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  • 101. Friedman, Ran
    et al.
    Caflisch, A
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis2008In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 73, no 4, p. 814-827Article in journal (Refereed)
  • 102.
    Friedman, Ran
    et al.
    University of Zürich, Switzerland.
    Caflisch, A.
    The Protonation State of the Catalytic Aspartates in Plasmepsin II2007In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 581, p. 4120-4124Article in journal (Refereed)
  • 103.
    Friedman, Ran
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Caflisch, Amedeo
    Department of Biochemistry, University of Zürich.
    Surfactant Effects on Amyloid Aggregation Kinetics2011In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 414, p. 303-312Article in journal (Refereed)
    Abstract [en]

    There is strong experimental evidence of the influence of surfactants (e.g., fatty acids) on the kinetics of amyloid fibril formation. However, the structures of mixed assemblies and interactions between surfactants and fibril-forming peptides are still not clear. Here, coarse-grained simulations are employed to study the aggregation kinetics of amyloidogenic peptides in the presence of amphiphilic lipids. The simulations show that the lower the fibril formation propensity of the peptides, the higher the influence of the surfactants on the peptide self-assembly kinetics. In particular, the lag phase of weakly aggregating peptides increases because of the formation of mixed oligomers, which are promoted by hydrophobic interactions and favorable entropy of mixing. A transient peak in the number of surfactants attached to the growing fibril is observed before reaching the mature fibril in some of the simulations. This peak originates from transient fibrillar defects consisting of exposed hydrophobic patches on the fibril surface, which provide a possible explanation for the temporary maximum of fluorescence observed sometimes in kinetic traces of the binding of small-molecule dyes to amyloid fibrils.

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  • 104.
    Friedman, Ran
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. University of Zürich, Switzerland.
    Caflisch, Amedeo
    University of Zürich, Switzerland.
    Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study2014In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 82, no 3, p. 399-404Article in journal (Refereed)
    Abstract [en]

    The C-terminal segment (residues 218–289) of the HET-s protein of the filamentous fungus Podosporina anserina is a prion-forming domain. The structural model of the HET-s(218–289) amyloid fibril based on solid-state nuclear magnetic resonance (NMR) restraints shows a β solenoid topology which is comprised of a β-sheet core and interconnecting loops. For the single-point mutants Phe286Ala and Trp287Ala, slower aggregation rates in vitro and loss of prionic infectivity have been reported recently. Here we have used molecular dynamics to compare the flexibility of the mutants and wild type. The simulations, initiated from a trimeric aggregate extracted from the NMR structural model, show structural stability on a 100-ns time scale for wild type and mutants. Analysis of the fluctuations along the simulations reveals that the mutants are less flexible than the wild type in the C-terminal segment at only one of the two external monomers. Analysis of interaction energy and buried accessible surface indicates that residue Phe286 in particular is stabilized in the Trp287Ala mutant. The simulation results provide an atomistic explanation of the suggestion (based on indirect experimental evidence) that flexibility at the protofibril end(s) is required for fibril elongation. Moreover, they provide further evidence that the growth of the HET-s amyloid fibril is directional.

  • 105.
    Friedman, Ran
    et al.
    Tel Aviv University, Israel.
    Fischer, Stefan
    Nachliel, Esther
    Scheiner, Steve
    Gutman, Menachem
    Minimum energy pathways for proton transfer between adjacent sites exposed to water2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 21, p. 6059-6070Article in journal (Refereed)
    Abstract [en]

    The capacity to transfer protons between surface groups is an innate property of many proteins. The transfer of a proton between donor and acceptor, located as far as 6−7 Å apart, necessitates the participation of water molecules in the process. In a previous study we investigated the mechanism of proton transfer (PT) between bulk exposed sites, a few ångströms apart, using as a model the proton exchange between the proton-binding sites of the fluorescein molecule in dilute aqueous solution.1 The present study expands the understanding of PT reactions between adjacent sites exposed to water through the calculation the minimum energy pathways (MEPs) by the conjugate peak refinement algorithm2 and a quantum-mechanical potential. The PT reaction trajectories were calculated for the fluorescein system with an increasing number of water molecules. The MEP calculations reveal that the transition state is highly strained and involves a supramolecular structure in which fluorescein and the interconnecting water molecules are covalently bonded together and the protons are shared between neighboring oxygens. These findings are in accord with the high activation energy, as measured for the reaction, and indicate that PT reactions on the surface proceed by a semi- or fully concerted rather than stepwise mechanism. A similar mechanism is assumed to be operative on the surface of proteins and renders water-mediated PT reactions as highly efficient as they are.

  • 106.
    Friedman, Ran
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Khalid, Syma
    Univ Southampton, UK.
    Aponte-Santamaria, Camilo
    Univ Los Andes, Colombia;Heidelberg Univ, Germany.
    Arutyunova, Elena
    Univ Alberta, Canada.
    Becker, Marlon
    Univ Munster, Germany.
    Boyd, Kevin J.
    Univ Connecticut, USA.
    Christensen, Mikkel
    Aarhus Univ, Denmark;Sinodanish Ctr Educ & Res, Peoples Republic of China.
    Coimbra, Joao T. S.
    Univ Porto, Portugal.
    Concilio, Simona
    Univ Salerno, Italy.
    Daday, Csaba
    Heidelberg Inst Theoret Studies, Germany.
    van Eerden, Floris J.
    Univ Groningen, Netherlands.
    Fernandes, Pedro A.
    Univ Porto, Portugal.
    Graeter, Frauke
    Heidelberg Univ, Germany;Heidelberg Inst Theoret Studies, Germany.
    Hakobyan, Davit
    Univ Munster, Germany.
    Heuer, Andreas
    Univ Munster, Germany.
    Karathanou, Konstantina
    Free Univ Berlin, Germany.
    Keller, Fabian
    Univ Munster, Germany.
    Lemieux, M. Joanne
    Univ Alberta, Canada.
    Marrink, Siewert J.
    Univ Groningen, Netherlands.
    May, Eric R.
    Univ Connecticut, USA.
    Mazumdar, Antara
    Univ Groningen, Netherlands.
    Naftalin, Richard
    Kings Coll London, UK.
    Pickholz, Monica
    Univ Buenos Aires, Argentina.
    Piotto, Stefano
    Univ Salerno, Italy.
    Pohl, Peter
    Johannes Kepler Univ Linz, Austria.
    Quinn, Peter
    Kings Coll London, UK.
    Ramos, Maria J.
    Univ Porto, Portugal.
    Schiott, Birgit
    Aarhus Univ, Denmark.
    Sengupta, Durba
    Natl Chem Lab, India.
    Sessa, Lucia
    Univ Salerno, Italy.
    Vanni, Stefano
    Univ Fribourg, Switzerland.
    Zeppelin, Talia
    Aarhus Univ, Denmark.
    Zoni, Valeria
    Univ Fribourg, Switzerland.
    Bondar, Ana-Nicoleta
    Free Univ Berlin, Germany.
    Domene, Carmen
    Univ Bath, UK;Univ Oxford, UK.
    Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology2018In: Journal of Membrane Biology, ISSN 0022-2631, E-ISSN 1432-1424, Vol. 251, no 5-6, p. 609-631Article, review/survey (Refereed)
    Abstract [en]

    This is a perspective article entitled "Frontiers in computational biophysics: understanding conformational dynamics of complex lipid mixtures relevant to biology" which is following a CECAM meeting with the same name.

  • 107.
    Friedman, Ran
    et al.
    University of Zürich, Switzerland.
    Pellarin, R
    Caflisch, A
    Amyloid aggregation on lipid bilayers and its impact on membrane permeability2009In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 387, no 2, p. 407-415Article in journal (Refereed)
  • 108.
    Friedman, Ran
    et al.
    University of Zürich, Switzerland.
    Pellarin, R
    Caflisch, A
    Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles2010In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 1, no 2, p. 471-474Article in journal (Refereed)
  • 109.
    Gagner, Viktor Ahlberg
    et al.
    University of Gothenburg, Sweden.
    Lundholm, Ida
    University of Gothenburg, Sweden.
    Garcia-Bonete, Maria-Jose
    University of Gothenburg, Sweden.
    Rodilla, Helena
    Chalmers University of Technology, Sweden.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Zhaunerchyk, Vitali
    University of Gothenburg, Sweden.
    Bourenkov, Gleb
    DESY, Germany.
    Schneider, Thomas
    DESY, Germany.
    Stake, Jan
    Chalmers University of Technology, Sweden.
    Katona, Gergely
    University of Gothenburg, Sweden.
    Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, p. 1-14, article id 19281Article in journal (Refereed)
    Abstract [en]

    Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.

  • 110.
    Georgoulia, Panagiota S.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Todde, Guido
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Bjelic, Sinisa
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    The catalytic activity of Abl1 single and compound mutations: Implications for the mechanism of drug resistance mutations in chronic myeloid leukaemia2019In: Biochimica et Biophysica Acta - General Subjects, ISSN 0304-4165, E-ISSN 1872-8006, Vol. 1863, no 4, p. 732-741Article in journal (Refereed)
    Abstract [en]

    Background

    Abl1 is a protein tyrosine kinase whose aberrant activation due to mutations is the culprit of several cancers, most notably chronic myeloid leukaemia. Several Abl1 inhibitors are used as anti-cancer drugs. Unfortunately, drug resistance limits their effectiveness. The main cause for drug resistance is mutations in the kinase domain (KD) of Abl1 that evolve in patients. The T315I mutation confers resistance against all clinically-available inhibitors except ponatinib. Resistance to ponatinib can develop by compound (double) mutations.

    Methods

    Kinetic measurements of the KD of Abl1 and its mutants were carried out to examine their catalytic activity. Specifically, mutants that lead to drug resistance against ponatinib were considered. Molecular dynamics simulations and multiple sequence analysis were used for explanation of the experimental findings.

    Results

    The catalytic efficiency of the T315I pan-resistance mutant is more than two times lower than that of the native KD. All ponatinib resistant mutations restore the catalytic efficiency of the enzyme. Two of them (G250E/T315I and Y253H/E255V) have a catalytic efficiency that is more than five times that of the native KD.

    Conclusions

    The measurements and analysis suggest that resistance is at least partially due to the development of a highly efficient kinase through subsequent mutations. The simulations highlight modifications in two structurally important regions of Abl1, the activation and phosphate binding loops, upon mutations.

    General significance

    Experimental and computational methods were used together to explain how mutations in the kinase domain of Abl1 lead to resistance against the most advanced drug currently in use to treat chronic myeloid leukaemia.

  • 111. Gibb, A.R.
    et al.
    Suckling, D.M.
    El-Sayed, A.M.
    Bohman, Björn
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Unelius, Rikard
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Dymock, J.J
    Larsen, M.L.
    Willoughby, B.E.
    (Z,E)-11,13-Hexadecadienyl Acetate: Sex Pheromone of the Grass Webworm Herpetogramma licarsisalis - Identification, Synthesis and Field Bioassays.2007In: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 33, no 4, p. 839-47Article in journal (Refereed)
  • 112.
    Gierow, Peter
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Jergil, B
    A spectrophotometric method for the determination of glucose-6-phosphatase activity1980In: Analytical biochemistry, Vol. 101, no 2, p. 305-309Article in journal (Refereed)
  • 113.
    Gierow, Peter
    et al.
    UNIV LUND, CTR CHEM, DEPT BIOCHEM, S-22007 LUND 7, SWEDEN .
    Jergil, B
    Spectrophotometric method for glucose 6-phosphate phosphatase1982In: Methods in enzymology, Vol. 89, p. 44-47Article in journal (Refereed)
  • 114.
    Giovannoli, Cristina
    et al.
    Univ Turin, Italy.
    Passini, Cinzia
    Univ Turin, Italy.
    Di Nardo, Fabio
    Univ Turin, Italy.
    Anfossi, Laura
    Univ Turin, Italy.
    Baggiani, Claudio
    Univ Turin, Italy.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Affinity Capillary Electrochromatography of Molecularly Imprinted Thin Layers Grafted onto Silica Capillaries Using a Surface-Bound Azo-Initiator and Living Polymerization2018In: Polymers, ISSN 2073-4360, E-ISSN 2073-4360, Vol. 10, no 2, article id 192Article in journal (Refereed)
    Abstract [en]

    Molecularly imprinted thin layers were prepared in silica capillaries by using two different surface polymerization strategies, the first using 4,4-azobis(4-cyanovaleric acid) as a surface-coupled radical initiator, and the second, S-carboxypropyl-S'-benzyltrithiocarbonate as a reversible addition-fragmentation chain transfer (RAFT) agent in combination with 2,2-azobisisobutyronitrile as a free radical initiator. The ability to generate imprinted thin layers was tested on two different polymerization systems: (i) a 4-vinylpyridine/ethylene dimethacrylate (4VP-EDMA) in methanol-water solution with 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as a template; and (ii) methacrylic acid/ethylene dimethacrylate (MAA-EDMA) in a chloroform solution with warfarin as the template molecule. The binding properties of the imprinted capillaries were studied and compared with those of the corresponding non-imprinted polymer coated capillaries by injecting the template molecule and by measuring its migration times relative to a neutral and non-retained marker. The role of running buffer hydrophobicity on recognition was investigated by studying the influence of varying buffer acetonitrile concentration. The 2,4,5-T-imprinted capillary showed molecular recognition based on a reversed phase mechanism, with a decrease of the template recognition in the presence of higher acetonitrile content; whereas warfarin-imprinted capillaries showed a bell-shaped trend upon varying the acetonitrile percentage, illustrating different mechanisms underlying imprinted polymer-ligand recognition. Importantly, the results demonstrated the validity of affinity capillary electrochromatography (CEC) to screen the binding properties of imprinted layers.

  • 115.
    Golker, Kerstin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Fundamental Studies on Molecularly Imprinted Materials2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The thesis focuses on fundamental studies aimed at elucidating factors that influence molecularly imprinted polymer (MIP) formation and ligand recognition. To this end, a series of computational techniques, in particular chemometrics and molecular dynamics (MD) in conjunction with polymer synthesis and physical characterization studies have been employed.

     

    In Paper I, the multivariate analysis method principal component analysis (PCA) was used to investigate the role of incubation media on polymer-ligand recognition, and results highlighted the importance of several solvent parameters on recognition. In Paper II, all-component MD simulations were used to examine the role of polymerization mixture stoichiometry on MIP-template recognition. Correlations between nature and extent of template complexation and recognition were observed. The influence of the acidic functionality of the methacrylic acid used in these polymers on polymer-template recognition and morphology was examined in Paper III. PCA was then used in Paper IV to identify relationships between interactions in the pre-polymerization mixture, polymer functionality, recognition and morphology using the polymers described in Paper II and III.

  • 116.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsson, Gustaf D.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Towards Molecular Dynamics-Based Rational Design of Polymeric Recognition Systems2010Conference paper (Refereed)
    Abstract [en]

    Molecular imprinting is a technique used to design polymeric recognition materials with selectivity for a predetermined structure. The molecular imprinting process generates cavities in the polymer matrix that are complementary in size, shape and functionality to the template-structure. The recognition properties of molecularly imprinted polymers (MIPs) are comparable to those of antibodies and enzymes, which make MIPs utilizable in a wide range of application areas including biomimetic assays and biosensors [1]. Previous studies have shown that the prepolymerization step is central for the establishment of high affinity binding sites in MIPs [2]. However, our understanding of the physical mechanisms underlying MIP formation and template recognition is still limited. With the rapid increase of computational power and the development of suitable software molecular dynamics (MD) simulation methods have become a valuable theoretical tool to aid our understanding of the molecular imprinting process, and even in the development of rational design strategies [2]. Recently the first simulation of a complete prepolymerization mixture was presented [3].

    Here we present 10 ns MD simulations of a series of all-component prepolymerization mixtures. The simulated systems were assembled with different molar ratios using the local anaesthetic bupivacaine as the template, methacrylic acid (MAA) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as the crosslinker, 2,2’-azobis-(2-methylpropionitrile) (AIBN) as the initiator and toluene as the solvent. The simulations were performed using the AMBER (v. 10.0 UCSF, San Francisco, CA) suite of programs (4) and the GAFF [6] force field. Molecular trajectories were evaluated with radial distribution functions and hydrogen bond analysis.

     

     

    References

    1. Alexander, C.; Andersson, H. S.; Andersson, L. I.; Ansell, R. J.; Kirsch, N.; Nicholls, I. A.; O´Mahony, J.; Whitcombe, J., J. Mol. Recognit. (2006), 19, 106-180
    2. Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron. (2009), 25, 543-552
    3. Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc. (2009), 131, 13297-13304
    4. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. Comput. Chem. (2009), 26, 1668-1688
    5. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. (2004), 25, 1157-1174

     

  • 117.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsson, Gustaf D.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Towards Molecular Dynamics-Based Rational Design of Synthetic Polymer Recognition Systems2010Conference paper (Refereed)
    Abstract [en]

    Molecularly imprinted polymers (MIPs) are polymeric receptors with selectivity for a predetermined structure. The molecular imprinting process generates cavities in a synthetic polymer matrix that are complementary in size, shape and functionality to the template. MIPs exhibit recognition properties analogous to their biological counterparts, such as antibodies, and can be utilized in a wide range of application areas [1]. Nonetheless, the physical mechanisms underlying MIP formation and template recognition are still poorly understood. Molecular dynamics (MD) based computer simulations are a valuable theoretical tool which may be used to aid our understanding of the molecular imprinting process, and even for the development of rational design strategies [2]. Recently the first MD simulation of a complete prepolymerization mixture was presented [3].

    In the present work, MD simulations of a series of all-component prepolymerization mixtures were performed, using the local anaesthetic bupivacaine as the template, methacrylic acid (MAA) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as the crosslinker, 2,2’-azobis-(2-methylpropionitrile) (AIBN) as the initiator and toluene as the solvent. The simulated systems differed in the molar fraction of MAA. Systems were evaluated with radial distribution functions and hydrogen bond analyses. By correlating the results with the rebinding behaviour of a series of synthesized MIPs the importance of the stoichiometry between template, functional monomer and crosslinker was highlighted. The analysis of the MD simulations revealed strong competition for hydrogen bonding between the carbonyl oxygen’s of MAA and EGDMA and the amide proton of bupivacaine. Moreover, the hydrogen bonding contact between EGDMA and bupivacaine remained nearly unaffected by the varied molar fraction MAA in the different systems demonstrating the role of the crosslinker being more important as generally accepted.

     

    References

    [1]             Alexander, C.; Andersson, H. S.; Andersson, L. I.; Ansell, R. J.; Kirsch, N.; Nicholls, I. A.; O´Mahony, J.; Whitcombe, J., J. Mol. Recognit., 19, 106-180 (2006)

    [2]            Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron., 25, 543-552 (2009)

    [3]            Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc., 131, 13297-13304 (2009)

  • 118.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Olsson, Gustaf D.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Towards the use of molecular dynamics as a predictive tool in the design of molecularly imprinted polymers2010Conference paper (Refereed)
    Abstract [en]

    Through the rapid increase in computational power and the development of suitable software, molecular dynamics (MD) has become a promising tool for use in the development of molecularly imprinted polymers (MIPs).1 MD is a computational method based on Newtonian mechanics, which enables the simultaneous simulation of thousands of discrete molecules, and can be used to establish the states of the molecular species present in MIP-prepolymerization mixtures. As detailed understanding of the molecular basis for formation of high affinity MIP sites is still lacking and the physical mechanism underlying specific recognition is still a matter of debate, the use of MD as a tool to investigate MIP-prepolymerization mixtures is highly motivated.1 Recently the first MD simulation of an all-component prepolymerization mixture was presented, which gave a detailed picture of the underlying monomer-template interactions important for the “molecular memory” in MIPs.2

    Here, we present results obtained from a series of MD simulations representing all-component MIP/REF prepolymerization mixtures assembled with differences in stoichiometries of functional and crosslinking monomer. In these mixtures, the local anaesthetic drug bupivacaine was used as a template, methacrylic acid as the functional monomer, ethylene dimethacrylate as crosslinking monomer, 2,2’-azobis-(2-methylpropionitrile) as the initiator and toluene as the solvent. Bupivacaine complexation in each system was evaluated with radial distribution functions and hydrogen bond analyses. By correlating the results with the rebinding behaviour of a series of synthesized bupivacaine-MIPs, the relationship between the degree of crosslinking and MIP-performance was highlighted.

    [1] Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron., 25, 543-552 (2009)

    [2] Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc., 131, 13297-13304 (2009)

  • 119.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Olsson, Gustaf D.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Rosengren, Annika M.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Influence of composition and morphology on template recognition in molecularly imprinted polymers2013In: Macromolecules, ISSN 0024-9297, E-ISSN 1520-5835, Vol. 46, no 4, p. 1408-1414Article in journal (Refereed)
    Abstract [en]

    A combination of theoretical and experimental studies has provided correlations between molecularly imprinted polymer composition, morphology, and recognition behavior obtained using a series of bupivacaine-imprinted methacrylic acid (MAA)–ethylene glycol dimethacrylate copolymers differing in molar ratios of the respective monomers. Results extracted from analysis of molecular dynamics (MD) trajectory data demonstrated that stability and frequency of interactions between bupivacaine and the monomers in the prepolymerization phase were strongly affected by minor changes in polymer composition, which in turn affected binding site affinity and heterogeneity of the imprinted polymers. Moreover, through the characterization of polymer morphology, we show that higher molar fractions of MAA resulted in polymeric materials with increased pore size, a feature that enhanced the binding capacity of the polymers. Furthermore, the results presented point at the strength of MD for predicting MIP-template binding capacity and affinity.

  • 120.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Rosengren, Annika M.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala University.
    A Functional Monomer Is Not Enough: Principal Component Analysis of the Influence of Template Complexation in Pre-Polymerization Mixtures on Imprinted Polymer Recognition and Morphology2014In: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 15, no 11, p. 20572-20584Article in journal (Refereed)
    Abstract [en]

    In this report, principal component analysis (PCA) has been used to explore the influence of template complexation in the pre-polymerization phase on template molecularly imprinted polymer (MIP) recognition and polymer morphology. A series of 16 bupivacaine MIPs were studied. The ethylene glycol dimethacrylate (EGDMA)-crosslinked polymers had either methacrylic acid (MAA) or methyl methacrylate (MMA) as the functional monomer, and the stoichiometry between template, functional monomer and crosslinker was varied. The polymers were characterized using radioligand equilibrium binding experiments, gas sorption measurements, swelling studies and data extracted from molecular dynamics (MD) simulations of all-component pre-polymerization mixtures. The molar fraction of the functional monomer in the MAA-polymers contributed to describing both the binding, surface area and pore volume. Interestingly, weak positive correlations between the swelling behavior and the rebinding characteristics of the MAA-MIPs were exposed. Polymers prepared with MMA as a functional monomer and a polymer prepared with only EGDMA were found to share the same characteristics, such as poor rebinding capacities, as well as similar surface area and pore volume, independent of the molar fraction MMA used in synthesis. The use of PCA for interpreting relationships between MD-derived descriptions of events in the pre-polymerization mixture, recognition properties and morphologies of the corresponding polymers illustrates the potential of PCA as a tool for better understanding these complex materials and for their rational design.

  • 121.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Bioorganic & Biophysical Chemistry Laboratory.
    Wiklander, Jesper G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Rosengren, Annika M.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala university.
    Hydrogen bond diversity in the pre-polymerization stage contributes to morphology and MIP-template recognition–MAA versus MMA2015In: European Polymer Journal, ISSN 0014-3057, E-ISSN 1873-1945, Vol. 66, p. 558-568Article in journal (Refereed)
    Abstract [en]

    This report demonstrates that the diversity of hydrogen bond interactions present in molecularly imprinted polymer pre-polymerization mixtures, typically associated with binding-site heterogeneity, can also contribute to morphological characteristics that may influence polymer–template recognition. Comparisons have been made between a series of bupivacaine molecularly imprinted methacrylic acid (MAA)–ethylene glycol dimethacrylate (EGDMA) copolymers and a series of analogous methyl methacrylate (MMA)–EGDMA copolymers using comprehensive molecular dynamics studies of the respective pre-polymerization mixtures, template–polymer binding studies and detailed BET surface area and BJH porosity analyses. The role of the carboxylic acid functionality of MAA, and in particular the acidic proton, in generating morphological features conducive to analyte access (slit-like rather than ink bottle-like structures) and recognition is discussed.

  • 122.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala University.
    The effect of crosslinking density on molecularly imprinted polymer morphology and recognition2016In: European Polymer Journal, ISSN 0014-3057, E-ISSN 1873-1945, Vol. 75, p. 423-430Article in journal (Refereed)
    Abstract [en]

    In this report, the crosslinking density of bupivacaine molecularly imprinted methacrylic acid (MAA)-ethylene glycol dimethacrylate (EGDMA) copolymers was investigated through replacement of EGDMA by methyl methacrylate (MMA). The effects were examined using a series of full-scale MD simulations of pre-polymerization mixtures, equilibrium rebinding studies on the corresponding synthesized polymers and morphology characterization through nitrogen sorption measurements. While the extent of hydrogen bonding between the functional monomer MAA and bupivacaine observed in the MD pre-polymerization mixtures was comparable in each of the systems studied, the decrease in degree of crosslinking impacted directly on polymer morphology as observed in BET and BJH studies of surface area and porosity. Further, decreases in the crosslinking density induced reductions in template rebinding capacity as seen from a series of radio-ligand binding studies, demonstrating the importance of crosslinking on the performance of molecularly imprinted MAA-EGDMA copolymers, the polymer system most commonly used in molecular imprinting science and technology. (C) 2016 Elsevier Ltd. All rights reserved.

  • 123.
    Golker, Kerstin
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala university.
    Olsson, Gustaf D.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala University.
    The influence of a methyl substituent on molecularly imprinted polymer morphology and recognition – Acrylic acid versus methacrylic acid2017In: European Polymer Journal, ISSN 0014-3057, E-ISSN 1873-1945, Vol. 92, p. 137-149Article in journal (Refereed)
    Abstract [en]

    In this report, we have investigated factors contributing to the morphology and template recognition of bupivacaine-imprinted copolymers of methacrylic acid (MAA) and ethyleneglycol dimethacrylate (EGDMA). To this end, MAA, the most commonly used functional monomer in non-covalent molecular imprinting protocols, was compared and contrasted with the closely related acrylic acid (AA) in terms of polymer morphologies, recognition characteristics, and molecular level events in the corresponding pre-polymerization mixtures. Two series of analogous bupivacaine-imprinted EGDMA-copolymers containing increasing fractions of either AA or MAA were studied through all-component MD simulations in the pre-polymerization phase, equilibrium binding experiments on corresponding synthesized polymers and morphology characterization by N2-sorption measurements. A higher degree of hydrogen bonding frequency between respective functional monomer and bupivacaine was recorded for the mixtures containing AA compared to those containing MAA. In contrast, results from binding experiments demonstrated higher binding capacities for the polymers prepared with MAA than for those prepared with AA, which is explained by differences in polymer morphology. The surface areas and pore volumes of the AA-polymers were higher than for the MAA-polymers and the overall pore structure in the AA-polymers was ink-bottle shaped while the pores in the MAA-polymers were slit-shaped. We suggest that the methyl substituent of MAA contributes to differences in the reaction kinetics for AA and MAA during polymerization and resulted in different morphologies, in particular pore shape, which affected mass-transfer and consequently the binding qualities of the materials. © 2017 Elsevier Ltd

  • 124.
    Grund Bäck, Lina
    Linnaeus University, Faculty of Technology, Department of Built Environment and Energy Technology.
    Electronic spectra and molar extinction coefficient of Cu2+ in mixed alkali-alkaline earth-silica glasses2015In: Physics and Chemistry of Glasses-European Journal of Glass Science and Technology Part B, ISSN 1753-3562, Vol. 56, no 1, p. 8-14Article in journal (Refereed)
    Abstract [en]

    CuO is a very common colorant in blue to turquoise-blue glasses. It is well known that the absorption peak at about 800 nm for silicate glasses is caused by Cu2+, octahedrally coordinated by 6 oxygen ions. It is also known that the [Cu+]/[Cu2+] ratio, the location of the absorption peak and the extinction coefficient of Cu2+ depends on the glass composition. Many investigations have been published with CuO as a colouring agent, but almost none with a mix of Na2O and K2O or CaO and BaO in the base glass. In this study, a base glass composition of 20R2O-10MO-70SiO2 (mol%, R=Na, K and M=Ca, Ba) is used and 0.40 mol% CuO is added. The molar extinction coefficient of Cu2+ is determined for the glasses and peak positions and heights are also presented and discussed.

  • 125.
    Grund Bäck, Lina
    et al.
    Linnaeus University, Faculty of Technology, Department of Built Environment and Energy Technology. RISE Research Institutes of Sweden, Sweden.
    Ali, Sharafat
    Linnaeus University, Faculty of Technology, Department of Built Environment and Energy Technology.
    Karlsson, Stefan
    RISE Research Institutes of Sweden, Sweden;Friedrich Schiller University of Jena, Germany.
    Wondraczek, Lothar
    Friedrich Schiller University of Jena, Germany.
    Jonson, Bo
    Linnaeus University, Faculty of Technology, Department of Built Environment and Energy Technology.
    X-ray and UV-Vis-NIR absorption spectroscopy studies of the Cu(I) and Cu(II) coordination environments in mixed alkali-lime-silicate glasses2019In: Journal of Non-Crystalline Solids: X, ISSN 2590-1591, article id 100029Article in journal (Refereed)
    Abstract [en]

    The local structures of Cu(I) and Cu(II) in (20-x)Na2O-xK2O-10CaO-70SiO2 glasses with a copper content of 0.4 mol% have been investigated by Cu K-edge extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES). Complementary data for Cu(II) was derived using UV–Vis-NIR spectroscopy. Indication for mainly linear two-fold coordination of the Cu+ ion was found by both EXAFS and XANES, but other coordination between Cu+ and O2– cannot be excluded. The Cu(I)O bond lengths were found to be 1.79–1.83 ± 0.02 Å. EXAFS results showed that Cu(II) was mostly present in a Jahn-Teller distorted environment with oxygen, an octahedron with four shorter Cu(II)O bonds and two longer in axial position. The equatorial bond lengths were found to be 1.89–1.91 ± 0.02 Å and the axial 2.20–2.24 ± 0.02 Å with no effect of the Jahn-Teller distortion of the octahedron when the glass composition was altered.

  • 126.
    Grund, Lina
    et al.
    Linnaeus University, Faculty of Technology, Department of Built Environment and Energy Technology.
    Ali, Sharafat
    Linnaeus University, Faculty of Technology, Department of Built Environment and Energy Technology.
    Jonson, Bo
    Linnaeus University, Faculty of Technology, Department of Built Environment and Energy Technology.
    Optical and Physical Properties of CuO-doped mixed alkali: alkaline earth silica glasses2014Conference paper (Refereed)
  • 127.
    Grund, Lina
    et al.
    Växjö University, Faculty of Mathematics/Science/Technology, School of Technology and Design.
    Jonson, Bo
    Växjö University, Faculty of Mathematics/Science/Technology, School of Technology and Design.
    Compositional effect on fining and oxygen activity in mixed alkali silicate glasses2007In: ICG 2007: XXI International Congress on Glass, ICG , 2007, p. 320-Conference paper (Refereed)
    Abstract [en]

    Antimony oxide has been used as fining agent for quite some time as a substitute for arsenic oxide in low temperature furnaces, not reaching temperatures high enough to activate sulphate compounds in the fining process. Due to environmentally issues, a substitution of antimony by a less toxic fining agent is becoming more urgent. However, since all the details of the mechanisms of fining/refining with antimony are not fully known, it is necessary to further study the present mechanisms and substitution possibilities.

    This study is done to monitor how changes in glass composition affect the fining result and the oxygen activity of the melt. Numbers of bubbles were determined in order to evaluate the fining efficiency. The oxygen activity measurement is a way to in situ monitor the fining characteristics. Na2O-K2O-CaO-SiO2 glasses were used with constant alkali oxide content but with varying ratio Na2O/K2O. The Sb2O3 content was 0,2 mol% and NaNO3 or KNO3 was added as oxidising agent.

    The oxygen activity has been measured electrochemically, both during the fining process and when the melt was in equilibrium with the surrounding atmosphere. To understand the nitrates contribution to the fining, the oxygen activity was measured in melts both with and without nitrate.

  • 128.
    Guo, Ming
    et al.
    Zhejiang Agr & Forestry Univ, Peoples Republic of China.
    Hu, Yinglu
    Zhejiang Agr & Forestry Univ, Peoples Republic of China.
    Wang, Lixia
    Zhejiang Agr & Forestry Univ, Peoples Republic of China.
    Brodelius, Peter E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Sun, Liping
    Zhejiang Agr & Forestry Univ, Peoples Republic of China.
    A facile synthesis of molecularly imprinted polymers and their properties as electrochemical sensors for ethyl carbamate analysis2018In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 8, no 69, p. 39721-39730Article in journal (Refereed)
    Abstract [en]

    New molecularly imprinted polymers (MIPs), which exhibit specific recognition of ethyl carbamate (EC) have been synthesized and studied. In this process, EC was the template molecule and -cyclodextrin derivatives were employed as functional monomers in the molecular imprinting technique (MIT). An EC molecularly imprinted sensor (EC-MIS) was prepared by using MIT surface modification. The EC-MIS was characterized by cyclic voltammetry, electrochemical impedance spectroscopy and differential pulse voltammetry. EC detection performance, binding parameters and dynamics mechanism were investigated. The result showed that the synthetic route designed was appropriate and that new MIP and EC-MIS were successfully prepared. The EC-MIS exhibited a good molecular recognition of EC. A linear relationship between current and EC concentration was observed using cyclic voltammetry and the detection limit was 5.86 g L-1. The binding constant (K = 4.75 x 10(6) L mol(-1)) between EC and the EC-MIS, as well as, the number of binding sites (n = 1.48) has been determined. The EC-MIS recognition mechanism for the EC is a two-step process. The sensor was applied for the determination of EC in Chinese yellow wines, and the results were in good agreement with the gas chromatography-mass spectrometry (GC-MS) method.

  • 129.
    Guo, Ming
    et al.
    Zhejiang A & F University, China.
    Lu, Xiaowang
    Zhejiang A & F University, China.
    Wang, Yan
    Zhejiang A & F University, China.
    Brodelius, Peter E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Comparison of the interaction between lactoferrin and isomeric drugs2017In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 173, p. 593-607Article in journal (Refereed)
    Abstract [en]

    The binding properties of pentacyclic triterpenoid isomeric drugs, i.e. ursolic acid (UA) and oleanolic acid (OA), to bovine lactoferrin (BLF) have been studied by molecule modeling, fluorescence spectroscopy, UV-visible absorbance spectroscopy and infrared spectroscopy (IR). Molecular docking, performed to reveal the possible binding mode or mechanism, suggested that hydrophobic interaction and hydrogen bonding play important roles to stabilize the complex. The results of spectroscopic measurements showed that the two isomeric drugs both strongly quenched the intrinsic fluorescence of BLF through a static quenching procedure although some differences between UM and OA binding strength and non-radiation energy transfer occurred within the molecules. The number of binding sites was 3.44 and 3.10 for UA and OA, respectively, and the efficiency of Forster energy transfer provided a distance of 0.77 and 1.21 nm for UA and OA, respectively. The conformation transformation of BLF affected by the drugs conformed to the "all-or-none" pattern. In addition, the changes of the ratios of alpha-helices, beta-sheets and beta-turns of BLF during the process of the interaction were obtained. The results of the experiments in combination with the calculations showed that there are two modes of pentacyclic triterpenoid binding to BLF instead of one binding mode only governed by the principle of the lowest bonding energy.

  • 130.
    Guo, Ming
    et al.
    Zhejiang Agr & Forestry Univ, Peoples Republi of China.
    Wang, Xiaomeng
    Zhejiang Agr & Forestry Univ, Peoples Republi of China.
    Lu, Xiaowang
    Zhejiang Agr & Forestry Univ, Peoples Republi of China.
    Wang, Hongzheng
    Zhejiang Agr & Forestry Univ, Peoples Republi of China.
    Brodelius, Peter E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    alpha-Mangostin Extraction from the Native Mangosteen (Garcinia mangostana L.) and the Binding Mechanisms of alpha-Mangostin to HSA or TRF2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 9, article id e0161566Article in journal (Refereed)
    Abstract [en]

    In order to obtain the biological active compound, alpha-mangostin, from the traditional native mangosteen (Garcinia mangostana L.), an extraction method for industrial application was explored. A high yield of a-mangostin (5.2%) was obtained by extraction from dried mangosteen pericarps with subsequent purification on macroporous resin HPD-400. The chemical structure of alpha-mangostin was verified mass spectrometry (MS), nuclear magnetic resonance (H-1 NMR and C-13 NMR), infrared spectroscopy (IR) and UV-Vis spectroscopy. The purity of the obtained alpha-mangostin was 95.6% as determined by HPLC analysis. The binding of native alpha-mangostin to human serum albumin (HSA) or transferrin (TRF) was explored by combining spectral experiments with molecular modeling. The results showed that amangostin binds to HSA or TRF as static complexes but the binding affinities were different in different systems. The binding constants and thermodynamic parameters were measured by fluorescence spectroscopy and absorbance spectra. The association constant of HSA or TRF binding to alpha-mangostin is 6.4832x10(5) L/mol and 1.4652x10(5) L/mol at 298 K and 7.8619x10(5) L/mol and 1.1582x10(5) L/mol at 310 K, respectively. The binding distance, the energy transfer efficiency between alpha-mangostin and HSA or TRF were also obtained by virtue of the Forster theory of non-radiation energy transfer. The effect of alpha-mangostin on the HSA or TRF conformation was analyzed by synchronous spectrometry and fluorescence polarization studies. Molecular docking results reveal that the main interaction between amangostin and HSA is hydrophobic interactions, while the main interaction between alpha-mangostin and TRF is hydrogen bonding and Van der Waals forces. These results are consistent with spectral results.

  • 131.
    Gustafsson, Niklas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Utveckling av grönsakskorv: Kartläggning av näringsrelaterade utmaningar med vegankost och förbättring av näringstäthet i korv baserad på grönsaker.2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Människor blir mer och mer medvetna om hur produktion och konsumtion av kött

    påverkar miljön och folkhälsan. Detta har gjort att vegetariska alternativ till kött blivit

    alltmer populära och att nya produkter i kategorin utvecklats. Ett företag som nappat på

    denna trend är Lindvalls Chark AB i Strömsnäsbruk. Företaget har sedan länge tillverkat

    vanlig korv men har nu börjat utveckla en korv som är helt baserad på grönsaker med

    veganer som målgrupp. Syftet med föreliggande arbete var att sammanställa

    information om de näringsrelaterade problemen som är associerade med en strikt

    vegankost. Vidare var syftet att utifrån informationen identifiera specifikt vilka

    vitaminer och mineraler som Lindvalls tilltänkta korv skulle, för att bättre passa

    målgruppen veganer. Syftet var även att identifiera i vilka råvaror som dessa vitaminer

    och mineraler återfinns och sedan att i praktiska försök testa hur de skulle fungera som

    ingredienser. Resultaten tyder på att sesamfrön och havregryn fungerar bra som

    ingredienser i det tilltänkta receptet, men i olika koncentrationer. Båda ingredienserna

    leder till en ökning av innehållet av järn, kalcium och zink jämfört med det erhållna

    prototyp-receptet.

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  • 132.
    Gustavsson, Maja
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Blodsocker- och insulinrespons efter intag av rågextrakt2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 133.
    Göransson, Frida
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lärares syn på användning och bedömning av laborationer i kemi2019Student paper other, 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Syftet med denna studie är att få en inblick i bedömning av laborationer i kemi och vilka svårigheter som kan finnas med det. Studien är kvalitativ och har fyra stycken forskningsfrågor som besvaras i resultatdiskussionen. Vad är lärares motiv till att genomföra laborationer i kemi? Vilka utmaningar ser lärare med laborationer i kemi? Hur ser lärare på bedömning av laborationer i kemi? Vilken/vilka bedömningsmetoder använder sig lärare av när de bedömer laborationer i kemi? För att ta reda på detta genomfördes 6 intervjuer med verksamma lärare i åk 4-9. Alla lärare är behöriga i ämnet NO och arbetade som NO-lärare när intervjuerna genomfördes. Det visade sig att flera lärare bedömde eleverna genom att göra observationer av laborationerna, de använde dock olika metoder för att dokumentera den kunskap eleverna visade sig ha. Lärarna använde laborationer i kemi till största del för att befästa elevernas kunskaper på ett effektivt sätt. I vissa avseende, som till exempel vid frågan om vad de ser att elevernas största utmaning med laborationer i kemi är, hade lärarna liknande svar. I andra avseenden, som exempelvis vid frågan om vad de själva ser som sin största utmaning vid laborationer i kemi, hade lärarna skilda svar.

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  • 134. Göransson, Ulf
    et al.
    Herrmann, Anders
    Burman, Robert
    Haugaard-Kedström (published under the name Haugaard-Jönsson), Linda M.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Rosengren, K. Johan
    University of Kalmar, School of Pure and Applied Natural Sciences.
    The conserved Glu in the cyclotide cycloviolacin O2 has a key structural role2009In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 10, no 14, p. 2354-2360Article in journal (Refereed)
    Abstract [en]

    Cyclotides are a large family of plant peptides that are characterised by a head-to-tail circular backbone and three disulfide bonds that are arranged in a cystine knot. This unique structural feature, which is referred to as a cyclic cystine knot, gives the cyclotides remarkable stability against chemical and biological degradation. In addition to their natural function as insecticides for plant defence, the cyclotides have a range of bioactivities with pharmaceutical relevance, including cytotoxicity against cancer cell lines. A glutamic acid residue, aside from the invariable disulfide array, is the most conserved feature throughout the cyclotide family, and it has recently been shown to be crucial for biological activity. Here we have used solution-state NMR spectroscopy to determine the three-dimensional structures of the potent cytotoxic cyclotide cycloviolacin O2, and an inactive analogue in which this conserved glutamic acid has been methylated. The structures of the peptides show that the glutamic acid has a key structural role in coordinating a set of hydrogen bonds in native cycloviolacin O2; this interaction is disrupted in the methylated analogue. The proposed mechanism of action of cyclotides is membrane disruption and these results suggest that the glutamic acid is linked to cyclotide function by stabilising the structure to allow efficient aggregation in membranes, rather than in a direct interaction with a target receptor.

  • 135.
    Hansen, Peter
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Treatment of aluminium oxide covered gallium phosphate surfaces for myosin II motor protein adhesion and motility2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    With their efficiency and nano-scaled size, cytoskeletal motors propose a promising addition to new technical innovations. These small workhorses are perfected by evolution and work with high proficiency in nanoscale environments. Since they utilize ATP as energy source they are rendered independent of an external power source. This opens up for the development of advanced mobile diagnostic devices that are as easy to use as a home-use pregnancy test. If they could deliver attached cargo molecules uni-directionally to different reaction chambers on lab-on-a-chip devices, they could replace the use of microfluids. This would include using topographically designed nanowire surfaces, such as aluminum oxide. This paper focuses on the design of a non-etching surface treatment for these gallium phosphate surfaces, which yield a high motility while yet being easy to reproduce. A step-by-step experiment was constructed and involves the use of various surface-cleaning and silanization procedures. The surfaces chemistry and morphology was analyzed with contact angle measurements, ellipsometry as well as in vitro motility assays. While a thought to be favorable surface chemistry was successfully attained utilizing 18 M sulphuric acid together with a following silanization using TMCS, a high motility was not. It was speculated that further manipulation of the silanization protocol and its chemicals could yield a more satisfactory result. 

  • 136.
    Hao, Mengshu
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Construction of transformation vectors and plant transformation of Artemisia annua L.2012Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
  • 137.
    Haraldsson, Jörgen
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Development of a Method for Measuring Pasta Quality Parameters2010Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this work the objective was to develop a method that would make it easier to quantitatively evaluate different quality parameters in pasta. This was done with the assistant of a texture analyzer from TexVol Instruments. The quality parameters that were investigated were hardness, resilience, elasticity and adhesiveness. Two different types of measurements were used to measure three different pasta brands. These were single cycle and hold until time. Before this was done the main parameters in the texture analyzer were tested and adjusted to suite the method. Most of the steps in the developed method worked satisfactorily but more studies have to be done to make the method useful in the daily work with pasta production and pasta development. With all tests in mind it could be said that the De Cecco pasta was the one with the best texture parameters. It had the highest hardness, elasticity and resilience and the lowest adhesiveness. The other two brands, Kungsörnen and Tomadini had lower but similar results. Further important studies to look into is if there`s a possibility to get a computer software that are more targeted on pasta measurement. Another important thing is if these pasta measurements can be done in a different way, perhaps just using a few spaghetti straws. It would also be interesting to study the protein network in an electron microscope because then it´s easier to understand what´s happening when pasta is prepared. Last but not least I think it´s important to do a organoleptic test to see if it´s possible to taste the measured results.

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  • 138.
    Harper, Aimee R.
    et al.
    New Zealand Inst Plant & Food Res Ltd, New Zealand.
    Unelius, C. Rikard
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. New Zealand Inst Plant & Food Res Ltd, New Zealand.
    Townsend, Richard J.
    AgResearch Ltd, Lincoln Res Ctr, New Zealand.
    Suckling, David Maxwell
    New Zealand Inst Plant & Food Res Ltd, New Zealand.
    Dose reduction and alternatives to the phenol pheromone in monitoring and management of the grass grub Costelytra zealandica2017In: Pest Management Science, ISSN 1526-498X, E-ISSN 1526-4998, Vol. 73, no 11, p. 2252-2258Article in journal (Refereed)
    Abstract [en]

    BACKGROUNDEndemic New Zealand grass grub Costelytra zealandica is a pest of introduced pasture that uses phenol as a sex pheromone. The pheromone could be used to monitor and manage grass grub populations, but the irritating properties and toxicity of phenol for human handlers, as well as the possible ecotoxicological effects, pose obstacles to the deployment of the pheromone. This study aimed to limit the use of phenol by dose-response studies and investigation into alternative attractants and synergists to phenol. RESULTSNo difference in trap catch was seen across the range of 1-100mg of phenol, while rates below this (0.001-0.1mg) caused a large drop in catches. Our results indicated that 1mg loading in lures was enough to indicate beetle presence over 1 week. 4-Hydroxybenzaldehyde and p-cresol proved unattractive in this study, both as single attractants and as synergists with phenol. Phenyl acetate, phenyl benzoate and diphenyl carbonate all formed phenol under hydrolytic conditions to act as successful propheromones, while phenyl acetate was found to be as attractive as phenol on its own. CONCLUSIONThis study described several ways to reduce or avoid the use of phenol in the field while maintaining lure effectiveness. (c) 2017 Society of Chemical Industry

  • 139.
    Harrysson, Louise
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Kalibreringav mikrovågsinstrumentet HK1-Mc för ostarna Herrgård 17 % och Grevé 17 %2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The present study investigated the water content and the height of the hard cheese varieties Herrgård with a fat content of 17% (H17%) and Grevé with a fat content of 17% (G17%). The aim of this study was to calibrate the microwave instrument HK1-Mc. The microwave instrument HK1-Mc uses the microwaves in combination with the product height and dielectric properties of water, to measure the water content in cheeses. The work began with a one-point calibration of the instrument, where obtained data were compared with assay values from an FTIR instrument, which was used as the reference method of analysis. The obtained measurement data from the microwave instrument and IR instrument where inserted into a spreadsheet program recommended by the manufacturer HK1-Mc, (Harrer & Kassen), from which the appropriate "slope" and "intercept" values were obtained for the microwave instrument. According to the measurements obtained on water from HK1-Mc respective FTIR instrument there is a correlation between the instruments of 1.1%.According to the measurements obtained from the instrument HK1-Mc, there is a correlation between water content and height of the cheeses, coefficient of determination of 60.4%, after calibration, this results can not be considered reasonable in the calibration of the instrument. According to measurements obtained from the reference instrument the relationship is significantly weaker, determintationskoefficient of 3.5% between water content and height after calibration, this value can be considered reasonable in the calibration of the instrument. The correlation between water content and height can be due to a change in the relationship between bound and free water because the height of the cheeses changes with time. The correlation may also be due to that the samples during calibration had a narrow distribution, which may have led to the “slope” of the calibration curve being incorrect. In the final stage of the work it was discovered that all of the previously calibrated channels in the microwave instrument provide a correlation between water content and height. The trend among all channels makes the current calibration unusable. There is a suspicion that the memory or height sensor of the instrument has been changed or influenced. Several other technical reasons can be the basis for the instrument's behavior. The cause / causes of the technical problems are under investigation.

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  • 140.
    Haugaard-Kedström, Linda M.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Structure and function of relaxins2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The relaxin/insulin superfamily is a group of peptide hormones that consists of ten members in human, namely relaxins 1-3, insulin-like peptides (INSL) 3-6, insulin and insulin-like growth factors (IGF) I-II. These peptides have various functions in the body, such as regulating growth, blood glucose levels,  collagen metabolism, germ cell maturation and appetite. Misregulation of these mechanisms is associated with disease and accordingly they are of interest as potential pharmaceutical targets. Structurally the hormones are characterised by two peptide chains, A and B, which are held together by one intra A-chain and two inter chain disulfide bonds. Four different G-protein coupled receptors (GPCR) called relaxin family peptide receptor (RXFP) 1-4 have been found to respond to stimuli by different relaxin peptides. RXFP3 and RXFP4 are classic peptide ligand GPCRs, whereas RXFP1 and RXFP2 are characterised by a large extracellular leucine rich-repeat domain. Relaxin-3, which is the relaxin family ancestor, is the only relaxin peptide known to be able to bind and activate both subtypes of GPCRs, namely RXFP1, RXFP3 and RXFP4.

    The aim of this thesis was to analyse the structure-function relationship of the relaxin ligands and receptors, and to use this information to develop selective ligands for the relaxin receptors, which can be used as drug leads or pharmacological tools for investigating the physiological roles of the RXFPs.

    The 3D structures of native INSL5 and relaxin-2 were determined by solution NMR spectroscopy. The peptides showed an insulin/relaxin-like overall fold. A relaxin chimera peptide, consisting of the A-chain from INSL5 and the B-chain from relaxin-3, R3/I5, which has been shown to be selective for RXFP3 and RXFP4 over RXFP1, was also subjected to NMR studies. The R3/I5 peptide maintained an insulin/relaxin-like overall fold, and the relaxin-3 B-chain adopted a conformation identical to that in native relaxin-3, confirming that the activity of R3/I5 can be directly related to its primary sequence. Furthermore, a truncation study was undertaken to ascertain the importance of the termini for structure and function. By using the knowledge generated from the structure-function relationship, a single-chain high affinity RXFP3 selective antagonist was developed.

    In conclusion, this thesis has contributed to broaden the knowledge of the structure-function relationship of the relaxin ligands and the development of a selective RXFP3 antagonist, which is currently a drug lead for treatment of neurological disorders including stress and obesity.

  • 141.
    Haugaard-Kedström, Linda M.
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Shabanpoor, Fazel
    Florey Neuroscience, The University of Melbourne.
    Hossain, Mohammed Akhter
    Florey Neuroscience, The University of Melbourne.
    Clark, Richard
    The University of Queensland, Institute for Molecular Bioscience .
    Ryan, Philip
    Florey Neuroscience, The University of Melbourne.
    Craik, David
    The University of Queensland, Institute for Molecular Bioscience .
    Gundlach, Andrew
    Florey Neuroscience, The University of Melbourne.
    Wade, John
    Florey Neuroscience, The University of Melbourne.
    Bathgate, Ross
    Florey Neuroscience, The University of Melbourne.
    Rosengren, K. Johan
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Design, synthesis, and characterization of a single-chain peptide antagonist for the relaxin-3 receptor RXFP32011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 13, p. 4965-4974Article in journal (Refereed)
  • 142.
    Haugaard-Kedström (published under the name Haugaard-Jönsson), Linda M.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hossain, Akther
    Daly, Norelle
    Bathgate, Ross
    Craik, David
    Wade, John
    Rosengren, Johan
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Structural characterization of a H3-INSL5 relaxin peptide chimera2007In: Proceedings of the 4th International Peptide Symposium / [ed] Wilce, Jackie, Cairns, Australia, 2007Conference paper (Refereed)
  • 143.
    Haugaard-Kedström (published under the name Haugaard-Jönsson), Linda M.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hossain, M. Akhter
    Daly, Norelle L.
    Bathgate, Ross A.D.
    Wade, John D.
    Craik, David J.
    Rosengren, K. Johan
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Structural Properties of Relaxin Chimeras: NMR Characterization of the R3/I5 Relaxin Peptide2009In: Annals of the New York Academy of Sciences, ISSN 0077-8923, E-ISSN 1749-6632, Vol. 1160, p. 27-30Article in journal (Refereed)
    Abstract [en]

    Relaxin-3 interacts with high potency with three relaxin family peptide receptors (RXFP1, RXFP3, and RXFP4). Therefore, the development of selective agonist and antagonist analogs is important for in vivo studies characterizing the biological significance of the different receptor-ligand systems and for future pharmaceutical applications. Recent reports demonstrated that a peptide selective for RXFP3 and RXFP4 over RXFP1 can be generated by the combination of the relaxin-3 B chain with the A chain from insulin-like peptide 5 (INSL5), creating an R3/I5 chimera. We have used NMR spectroscopy to determine the three-dimensional structure of this peptide to gain structural insights into the consequences of combining chains from two different relaxins. The R3/I5 structure reveals a similar backbone conformation for the relaxin-3 B chain compared to native relaxin-3, and the INSL5 A chain displays a relaxin/insulin-like fold with two parallel helices. The findings indicate that binding and activation of RXFP3 and RXFP4 mainly require the B chain and that the A chain functions as structural support. RXFP1, however, demonstrates a more complex binding mechanism, involving both the A chain and the B chain. The creation of chimeras is a promising strategy for generating new structure-activity data on relaxins.

  • 144.
    Haugaard-Kedström (published under the name Haugaard-Jönsson), Linda M.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hossain, M. Akhter
    Daly, Norelle L.
    Craik, David J.
    Wade, John D.
    Rosengren, K. Johan
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Structure of the human insulin-like peptide 5 and characterization of conserved hydrogen bonds and electrostatic interactions within the relaxin framework2009In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 419, p. 619-627Article in journal (Refereed)
    Abstract [en]

    INSL5 (insulin-like peptide 5) is a two-chain peptide hormone related to insulin and relaxin. It was recently discovered through searches of expressed sequence tag databases and, although the fulfil biological significance of INSL5 is still being elucidated, high expression in peripheral tissues such as the colon, as well as in the brain and hypothalamus, suggests roles in gut contractility and neuroendocrine signalling. INSL5 activates the relaxin family peptide receptor 4 with high potency and appears to be the endogenous ligand for this receptor, on the basis of overlapping expression profiles and their apparent co-evolution. In the present Study, we have used solution-state NMR to characterize the three-dimensional structure of synthetic human INSL5. The structure reveals an insulin/relaxin-like fold with three helical segments that are braced by three disulfide bonds and enclose a hydrophobic core. Furthermore, we characterized in detail the hydrogen-bond network and electrostatic interactions between charged groups in INSL5 by NMR-monitored temperature and pH titrations and Undertook a comprehensive structural comparison with other members of the relaxin family, thus identifying the conserved structural features of the relaxin fold. The B-chain helix, which is the primary receptor-binding site of the relaxins, is longer in INSL5 than in its close relative relaxin-3. As this feature results in a different positioning of the receptor-activation domain Arg(B23) and Trp(B24), it may be an important contributor to the difference in biological activity observed for these two peptides. Overall, the structural Studies provide mechanistic insights into the receptor selectivity of this important family of hormones. 

  • 145.
    Haugaard-Kedström (published under the name Haugaard-Jönsson), Linda M.
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Hossain, Mohammed Akhter
    Daly, Norelle L.
    Bathgate, Ross A.D.
    Wade, John D.
    Craik, David J.
    Rosengren, Johan
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Structure of the R3/I5 chimeric relaxin peptide, a selective GPCR135 and GPCR142 agonist2008In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 283, no 35, p. 23811-23818Article in journal (Refereed)
    Abstract [en]

    The human relaxin family comprises seven peptide hormones with various biological functions mediated through interactions with G-protein-coupled receptors. Interestingly, among the hitherto characterized receptors there is no absolute selectivity toward their primary ligand. The most striking example of this is the relaxin family ancestor, relaxin-3, which is an agonist for three of the four currently known relaxin receptors: GPCR135, GPCR142, and LGR7. Relaxin-3 and its endogenous receptor GPCR135 are both expressed predominantly in the brain and have been linked to regulation of stress and feeding. However, to fully understand the role of relaxin-3 in neurological signaling, the development of selective GPCR135 agonists and antagonists for in vivo studies is crucial. Recent reports have demonstrated that such selective ligands can be achieved by making chimeric peptides comprising the relaxin-3 B-chain combined with the INSL5 A-chain. To obtain structural insights into the consequences of combining A-and B-chains from different relaxins we have determined the NMR solution structure of a human relaxin-3/INSL5 chimeric peptide. The structure reveals that the INSL5 A-chain adopts a conformation similar to the relaxin-3 A-chain, and thus has the ability to structurally support a native-like conformation of the relaxin-3 B-chain. These findings suggest that the decrease in activity at the LGR7 receptor seen for this peptide is a result of the removal of a secondary LGR7 binding site present in the relaxin-3 A-chain, rather than conformational changes in the primary B-chain receptor binding site. 

  • 146.
    Hemmilä, Venla
    Linnaeus University, Faculty of Technology, Department of Forestry and Wood Technology.
    Towards low-emitting and sustainable particle and fibreboards: Formaldehyde emission test methods and adhesives from biorefinery lignins2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    High volumes, fast production speed, and low material costs have been historically the driving factors of the particle- and fibreboard industries. However, in recent years the fossil-fuel dependency and health issues of the formaldehyde-containing adhesives used in the production have gained attention from both legislators and consumers. The latest example of legislation development is the change that the Federal Ministry for the Environment, Nature Conservation and Nuclear Safety of Germany  (Bundesministerium für Umwelt, Naturschutz und Nukleare Sicherheit) made to their testing method, effectively lowering the formaldehyde emission levels of wood-based panels in Germany from the European emission level of 0.1 ppm (E1, EN 717-1) to 0.05 ppm. As the emission levels of requirements decrease, market opportunities arise for formaldehyde-free bio-based adhesive systems. The aim of this thesis was thus to evaluate the different formaldehyde test methods at low emission levels (<0.05 ppm), and to explore new adhesive alternatives to the formaldehyde and petroleum-based systems used today.

    As formaldehyde emissions decrease, choosing the right measurement method becomes increasingly important. Repeatability and correlation between the main European and American formaldehyde measurement chambers, described in EN 717-1 and ASTM D 6007 standards respectively, were determined. In addition, an alternative fast factory method based on emissions was evaluated, and the effect of reducing the conditioning time before emission measurements was investigated. A literature research was conducted on different bio-based raw materials in order to review their potential, from both scientific and industrial viewpoints, as alternatives to the current petroleum-derived and formaldehyde-based adhesives. Lignin residues from biorefinery processes were chosen for further testing due to their increasing volumes and potential to suit various pathways for adhesive making. Three different biorefinery lignins were compared, and ammonium lignosulfonate was chosen for making adhesives for particleboards by using one petroleum-based and one bio-based crosslinker.

    The main conclusion of the formaldehyde emission part of the thesis was that formaldehyde emissions can be measured both accurately and quickly at low levels using chamber methods, even at factory environment. There was a good correlation between the American D 6007 and European EN 717-1 chamber methods at emission levels <0.05 ppm for both particleboards (r2 = 0.9167) and fibreboards (r2 = 0.9443). Further understanding on the effect of edge-sealing of boards and analytical methods described in the standards was obtained. It was confirmed that a fast chamber method with 1 day conditioning and 15 minutes measuring time could be used for factory formaldehyde control for most board types.

    The bio-based adhesives’ literature review revealed a large amount of studies on different sustainable adhesive systems, some of which seem promising. Both soy protein and tannin were found to be partially commercialized, with certain pre-requisites. Kraft-lignin was especially well researched, but was found to be difficult to use for other applications than partial replacement of phenol in phenol-formaldehyde (PF) adhesives due to poor water solubility and purity. Lignin residues from biorefinery processes were found to be a less studied, growing raw-material source with a lot of potential. Thus, supercritical water hydrolysis lignin (SCWH) and two biorefinery lignosulfonates were chemically and thermally characterized, and evaluated as raw materials for value-added applications, including adhesives. SCWH lignin was found to have more β-R linkages and lower amount of impurities than the lignosulfonates. High amount of phenolic hydroxyl groups indicated that SCWH would be well suited for phenol replacement in PF adhesives. The two lignosulfonates had more aliphatic hydroxyl groups, which can be interesting for other crosslinking reactions than PF. Ammonium lignosulfonate (ALS) was chosen for further evaluation as having slightly better properties than sodium lignosulfonate (SLS). ALS was combined with one bio-based crosslinker, furfuryl alcohol (FOH), and one synthetic crosslinker, 4,4’-diphenylmethane diisocyanate (pMDI), and tested as particleboard adhesive. Although in veneer tensile shear strength testing the crosslinkers worked equally well, pMDI provided significantly better results in particleboards. In addition, higher emissions than what can be expected from wood particles alone were detected from the particleboard samples crosslinked with FOH, even though FOH can be classified as non-formaldehyde added adhesive system. Further research is needed to elucidate how much the lignin contributes to the final adhesion strength when it is used together with pMDI.

    This thesis has provided new insights on formaldehyde emissions and bio-based adhesives towards healthier and more sustainable particle- and fibreboards. It has been proven that formaldehyde emissions can be measured accurately at emission levels of wood, enabling comparisons of formaldehyde-free systems. Formaldehyde-free adhesives based on a biorefinery lignin type and pMDI showed promising results for particleboards. However, these results need to be improved by different modifications of the lignin in order to bring the adhesive system to the economical and performance level required by the particleboard industry.

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  • 147.
    Henriksson, Julia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Characterization of Composition of the Fat-rich Residues from Grease Separators2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Fat, oil, and grease (FOG) deposits in wastewater systems reduce sewer diameter and can completely block the pipe, leading to sanitary sewer overflows (SSOs). This impacts both public health and the environment. Grease separators (GSs) are tanks that have the ability to prevent a substantial part of the incoming FOG from entering the sewer system. The aim of this study was to characterize the fatty acid profile and the change over time in fat content, free fatty acids (FFAs) and dry solids in FOG-rich residues from three GSs in the Stockholm region. One of these GSs was treated with a biological system (GOR BioSystem™). The results show a lower amount of fat and dry solids in the biologically treated GS compared with the two untreated. The proportion of FFAs is high from the beginning of the study period in grease caps from all GSs analyzed. The predominant fatty acids in FOG was in this study palmitic (C16:0), stearic (C18:0), oleic (C18:1) and linoleic acid (C18:2), which is consistent with previous studies. However, there was a higher content of palmitic acid (C16:0) and saturated fatty acids in the grease caps from the treated GS. The untreated GSs had a higher content of oleic acid (C18:1) and unsaturated fatty acid, which in one of these GSs decreased during the study period. In conclusion, the change in the fatty acid profile in FOG-rich residues did not follow the same pattern in the different GSs and the results were inconclusive. Further studies, with a longer time perspective, are needed in this area.

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  • 148.
    Henschel, Henning
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Rosengren, Annika M.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Insights into the Isomerisation Mechanism of Warfarin2010Conference paper (Refereed)
    Abstract [en]

    Warfarin is one of the most commonly used drugs in anticoagulent therapy. Notwithstanding its wide use, achieving correct dosage is often a major challenge due to its narrow therapeutic window.[1] The bioavailability of warfarin is believed to be greatly influenced by the environment-dependent composition of the ensemble of isomers present. While the different structures of warfarin have been discussed in earlier publications,[2] details of the mechanism underlying the formation of the cyclic hemiacetal (Figure 1) had not yet been investigated.

    Figure 1. Cyclization reaction of warfarin.

    Figure 2. Transition state in presence of one water molecule.

     

    We have now studied the reaction by means of density functional calculations. Comparison of results from calculations performed on the isolated warfarin molecule and in presence of water molecules (compare Figure 2) highlight the importance of intermolecular interactions in the key proton transfer step for the reaction to proceed. A viable model for the mechanism underlying the isomerisation shall be presented.

     

     

    References

    [1]             J. Ansell, J. Hirsh, L. Poller, H. Bussey, A. Jacobsen and E. Hylek, Chest, 126, 204S (2004).

    [2]            B. C. G. Karlsson, A. M. Rosengren, P. O. Andersson and I. A. Nicholls, J. Phys. Chem. B, 111,10520 (2007).

  • 149.
    Henschel, Henning
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Rosengren, Annika M.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    The Mechanistic Basis for Warfarin’s Structural Diversity and Implications for Its Bioavailability2010In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 958, p. 7-9Article in journal (Refereed)
    Abstract [en]

    The anticoagulent drug warfarin exhibits chameleon-like isomerism, where the environment-dependent composition of the ensemble of structures greatly influences its bioavailability. Here, the mechanism of conversion between the major isomeric forms is studied. The dramatic differences in transition state energies, as determined by density functional calculations, highlight the necessity for the involvement of intermolecular interactions in the key proton transfer step. A viable model for the mechanism underlying the isomerization reactions is presented.

  • 150.
    Henschel, Henning
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Kirsch, Nicole
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Hedin-Dahlström, Jimmy
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Whitcombe, MJ
    Wikman, Susanne
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Nicholls, Ian A.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Effect of the cross-linker on the general performance and temperature dependent behaviour of a molecularly imprinted polymer catalyst of a Diels-Alder reaction2011In: Journal of Molecular Catalysis B: Enzymatic, ISSN 1381-1177, E-ISSN 1873-3158, Vol. 72, no 3-4, p. 199-205Article in journal (Refereed)
    Abstract [en]

    Here we present a series of molecularly imprinted polymers capable of catalysing the Diels-Alder reaction between benzyl 1,3-butadienylcarbamate (1) and N,N-dimethyl acrylamide (2). The polymer systems studied here demonstrated an unusual cross-linker and temperature dependent behaviour, namely that polymer catalysis of the Diels-Alder reaction was lower at elevated temperature, in contrast to the solution reaction. Furthermore, not only was the catalytic activity significantly influenced by the choice of cross-linker, but in a similar fashion also the extent of the temperature effect, indicating a close relationship between catalysis and the observed inhibition. Molecular dynamics simulations of both the polymer systems studied were used to provide insight into the molecular background of transition state stabilisation, and differences in properties of the systems based on different cross-linkers.

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