photoprotected species. The extent to which the latter pathway contributes is affected by the nature of buffer salts in the irradiated solution. It was more prominent in an amine-based buffer (MOPS) than in phosphate buffer.
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| 44. |
- Corrie, J, et al.
(författare)
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Photochemistry and thermal decarboxylation of alpha-phosphoryloxy-p-nitrophenylacetates
- 2009
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Ingår i: Photochemistry and Photobiology. - : Wiley. - 0031-8655 .- 1751-1097. ; 85, s. 1089-1096
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Tidskriftsartikel (refereegranskat)abstract
- α-Carboxy-4-nitrobenzyl phosphate 4 and its derived monomethyl phosphate ester 5 were synthesized and purified by anion-exchange chromatography. A gradient of LiCl was necessary for elution of the anion-exchange column to avoid unexpected thermal decarboxylation that occurred during vacuum evaporation when the volatile triethylammonium bicarbonate buffer was used. Photolysis of each compound was accompanied by decarboxylation, and 4 released inorganic phosphate with near-100% stoichiometry. Time-resolved infrared spectroscopy of the photolysis reaction, coupled with density functional theory calculations of vibrational frequencies, enabled us to infer a mechanism for the photolytic pathway, although there was some evidence for a second pathway also being operative. In contrast to the results for 4, photolysis of 5 appeared to release little or no monomethyl phosphate.
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| 45. |
- De Oliveira, Danilo Hirabae, et al.
(författare)
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Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
-
Tidskriftsartikel (refereegranskat)abstract
- The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an α-helix to β-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into β-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.
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| 46. |
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| 47. |
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| 48. |
- Eliaz, D., et al.
(författare)
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Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Silk is a unique, remarkably strong biomaterial made of simple protein building blocks. To date, no synthetic method has come close to reproducing the properties of natural silk, due to the complexity and insufficient understanding of the mechanism of the silk fiber formation. Here, we use a combination of bulk analytical techniques and nanoscale analytical methods, including nano-infrared spectroscopy coupled with atomic force microscopy, to probe the structural characteristics directly, transitions, and evolution of the associated mechanical properties of silk protein species corresponding to the supramolecular phase states inside the silkworm's silk gland. We found that the key step in silk-fiber production is the formation of nanoscale compartments that guide the structural transition of proteins from their native fold into crystalline beta-sheets. Remarkably, this process is reversible. Such reversibility enables the remodeling of the final mechanical characteristics of silk materials. These results open a new route for tailoring silk processing for a wide range of new material formats by controlling the structural transitions and self-assembly of the silk protein's supramolecular phases.
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| 49. |
- Engblom, Jakob, et al.
(författare)
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Der ausgequetschte Code (3 part article)
- 2003
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Ingår i: Elektronik. ; :8, 10, 12
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This article was published in three parts, over three Issues of the German magazine "Elektronik". It covers how to efficiently program C for small embedded systems. It was published in cooperation with IAR Systems Germany AG.
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| 50. |
- Eremina, Nadejda, 1985-
(författare)
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Infrared spectroscopic studies : from small molecules to large
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Infrared light (IR) was first discovered by Friedrich Wilhelm Herschel in 1800. However, until 1940’s, molecular IR studies involved only water and small organic molecules, because of the long measurement times. Development Fourier transform infrared spectroscopy (FTIR) has minimized the time required to obtain data, making it possible to investigate bigger biological systems, e.g. proteins and nucleic acids.This thesis concentrates on the applications of different IR spectroscopic techniques to a variety of biological systems and development of new approaches to study complicated biological events.The first paper in this work concerns using so-called caged compounds to study the aggregation of Alzheimer’s Aβ-peptide which is linked to the formation of neurotoxic fibrils in the brain. By adding caged-sulfate to the Aβ samples we were able to change the pH of the sample, while recording IR data and study fibril formation in a time-resolved manner. Then we used caged–ADP to study the production of ATP and creatine, mediated by creatine kinase (CK). Using CK as a helper enzyme we studied the effects of the phosphate binding on the secondary structure of SR Ca2+ATPse and determined the structural differences between two similar states Ca2E1ADP and Ca2E1ATP.In the second part of the thesis we used ATR-FTIR spectroscopy and a specially designed dialysis setup, to develop a general method to detect ligand binding events by observing the IR absorbance changes in the water hydration shell around the molecules. The same method was used to determine the binding of DNA to the transcription factors of the E2F family. E2F proteins play main part in the gene regulatory networks that control cell development. However how they recognize their DNA-binding sites and the mechanism of binding is not well understood. By using ATR-FTIR, we observed the changes in the secondary structure of the proteins, as well as the distortions to the DNA upon E2F-DNA complex formation.
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