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  • 1.
    Abdullatif, Zina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjuksköterskors bidrag till farmakovigilans arbete i Sverige En retrospektiv analys av alla sjuksköterskors biverkningsrapporter år 2015: En retrospektiv analys av alla sjuksköterskors biverkningsrapporter år 20152016Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 2.
    Abed, Shahla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Läkemedel mot Bcl-2 överuttryckande resistenta Prostatatumörer: Läkemedel mot Bcl-2 överuttryckande resistenta Prostatatumörer2015Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 3. Accinelli, Cesare
    et al.
    Saccà, Maria Ludovica
    Batisson, Isabelle
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mencarelli, Mariangela
    Grabic, Roman
    Removal of oseltamivir (Tamiflu) and other selected pharmaceuticals from wastewater using a granular bioplastic formulation entrapping propagules of Phanerochaete chrysosporium2010In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 81, no 3, 436-43 p.Article in journal (Refereed)
    Abstract [en]

    The capacity of the ligninolytic fungus Phanerochaete chrysosporium to degrade a wide variety of environmentally persistent xenobiotics has been largely reported in the literature. Beside other factors, one barrier to a wider use of this bioremediation fungus is the availability of effective formulations that ensure easy preparation, handling and application. In this series of laboratory experiments, we evaluated the efficiency of a granular bioplastic formulation entrapping propagules of P. chrysosporium for removal of four selected pharmaceuticals from wastewater samples. Addition of inoculated granules to samples of the wastewater treatment plant of Bologna significantly increased the removal of the antiviral drug oseltamivir (Tamiflu), and the antibiotics, erythromycin, sulfamethoxazol, and ciprofloxacin. Similar effects were also observed in effluent water. Oseltamivir was the most persistent of the four active substances. After 30d of incubation, approximately two times more oseltamivir was removed in bioremediated wastewater than controls. The highest removal efficiency of the bioplastic formulation was observed with the antibiotic ciprofloxacin. Microbiological DNA-based analysis showed that the bioplastic matrix supported the growth of P. chrysosporium, thus facilitating its adaptation to unusual environment such as wastewater.

  • 4. Accinelli, Cesare
    et al.
    Saccà, Maria Ludovica
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mencarelli, Mariangela
    Lindberg, Richard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olsen, Björn
    Dissipation and removal of oseltamivir (Tamiflu) in different aquatic environments2010In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 79, no 8, 891-897 p.Article in journal (Refereed)
    Abstract [en]

    The antiviral drug oseltamivir (Tamiflu) has received recent attention due to the potential use as a first-line defense against H5N1 and H1N1 influenza viruses. Research has shown that oseltamivir is not removed during conventional wastewater treatments, thus having the potential to enter surface water bodies. A series of laboratory experiments investigated the fate and the removal of oseltamivir in two surface water ecosystems of Japan and in a municipal wastewater treatment plant located in Northern Italy. Persistence of oseltamivir in surface water ranged from non-detectable degradation to a half-life of 53d. After 40d, <3% of radiolabeled oseltamivir evolved as (14)CO(2). The presence of sediments (5%) led to a significant increase of oseltamivir degradation and mineralization rates. A more intense mineralization was observed in samples of the wastewater treatment plant when applying a long incubation period (40d). More precisely, 76% and 37% of the initial radioactivity applied as (14)C-oseltamivir was recovered as (14)CO(2) from samples of the biological tank and effluent water, respectively. Two bacterial strains growing on oseltamivir as sole carbon source were isolated and used for its removal from synthetic medium and environmental samples, including surface water and wastewater. Inoculation of water and wastewater samples with the two oseltamivir-degrading strains showed that mineralization of oseltamivir was significantly higher in both inoculated water and wastewater, than in uninoculated controls. Denaturing gradient gel electrophoresis and quantitative PCR analysis showed that Tamiflu would not affect the microbial population of surface water and wastewater.

  • 5. Acharya, Shravan S.
    et al.
    Easton, Christopher D.
    McCoy, Thomas M.
    Spiccia, Leone
    Ohlin, C. André
    Umeå University, Faculty of Science and Technology, Department of Chemistry. School of Chemistry, Monash University, Clayton, Australia.
    Winther-Jensen, Bjorn
    Diverse composites of metal-complexes and PEDOT facilitated by metal-free vapour phase polymerization2017In: Reactive & functional polymers, ISSN 1381-5148, E-ISSN 1873-166X, Vol. 116, 101-106 p.Article in journal (Refereed)
    Abstract [en]

    Abstract Oxidative polymerization for the manufacture of conducting polymers such as poly(3,4-ethylenedioxy-thiophene) has traditionally employed iron(III) salts. Demonstrated in this study is vapour phase polymerization of 3,4-ethylenedio- xythiophene using a metal-free oxidant, ammonium persulfate, leading to films with an estimated conductivity of 75 S/cm. Additionally, a route for embedding active transition metal complexes into these poly(3,4-ethylenedioxythiophene)/-poly(styrene-4-sulfonate) (PEDOT/PSS) films via vapour assisted complexation is outlined. Here, the vapour pressure of solid ligands around their melting temperatures was exploited to ensure complexation to metal ions added into the oxidant mixture prior to polymerization of PEDOT. Four composite systems are discussed, viz. PEDOT/PSS embedded with tris(8-hydroxyquinolinato)cobalt(III), tris(2,2-bipyridine)cobalt(II), tris(1,10- phenanthroline)cobalt(II) and tris(8-hyd-roxyquinolinato)aluminium(III). Using these composites, electrochemical reduction of nitrite to ammonia with a faradaic efficiency of 61% was reported.

  • 6. Acharya, Shravan
    et al.
    Winther-Jensen, Bjorn
    Spiccia, Leone
    Ohlin, André C.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Rates of water exchange in 2,2'-bipyridine and 1,10-phenanthroline complexes of CoII and MnII2017In: Australian journal of chemistry (Print), ISSN 0004-9425, E-ISSN 1445-0038, Vol. 70, no 6, 751-754 p.Article in journal (Refereed)
    Abstract [en]

    The rates and activation parameters of water exchange at pH 3.0 have been determined using variable temperature 17O NMR spectroscopy for four CoII complexes and one MnII complex: [Co(bpy)(H2O)4]2+, [Co(bpy)2 (H2O)2]2+, [Co(phen)-(H2O)4]2+, [Co(phen)2 (H2O)2]2+, and [Mn(bpy)(H2O)4]2+ (bpy = 2,2′-bipyridyl and phen = 1,10-phenanthroline). Substitution of aquo ligands with 1,10-phenanthroline or 2,2′-bipyridyl leads to an increase in the rate of exchange in the manganese complexes, from k298 (1.8 ± 0.1) × 107 s-1 for [Mn(H2O)6]2+ to (7.2 ± 0.3) × 107 s-1 for [Mn(phen)2 (H2O)2]2+, whereas the trends are more complex for the cobalt complexes. We have used the new data in conjunction with literature data for similar complexes to analyse the effect of M–OH2 distance and degree of substitution.

  • 7.
    Addario, Barbara
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Alpha-actinin - an amazing journey through time and species2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In eukaryotes, the actin cytoskeleton plays an important role in a large variety of cellular events. Its reorganization is regulated by a plethora of actin-modulating proteins, such as α-actinin.

    α-actinin is a ubiquitous actin-binding protein that belongs to the spectrin superfamily. This family, besides α-actinin, includes spectrin, dystrophin and utrophin. Phylogenetic analyses have indicated that the family members arose after several intragene duplications and rearrangements of a common ancestral α-actinin isoform. Up to the invertebrate-vertebrate bifurcation, organisms seemed to have a single, calcium-dependent α‑actinin. After the split, invertebrates have kept this single isoform, in contrast to vertebrates that acquired four distinct isoforms. Of the four vertebrate α-actinin isoforms, the two present in non-muscle cells are typically calcium sensitive while the two muscle isoforms are calcium insensitive.

    α-actinin in higher organisms is characterized by the presence of three distinct structural domains: a highly conserved N-terminal actin-binding domain, a central rod domain with four spectrin repeats and a calcium-binding C terminus with EF-hand motifs. In some primitive organisms, such as protozoa and fungi, the rod domain of α-actinin contains only one or two spectrin repeats. With the completion of an ever increasing number of genomes, new and atypical α‑actinin sequences had been available that have not been characterized yet. To obtain a firmer understanding of the evolutionary history of α-actinin, the main objective of this study was to identify, purify and biochemically characterize atypical α‑actinin or α‑actinin-like proteins of the parasite Entamoeba histolytica and of the fungus Schizosaccharomyces pombe. Our results show that both isoforms, despite the much shorter rod domain, are able to bind and cross-link actin filaments and therefore can be considered genuine α-actinins. 

  • 8.
    Addario, Barbara
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Backman, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Alpha-actinin of Schizosaccharomyces pombeManuscript (preprint) (Other academic)
  • 9.
    Addario, Barbara
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Backman, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The domain structure of Entamoeba α-actinin22010In: Cellular & Molecular Biology Letters (Druk), ISSN 1425-8153, E-ISSN 1689-1392, Vol. 15, no 4, 665-78 p.Article in journal (Refereed)
    Abstract [en]

    Entamoeba histolytica, a major agent of human amoebiasis, expresses two distinct forms of α-actinin, a ubiquitous actin-binding protein that is present in most eukaryotic organisms. In contrast to all metazoan α-actinins, in both isoforms the intervening rod domain that connects the N-terminal actin-binding domain with the C-terminal EF-hands is much shorter. It is suggested that these α-actinins may be involved in amoeboid motility and phagocytosis, so we cloned and characterised each domain of one of these α-actinins to better understand their functional role. The results clearly showed that the domains have properties very similar to those of conventional α-actinins.

  • 10.
    Addario, Barbara
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Huang, Shenghua
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sauer, Uwe
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Backman, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Crystallization and preliminary X-ray analysis of the Entamoeba histolytica α-actinin-2 rod domain2011In: Acta Crystallographica. Section F: Structural Biology and Crystallization Communications, ISSN 1744-3091, E-ISSN 1744-3091, Vol. 67, no 10, 1214-1217 p.Article in journal (Refereed)
    Abstract [en]

    -Actinins form antiparallel homodimers that are able to cross-link actin filaments. The protein contains three domains: an N-terminal actin-binding domain followed by a central rod domain and a calmodulin-like EF-hand domain at the C-terminus. Here, crystallization of the rod domain of Entamoeba histolytica -actinin-2 is reported; it crystallized in space group P212121, with unit-cell parameters a = 47.8, b = 79.1, c = 141.8 Å. A Matthews coefficient VM of 2.6 Å3 Da-1 suggests that there are two molecules and 52.5% solvent content in the asymmetric unit. A complete native data set extending to a d-spacing of 2.8 Å was collected on beamline I911-2 at MAX-lab, Sweden.

     

  • 11. Addario, Barbara
    et al.
    Sandblad, Linda
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Persson, Karina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Backman, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Characterisation of Schizosaccharomyces pombe alpha-actinin2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, e1858Article in journal (Refereed)
    Abstract [en]

    The actin cytoskeleton plays a fundamental role in eukaryotic cells. Its reorganization is regulated by a plethora of actin-modulating proteins, such as a-actinin. In higher organisms, alpha-actinin is characterized by the presence of three distinct structural domains: an N-terminal actin-binding domain and a C-terminal region with EF-hand motif separated by a central rod domain with four spectrin repeats. Sequence analysis has revealed that the central rod domain of alpha-actinin from the fission yeast Schizosaccharomyces pombe consists of only two spectrin repeats. To obtain a firmer understanding of the structure and function of this unconventional alpha-actinin, we have cloned and characterized each structural domain. Our results show that this alpha-actinin isoform is capable of forming dimers and that the rod domain is required for this. However, its actin-binding and cross-linking activity appears less efficient compared to conventional alpha-actinins. The solved crystal structure of the actin-binding domain indicates that the closed state is stabilised by hydrogen bonds and a salt bridge not present in other a-actinins, which may reduce the affinity for actin.

  • 12. Adebahr, J
    et al.
    Forsyth, M
    Gavelin, P
    Jacobsson, P
    Orädd, Greger
    Umeå University, Faculty of Science and Technology, Chemistry.
    Ion and Solvent Dynamics in Gel Electrolytes Based on Ethylene Oxide Grafted Acrylate Polymers2002In: The Journal of Physical Chemistry B, Vol. 106, no 47, 12119-12123 p.Article in journal (Refereed)
    Abstract [en]

    Multinuclear pulsed field gradient NMR measurements and rheological viscosity measurements were performed on three series of polymer gel electrolytes. The gels were based on a lithium salt electrolyte swollen into a copolymer matrix comprising an acrylate backbone and ethylene oxide side chains. In each series the side chains differed in length and number, but the acrylate-to-ethylene oxide ratio was kept constant. It was found that the self-diffusion coefficient of the cations was much lower than that of the anions, and that it decreased rapidly when the side chains got longer. In contrast, the self-diffusion coefficient of the anions was found to be independent of chain length. In the gel electrolytes, the diffusion coefficients of the solvent molecules are relatively constant despite an increased viscosity with increasing length of the side chains. However, in salt-free gels made for comparison, the diffusion coefficients of the solvent molecules decreased with increasing length of the side chains, which is consistent with an increased viscosity.

  • 13. Adnan, Muhammad
    et al.
    Iqbal, Javed
    Bibi, Shamsa
    Hussain, Riaz
    Akhtar, Muhammad Nadeem
    Rashid, Muhammad Abid
    Eliasson, Bertil
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ayub, Khurshid
    Fine Tuning the Optoelectronic Properties of Triphenylamine Based Donor Molecules for Organic Solar Cells2017In: Zeitschrift fur physikalische Chemie (Munchen. 1991), ISSN 0942-9352, Vol. 231, no 6, 1127-1139 p.Article in journal (Refereed)
    Abstract [en]

    Geometrical parameters, electronic structures and photophysical properties of three new triphenylamine (TPA) and diphenylamine (DPA) based electron donor materials M1-M3 (for organic solar cells) have been investigated through density functional theory (DFT) methods at the B3LYP/6-31G(d) level of the theory. TPA and DPA are used as donor moieties due to their electron donating ability while benzothiazole, cyanide and cyanomethylacetate (CMA) moieties have been taken as acceptor moieties. The time dependent-DFT (TD-DFT) method has been employed [TD-B3LYP/6-31G (d)] for the computation of excited state properties in the gas phase and in solvent (chloroform). The polarization continuum model is applied for calculations in the solvent phase. The designed molecules exhibited broad absorption in the visible and near infra-red region of spectrum with respect to a reference molecule "R" of a similar class of compounds. Based on reorganization energies calculations, these materials could act as excellent hole transport materials.

  • 14. Aeppli, Christoph
    et al.
    Holmstrand, Henry
    Bastviken, David
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gustafsson, Orjan
    Investigating formation and degradation of polychlorinated phenols in the environment using chlorine and carbon stable isotope fractionation2011In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 242, 214-ENVR- p.Article in journal (Refereed)
  • 15. Aeppli, Christoph
    et al.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Holmstrand, Henry
    Gustafsson, Örjan
    Use of Cl and C Isotopic Fractionation to Identify Degradation and Sources of Polychlorinated Phenols: Mechanistic Study and Field Application2013In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 47, no 2, 790-797 p.Article in journal (Refereed)
    Abstract [en]

    The widespread use of chlorinated phenols (CPs) as a wood preservative has led to numerous contaminated sawmill sites. However, it remains challenging to assess the extent of in situ degradation of CPs. We evaluated the use of compound-specific chlorine and carbon isotope analysis (Cl- and C-CSIA) to assess CP biotransformation. In a laboratory system, we measured isotopic fractionation during oxidative 2,4,6-trichlorophenol dechlorination by representative soil enzymes (C. fumago chloroperoxidase, horseradish peroxidase, and laccase from T. versicolor). Using a mathematical model, the validity of the Rayleigh approach to evaluate apparent kinetic isotope effects (AKIE) was confirmed. A small but significant Cl-AKIE of 1.0022 ± 0.0006 was observed for all three enzymes, consistent with a reaction pathway via a cationic radical species. For carbon, a slight inverse isotope effect was observed (C-AKIE = 0.9945 ± 0.0019). This fractionation behavior is clearly distinguishable from reported reductive dechlorination mechanisms. Based on these results we then assessed degradation and apportioned different types of technical CP mixtures used at two former sawmill sites. To our knowledge, this is the first study that makes use of two-element CSIA to study sources and transformation of CPs in the environment.

  • 16.
    Afvander, Åsa
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Development of a working method for the study of a distillation process: Distillation of a multicomponent system2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 17.
    Agharbi, Mariam
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hva ønsker den norske kunden seg av helsetjenester i apotek?: Kartlegging og utforming av blodtrykksmåling som en etterspurt helsetjeneste i norske apotek.2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 18.
    Aghester, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hyperspektral bildanalys av pulverblandningar innehållande mannitol och natriumsalicylat: Effekt av partikelstorlek och blandningstid2014Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 19.
    Aglar, Öznur
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Design and synthesis of inhibitors of the ADP ribosylating toxin ExoS: Targeting the Type III Secretion System (T3SS) of Pseudomonas aeruginosa.2016Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 20. Agrawal, Ganesh Kumar
    et al.
    Job, Dominique
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Barkla, Bronwyn J.
    Chen, Sixue
    Deswal, Renu
    Luethje, Sabine
    Amalraj, Ramesh Sundar
    Tanou, Georgia
    Ndimba, Bongani Kaiser
    Cramer, Rainer
    Weckwerth, Wolfram
    Wienkoop, Stefanie
    Dunn, Michael J.
    Kim, Sun Tae
    Fukao, Yochiro
    Yonekura, Masami
    Zolla, Lello
    Rohila, Jai Singh
    Waditee-Sirisattha, Rungaroon
    Masi, Antonio
    Wang, Tai
    Sarkar, Abhijit
    Agrawal, Raj
    Renaut, Jenny
    Rakwal, Randeep
    INPPO Actions and Recognition as a Driving Force for Progress in Plant Proteomics: Change of Guard, INPPO Update, and Upcoming Activities2013In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 13, no 21, 3093-3100 p.Article in journal (Other academic)
    Abstract [en]

    The International Plant Proteomics Organization (INPPO) is a non-profit organization whose members are scientists involved or interested in plant proteomics. Since the publication of the first INPPO highlights in 2012, continued progress on many of the organization's mandates/goals has been achieved. Two major events are emphasized in this second INPPO highlights. First, the change of guard at the top, passing of the baton from Dominique Job, INPPO founding President to Ganesh Kumar Agrawal as the incoming President. Ganesh K. Agrawal, along with Dominique Job and Randeep Rakwal initiated the INPPO. Second, the most recent INPPO achievements and future targets, mainly the organization of first the INPPO World Congress in 2014, tentatively planned for Hamburg (Germany), are mentioned.

  • 21. Agrawal, Ganesh Kumar
    et al.
    Sarkar, Abhijit
    Agrawal, Raj
    Ndimba, Bongani Kaiser
    Tanou, Georgia
    Dunn, Michael J
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Cramer, Rainer
    Wienkoop, Stefanie
    Chen, Sixue
    Rafudeen, Mohammed Suhail
    Deswal, Renu
    Barkla, Bronwyn J
    Weckwerth, Wolfram
    Heazlewood, Joshua L
    Renaut, Jenny
    Job, Dominique
    Chakraborty, Niranjan
    Rakwal, Randeep
    Boosting the Globalization of Plant Proteomics through INPPO: Current Developments and Future Prospects2012In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 12, no 3, 359-368 p.Article in journal (Refereed)
    Abstract [en]

    The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO community, and also due to the wide encouragement and support from the communities (scientific and non-scientific).

  • 22.
    Aguilar, Ximena
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Folding and interaction studies of subunits in protein complexes2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis.

    Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements.

    The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%).

    The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and

    VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25.

    The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

  • 23.
    Aguilar, Ximena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Blomberg, Jeanette
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Olofsson, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Schleucher, Jurgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Björklund, Stefan
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Interaction Studies of the Human and Arabidopsis thaliana Med25-ACID Proteins with the Herpes Simplex Virus VP16-and Plant-Specific Dreb2a Transcription Factors2014In: PLoS ONE, ISSN 1932-6203, Vol. 9, no 5, e98575- p.Article in journal (Refereed)
    Abstract [en]

    Mediator is an evolutionary conserved multi-protein complex present in all eukaryotes. It functions as a transcriptional coregulator by conveying signals from activators and repressors to the RNA polymerase II transcription machinery. The Arabidopsis thaliana Med25 (aMed25) ACtivation Interaction Domain (ACID) interacts with the Dreb2a activator which is involved in plant stress response pathways, while Human Med25-ACID (hMed25) interacts with the herpes simplex virus VP16 activator. Despite low sequence similarity, hMed25-ACID also interacts with the plant-specific Dreb2a transcriptional activator protein. We have used GST pull-down-, surface plasmon resonance-, isothermal titration calorimetry and NMR chemical shift experiments to characterize interactions between Dreb2a and VP16, with the hMed25 and aMed25-ACIDs. We found that VP16 interacts with aMed25-ACID with similar affinity as with hMed25-ACID and that the binding surface on aMed25-ACID overlaps with the binding site for Dreb2a. We also show that the Dreb2a interaction region in hMed25-ACID overlaps with the earlier reported VP16 binding site. In addition, we show that hMed25-ACID/Dreb2a and aMed25-ACID/Dreb2a display similar binding affinities but different binding energetics. Our results therefore indicate that interaction between transcriptional regulators and their target proteins in Mediator are less dependent on the primary sequences in the interaction domains but that these domains fold into similar structures upon interaction.

  • 24.
    Aguilar, Ximena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Weise, Christoph
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wolf-Watz, Magnus
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wittung-Stafshede, Pernilla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Macromolecular crowding extended to a heptameric system: the co-chaperonin protein 102011In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 50, no 14, 3034-3044 p.Article in journal (Refereed)
    Abstract [en]

    Experiments on monomeric proteins have shown that macromolecular crowding can stabilize toward heat perturbation and also modulate native-state structure. To assess the effects of macromolecular crowding on unfolding of an oligomeric protein, we here tested the effects of the synthetic crowding agent Ficoll 70 on human cpn10 (GroES in E. coli), a heptameric protein consisting of seven identical β-barrel subunits assembling into a ring. Using far-UV circular dichroism (CD), tyrosine fluorescence, nuclear magnetic resonance (NMR), and cross-linking experiments, we investigated thermal and chemical stability, as well as the heptamer-monomer dissociation constant, without and with crowding agent. We find that crowding shifts the heptamer-monomer equilibrium constant in the direction of the heptamer. The cpn10 heptamer is both thermally and thermodynamically stabilized in 300 mg/mL Ficoll 70 as compared to regular buffer conditions. Kinetic unfolding experiments show that the increased stability in crowded conditions, in part, is explained by slower unfolding rates. A thermodynamic cycle reveals that in presence of 300 mg/mL Ficoll the thermodynamic stability of each cpn10 monomer increases by over 30%, whereas the interfaces are stabilized by less than 10%. We also introduce a new approach to analyze the spectroscopic data that makes use of multiple wavelengths: this provides robust error estimates of thermodynamic parameters.

  • 25. Ahl, Ing-Marie
    et al.
    Lindberg, Mikael J
    Umeå University, Faculty of Science and Technology, Chemistry.
    Tibell, Lena A E
    Coexpression of yeast copper chaperone (yCCS) and CuZn-superoxide dismutases in Escherichia coli yields protein with high copper contents2004In: Protein Expression and Purification, ISSN 1046-5928, Vol. 37, no 2, 311-9 p.Article in journal (Refereed)
    Abstract [en]

    To fully understand the function of the Cu- and Zn-containing superoxide dismutases in normal and disordered cells, it is essential to study protein variants with full metal contents. We describe the use of an Escherichia coli-based expression system for the overproduction of human intracellular wild type CuZn-superoxide dismutase (SOD), the CuZnSOD variant F50E/G51E (monomeric), two amyotrophic lateral sclerosis-related mutant CuZnSOD variants (D90A and G93A), and PseudoEC-SOD, all with high Cu contents. This system is based on coexpression of the SOD variants with the yeast copper chaperone yCCS during growth in a medium supplemented with Cu(2+) and Zn(2+). The recombinant SOD enzymes were all found in the cytosol and represented 30-50% of the total bacterial protein. The enzymes were purified to homogeneity and active enzymes were obtained in high yield. The resulting proteins were characterized through immunochemical reactivity and specific activity analyses, in conjunction with mass-, photo-, and atomic absorption-spectroscopy.

  • 26.
    Ahlinder, Jon
    et al.
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Mathisen, Peter
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Nilsson, Elin
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Forsman, Mats
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Andersson, Agneta
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Thelaus, Johanna
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Oligotyping reveals divergent responses of predation resistant bacteria to aquatic productivity and plankton compositionManuscript (preprint) (Other academic)
    Abstract [en]

    Predation-resistance has been suggested to be a key for persistence of pathogenic bacteria in aquatic environments. Little is known about driving factors for different types of protozoa resistant bacteria (PRB). We studied if presence of PRB is linked to specific plankton taxa, the aquatic nutrient state, or predation pressure on bacteria. Nineteen freshwater systems were sampled and analyzed for PRB, plankton composition and physicochemical variables. Three PRB genera were identified; Pseudomonas, Mycobacterium and Rickettsia. Use of minimum entropy decomposition algorithm and phylogenetic analysis showed that different nodes (representing OTUs of high taxonomic resolution) matched to environmental isolates of the three genera. Links between the PRB genera and specific plankton taxa were found, but showed different relationships depending on if 18S rRNA OTU or microscopy data were used in the analysis. Mycobacterium spp. was negatively correlated to aquatic nutrient state, while Pseudomonas showed the opposite pattern. Rickettsia spp. was positively related to predation pressure on bacteria. Both Mycobacterium and Rickettsia were more abundant in systems with high eukaryotic diversity, while Pseudomonas occurred abundantly in waters with low prokaryotic diversity. The different drivers may be explained by varying ecological strategies, where Mycobacterium and Rickettsia are slow growing and have an intracellular life style, while Pseudomonas is fast growing and opportunistic. Here we give an insight to the possibilities of newly advanced methods such as sequencing and oligotyping to link potential pathogens with biomarkers. This as a tool to assist predictions of the occurrence and persistence of environmental pathogens.

  • 27.
    Ahlkvist, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Formic and Levulinic Acid from Cellulose via Heterogeneous Catalysis2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The chemical industry of today is under increased pressure to develop novel green materials, bio-fuels as well as sustainable chemicals for the chemical industry. Indeed, the endeavour is to move towards more eco-friendly cost efficient production processes and technologies and chemical transformation of renewables has a central role considering the future sustainable supply of chemicals and energy needed for societies. In the Nordic countries, the importance of pulping and paper industry has been particularly pronounced and the declining European demand on these products as a result of our digitalizing world has forced the industry to look at alternative sources of revenue and profitability. In this thesis, the production of levulinic and formic acid from biomass and macromolecules has been studied. Further, the optimum reaction conditions as well as the influence of the catalyst and biomass type were also discussed.

    Nordic sulphite and sulphate (Kraft) cellulose originating from two Nordic pulp mills were used as raw materials in the catalytic synthesis of green platform chemicals, levulinic and formic acids, respectively. The catalyst of choice used in this study was a macro-porous, cationic ion-exchange resin, Amberlyst 70, for which the optimal reaction conditions leading to best yields were determined. Cellulose from Nordic pulp mills were used as raw materials in the catalytic one-pot synthesis of ‘green’ levulinic and formic acid. The kinetic experiments were performed in a temperature range of 150–200 °C and an initial substrate concentration regime ranging from 0.7 to 6.0 wt %. It was concluded that the most important parameters in the one-pot hydrolysis of biomass were the reaction temperature, initial reactant concentration, acid type as well as the raw material applied. The reaction route includes dehydration of glucose to hydroxymethylfurfural as well as its further rehydration to formic and levulinic acids. The theoretical maximum yield can hardly be obtained due to formation of humins. For this system, maximum yields of 59 mol % and 68 mol % were obtained for formic and levulinic acid, respectively. The maximum yields were separately obtained in a straight-forward conversion system only containing cellulose, water and the heterogeneous catalyst. These yields were achieved at a reaction temperature of 180 °C and an initial cellulose intake of 0.7 wt % and belong to the upper range for solid catalysts so far presented in the literature.

    The reaction network of the various chemical species involved was investigated and a simple mechanistic approach involving first order reaction kinetics was developed. The concept introduces a one-pot procedure providing a feasible route to green platform chemicals obtained via conversion of coniferous soft wood pulp to levulinic and formic acids, respectively. The model was able to describe the behaviour of the system in a satisfactory manner (degree of explanation 97.8 %). Since the solid catalyst proved to exhibit good mechanical strength under the experimental conditions applied here and a one-pot procedure providing a route to green platform chemicals was developed. A simplified reaction network of the various chemical species involved was investigated and a mechanistic approach involving first order reaction kinetics was developed.

  • 28.
    Ahlkvist, Johan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ajaikumar, Samikannu
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, William
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    One-pot catalytic conversion of Nordic pulp media into green platform chemicals2013In: Applied Catalysis A: General, ISSN 0926-860X, E-ISSN 1873-3875, Vol. 454, 21-29 p.Article in journal (Refereed)
    Abstract [en]

    In this paper, both sulphite and sulphate (Kraft) cellulose from Nordic pulp mills were used as raw materials in the catalytic one-pot synthesis of green platform chemicals, levulinic and formic acids, respectively. The catalyst of choice was a macro-porous, cationic ion-exchange resin, Amberlyst 70. The optimal reaction conditions were determined and the influence of various gas atmospheres was investigated. The maximum yields of 53% formic acid and 57% of levulinic acid were separately obtained in a straight-forward conversion system only containing cellulose, water and the heterogeneous catalyst. The concept introduces a one-pot procedure providing a feasible route to green platform chemicals obtained via conversion of coniferous soft wood pulp to levulinic and formic acids, respectively.

  • 29.
    Ahlkvist, Johan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mäki-Arvela, Päivi
    Åbo Akademi.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Åbo Akademi University, Process Chemistry Centre, Åbo Akademi University, Industrial Chemistry & Reaction Engineering., Finland.
    Macro-molecules as a source of levulinic acid2014In: International Review of Chemical Engineering, ISSN 2035-1755, Vol. 16, no 1, 44-58 p.Article in journal (Refereed)
    Abstract [en]

    The production of levulinic acid from biomass and macromolecules has been reviewed. It was concluded that the most important parameters in the one-pot hydrolysis of biomass, also including dehydration of glucose to hydroxymethylfurfural as well as its further rehydration to formic and levulinic acids, respectively, are the reaction temperature, initial reactant concentration, acid type as well as the raw material applied. The theoretical maximum yield can hardly be obtained due to formation of humins. Further, the optimum reaction conditions as well as the influence of the catalyst and biomass type are also discussed.

  • 30.
    Ahlkvist, Johan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Samikannu, Ajaikumar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, William
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wärnå, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo, Finland.
    Salmi, Tapio
    Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo, Finland.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo, Finland.
    Reaction Network upon One-pot Catalytic Conversion of Pulp2013In: / [ed] Sauro Pierucci, Jiří J. Klemeš, AIDIC - associazione italiana di ingegneria chimica, 2013, Vol. 32, 649-654 p.Conference paper (Refereed)
    Abstract [en]

    Nordic sulphite and sulphate (Kraft) cellulose originating from Nordic pulp mills were used as raw materials in the catalytic synthesis of green platform chemicals, levulinic and formic acids, respectively. The catalyst of choice used in this study was a macro-porous, cationic ion-exchange resin Amberlyst 70 for which the optimal reaction conditions leading to best yields were determined. For this system, maximum yields of 53 mol-% and 57 mol-% were obtained for formic and levulinic acid, respectively. The reaction network of the various chemical species involved was investigated and a simple mechanistic approach involving first order reaction kinetics was developed. The prototype model was able to describe the behaviour of the system in a satisfactory manner.

  • 31.
    Ahlkvist, Johan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Samikannu, Ajaikumar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Catalytic conversion of lignocellulosic materials2010Conference paper (Other academic)
  • 32.
    Ahlkvist, Johan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wärnå, Johan
    Åbo Akademi.
    Salmi, Tapio
    Åbo Akademi.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Experimental and Kinetic Modelling Studies upon Conversion of Nordic Pulp into Levulinic AcidManuscript (preprint) (Other academic)
    Abstract [en]

    In this paper, sulphite cellulose from a Swedish pulp mill was applied as the raw material upon catalytic, one-pot synthesis of green platform chemicals – levulinic and formic acids. Cationic ion-exchange resin, Amberlyst 70, was the catalyst of choice and the optimal reaction conditions leading to best yields were determined. The kinetic experiments were performed in a temperature range of 180–200 °C and an initial substrate concentration regime ranging from 0.7 to 6.0 wt %. For this system, maximum theoretical yields of around 59 mol % and 68 mol % were obtained for formic and levulinic acid, respectively. These yields were achieved at a reaction temperature of 180 °C and an initial cellulose intake of 0.7 wt %. A simplified reaction network of the various chemical species involved was investigated and a mechanistic approach involving first order reaction kinetics was developed. The model was able to describe the behaviour of the system in a satisfactory manner (degree of explanation 97.8 %). Since the solid catalyst proved to exhibit good mechanical strength under the experimental conditions applied here, the concept introduces a one-pot procedure providing a route to green platform chemicals from coniferous soft wood pulp to produce levulinic and formic acids, respectively.

  • 33.
    Ahlkvist, Johan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wärnå, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University,Turku, Finland.
    Salmi, Tapio
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University,Turku, Finland.
    Heterogeneously catalyzed conversion of nordic pulp to levulinic and formic acids2016In: Reaction Kinetics, Mechanisms and Catalysis, ISSN 1878-5190, E-ISSN 1878-5204, Vol. 119, no 2, 415-427 p.Article in journal (Refereed)
    Abstract [en]

    Herein, one-pot conversion of cellulose to platform chemicals, formic and levulinic acids was demonstrated. The catalyst selected was an affordable, acidic ion-exchange resin, Amberlyst 70, whereas the cellulose used was sulfite cellulose delivered by a Swedish pulp mill. Furthermore, in an attempt to better understand the complex hydrolysis network of the polysaccharide, kinetic experiments were carried out to pinpoint the optimal reaction conditions with an initial substrate concentration of 0.7–6.0 wt% and a temperature range of 180–200 °C. Higher temperatures could not be used due to the limitations in the thermal stability of the catalyst. Overall, maximum theoretical yields of 59 and 68 mol% were obtained for formic and levulinic acid, respectively. The parameters allowing for the best performance were reaction temperature of 180 °C and initial cellulose concentration of 0.7 wt%. After studying the behavior of the system, a simplified reaction network in line with a mechanistic approach was developed and found to follow first order reaction kinetics. A satisfactory fit of the model to the experimental data was achieved (97.8 % degree of explanation). The catalyst chosen exhibited good mechanical strength under the experimental conditions and thus, a route providing green platform chemicals from soft wood pulp from coniferous trees (mixture of Scots Pine and Norway Spruce) was demonstrated.

  • 34.
    Ahmad, Bayar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Apotekverksamhetens regler i Holland: – skillnader och likheter mellan Sverige och Holland2014Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 35.
    Ahmad, Bayar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Apotekverksamhetens regler i Holland – skillnader och likheter mellan Sverige och Holland2014Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 36.
    Ahmad, Raghad
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sambandet mellan neuroleptika och det metabola syndromet2014Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 37.
    Ahmed, Zina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Poly-ADP ribos polymeras (PARP) inhibitorers effekt på bröstcancer: Poly-ADP ribos polymeras (PARP) inhibitorers effekt på bröstcancer2015Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
  • 38. Aid, T.
    et al.
    Hyvarinen, S.
    Vaher, M.
    Koel, M.
    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, Åbo-Turku, Finland.
    Saccharification of lignocellulosic biomasses via ionic liquid pretreatment2016In: Industrial crops and products (Print), ISSN 0926-6690, E-ISSN 1872-633X, Vol. 92, 336-341 p.Article in journal (Refereed)
    Abstract [en]

    The current work focuses on the pretreatment efficiency of ILs combined with heat for woody biomass consisting of spruce, birch and pine as well as winter wheat straw. The latter was investigated as a comparison and with the aim to enhance its digestibility during enzymatic hydrolysis whereby the influence of IL-treatment to cellulose resistance for hydrolysis was investigated. Considering the wood species, the most common and industrially important wood species in Northern Europe were chosen in the present work and the goal was to obtain fermentable sugars and their degradation product, i.e. 5-hydroxymethylfurfural (5-HMF), which is known valuable platform chemical. Further, the differences in the yields of IL-obtainable carbohydrates between these species were studied. The highest sugar yields were obtained to glucose in the case of spruce and arabinose in the case of pine sapwood, 12.07 and 7.72 mmol/L, respectively. The highest 5-HMF yield was obtained for spruce heartwood (9.18 mmol/L) with longer treatment time, such as 100h. However, regarding woody biomass, the present work was focused more on the study and analysis of the IL-containing liquid part, wood hydrolysate, after IL-treatment aiming to answer the analysis challenges related to this fraction.

  • 39.
    Aigner, Harald
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Characterization of FtsH proteases in the annual plant Arabidopsis thaliana2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background FtsH is an ATP-dependent membrane-bound metalloprotease. A. thaliana contains 12 FtsH proteases localized in membranes of chloroplasts and mitochondria where they form homo- or hetero-hexameric complexes. FtsH11 – the main subject of this thesis – is located in the chloroplast envelope.

     

    Methods

    • Field studies with A. thaliana to determine Darwinian fitness. A growth under outdoor conditions often allows discovering of phenotypes that are unascertainable in the controlled environment of growth chambers.
    • Proteomic methods to discover fragments of substrate proteins (limited proteolysis) and changes in the proteome of FtsH protease deficient mutants.

     

    Results ftsh11 has increased amount of: RuBisCO activase, several Calvin cycle enzymes, two enzymes involved in starch synthesis and some chaperons. Some of those enzymes have been identified as possible substrates of FtsH11. Under long photoperiods ftsh11 develops a chlorotic phenotype accompanied by decreasing NADP+/NADPH ratio and increase of ROS damaged proteins. 

  • 40.
    Aigner, Harald
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Comparison of hypothetical 3D-structures of Arabidopsis thaliana FtsH Proteases with the aim to predict FtsH complex formationManuscript (preprint) (Other academic)
    Abstract [en]

    In Arabidopsis thaliana 12 metallo proteases of the FtsH family are located in the organellar membranes of chloroplasts and mitochondria. While it is known for the Arabidopsis FtsH proteases FtsH1, 2, 5 and 8 to form a hetero–oligomeric, hexameric complex in the chloroplast thylakoid membrane and for FtsH3 and 10 in the inner membrane of mitochondria, no data are available for the remaining (low abundant) FtsH proteases . We compared the sequence identity of amino acids predicted to be relevant in complex formation of FtsH proteases in order to predict additional hetero-oligomeric FtsH complexes. Focus was set on FtsH11 and FtsH4, two subunits that might form a complex in mitochondria. 

  • 41.
    Aigner, Harald
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Searching for substrates of the metallo protease FtsH11 of Arabidopsis thaliana using N-terminal proteomics2012Manuscript (preprint) (Other academic)
    Abstract [en]

    FtsH11 is a membrane-bound metalloprotease localized in mitochondria and in the chloroplast envelope of Arabidopsis thaliana. An ftsh11 knock-out mutant has been shown to develop a chlorotic phenotype in prolonged photoperiods. The proteome of the ftsh11 chloroplast revealed increased abundance of several Calvin cycle enzymes, chaperones and some other proteins, however, none of those proteins could be verified to be an FtsH11 substrate (Harald Aigner, Raik Wagner, Lars L.E. Sjögren, Holger Eubel, A. Harvey Millar, Adrian K. Clarke, Christiane Funk, 2012, manuscript submitted). Here, we have used positional proteomics to identify peptides that report FtsH11 processing events. In this work we were able to identify seven chloroplast-localized proteins that are processed in wild type, but not in ftsh11.  

  • 42.
    Aigner, Harald
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wagner, Raik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjögren, Lars
    Eubel, Holger
    Millar, Harvey
    Clarke, Adrian
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    FtsH11 protease is required for Arabidopsis thaliana to adapt to gtowth in continuous lightManuscript (preprint) (Other academic)
    Abstract [en]

    Continuous light can increase greenhouse food production; however, some of the most important greenhouse horticulture crops are not able to adapt to long photoperiods. Here, we provide evidence that knock-out of the FtsH11 protease causes molecular differences that prevent Arabidopsis thaliana to adapt to prolonged photoperiods. Previously this protease had been shown to be critical for thermotolerance (Chen et al. 2006). We demonstrate that knock-out mutants deficient of FtsH11 develop chlorosis when shifted to continuous light. When grown under normal growth conditions and short days, ftsh11 displayed changes in protein amount of chloroplast proteins involved in the photosynthetic light reaction and the Calvin cycle as well as of the FtsH12 protease. The proteomic changes are accompanied by reduced non-photochemical quenching and faster state transition. A shift to continuous light further enhanced these effects and induced morphological changes of the chloroplast and chlorosis. No changes in the mitochondrial proteome were observed between wild type and ftsh11.

  • 43.
    Aisenbrey, Christopher
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Bechinger, Burkhard
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Chemistry.
    Macromolecular Crowding at Membrane Interfaces: Adsorption and Alignment of Membrane Peptides2008In: Journal of Molecular Biology, ISSN 1089-8638, Vol. 375, 376-85 p.Article in journal (Refereed)
    Abstract [en]

    Association of proteins to cellular membranes is involved in various biological processes. Various theoretical models have been developed to describe this adsorption mechanism, commonly implying the concept of an ideal solution. However, due to the two-dimensional character of membrane surfaces intermolecular interactions between the adsorbed molecules become important. Therefore previously adsorbed molecules can influence the adsorption behavior of additional protein molecules and their membrane-associated structure. Using the model peptide LAH4, which upon membrane-adsorption can adopt a transmembrane as well as an in-planar configuration, we carried out a systematic study of the correlation between the peptide concentration in the membrane and the topology of this membrane-associated polypeptide. We could describe the observed binding behavior by establishing a concept, which includes intermolecular interactions in terms of a scaled particle theory.

    High surface concentration of the peptide shifts the molecules from an in-planar into a transmembrane conformation, a process driven by the reduction of occupied surface area per molecule. In a cellular context, the crowding-dependent alignment might provide a molecular switch for a cell to sense and control its membrane occupancy. Furthermore, crowding might have pronounced effects on biological events, such as the cooperative behavior of antimicrobial peptides and the membrane triggered aggregation of amyloidogenic peptides.

  • 44.
    Aisenbrey, Christopher
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Bertani, Philippe
    Henklein, Peter
    Bechinger, Burkhard
    Structure, dynamics and topology of membrane polypeptides by oriented 2H solid-state NMR spectroscopy2007In: European Biophysics Journal, ISSN 0175-7571 (Print) 1432-1017 (Online), Vol. 36, no 4-5, 451-60 p.Article in journal (Refereed)
    Abstract [en]

    Knowledge of the structure, dynamics and interactions of polypeptides when associated with phospholipid bilayers is key to understanding the functional mechanisms of channels, antibiotics, signal- or translocation peptides. Solid-state NMR spectroscopy on samples uniaxially aligned relative to the magnetic field direction offers means to determine the alignment of polypeptide bonds and domains relative to the bilayer normal. Using this approach the 15N chemical shift of amide bonds provides a direct indicator of the approximate helical tilt, whereas the 2H solid-state NMR spectra acquired from peptides labelled with 3,3,3-2H3-alanines contain valuable complimentary information for a more accurate analysis of tilt and rotation pitch angles. The deuterium NMR line shapes are highly sensitive to small variations in the alignment of the Cα–Cβ bond relative to the magnetic field direction and, therefore, also the orientational distribution of helices relative to the membrane normal. When the oriented membrane samples are investigated with their normal perpendicular to the magnetic field direction, the rate of rotational diffusion can be determined in a semi-quantitative manner and thereby the aggregation state of the peptides can be analysed. Here the deuterium NMR approach is first introduced showing results from model amphipathic helices. Thereafter investigations of the viral channel peptides Vpu1–27 and Influenza A M222–46 are shown. Whereas the 15N chemical shift data confirm the transmembrane helix alignments of these hydrophobic sequences, the deuterium spectra indicate considerable mosaic spread in the helix orientations. At least two peptide populations with differing rotational correlation times are apparent in the deuterium spectra of the viral channels suggesting an equilibrium between monomeric peptides and oligomeric channel configurations under conditions where solid-state NMR structural studies of these peptides have previously been performed.

  • 45.
    Aisenbrey, Christopher
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Borowik, Tomasz
    Byström, Roberth
    Umeå University, Faculty of Science and Technology, Chemistry.
    Bokvist, Marcus
    Umeå University, Faculty of Science and Technology, Chemistry.
    Lindström, Fredrick
    Umeå University, Faculty of Science and Technology, Chemistry.
    Misiak, Hanna
    Sani, Marc-Antoine
    Umeå University, Faculty of Science and Technology, Chemistry.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Chemistry.
    How is protein aggregation in amyloidogenic diseases modulated by biological membranes?2008In: European Biophysics Journal, ISSN 0175-7571, European Biophysics Journal, ISSN 1432-1017 (Online), Vol. 37, no 3, 247-55 p.Article in journal (Refereed)
    Abstract [en]

    The fate of proteins with amyloidogenic properties depends critically on their immediate biochemical environment. However, the role of biological interfaces such as membrane surfaces, as promoters of pathological aggregation of amyloidogenic proteins, is rarely studied and only established for the amyloid-β protein (Aβ) involved in Alzheimer’s disease, and α-synuclein in Parkinsonism. The occurrence of binding and misfolding of these proteins on membrane surfaces, is poorly understood, not at least due to the two-dimensional character of this event. Clearly, the nature of the folding pathway for Aβ protein adsorbed upon two-dimensional aggregation templates, must be fundamentally different from the three-dimensional situation in solution. Here, we summarize the current research and focus on the function of membrane interfaces as aggregation templates for amyloidogenic proteins (and even prionic ones). One major aspect will be the relationship between membrane properties and protein association and the consequences for amyloidogenic products. The other focus will be on a general understanding of protein folding pathways on two-dimensional templates on a molecular level. Finally, we will demonstrate the potential importance of membrane-mediated aggregation for non-amphiphatic soluble amyloidogenic proteins, by using the SOD1 protein involved in the amyotrophic lateral sclerosis syndrome.

  • 46.
    Aisenbrey, Christopher
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Byström, Roberth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Oliveberg, Mikael
    Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    SOD1 associates to membranes in its folded apo-stateManuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

    Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease accompanied by misfolding and intracellular deposition of superoxide dismutase 1 (SOD1). Although the molecular details behind this misfolding process are yet poorly understood, increasing evidence suggest that SOD1 is most susceptible to misfolding in its metal-free and relatively unstable apo-state. Here, we addressed the question, if misfolding and aggregation of SOD1 involves erroneous interactions with membranes as has been implicated for the Aβ peptide in Alzheimers disease. To examine this possibility we subjected various apo SOD1 variants to the presence of different membrane systems. The results reveal that wild type apoSOD1 but to less extent destabilized ALS mutations interact with charged vesicles under physiologically relevant conditions, thereby acquiring pronounced helical structural features. As the data further show, the protein binds to the membranes by an electrostatically driven mechanism, which requires a folded apo-state conformation and a negative membrane surface potential. Unfolded SOD1 molecules show no appreciable affinity to the membrane surfaces yielding a correlation between increased stability, i. e. occupancy of folded molecules and extend of membrane association. Since this trend opposes the correlation between decreased SOD1 stability and progression of neural damage, the results suggest that membrane association is not part of the ALS mechanism. An explanation could be that the observed membrane association of apo SOD1 is reversible and does not ‘bleed out’ in irreversible aggregation as observed for other precursors of protein-misfolding diseases.

  • 47.
    Aisenbrey, Christopher
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Cusan, Monica
    Lambotte, Stephan
    Jasperse, Pieter
    Georgescu, Julia
    Harzer, Ulrike
    Bechinger, Burkhard
    Specific Isotope Labeling of Colicin E1 and B Channel Domains For Membrane Topological Analysis by Oriented Solid-State NMR Spectroscopy2008In: ChemBioChem, Vol. 9, no 6, 944-51 p.Article in journal (Refereed)
    Abstract [en]

    An approach is presented to selectively label the methionines of the colicin E1 and B channel domains, each about 200 residues in size, and use them for oriented solid-state NMR investigations. By combining site-directed mutagenesis, bacterial overexpression in a methionine auxotroph E. coli strain and biochemical purification, quantitative amounts of the proteins for NMR structural investigations were obtained. The proteins were selectively labeled with 15N at only one, or at a few, selected sites. Multidimensional heteronuclear correlation high-resolution NMR spectroscopy and mass spectrometry were used to monitor the quality of isotopic labeling. Thereafter the proteins were reconstituted into oriented phospholipid bilayers and investigated by proton-decoupled 15N solid-state NMR spectroscopy. The colicin E1 thermolytic fragment that carries a single 15N methionine within its hydrophobic helix 9 region exhibited 15N resonances that are characteristic of helices that are oriented predominantly parallel to the membrane surface at low temperature, and a variety of alignments and conformations at room temperature. This suggests that the protein can adopt both umbrella and pen-knife conformations.

  • 48.
    Aisenbrey, Christopher
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Sizun, Christina
    Koch, Joachim
    Herget, Meike
    Abele, Rupert
    Bechinger, Burkhard
    Tampé, Robert
    Structure and dynamics of membrane-associated ICP47, a viral inhibitor of the MHC I antigen-processing machinery2006In: The Journal of Biological Chemistry, ISSN 0021-9258, Vol. 281, no 41, 30365-72 p.Article in journal (Refereed)
    Abstract [en]

    To evade the host's immune response, herpes simplex virus employs the immediate early gene product ICP47 (IE12) to suppress antigen presentation to cytotoxic T-lymphocytes by inhibition of the ATP-binding cassette transporter associated with antigen processing (TAP). ICP47 is a membrane-associated protein adopting an alpha-helical conformation. Its active domain was mapped to residues 3-34 and shown to encode all functional properties of the full-length protein. The active domain of ICP47 was reconstituted into oriented phospholipid bilayers and studied by proton-decoupled 15N and 2H solid-state NMR spectroscopy. In phospholipid bilayers, the protein adopts a helix-loop-helix structure, where the average tilt angle of the helices relative to the membrane surface is approximately 15 degrees (+/- 7 degrees ). The alignment of both structured domains exhibits a mosaic spread of approximately 10 degrees . A flexible dynamic loop encompassing residues 17 and 18 separates the two helices. Refinement of the experimental data indicates that helix 1 inserts more deeply into the membrane. These novel insights into the structure of ICP47 represent an important step toward a molecular understanding of the immune evasion mechanism of herpes simplex virus and are instrumental for the design of new therapeutics.

  • 49.
    Aisenbrey, Christopher
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Sudheendra, U. S.
    Ridley, Helen
    Bertani, Philippe
    Marquette, Arnaud
    Nedelkina, Svetlana
    Lakey, Jeremy H.
    Bechinger, Burkhard
    Helix orientations in membrane-associated Bcl-XL determined by 15N-solid-state NMR spectroscopy2007In: European Biophysics Journal, ISSN 0175-7571 (Print) 1432-1017 (Online), Vol. 37, no 1, 71-80 p.Article in journal (Refereed)
    Abstract [en]

    Controlled cell death is fundamental to tissue hemostasis and apoptosis malfunctions can lead to a wide range of diseases. Bcl-xL is an anti-apoptotic protein the function of which is linked to its reversible interaction with mitochondrial outer membranes. Its interfacial and intermittent bilayer association makes prediction of its bound structure difficult without using methods able to extract data from dynamic systems. Here we investigate Bcl-xL associated with oriented lipid bilayers at physiological pH using solid-state NMR spectroscopy. The data are consistent with a C-terminal transmembrane anchoring sequence and an average alignment of the remaining helices, i.e. including helices 5 and 6, approximately parallel to the membrane surface. Data from several biophysical approaches confirm that after removal of the C-terminus from Bcl-xL its membrane interactions are weak. In the presence of membranes Bcl-xL can still interact with a Bak BH3 domain peptide suggesting a model where the hydrophobic C-terminus of the protein unfolds and inserts into the membrane. During this conformational change the Bcl-xL hydrophobic binding pocket becomes accessible for protein–protein interactions whilst the structure of the N-terminal region remains intact.

  • 50.
    Ajaikumar, Samikannu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ahlkvist, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, William
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Boström, Dan
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics, Energy Technology and Thermal Process Chemistry.
    Kordas, K
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Highly active and selective bimetallic catalysts supported on transition metal oxides for the oxidation of α-pinene using molecular oxygen2010Conference paper (Other academic)
1234567 1 - 50 of 3829
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