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  • 301.
    Bengtsson, Åsa
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjöberg, Staffan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Surface complexation and proton-promoted dissolution in aqueous apatite systems2009In: Pure and Applied Chemistry, ISSN 0033-4545, E-ISSN 1365-3075, Vol. 81, no 9, p. 1569-1584Article in journal (Refereed)
    Abstract [en]

    Abstract: The dissolution of hydroxyapatite (HAP) and fluorapatite (FAP) has been studied (25 °C, 0.1 M NaCl medium) within the pH ranges 2–11 (FAP) and 4–10 (HAP). A range of techniques has been utilized to achieve understanding in how these two abundant minerals may interact with their natural surroundings (e.g., body fluids and soil environments). Synthetic crystalline HAP and FAP were prepared, and both minerals were found to undergo a phase transformation generated during a dialysis step of the synthetic routes. Surface-deficient layers with the nonstoichiometric compositions Ca8.4(HPO4)1.6(PO4)4.4(OH)0.4 and Ca9(HPO4)2(PO4)4F2 were identified. The equilibrium analysis of experimental solubility data of the two apatite systems was based upon potentiometric titration data, batch experiments, and zeta-potential measurements in combination with information provided by X-ray photoelectron spectroscopy (XPS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. The analysis required, besides the two solubility equilibria, the formation of surface protonation/deprotonation reactions, re-adsorption processes involving phosphate and fluoride ions as well as an ion exchange reaction (≡F + H2O ⇋ ≡OH + H+ + F) to fully describe the dissolution characteristics of the two apatite systems. The resulting model also agrees with observations from XPS and solubility data, claiming the formation of CaF2(s) in the most acidic pH range of the FAP system. In addition, calculated isoelectric points (pHiep) are in agreement with values from surface charge measurements showing pHiep (HAP) = 8.1 and pHiep (FAP) = 5.7.

  • 302.
    Bengtsson, Åsa
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjöberg, Staffan
    Persson, Per
    Solubility and Adsorption Characterisics of Non-Stoichiometric Surface Layers of Hydroxyapatite with some Organic Carboxylic Ligands: An ATR-FTIR Spectroscopic and Thermodynamic Modeling StudyManuscript (preprint) (Other (popular science, discussion, etc.))
  • 303. Bengtsson-Palme, Johan
    et al.
    Boulund, Fredrik
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kristiansson, Erik
    Larsson, D. G. Joakim
    Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India2014In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5Article in journal (Refereed)
    Abstract [en]

    There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.

  • 304. Bengtsson-Palme, Johan
    et al.
    Hammarén, Rickard
    Pal, Chandan
    Östman, Marcus
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Björlenius, Berndt
    Flach, Carl-Fredrik
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kristiansson, Erik
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, D.G. Joakim
    Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics2016In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 572, p. 697-712Article in journal (Refereed)
    Abstract [en]

    Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.

  • 305.
    Benlloch, Reyes
    et al.
    Department of Forest Genetics and Plant Physiology, SLU.
    Shevela, Dmitriy
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hainzl, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Grundström, Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Shutova, Tatyana
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Samuelsson, Göran
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sauer-Eriksson, Elisabeth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Crystal structure and functional characterization of Photosystem II-associated carbonic anhydrase CAH3 in Chlamydomonas reinhardtii2015In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 167, no 3, p. 950-962Article in journal (Refereed)
    Abstract [en]

    In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates.The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place inphotosystem II (PSII). Recent studies show that in higher plants, HCO3– increases PSII activity by acting as a mobile acceptor ofthe protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested toimprove proton removal from PSII, possibly by rapid reformation of HCO3– from CO2. In this study, we investigated the interplaybetween PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometrymeasurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen underillumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and2.7-Å resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature notpreviously observed in a-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 functionwith dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3– on PSIIactivity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSIIpreparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at lowpH and CO2 concentration.

  • 306. Ben-Menachem, Gil
    et al.
    Byström, Tomas
    Umeå University, Faculty of Science and Technology, Chemistry.
    Rechnitzer, Hagai
    Rottem, Shlomo
    Rilfors, Leif
    Umeå University, Faculty of Science and Technology, Chemistry.
    Lindblom, Göran
    Umeå University, Faculty of Science and Technology, Chemistry.
    The physico-chemical characteristics of the phosphocholine-containing glycoglycerolipid MfGL-II govern the permeability properties of Mycoplasma fermentans2001In: The FEBS Journal, European Journal of Biochemistry, Vol. 268, no 13, p. 3694-3701Article in journal (Refereed)
    Abstract [en]

    Mycoplasma fermentans seems to be involved in several pathogenic condtions in humans, and is among other things capable of fusing with T-cells and lymphocytes. The choline-containing phosphoglycolipid 6'-O-(3"-phosphocholine-2"-amino-1"-phospho-1",3"-propanediol)-α-d-glucopyranosyl-(1'→3)-1,2-diacylglycerol (MfGL-II) in the membrane of M. fermentans has been suggested to enhance the fusion process, and the characteristics of MfGL-II were therefore investigated. When a cell culture ages the fraction of MfGL-II increases, and the fraction of the other major membrane lipid, phosphatidylglycerol (PtdGro), decreases concomitantly. Swelling experiments showed that the permeability and osmotic fragility are markedly reduced in aged cells. MfGL-II is selectively released into the surrounding medium when aged M. fermentans cells are incubated in buffer containing EDTA. The physico-chemical properties of MfGL-II were studied by NMR spectroscopy and differential scanning calorimetry, and they can explain the biochemical results. The temperature for the transition between gel and lamellar liquid crystalline (Lα) phases is 35–45 °C higher for MfGL-II than for PtdGro, which most probably gives rise to the reduced permeability in aged cells. At high water contents MfGL-II forms an Lα phase and isotropic aggregates which were interpreted to be vesicles with a radius of ≈ 450 Å. It is proposed that MfGL-II forms vesicles in the surrounding medium when it is released from the cell membrane. Neither EDTA nor Ca2+ ions have a significant influence on the aggregate structures formed by MfGL-II. Our results indicate that MfGL-II has no fusogenic properties. It is more probable that a recently identified lysolipid in the M. fermentans membrane acts as a fusogen.

  • 307. Beranová, Lenka
    et al.
    Humpolíčková, Jana
    Sýkora, Jan
    Benda, Aleš
    Cwiklik, Lukasz
    Jurkiewicz, Piotr
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hof, Martin
    Effect of heavy water on phospholipid membranes: experimental confirmation of molecular dynamics simulations2012In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, no 42, p. 14516-14522Article in journal (Refereed)
    Abstract [en]

    Although there were experimental indications that phospholipid bilayers hydrated with D(2)O express different biophysical properties compared with hydration by ordinary H(2)O, a molecular concept for this behavior difference was only recently proposed by a molecular dynamics simulations study [T. Róg et al., J. Phys. Chem. B, 2009, 113, 2378-2387]. Here we attempt to verify those theoretical predictions by fluorescence measurements on 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes. Specifically, we determine the water isotope effect on headgroup hydration and mobility, lateral lipid diffusion and lipid backbone packing. Time-dependent fluorescence shift experiments show significantly slower dynamics and lower hydration of the headgroup region for a bilayer hydrated with D(2)O, an observation in good agreement with the calculated predicted differences in duration of lipid-lipid and lipid-water bridges and extent of water penetration into the bilayer, respectively. The water isotope effect on the lipid order parameter of the bilayer core (measured by fluorescence anisotropy) and lateral diffusion of lipid molecules (determined by two-focus fluorescence correlation spectroscopy) is close to the experimental errors of the experiments, however also refers to slightly more rigid organization of phospholipid bilayers in heavy water. This study confirms the view that the water isotope effect can be particularly found in time-resolved physicochemical properties of the membrane. Together with the simulations our experiments provide a comprehensive, molecular view on the effect of D(2)O on phospholipid bilayers.

  • 308.
    Berg, Anders
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry. Faculty of Teacher Education, Mathematics, Technology and Science Education.
    Bergendahl, Christina
    Umeå University, Faculty of Science and Technology, Chemistry.
    Lundberg, Bruno
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tibell, Lena
    Umeå University, Faculty of Science and Technology, Chemistry.
    Benefiting from an open-ended experiment? A comparison of attitudes to, and outcomes of, an expository versus an open-inquiry version of the same experiment2003In: International Journal of Science Education, Vol. 25, no 3, p. 351-72Article in journal (Refereed)
    Abstract [en]

    In this article we compare outcomes of an open-inquiry and an expository version of a chemistry laboratory experiment at university level for 190 students. The aim of the study was to investigate if these two versions would result in different outcomes depending on the students' attitudes towards learning. We used a questionnaire to find out their attitude position prior to the laboratory experiment. The outcome in the different versions of the experiment was evaluated by interviews, questions asked during the experiment and students self-evaluations. The main findings were that the open-inquiry version shows the most positive outcomes regarding learning outcome, preparation time, time spent in the laboratory and student perception of the experiment. The students with low attitude position needed more support to meet the challenge of an open-inquiry experiment, the support being a clearer explanation of the aims, and feedback from the instructor during the experiment.

  • 309.
    Berg, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Narkotika som läkemedel: Behandling med centralstimulantia hos barn med ADHD – Effekter och biverkningar2015Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 310.
    Berg, C. Anders R.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Analysis of university chemistry students’ questions and focus during laboratory work.Manuscript (Other academic)
  • 311.
    Berg, C. Anders R.
    Umeå University, Faculty of Teacher Education, Mathematics, Technology and Science Education. Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Factors related to observed attitude change toward learning chemistry among university students2005In: Chemistry education, ISSN 1109-4028, E-ISSN 1109-4028, Chemistry Education Research and Practice, Vol. 6, no 1, p. 1-18Article in journal (Refereed)
    Abstract [en]

    To gain insight into factors associated with changes in attitude toward learning chemistry, six students who displayed major attitude changes were identified through a pre- and post-course attitude questionnaire administered to sixty-six first-year university chemistry students. Those with largest attitude changes, both positive and negative, were selected to highlight the contrast between students. The six students were interviewed; descriptions of their one-semester chemistry course experiences were analyzed to identify factors associated with their change in attitude. A positive attitude change was associated with evidence of motivated behaviour, while a negative change was linked to less motivated behaviour. Students addressed similar factors in the educational setting, but students with positive attitude changes exhibited fewer negative views of educational factors, while students with negative attitude changes showed an opposite pattern. Since the same factors, students’ perceived level of teacher empathy for their efforts at chemistry learning, affected both groups, this indicates a possibility for changes in educational setting beneficial to all students.

  • 312.
    Berg, C. Anders R.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Learning Chemistry at the University level: Student attitudes, motivation, and design of the learning environment2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The main purpose of the research this thesis is based upon was to study students’ attitudes towards learning chemistry at university level and their motivation from three perspectives. How can students’ attitudes towards learning chemistry be assessed? How can these attitudes be changed? How are learning situations experienced by students with different attitude positions?

    An attitude questionnaire, assessing views of knowledge, learning assessments, laboratory activities, and perceived roles of instructors and student, was used to estimate students’ attitude positions. It was shown that a positive attitude was related to motivated student behaviour. Furthermore, it was shown that factors in the educational context, such as the teachers’ empathy for students learning chemistry, had affected the students. It was also found that students holding different attitude positions showed different learning outcomes and differed in their perceptions of the learning situation. Students’ holding a more relativistic attitude more readily accepted the challenges of open experiments and other more demanding tasks than those holding a dualistic attitude.

    In addition, the teachers were found to play important roles in the way the tasks were perceived and the development of students’ ideas. In studied laboratory activities open tasks resulted in positive student engagement and learning outcomes. Preparative exercises, such as a computer simulation of the phenomena to be investigated, affected students’ focus during laboratory work, encouraging them to incorporate more theoretical considerations and increasing their ability to use chemical knowledge. Finally, it was shown that students’ focus during laboratory work is reflected in the questions they ask the teacher, implying that questions could be used as tools to evaluate laboratory teaching and learning processes.

    The findings imply that students’ attitudes towards learning and motivation, and the design of learning situations, are key factors in the attainment of desirable higher educational goals such as the ability to judge, use, and develop knowledge. For universities encountering students with increasingly diverse attitudes, motivation and prior knowledge, these are important considerations if they are to fulfil their commissions to provide high quality learning environments and promote high quality learning.

  • 313. Berg, C
    et al.
    Säfholm, M
    Jansson, E
    Olsson, A J
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brandt, I
    Combined exposure to progestin and oestrogen mixtures: Effects on vitellogenin and hormone receptor mRNA expression2012In: Comparative Biochemistry and Physiology A, ISSN 1095-6433, E-ISSN 1531-4332, Vol. 163, no 1, p. S56-S57Article in journal (Other academic)
  • 314. Berg, Cecilia
    et al.
    Bäckström, Tobias
    Winberg, Svante
    Lindberg, Richard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brandt, Ingvar
    Developmental exposure to fluoxetine modulates the serotonin system in hypothalamus2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 1, article id e55053Article in journal (Refereed)
    Abstract [en]

    The selective serotonin reuptake inhibitor (SSRI) fluoxetine (FLU, Prozac®) is commonly prescribed for depression in pregnant women. This results in SSRI exposure of the developing fetus. However, there are knowledge gaps regarding the impact of SSRI exposure during development. Given the role of serotonin in brain development and its cross-talk with sex hormone function, we investigated effects of developmental exposure to pharmacologically relevant concentrations of FLU (3 and 30 nM (measured)) on brain neurotransmitter levels, gonadal differentiation, aromatase activity in brain and gonads, and the thyroid system, using the Xenopus tropicalis model. Tadpoles were chronically exposed (8 weeks) until metamorphosis. At metamorphosis brains were cryosectioned and levels of serotonin, dopamine, norepinephrine, and their metabolites 5-hydroxyindoleacetic acid, 3,4-dihydroxyphenylacetic acid, and homovanillic acid were measured in discrete regions (telencephalon, hypothalamus and the reticular formation) of the cryosections using high-performance liquid chromatography. Exposure to 30 nM FLU increased the concentration of 5-hydroxyindoleacetic acid in hypothalamus compared with controls. FLU exposure did not affect survival, time to metamorphosis, thyroid histology, gonadal sex differentiation, or aromatase activity implying that the effect on the serotonergic neurotransmitter system in the hypothalamus region was specific. The FLU concentration that impacted the serotonin system is lower than the concentration measured in umbilical cord serum, suggesting that the serotonin system of the developing brain is highly sensitive to in utero exposure to FLU. To our knowledge this is the first study showing effects of developmental FLU exposure on brain neurochemistry. Given that SSRIs are present in the aquatic environment the current results warrant further investigation into the neurobehavioral effects of SSRIs in aquatic wildlife.

  • 315.
    Berg, Elin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Adsorption of organic andinorganic compounds onactivated carbon and biochar2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 316.
    Berg, Isak
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Analysis of α-actinin in Phytophthora infestans2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 317.
    Berg, Lotta
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Exploring non-covalent interactions between drug-like molecules and the protein acetylcholinesterase2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The majority of drugs are small organic molecules, so-called ligands, that influence biochemical processes by interacting with proteins. The understanding of how and why they interact and form complexes is therefore a key component for elucidating the mechanism of action of drugs. The research presented in this thesis is based on studies of acetylcholinesterase (AChE). AChE is an essential enzyme with the important function of terminating neurotransmission at cholinergic synapses. AChE is also the target of a range of biologically active molecules including drugs, pesticides, and poisons. Due to the molecular and the functional characteristics of the enzyme, it offers both challenges and possibilities for investigating protein-ligand interactions. In the thesis, complexes between AChE and drug-like ligands have been studied in detail by a combination of experimental techniques and theoretical methods. The studies provided insight into the non-covalent interactions formed between AChE and ligands, where non-classical CH∙∙∙Y hydrogen bonds (Y = O or arene) were found to be common and important. The non-classical hydrogen bonds were characterized by density functional theory calculations that revealed features that may provide unexplored possibilities in for example structure-based design. Moreover, the study of two enantiomeric inhibitors of AChE provided important insight into the structural basis of enthalpy-entropy compensation. As part of the research, available computational methods have been evaluated and new approaches have been developed. This resulted in a methodology that allowed detailed analysis of the AChE-ligand complexes. Moreover, the methodology also proved to be a useful tool in the refinement of X-ray crystallographic data. This was demonstrated by the determination of a prereaction conformation of the complex between the nerve-agent antidote HI-6 and AChE inhibited by the nerve agent sarin. The structure of the ternary complex constitutes an important contribution of relevance for the design of new and improved drugs for treatment of nerve-agent poisoning. The research presented in the thesis has contributed to the knowledge of AChE and also has implications for drug discovery and the understanding of biochemical processes in general.

  • 318.
    Berg, Lotta
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Andersson, C. David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Artursson, Elisabet
    Hornberg, Andreas
    Tunemalm, Anna-Karin
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ekstrom, Fredrik
    Targeting Acetylcholinesterase: Identification of Chemical Leads by High Throughput Screening, Structure Determination and Molecular Modeling2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 11, article id e26039Article in journal (Refereed)
    Abstract [en]

    Acetylcholinesterase (AChE) is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia) to treat cholinergic deficiencies (e. g. in Alzheimer's disease), but may also act as dangerous toxins (e. g. nerve agents such as sarin). Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS). Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685.mAChE) is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical characterization, crystallography and computational chemistry provide a route to novel AChE inhibitors and reactivators.

  • 319.
    Berg, Lotta
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mishra, Brijesh Kumar
    Andersson, C. David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ekström, Fredrik
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes2016In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 22, no 8, p. 2672-2681Article in journal (Refereed)
    Abstract [en]

    Molecular recognition events in biological systems are driven by non-covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CHY type involving electron-deficient CH donors using dispersion-corrected density functional theory (DFT) calculations applied to acetylcholinesterase-ligand complexes. The strengths of CHY interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non-activated CHY interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CHY interactions when analysing protein-ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.

  • 320.
    Berg, Lotta
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Niemiec, Moritz S.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Qian, Weixing
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Andersson, C. David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wittung-Stafshede, Pernilla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ekström, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, European CBRNE Center.
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Similar but Different: Thermodynamic and Structural Characterization of a Pair of Enantiomers Binding to Acetylcholinesterase2012In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 51, no 51, p. 12716-12720Article in journal (Refereed)
    Abstract [en]

    Take a closer look: Unexpectedly, a pair of enantiomeric ligands proved to have similar binding affinities for acetylcholinesterase. Further studies indicated that the enantiomers exhibit different thermodynamic profiles. Analyses of the noncovalent interactions in the protein-ligand complexes revealed that these differences are partly due to nonclassical hydrogen bonds between the ligands and aromatic side chains of the protein.

  • 321.
    Bergemalm, Daniel
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    Forsberg, Karin
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Jonsson, P Andreas
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    Graffmo, Karin S
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Brännström, Thomas
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Andersen, Peter M
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Marklund, Stefan L
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    Changes in the spinal cord proteome of an amyotrophic lateral sclerosis murine model determined by differential in-gel electrophoresis2009In: Molecular and cellular proteomics, ISSN 1535-9484, Vol. 8, no 6, p. 1306-1317Article in journal (Refereed)
    Abstract [en]

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by loss of motor neurons resulting in progressive paralysis. To date, more than 140 different mutations in the gene encoding CuZn-superoxide dismutase (SOD1) have been associated with ALS. Several transgenic murine models exist in which various mutant SOD1s are expressed. We have used differential in-gel electrophoresis (DIGE) to analyze the changes in the spinal cord proteome induced by expression of the unstable SOD1 truncation mutant G127insTGGG (G127X) in mice. Unlike mutants used in most other models, G127X lacks SOD activity and is present at low levels, thus reducing the risk of overexpression artifacts. The mice were analyzed at their peak body weights, just before onset of symptoms. Variable importance plot (VIP) analysis showed that 420 of 1,800 detected protein spots contributed significantly to the differences between the groups. By MALDI-TOF MS analysis, 54 proteins were identified. One spot was found to be a covalently linked mutant SOD1 dimer, apparently analogous to SOD1 immunoreactive bands migrating at double the molecular weight of SOD1 monomers previously detected in humans and mice carrying mutant SOD1s and in sporadic ALS cases. Analyses of affected functional pathways, and the subcellular representation of alterations suggest that the toxicity exerted by mutant SODs induces oxidative stress and affects mitochondria, cellular assembly/organization, and protein degradation.

  • 322.
    Bergendahl, Christina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Development of competence in biochemical experimental work: Assessment of complex learning at university level2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biochemistry is part of life science: a fast developing multidisciplinary area. The overall aims of this thesis and the work underlying it were to find ways in which to develop competence in biochemistry at university level and to assess complex learning. A particular interest was the development of experimental work as a means to promote learning.

    The study focuses on changes made in two educational settings. The aim of the changes was to develop competence, amongst both students and teachers. Therefore, the research in the three first papers has in some aspects, and to different extent, the characteristics of action research. Broadly, the changes can be described as making experiments more open, with multiple formative and authentic assessment methods involving both students and teachers. The empirical studies included questionnaires, interviews, questions asked during experimental work, written material as formulated objectives, examination questions and answers, reports, other products; and grades/judgements made by teachers and students. Collected data were analyzed in several different ways. Statistical methods included the use of mean values, paired T-tests, Spearman rank correlation coefficients and Principal Component Analysis. Interview data as well as some questionnaire data were analyzed using analytical induction techniques. Some categories were based on thematic content analysis, while others were based on Bloom’s taxonomy. Students’ attitude positions were categorized according to Perry’s framework.

    The main results can be summarized as follows;

    The students’ learning was improved by open ended versions of experimental work, according to both their and the researchers’ opinions. Planning, approaching problems from different perspectives and evaluating the results of their own experimental work promote the students’ capacity for higher order cognitive thinking. However, the synthesis level constitutes a threshold and particular support is needed for students with a more dualistic view of teaching, learning and experimental work.

    Introducing formative and authentic assessment is a way to help students to make progress, and to develop competence. The importance was clearly demonstrated of involving both teachers and students in discussions of aims and criteria and of making them explicit. Feedback from teachers’ and students’ own reflective activities about subject content, and their learning as well as affective factors were shown to be central for complex learning. Based on our studies, areas were identified for the critical development of competence and for promoting learning in biochemistry at university level. These areas are; multidisciplinary and complex learning, communication skills of different types, metacognitive perspectives, attitude development, and affective factors.

    The students see experimental work as crucial for their learning and therefore important in terms of assessment. Therefore, experimental work can and ought to be assessed. However, similarities and discrepancies were observed between students’ and teachers’ perspectives for both the aims and assessment of experimental work. Our conclusion is that a combination of assessment methods is needed in order to be able to make a high qualitative assessment.

  • 323.
    Bergendahl, Christina
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tibell, Lena
    Boosting complex learning by strategic assessment and course design2004In: Faseb Journal, ISSN 0892-6638, Vol. 18, no 8, p. C206-C207Article in journal (Other (popular science, discussion, etc.))
  • 324.
    Bergendahl, Christina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tibell, Lena
    Department of Biomedicine and Surgery, Linköping .
    Boosting complex learning by strategic assessment and course design2005In: Journal of Chemical Education, ISSN 0021-9584, E-ISSN 1938-1328, Vol. 82, no 4, p. 645-651Article in journal (Refereed)
    Abstract [en]

    Learning quality depends on the assessment methods used, as well as other factors. By choosing adequate assessments and involving students in the process of learning, students can gain a deeper understanding of the content and its context while developing related skills. In this study we describe a practical university-level biochemistry course that focuses on understanding protein separation and analysis techniques and especially on their application. The course was designed to examine the effects of a strategic use of differentassessment methods and an analysis of the resulting outcomes. We used quantitative as well as qualitative methods, including a simplified variant of the Bloom taxonomy, statistical methods, principle component analysis, inquires, and interviews. We conclude that astrategic choice of assessments and instructional design can be used to achieve morecomplex learning. We did not find any single teaching or assessment method to be clearly the best for enhancing higher-order thinking or achieving all learning objectives; rather a combination of different methods (i.e., a strategic choice) seems the best approach.

  • 325.
    Bergendahl, V.C.B.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Action Research as a Means of Professional Development: Reflections on Research and Action in University Chemistry Education.2003In: Journal of In-service Education, Vol. 29, no 3, p. 363-374Article in journal (Refereed)
  • 326.
    Bergendahl, V.C.B.
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tibell, L.A.E.
    Aims and Assessment of Laboratory Based Project work in a Master’s Level Biochemistry Course.: Students’ and Teachers’ Perspectives.Manuscript (Other academic)
  • 327. Bergenstråhle-Wohlert, Malin
    et al.
    Berglund, Lars A
    Brady, John W
    Larsson, P Tomas
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wohlert, Jakob
    Concentration enrichment of urea at cellulose surfaces: results from molecular dynamics simulations and NMR spectroscopy2012In: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 19, no 1, p. 1-12Article in journal (Refereed)
    Abstract [en]

    A combined solid-state NMR and Molecular Dynamics simulation study of cellulose in urea aqueous solution and in pure water was conducted. It was found that the local concentration of urea is significantly enhanced at the cellulose/solution interface. There, urea molecules interact directly with the cellulose through both hydrogen bonds and favorable dispersion interactions, which seem to be the driving force behind the aggregation. The CP/MAS 13C spectra was affected by the presence of urea at high concentrations, most notably the signal at 83.4 ppm, which has previously been assigned to C4 atoms in cellulose chains located at surfaces parallel to the (110) crystallographic plane of the cellulose Iβ crystal. Also dynamic properties of the cellulose surfaces, probed by spin-lattice relaxation time 13CT 1 measurements of C4 atoms, are affected by the addition of urea. Molecular Dynamics simulations reproduce the trends of the T 1measurements and lends new support to the assignment of signals from individual surfaces. That urea in solution is interacting directly with cellulose may have implications on our understanding of the mechanisms behind cellulose dissolution in alkali/urea aqueous solutions.

  • 328.
    Bergfors, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Betablockerare somförebyggande behandling avsymtom vid ärftligt långt QTsyndrom2014Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 329.
    Bergknut, Magnus
    Umeå University, Faculty of Science and Technology, Chemistry.
    Characterization of PAH-contaminated soils focusing on availability, chemical composition and biological effects2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The risks associated with a soil contaminated by polycyclic aromatic hydrocarbons (PAHs) are generally assessed by measuring individual PAHs in the soil and correlating the obtained amounts to known adverse biological effects of the PAHs. The validity of such a risk estimation is dependent on the presence of additional compounds, the availability of the compounds (including the PAHs), and the methods used to correlate the measured chemical data and biological effects. In the work underlying this thesis the availability, chemical composition and biological effects of PAHs in samples of soils from PAH-contaminated environments were examined. It can be concluded from the results presented in the included papers that the PAHs in the studied soils from industrial sites were not generally physically trapped in soil material, indicating that the availability of the PAHs was not restricted in this sense. However, the bioavailable fraction of the PAHs, as assessed by bioassays with the earthworm Eisenia Fetida, could not be assessed by a number of abiotic techniques (including: solid phase micro extraction, SPME; use of semi-permeable membrane devices, SPMDs; leaching with various solvent mixtures, leaching using additives, and sequential leaching) and it seems to be difficult to find a chemical method that can accurately assess the bioavailability of PAHs. Furthermore, it was shown that PAH-polluted samples may be extensively chemically characterized by GC-TOFMS using peak deconvolution, and over 900 components can be resolved in a single run. The chemical characterization also revealed that samples that appeared to be similar in terms of their PAH composition were heterogeneous in terms of their overall composition. Finally, single compounds from this large set of compounds, which correlated with different biological effects, could be identified using the multivariate technique partial least squares projections to latent structures (PLS). This indicates that PLS may provide a valid alternative to Effect Directed Analysis (EDA), an established method for finding single compounds that correlate to the toxicity of environmental samples. Thus, the instrumentation and data evaluation tools used in this thesis are clearly capable of providing a broad chemical characterization as well as linking the obtained chemical data to results from bioassays. However, the link between the chemical analyses and the biological tests could be improved as as an organic solvent that solubilised virtually all of the contaminants was used during the chemical analysis while the biological tests were performed in an aqueous solution with limited solubility for a number of compounds. Consequently the compounds probably have a different impact in the biological tests than their relative abundance in profiles obtained by standard chemical analyses suggests. The availability and bioavailability of contaminants in soil also has to be studied further, and such future studies should focus on the molecular interactions between the contaminants and different compartments of the soil. By doing so, detailed knowledge could be obtained which could be applied to a number of different contaminants and soil types. Such studies would generate the data needed for molecular-based modelling of availability and bioavailability, which would be a big step forward compared to current risk assessment practices.

  • 330.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Eriksson, Lennart
    Nyman, Madeleine
    Andersson, Patrik
    Umeå University, Faculty of Science and Technology, Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Chemistry.
    Novel multivariate methods for evaluation of PCB levels, and of CYP1A, vitamin E, and haematological parameters as PCB-exposure biomarkers, in seal2005In: Organohalogen Compounds, Vol. 67, p. 1867-70Article in journal (Refereed)
  • 331.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Frech, Kristina
    Umeå University, Faculty of Science and Technology, Chemistry.
    Andersson, Patrik L.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Chemistry.
    Characterization and classification of complex PAH samples using GC-qMS and GC-TOFMS2006In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 65, no 11, p. 2208-2215Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to compare the polycyclic aromatic hydrocarbon (PAH) contents in a number of complex samples, including soil samples from industrial sites, anti-skid sand, urban dust and ash samples from municipal solid waste incinerators. The samples were characterized by routine analysis of PAHs (gas chromatography–quadrupole mass spectrometry) and gas chromatography–time of flight mass spectrometry (GC–TOFMS). Classification of the samples by principal component analysis (PCA) according to their composition of PAHs revealed that samples associated with traffic and the municipal incinerator formed homogeneous clusters, while the PAH-contaminated soils clustered in separate groups. Using spectral data to resolve co-eluting chromatographic peaks, 962 peaks could be identified in the GC–TOFMS analysis of a pooled sample and 123–527 peaks in the individual samples. Many of the studied extracts included a unique set of chemicals, indicating that they had a much more diverse contamination profile than their PAH contents suggested. Compared to routine analysis, GC–TOFMS provided more detailed information about each sample and in this study a large number of alkylated PAHs were found to be associated with the corresponding unsubstituted PAHs. The possibility to filter peaks according to different criteria (e.g. to include only peaks that were detected in the analysis of another sample) was explored and used to identify unique as well as common compounds within samples. This procedure could prove to be valuable for obtaining relevant chemical data for use in conjunction with results from various biological test systems.

  • 332.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kitti, Anna
    Umeå University, Faculty of Science and Technology, Chemistry.
    Lundstedt, Staffan
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Chemistry.
    Assessment of the availability of polycyclic aromatic hydrocarbons from gasworks soil using different extraction solvents and techniques2004In: Environmental Toxicology and Chemistry, ISSN 0730-7268, E-ISSN 1552-8618, Vol. 23, no 8, p. 1861-1866Article in journal (Refereed)
    Abstract [en]

    This study was designed to assess the availability of polycyclic aromatic hydrocarbons (PAHs) present at a gasworks site to different soil remediation techniques. The study examined the effect on PAH availability of using different organic solvents, the degree of pretreatment, and the extraction time. In total, 25 PAHs (with two to six fused rings) and five carbonyl derivatives were measured. The results indicated that the PAHs and their derivatives were bound loosely to the surface of the studied soil and that there were no significant kinetic boundaries associated with the extraction of the PAHs. Furthermore, it was concluded that the studied soil was not suitable for bioremediation, as the concentration of PAHs with low molecular weight were limited. However, pressurized liquid extraction (PLE) with methanol as the solvent extracted 97% of all PAHs and PAH-derivatives, indicating that extraction may be effective as part of a soil remediation technique for old gasworks soils.

  • 333.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kucera, Adam
    Frech, Kristina
    Umeå University, Faculty of Science and Technology, Chemistry.
    Andersson, Erika
    Engwall, Magnus
    Rannung, Ulf
    Koci, Vladimir
    Andersson, Patrik
    Umeå University, Faculty of Science and Technology, Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Chemistry.
    Identification of potentially toxic compounds in complex extracts of environmental samples using GC-MS and multivariate data analysis2007In: Environmental Toxicology and Chemistry, ISSN 0730-7268, E-ISSN 1552-8618, Vol. 26, no 2, p. 208-17Article in journal (Refereed)
    Abstract [en]

    In this study, we examined 31 samples of varying chemical composition, including samples of soils from gasworks, coke production sites, and sites where wood preservatives were heavily used; ash and soot from municipal solid waste incinerators; antiskid sand; and dust from areas with heavy road traffic. The samples were comprehensively chemically characterized, especially their polycyclic aromatic compound contents, using gas chromatography–time-of-flight mass spectrometry, whereas their biological effects were assessed using dehydrogenase activity, root growth (Hordeum vulgare), reproduction of springtails (Folsomia candida), algal growth (Desmodesmus subspicatus), germinability (Sinapis alba), Vibrio fischeri, DR-CALUX, and Ames Salmonella assays. The number of compounds detected in the samples ranged from 123 to 527. Using the multivariate regression technique of partial-least-squares projections to latent structures, it was possible to find individual compounds that exhibited strong correlations with the different biological responses. Some of the results, however, indicate that a broader chemical characterization may be needed to identify all the compounds that may cause the measured biological responses.

  • 334.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Laudon, Hjalmar
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, Anna
    Gocht, Tilman
    Wiberg, Karin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Atmospheric deposition, retention, and stream export of dioxins and PCBs in a pristine boreal catchment2011In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 159, no 6, p. 1592-1598Article in journal (Refereed)
    Abstract [en]

    The mass-balance between diffuse atmospheric deposition of organic pollutants, amount of pollutants retained by the terrestrial environment, and levels of pollutants released to surface stream waters was studied in a pristine northern boreal catchment. This was done by comparing the input of atmospheric deposition of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) and PCBs with the amounts exported to surface waters. Two types of deposition samplers were used, equipped with a glass fibre thimble and an Amberlite sampler respectively. The measured fluxes showed clear seasonality, with most of the input and export occurring during winter and spring flood, respectively. The mass balance calculations indicates that the boreal landscape is an effective sink for PCDD/Fs and PCBs, as 96.0-99.9 % of received bulk deposition was retained, suggesting that organic pollutants will continue to impact stream water in the region for an extended period of time.

  • 335.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Laudon, Hjalmar
    Wiberg, Karin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dioxins, PCBs, and HCB in soil and peat profiles from a pristine boreal catchment2010In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 158, no 7, p. 2518-2525Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to explore how atmospherically derived soil pollution is affected by environmental processes at two typical boreal catchment landscape type settings: wetlands and forested areas. Measurements of hydrophobic organic compounds (HOCs) in forest soil and peat from an oligotrophic mire at various depths were performed at a remote boreal catchment in northern Sweden. HOCs in peat were evenly distributed throughout the body of the mire while levels of HOCs in the forest soil increased with increased amount of organic matter. Evaluation of HOC composition by principal component analysis (PCA) showed distinct differences between surface soils and deeper soil and peat samples. This was attributed to vertical transport, degradation and/or shifting sources over time. The calculated net vertical transport differed between surface layers (0.3%) and deeper soils (8.0%), suggesting that vertical transport conditions and processes differ in the deeper layers compared to the surface layers.

  • 336.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Meijer, Sandra
    Halsall, Crispin
    Ågren, Anneli
    Laudon, Hjalmar
    Köhler, Stephan
    Jones, Kevin C
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wiberg, Karin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Modelling the fate of hydrophobic organic contaminants in a boreal forest catchment: a cross disciplinary approach to assessing diffuse pollution to surface waters2010In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 158, no 9, p. 2964-2969Article in journal (Refereed)
    Abstract [en]

    The fate of hydrophobic organic compounds (HOCs) in soils and waters in a northern boreal catchment was explored through the development of a chemical fate model in a well-characterised catchment system dominated by two land types: forest and mire. Input was based solely on atmospheric deposition, dominated by accumulation in the winter snowpack. Release from soils was governed by the HOC concentration in soil, the soil organic carbon fraction and soil-water DOC content. The modelled export of selected HOCs in surface waters ranged between 11 and 250ng day(-1) during the snow covered period, compared to 200 and 9600ng/d during snow-melt; highlighting the importance of the snow pack as a source of these chemicals. The predicted levels of HOCs in surface water were in reasonable agreement to a limited set of measured values, although the model tended to over predict concentrations of HOCs for the forested sub-catchment, by over an order of magnitude in the case of hexachlorobenzene and PCB 180. This possibly reflects both the heterogeneity of the forest soils and the complicated and changing hydrology experienced between the different seasons.

  • 337. Bergknut, Magnus
    et al.
    Persson, Per
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Skyllberg, Ulf
    Molecular characterization of brominated persistent pollutants using extended X-ray absorption fine structure (EXAFS) spectroscopy2008In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 390, no 3, p. 921-928Article in journal (Refereed)
    Abstract [en]

    X-ray absorption fine structure (EXAFS) spectroscopy spectra were collected for three brominated persistent pollutants: 6-bromo-2,4,5-trichlorophenol (BrTriClP), pentabromophenol (PentaBrP) and 3,3',5,5'-tetrabromobisphenol A (TBBA). The substances were selected to be symmetrical (BrTriClP and TBBA) or asymmetrical (PentaBrP) with respect to the atomic Br positions and to differ in the number of bromine and other halide atoms, as well as their relative positions. The asymmetrical PentaBrP was modelled with special detail as not all bromine atoms have identical coordination environments. The studied substances displayed unique EXAFS spectra, which could be used to determine the molecular structure in fair detail. We conclude that EXAFS spectroscopy is a suitable technique for molecular characterization of the comparatively complex molecules within the class of compounds of brominated organic persistent pollutants. A detailed understanding of the EXAFS spectra of the pure compounds opens up possibilities to study the interactions with soil and sediment matrices by means of EXAFS spectroscopy. Figure Brominated organic persistent pollutants are characterized by EXAFS spectroscopy.

  • 338.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Sehlin, E
    Lundstedt, Staffan
    Umeå University, Faculty of Science and Technology, Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Chemistry.
    Assessment of bioavailability of PAHs by comparison of uptake in earthworm (Eisenia foetida) and different echniques including leaching, HPCD, SPME and SPMD2005In: Organohalogen Compounds, p. 2580-Article in journal (Refereed)
  • 339.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Sehlin, Emma
    Umeå University, Faculty of Science and Technology, Chemistry.
    Lundstedt, Staffan
    Umeå University, Faculty of Science and Technology, Chemistry.
    Andersson, Patrik L
    Umeå University, Faculty of Science and Technology, Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Chemistry.
    Comparison of techniques for estimating PAH bioavailability: uptake in Eisenia fetida, passive samplers and leaching using various solvents and additives.2007In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 145, no 1, p. 154-60Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to evaluate different techniques for assessing the availability of polycyclic aromatic hydrocarbons (PAHs) in soil. This was done by comparing the amounts (total and relative) taken up by the earthworm Eisenia fetida with the amounts extracted by solid-phase microextraction (SPME), semi-permeable membrane devices (SPMDs), leaching with various solvent mixtures, leaching using additives, and sequential leaching. Bioconcentration factors of PAHs in the earthworms based on equilibrium partitioning theory resulted in poor correlations to observed values. This was most notable for PAHs with high concentrations in the studied soil. Evaluation by principal component analysis (PCA) showed distinct differences between the evaluated techniques and, generally, there were larger proportions of carcinogenic PAHs (4–6 fused rings) in the earthworms. These results suggest that it may be difficult to develop a chemical method that is capable of mimicking biological uptake, and thus estimating the bioavailability of PAHs.

    The total and relative amounts of PAHs extracted by abiotic techniques for assessing the bioavailability of PAHs was found to differ from the amounts taken up by Eisenia fetida.

    Keywords: Bioavailability; Polycyclic aromatic hydrocarbons; Earthworms; Leaching; Hydroxypropyl-β-cyclodextrin; Solid-phase microextraction; Semi-permeable membrane device

  • 340.
    Bergknut, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wiberg, Karin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Klaminder, Jonatan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Vertical and lateral redistribution of POPs in soils developed along a hydrological gradient2011In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 45, no 24, p. 10378-10384Article in journal (Refereed)
    Abstract [en]

    Study of the dispersion of persistent organic pollutants (POPs) throughout the environment is necessitated by their toxicological properties and propensity to accumulate in biota. In this study, we use data from the analysis of three (210)Pb dated soil profiles collected along a 30-m hydrological gradient to demonstrate postdepositional mobility of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) and polychlorinated biphenyls (PCBs). We found that (i) humus originating from litter exposed to surface fallout during the 1960-1970s contains the highest concentrations of PCDD/Fs and PCBs in the O-horizon of the soils; (ii) accumulation rates of PCDD/Fs and PCBs in the O-horizon (similar to 5.0 and similar to 210 mu g m(-2) yr(-1)) constituted only 9.1% and 3.5%, respectively, of the measured annual input, demonstrating that a minor fraction of the deposited material is retained within the O-horizon; (iii) POP inventories in the upper 0.5-0.9 m of the mineral soil constituted a considerable part (40-70%) of the total pool stored in the soil, implying significant vertical translocation of atmospheric derived POPs; and (iv) increasing downslope inventories of POPs suggest a lateral downward transport of POPs from uphill soils. The findings challenge the commonly accepted view that POPs fallout is effectively retained within O-horizons.

  • 341.
    Berglind, Rune
    et al.
    Umeå University, Faculty of Science and Technology, European CBRNE Center.
    Leffler, Per
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Occupational and Environmental Medicine.
    Sjöström, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Interactions between pH, potassium, calcium, bromide, and phenol and their effects on the bioluminescence of Vibrio fischeri2010In: Journal of Toxicology and Environmental Health, ISSN 1528-7394, E-ISSN 1087-2620, Vol. 73, no 16, p. 1102-1112Article in journal (Refereed)
    Abstract [en]

    Little attention has been paid to how the light produced by the bacterium Vibrio fischeri in the Microtox assay is dependent on the concentration of essential ions such as sodium and potassium, and whether the concentrations of these ions affect the sensitivity of the test system to toxic chemicals. Five selected factors, pH, potassium (K(+)), calcium (Ca(2+)), bromide (Br(-)), and phenol (Phe), were simultaneously varied over a set of systematically planned experiments according to a D-optimal design that supported the estimation of a model with linear, quadratic, and two-factor interatcions of the studied factors. The bacterial light production represented by the gamma values in the Microtox assay for the 24 selected combinations of factors was measured at 5 and 15 min. The gamma values varied from negative to positive values greater than 1, indicating stimulation and inhibition of bacterial light production, respectively. The relationship between the gamma values and the factor settings was investigated with multiple linear regression. After 5 min of exposure, the light production was significantly affected by linear and quadratic terms for K(+), pH, and Phe and an interaction between pH and Phe. The situation was more complex after 15 min of exposure, since in addition significant interactions were found for K x Phe and Ca x pH. The tolerance of V. fischeri to Phe was enhanced by increasing the K and Ca concentrations. Data indicate that the ion composition and pH of the sample, as well as the diluents, need to be considered when the toxicity of salts, water samples, and extracts of sediments and soils are tested using commercially certified toxicity test kits.

  • 342.
    Berglund, Anders
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brorsson, Ann-Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jonsson, Bengt-Harald
    Sethson, Ingmar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The equilibrium unfolding of MerP characterized by multivariate analysis of 2D NMR data2005In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 172, no 1, p. 24-30Article in journal (Refereed)
    Abstract [en]

    A general problem when analysing NMR spectra that reflect variations in the environment of target molecules is that different resonances are affected to various extents. Often a few resonances that display the largest frequency changes are selected as probes to reflect the examined variation, especially in the case, where the NMR spectra contain numerous resonances. Such a selection is dependent on more or less intuitive judgements and relying on the observed spectral variation being primarily caused by changes in the NMR sample. Second, recording changes observed for a few (albeit significant) resonances is inevitably accompanied by not using all available information in the analysis. Likewise, the commonly used chemical shift mapping (CSM) [Biochemistry 39 (2000) 26, Biochemistry 39 (2000) 12595] constitutes a loss of information since the total variation in the data is not retained in the projection into this single variable. Here, we describe a method for subjecting 2D NMR time-domain data to multivariate analysis and illustrate it with an analysis of multiple NNIR experiments recorded at various folding conditions for the protein MerP. The calculated principal components provide an unbiased model of variations in the NNIR spectra and they can consequently be processed as NMR data, and all the changes as reflected in the principal components are thereby made available for visual inspection in one single NMR spectrum. This approach is much less laborious than consideration of large numbers of individual spectra, and it greatly increases the interpretative power of the analysis.

  • 343.
    Berglund, Anders
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Head, Richard D
    Welsh, Eric A
    Marshall, Garland R
    ProVal: A protein-scoring function for the selection of native and near-native folds2004In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 54, no 2, p. 289-302Article in journal (Refereed)
    Abstract [en]

    A low-resolution scoring function for the selection of native and near-native structures from a set of predicted structures for a given protein sequence has been developed. The scoring function, ProVal (Protein Validate), used several variables that describe an aspect of protein structure for which the proximity to the native structure can be assessed quantitatively. Among the parameters included are a packing estimate, surface areas, and the contact order. A partial least squares for latent variables (PLS) model was built for each candidate set of the 28 decoy sets of structures generated for 22 different proteins using the described parameters as independent variables. The C(alpha) RMS of the candidate structures versus the experimental structure was used as the dependent variable. The final generalized scoring function was an average of all models derived, ensuring that the function was not optimized for specific fold classes or method of structure generation of the candidate folds. The results show that the crystal structure was scored best in 64% of the 28 test sets and was clearly separated from the decoys in many examples. In all the other cases in which the crystal structure did not rank first, it ranked within the top 10%. Thus, although ProVal could not distinguish between predicted structures that were similar overall in fold quality due to its inherently low resolution, it can clearly be used as a primary filter to eliminate approximately 90% of fold candidates generated by current prediction methods from all-atom modeling and further evaluation. The correlation between the predicted and actual C(alpha) RMS values varies considerably between the candidate fold sets.

  • 344.
    Berglund, Anders
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kettaneh, Nouna
    Umetrics Inc., Kinnelon, NJ, USA.
    Uppgård, Lise-Lott
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wold, Svante
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bendwell, Nancy
    Tembec Inc., Temiscaming, Quebec, Canada.
    Cameron, Dave R
    Tembec Inc., Temiscaming, Quebec, Canada.
    The GIFI approach to non-linear PLS modeling2001In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 15, no 4, p. 321-36Article in journal (Refereed)
    Abstract [en]

    The GIFI approach to non-linear modeling involves the transformation of quantitative variables to a set of 1/0 dummies in a similar manner to the way qualitative variables are coded. This is followed by analyzing the sets of 1/0 dummies by principal component analysis, multiple regression or, as discussed here, PLS. The patterns of the resulting coefficients indicate the nature of the non-linearities in the data. Here the potential uses and limitations of PLS regression, in combination with four variants of GIFI coding, are investigated using both simulated and empirical data sets.

  • 345.
    Berglund, Anders
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sethson, Ingmar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Analysis of 2D-NMR data in the time domain, a study of the unfolding of MERP2004In: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0065-7727, Vol. 228, no 1, p. U111-U111Article in journal (Other academic)
  • 346. Berglund, Bjorn
    et al.
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindgren, Per-Eric
    Urban wastewater effluent increases antibiotic resistance gene concentrations in a receiving northern european river2015In: Environmental Toxicology and Chemistry, ISSN 0730-7268, E-ISSN 1552-8618, Vol. 34, no 1, p. 192-196Article in journal (Refereed)
    Abstract [en]

    Antibiotic-resistant bacteria are an emerging global problem that threatens to undermine important advances in modern medicine. The environment is likely to play an important role in the dissemination of antibiotic-resistance genes (ARGs) among both environmental and pathogenic bacteria. Wastewater treatment plants (WWTPs) accumulate both chemical and biological waste from the surrounding urban milieu and have therefore been viewed as potential hotspots for dissemination and development of antibiotic resistance. To assess the effect of wastewater effluent on a river that flows through a Swedish city, sediment and water samples were collected from Stangan River, both upstream and downstream of an adjacent WWTP over 3 mo. Seven ARGs and the integrase gene on class 1 integrons were quantified in the collected sediment using real-time polymerase chain reaction (PCR). Liquid chromatography-mass spectrometry was used to assess the abundance of 10 different antibiotics in the water phase of the samples. The results showed an increase in ARGs and integrons downstream of the WWTP. The measured concentrations of antibiotics were low in the water samples from the Stangan River, suggesting that selection for ARGs did not occur in the surface water. Instead, the downstream increase in ARGs is likely to be attributable to accumulation of genes present in the treated effluent discharged from the WWTP. Environ Toxicol Chem 2015;34:192-196. (c) 2014 SETAC

  • 347. Berglund, Björn
    et al.
    Khan, Ghazanfar Ali
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindberg, Richard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindgren, Per-Eric
    Abundance and dynamics of antibiotic resistance genes and integrons in lake sediment microcosms2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 9, article id e108151Article in journal (Refereed)
    Abstract [en]

    Antibiotic resistance in bacteria causing disease is an ever growing threat to the world. Recently, environmental bacteria have become established as important both as sources of antibiotic resistance genes and in disseminating resistance genes. Low levels of antibiotics and other pharmaceuticals are regularly released into water environments via wastewater, and the concern is that such environmental contamination may serve to create hotspots for antibiotic resistance gene selection and dissemination. In this study, microcosms were created from water and sediments gathered from a lake in Sweden only lightly affected by human activities. The microcosms were exposed to a mixture of antibiotics of varying environmentally relevant concentrations (i.e., concentrations commonly encountered in wastewaters) in order to investigate the effect of low levels of antibiotics on antibiotic resistance gene abundances and dynamics in a previously uncontaminated environment. Antibiotic concentrations were measured using liquid chromatography-tandem mass spectrometry. Abundances of seven antibiotic resistance genes and the class 1 integron integrase gene, intL1, were quantified using real-time PCR. Resistance genes sulI and ermB were quantified in the microcosm sediments with mean abundances 5 and 15 gene copies/10(6) 16S rRNA gene copies, respectively. Class 1 integrons were determined in the sediments with a mean concentration of 3.86x10(4) copies/10(6) 16S rRNA gene copies. The antibiotic treatment had no observable effect on antibiotic resistance gene or integron abundances.

  • 348. Berglund, Björn
    et al.
    Khan, Ghazanfar Ali
    Weisner, Stefan E. B.
    Ehde, Per Magnus
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindgren, Per-Eric
    Efficient removal of antibiotics in surface-flow constructed wetlands, with no observed impact on antibiotic resistance genes2014In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 476-477, p. 29-37Article in journal (Refereed)
    Abstract [en]

    Recently, there have been growing concerns about pharmaceuticals including antibiotics as environmental contaminants. Antibiotics of concentrations commonly encountered in wastewater have been suggested to affect bacterial population dynamics and to promote dissemination of antibiotic resistance. Conventional wastewater treatment processes do not always adequately remove pharmaceuticals causing environmental dissemination of low levels of these compounds. Using constructed wetlands as an additional treatment step after sewage treatment plants have been proposed as a cheap alternative to increase reduction of wastewater contaminants, however this means that the natural microbial community of the wetlands becomes exposed to elevated levels of antibiotics. In this study, experimental surface-flow wetlands in Sweden were continuously exposed to antibiotics of concentrations commonly encountered in wastewater. The aim was to assess the antibiotic removal efficiency of constructed wetlands and to evaluate the impact of low levels of antibiotics on bacterial diversity, resistance development and expression in the wetland bacterial community. Antibiotic concentrations were measured using liquid chromatography-mass spectrometry and the effect on the bacterial diversity was assessed with 16S rRNA-based denaturing gradient gel electrophoresis. Real-time PCR was used to detect and quantify antibiotic resistance genes and integrons in the wetlands, during and after the exposure period. The results indicated that the antibiotic removal efficiency of constructed wetlands was comparable to conventional wastewater treatment schemes. Furthermore, short-term treatment of the constructed wetlands with environmentally relevant concentrations (i.e. 100-2000 ng x 1(-1)) of antibiotics did not significantly affect resistance gene concentrations, suggesting that surface-flow constructed wetlands are well-suited for wastewater treatment purposes. (c) 2014 Elsevier B.V. All rights reserved.

  • 349. Berglund, Björn
    et al.
    Khan, Ghazanfar Ali
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Weisner, Stefan E.B.
    Ehde, Per Magnus
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindgren, Per-Eric
    Exposure of constructed wetlands to environmental concentrations of antibiotics show no effect on antibiotic resistance gene selection and expressionManuscript (preprint) (Other academic)
  • 350. Berglund, Linn
    et al.
    Anugwom, Ikenna
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Turku, Finland.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Aitomäki, Yvonne
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Turku, Finland.
    Oksman, Kristiina
    Switchable ionic liquids enable efficient nanofibrillation of wood pulp2017In: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 24, no 8, p. 3265-3279Article in journal (Refereed)
    Abstract [en]

    Use of switchable ionic liquid (SIL) pulp offers an efficient and greener technology to produce nanofibers via ultrafine grinding. In this study, we demonstrate that SIL pulp opens up a mechanically efficient route to the nanofibrillation of wood pulp, thus providing both a low cost and chemically benign route to the production of cellulose nanofibers. The degree of fibrillation during the process was evaluated by viscosity and optical microscopy of SIL treated, bleached SIL treated and a reference pulp. Furthermore, films were prepared from the fibrillated material for characterization and tensile testing. It was observed that substantially improved mechanical properties were attained as a result of the grinding process, thus signifying nanofibrillation. Both SIL treated and bleached SIL treated pulps were fibrillated into nanofibers with fiber diameters below 15 nm thus forming networks of hydrophilic nature with an intact crystalline structure. Notably, it was found that the SIL pulp could be fibrillated more efficiently than traditional pulp since nanofibers could be produced with more than 30% less energy when compared to the reference pulp. Additionally, bleaching reduced the energy demand by further 16%. The study demonstrated that this switchable ionic liquid treatment has considerable potential in the commercial production of nanofibers due to the increased efficiency in fibrillation.

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