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  • 1.
    Altincekic, Nadide
    et al.
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Jores, Nathalie
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Löhr, Frank
    Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany; Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Frankfurt, Germany.
    Richter, Christian
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Ehrhardt, Claus
    Department of Biochemistry, University of Zurich, Zurich, Switzerland.
    Blommers, Marcel J. J.
    SavernaTherapeutics, Biel-Benken, Switzerland.
    Berg, Hannes
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Öztürk, Sare
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany.
    Gande, Santosh L.
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Linhard, Verena
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Orts, Julien
    Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, Vienna, Austria.
    Abi Saad, Marie Jose
    Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, Vienna, Austria.
    Bütikofer, Matthias
    Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zürich, Switzerland.
    Kaderli, Janina
    Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zürich, Switzerland.
    Karlsson, B. Göran
    Swedish NMR Centre, Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden; SciLifeLab, University of Gothenburg, Göteborg, Sweden.
    Brath, Ulrika
    Swedish NMR Centre, Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sauer, Uwe H.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Perrakis, Anastassis
    Oncode Institute and Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, Netherlands.
    Langer, Julian
    Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
    Banci, Lucia
    Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, Sesto Fiorentino, Italy.
    Cantini, Francesca
    Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, Sesto Fiorentino, Italy.
    Fragai, Marco
    Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, Sesto Fiorentino, Italy.
    Grifagni, Deborah
    Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy.
    Barthel, Tatjana
    Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, Berlin, Germany.
    Wollenhaupt, Jan
    Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, Berlin, Germany.
    Weiss, Manfred S.
    Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, Berlin, Germany.
    Robertson, Angus
    NIH, LCP NIDDK, MD, Bethesda, United States.
    Bax, Adriaan
    NIH, LCP NIDDK, MD, Bethesda, United States.
    Sreeramulu, Sridhar
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Schwalbe, Harald
    Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt, Germany; Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt, Germany.
    Targeting the main protease (Mpro, nsp5) by growth of fragment scaffolds exploiting structure-based methodologies2023In: ACS Chemical Biology, ISSN 1554-8929, E-ISSN 1554-8937Article in journal (Refereed)
    Abstract [en]

    The main protease Mpro, nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with Mpro. These investigations resulted in the four-armed compound 35b that binds directly to Mpro. 35b could be cocrystallized with Mpro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.

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  • 2. Anugwom, Ikenna
    et al.
    Eta, Valerie
    Virtanen, Pasi
    Mäki-Arvela, Paivi
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Yibo, Ma
    Hummel, Micheal
    Sixta, Herbert
    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.
    Towards optimal selective fractionation for Nordic woody biomass using novel amine–organic superbase derived switchable ionic liquids (SILs)2014In: Biomass and Bioenergy, ISSN 0961-9534, E-ISSN 1873-2909, Vol. 70, p. 373-381Article in journal (Refereed)
    Abstract [en]

    Abstract Improved fractionation process conditions for wood dissolution with switchable ionic liquids (SILs) were determined. The short time, high temperature (STHT) system was introduced as a selective and efficient way to extract components from lignocellulosic material. A SIL based on monoethanol amine (MEA) and 1,8-diazabicyclo-[5.4.0]-undec-7-ene (DBU) formed via coupling with SO2, was applied as a solvent in a 1:3 weight ratio with water. In essence, selective dissolution of mainly lignin was achieved by means of the aqueous SIL at 160 °C (∼6.1 bar corresponding to the vapor pressure of water) in 2 h and in a pressure vessel, for both hard- and soft-wood. About 95 wt-% of wood lignin was extracted. The dissolved components in the spent SIL were recovered by the addition of an anti-solvent whereupon over 70% of the dissolved components were recovered; the recovered fraction contained 19 wt-% hemicellulose while the rest of the material was in essence lignin. The non-dissolved, fluffy material contained ∼70 wt-% cellulose and ∼20 wt-% hemicellulose – a consistency resembling that of Kraft pulp.

  • 3. Anugwom, Ikenna
    et al.
    Eta, Valerie
    Virtanen, Pasi
    Mäki-Arvela, Päivi
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hummel, Michael
    Sixta, Herbert
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Switchable ionic liquids as delignification solvents for lignocellulosic materials2014In: ChemSusChem, ISSN 1864-5631, E-ISSN 1864-564X, Vol. 7, no 4, p. 1170-1176Article in journal (Refereed)
    Abstract [en]

    The transformation of lignocellulosic materials into potentially valuable resources is compromised by their complicated structure. Consequently, new economical and feasible conversion/fractionation techniques that render value-added products are intensely investigated. Herein an unorthodox and feasible fractionation method of birch chips (B. pendula) using a switchable ionic liquid (SIL) derived from an alkanol amine (monoethanol amine, MEA) and an organic super base (1,8-diazabicyclo-[5.4.0]-undec-7-ene, DBU) with two different trigger acid gases (CO2 and SO2 ) is studied. After SIL treatment, the dissolved fractions were selectively separated by a step-wise method using an antisolvent to induce precipitation. The SIL was recycled after concentration and evaporation of anti-solvent. The composition of undissolved wood after MEA-SO2 -SIL treatment resulted in 80 wt % cellulose, 10 wt % hemicelluloses, and 3 wt % lignin, whereas MEA-CO2 -SIL treatment resulted in 66 wt % cellulose, 12 wt % hemicelluloses and 11 wt % lignin. Thus, the MEA-SO2 -SIL proved more efficient than the MEA-CO2 -SIL, and a better solvent for lignin removal. All fractions were analyzed by gas chromatography (GC), Fourier transform infrared spectroscopy (FT-IR), (13) C nuclear magnetic resonance spectroscopy (NMR) and Gel permeation chromatography (GPC).

  • 4. Anugwom, Ikenna
    et al.
    Lahtela, Ville
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kiljunen, Samantha
    Karki, Timo
    Kallioinen-Manttari, Mari
    Esterified Lignin from Construction and Demolition Waste (CDW) as a Versatile Additive for Polylactic-Acid (PLA) Composites-The Effect of Artificial Weathering on its Performance2022In: Global Challenges, E-ISSN 2056-6646, Vol. 6, no 8, article id 2100137Article in journal (Refereed)
    Abstract [en]

    Demand for sustainable packaging and building materials has increased the need for biobased additives. Biocomposites can often be exposed to different weather conditions and UV irradiation. Thus, additives to prevent the negative impact of weathering are generally added to composites. This study aims to evaluate using esterified lignin as an additive against weathering effects in polylactic-acid (PLA) composites. Lignin is extracted from construction and demolition waste (CDW) wood using a deep eutectic solvent then esterified and tested as an additive in the fabrication of biobased composites. For comparison, lignin from birch is used as a raw material for an additive. Esterification is confirmed by solid-state N MR analysis. Samples are exposed to artificial weathering for 700 hours and their impact strength and color change properties are measured. The results indicate that esterified lignin from CDW (CDW e-lignin) as an additive protects the biocomposite from the weathering impact. The sample containing the CDW e-lignin as an additive suffers only a 4.3% of reduction of impact strength, while the samples that contain commercial additives lose clearly more of their impact strength (from 23.1% to 61.1%). Based on the results CDW e-lignin is a good additive to prevent weathering. As a conclusion, the esterified lignin from CDW, is a versatile additive for composite production.

  • 5. Anugwom, Ikenna
    et al.
    Maki-Arvela, Paivi
    Virtanen, Pasi
    Willfor, Stefan
    Damlin, Pia
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Treating birch wood with a switchable 1,8-diazabicyclo-[5.4.0]-undec-7-ene-glycerol carbonate ionic liquid2012In: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 66, no 7, p. 809-815Article in journal (Refereed)
    Abstract [en]

    The suitability of a new switchable ionic liquid (SIL) has been investigated as a solvent for fractionation of lignocellulosic materials. SIL was prepared from inexpensive chemicals, e. g., glycerol, CO2, and 1,8-diazabicyclo-[5.4.0]-undec-7-ene (DBU). Fresh Nordic birch wood (B. pendula) was treated with the SIL for a time period of 1-5 days at 100 degrees C and under atmospheric pressure. Upon SIL treatment, at best, 57 % of the hemicelluloses were dissolved and 50 % of lignins were dissolved from the native birch. The slightly fibrillated SIL treated chips contained about 55 % cellulose. Up to 76 % of the recovered species removed from the spent SIL liquor was originating from hemicelluloses, mainly from xylan. The spent SILs were reused for fresh wood dissolution in four consecutive cycles and each time the wood dissolution efficiency was similar. SILs could offer affordable (easy-to-synthesize) solvent systems for partial elimination of hemicelluloses and lignin from wood. SILs can also be prepared in-situ and on-site.

  • 6.
    Anugwom, Ikenna
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo-Turku FI-20500, Finland.
    Rujana, L.
    Wärnå, J.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    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-Turku FI-20500, Finland.
    In quest for the optimal delignification of lignocellulosic biomass using hydrated, SO2 switched DBU MEASIL switchable ionic liquid2016In: Chemical Engineering Journal, ISSN 1385-8947, E-ISSN 1873-3212, Vol. 297, p. 256-264Article in journal (Refereed)
    Abstract [en]

    In this paper, various process parameters aiming at optimal short-time-high-temperature (STHT) process were studied upon fractionation of Nordic woody biomass into its primary constituents. Highly diluted, aqueous 'SO2-switched' switchable ionic liquid (SIL) based on an alkanol amine (monoethanol amine, MEA) and an organic superbase (1,8-diazabicyclo-[5.4.0]-undec-7-ene, DBU) was applied. The ultimate goal was to develop a more sustainable, environmentally friendly and cost efficient systems for efficient separation of the lignocellulosic fractions. One of the main products from the SIL fractionation is cellulose-rich pulp with very low lignin content, complemented with hemicelluloses. The NMR results reveal that substantial removal of lignin occurs even when relatively low amount of SIL was used. Further, a simple mathematical model describing the dissolution of the lignocellulose components (hemicellulose and lignin) and weight loss of wood as a function of time is described. Moreover, the most efficient process involved the use of SpinChem (R) rotating bed reactor while upon use of a flow through (loop) reactor, promising results were obtained at a treatment time of 4 h. Still, all the reactor systems studied gave rise to a rather low removal of hemicelluloses which mean that the solvent system is primary selective towards lignin dissolution.

  • 7. Berglund, Linn
    et al.
    Anugwom, Ikenna
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Turku, Finland.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Aitomäki, Yvonne
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Turku, Finland.
    Oksman, Kristiina
    Switchable ionic liquids enable efficient nanofibrillation of wood pulp2017In: Cellulose, ISSN 0969-0239, E-ISSN 1572-882X, Vol. 24, no 8, p. 3265-3279Article in journal (Refereed)
    Abstract [en]

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

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  • 8.
    Blomberg, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kreye, Paul
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sethson, Ingmar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brickmann, Kay
    AstraZeneca R&D Mölndal, Mölndal, Sweden.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Synthesis and conformational studies of a β-turn mimetic incorporated in Leu-enkephalin2004In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 69, no 10, p. 3500-3508Article in journal (Refereed)
    Abstract [en]

    A β-turn mimetic in which the four amino acids of a β-turn have been replaced by a 10-membered ring has been designed, synthesized, and subjected to conformational studies. In the mimetic, the intramolecular COi − HNi+3 hydrogen bond that is often found in β-turns has been replaced by an ethylene bridge. In addition, the amide bond between residues i and i + 1 was exchanged for a methylene ether isoster. Such a β-turn mimetic, based on the first four residues of Leu-enkephalin (Tyr-Gly-Gly-Phe-Leu), was prepared in 15 steps. The synthesis relied on a β-azido alcohol prepared in five steps from Cbz-Tyr(tBu)-OH as a key, i-position building block. tert-Butyl bromoacetate, glycine, and a Phe-Leu dipetide were then used as building blocks for positions i + 1, i + 2, and i + 3, respectively. Conformational studies based on 1H NMR data showed that the β-turn mimetic was flexible, but that it resembled a type-II β-turn at low temperature. This low energy conformer closely resembled the structure determined for crystalline Leu-enkephalin.

  • 9.
    Chambi, Diego
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Instituto de Investigacion y Desarrollo de Procesos Quimicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andres, P.O. Box 12958, La Paz, Bolivia; Viceministerio de Producción Industrial a Mediana y Gran Escala, Ministerio de Desarrollo Productivo y Economía Plural, P.O. Box 12958, La Paz, Bolivia.
    Lundqvist, Jenny
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Nygren, Erik
    Department of Agrifood and Bioscience, RISE Research Institutes of Sweden AB, P.O. Box 857, Borås, Sweden.
    Romero-Soto, Luis
    Instituto de Investigacion y Desarrollo de Procesos Quimicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andres, P.O. Box 12958, La Paz, Bolivia.
    Marin, Katherine
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Instituto de Investigacion y Desarrollo de Procesos Quimicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andres, P.O. Box 12958, La Paz, Bolivia.
    Gorzsás, András
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Carlborg, Markus
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Broström, Markus
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Sundman, Ola
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Carrasco, Cristhian
    Instituto de Investigacion y Desarrollo de Procesos Quimicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andres, P.O. Box 12958, La Paz, Bolivia.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Martín, Carlos
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.
    Production of Exopolysaccharides by Cultivation of Halotolerant Bacillus atrophaeus BU4 in Glucose-and Xylose-Based Synthetic Media and in Hydrolysates of Quinoa Stalks2022In: Fermentation, E-ISSN 2311-5637, Vol. 8, no 2, article id 79Article in journal (Refereed)
    Abstract [en]

    A halotolerant, exopolysaccharide-producing bacterium isolated from the Salar de Uyuni salt flat in Bolivia was identified as Bacillus atrophaeus using next-generation sequencing. Comparisons indicate that the genome most likely (p-value: 0.0024) belongs to a subspecies previously not represented in the database. The growth of the bacterial strain and its ability to produce exopolysaccharides (EPS) in synthetic media with glucose or xylose as carbon sources, and in hydrolysates of quinoa stalks, was investigated. The strain grew well in all synthetic media, but the growth in glucose was better than that in xylose. Sugar consumption was better when initial concentrations were low. The growth was good in enzymatically produced cellulosic hydrolysates but was inhibited in hemicellulosic hydrolysates produced using hydrothermal pretreatment. The EPS yields were up to 0.064 g/g on initial glucose and 0.047 g/g on initial xylose, and was higher in media with relatively low sugar concentrations. The EPS was isolated and purified by a sequential procedure including centrifugation, cold ethanol precipitation, trichloroacetic acid treatment, dialysis, and freeze-drying. Glucose and mannose were the main sugars identified in hydrolyzed EPS. The EPS was characterized by size-exclusion chromatography, Fouriertransform infrared (FTIR) spectroscopy, heteronuclear single-quantum coherence nuclear magnetic resonance (HSQC NMR) spectroscopy, scanning electron microscopy, X-ray diffraction, and thermogravimetric analysis. No major differences were elucidated between EPS resulting from cultivations in glucoseor-xylose-based synthetic media, while some divergences with regard to molecular-weight averages and FTIR and HSQC NMR spectra were detected for EPS from hydrolysate-based media.

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  • 10.
    Derba-Maceluch, Marta
    et al.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Mitra, Madhusree
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Liu, Xiaokun
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Barbut, Félix R.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Abreu, Ilka N.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Donev, Evgeniy N.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Urbancsok, János
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Moritz, Thomas
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tsang, Adrian
    Centre for Structural and Functional Genomics, Concordia University, QC, Montreal, Canada.
    Powlowski, Justin
    Centre for Structural and Functional Genomics, Concordia University, QC, Montreal, Canada.
    Master, Emma R.
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, Toronto, Canada.
    Mellerowicz, Ewa J.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls2023In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 238, no 1, p. 297-312Article in journal (Refereed)
    Abstract [en]

    Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood.

    We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions.

    The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds.

    These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.

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  • 11. Dominguez, Pia Guadalupe
    et al.
    Donev, Evgeniy
    Derba-Maceluch, Marta
    Bünder, Anne
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tomásková, Ivana
    Mellerowicz, Ewa J.
    Niittylä, Totte
    Sucrose synthase determines carbon allocation in developing wood and alters carbon flow at the whole tree level in aspen2021In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 229, no 1, p. 186-198Article in journal (Refereed)
    Abstract [en]

    Despite the ecological and industrial importance of biomass accumulation in wood, the control of carbon (C) allocation to this tissue and to other tree tissues remain poorly understood. We studied sucrose synthase (SUS) to clarify its role in biomass formation and C metabolism at the whole tree level in hybrid aspen (Populus tremula x tremuloides). To this end, we analysed source leaves, phloem, developing wood, and roots ofSUSRNAitrees using a combination of metabolite profiling, 13CO2 pulse labelling experiments, and long-term field experiments. The glasshouse grownSUSRNAitrees exhibited a mild stem phenotype together with a reduction in wood total C. The 13CO2 pulse labelling experiments showed an alteration in the C flow in all the analysed tissues, indicating that SUS affects C metabolism at the whole tree level. This was confirmed when theSUSRNAitrees were grown in the field over a 5-yr period; their stem height, diameter and biomass were substantially reduced. These results establish that SUS influences C allocation to developing wood, and that it affects C metabolism at the whole tree level.

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  • 12. Ekstrand, E.-M
    et al.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Svensson, B. H.
    Yekta, S. Shakeri
    Björn, A.
    Methane potentials and organic matter characterization of wood fibres from pulp and paper mills: The influence of raw material, pulping process and bleaching technique2020In: Biomass and Bioenergy, ISSN 0961-9534, E-ISSN 1873-2909, Vol. 143, article id 105824Article in journal (Refereed)
    Abstract [en]

    During the process of pulp- and papermaking, large volumes of fibre-rich primary sludge are generated. Anaerobic digestion of primary sludge offers a substantial potential for methane production as an alternative approach to the inefficient energy recoveries by commonly used incineration techniques. However, a systematic study of the importance of upstream process techniques for the methane potential of pulp fibres is lacking. Therefore, biochemical methane potentials were determined at mesophilic conditions for 20 types of fibres processed by a variety of pulping and bleaching techniques and from different raw materials. This included fibres from kraft, sulphite, semi-chemical, chemical thermo-mechanical (CTMP) and thermo-mechanical pulping plants and milled raw wood. The pulping technique was clearly important for the methane potential, with the highest potential achieved for kraft and sulphite fibres (390–400 Nml CH4 g VS−1). For raw wood and CTMP, hardwood fibres gave substantially more methane than the corresponding softwood fibres (240 compared to 50 Nml CH4 g VS−1 and 300 compared to 160 Nml CH4 g VS−1, respectively). Nuclear magnetic resonance characterization of the organic content demonstrated that the relative lignin content of the fibres was an important factor for methane production, and that an observed positive effect of bleaching on the methane potential of softwood CTMP fibres was likely related to a higher degree of deacetylation and improved accessibility of the hemicellulose. In conclusion, fibres from kraft and sulphite pulping are promising substrates for methane production irrespective of raw material or bleaching, as well as fibres from CTMP pulping of hardwood.

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  • 13.
    Erhagen, Björn
    et al.
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Öquist, Mats
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Haei, Mahsa
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Ilstedt, Ulrik
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Nilsson, Mats B
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Temperature response of litter and soil organic matter decomposition is determined by chemical composition of organic material2013In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 19, no 12, p. 3858-3871Article in journal (Refereed)
    Abstract [en]

    The global soil carbon pool is approximately three times larger than the contemporary atmospheric pool, therefore even minor changes to its integrity may have major implications for atmospheric CO2 concentrations. While theory predicts that the chemical composition of organic matter should constitute a master control on the temperature response of its decomposition, this relationship has not yet been fully demonstrated. We used laboratory incubations of forest soil organic matter (SOM) and fresh litter material together with NMR spectroscopy to make this connection between organic chemical composition and temperature sensitivity of decomposition. Temperature response of decomposition in both fresh litter and SOM was directly related to the chemical composition of the constituent organic matter, explaining 90% and 70% of the variance in Q10 in litter and SOM respectively. The Q10 of litter decreased with increasing proportions of aromatic and O-aromatic compounds, and increased with increased contents of alkyl- and O-alkyl carbons. In contrast, in SOM, decomposition was affected only by carbonyl compounds. To reveal why a certain group of organic chemical compounds affected the temperature sensitivity of organic matter decomposition in litter and SOM, a more detailed characterisation of the (13) C aromatic region using Heteronuclear Single Quantum Coherence (HSQC) was conducted. The results revealed considerable differences in the aromatic region between litter and SOM. This suggests that the correlation between chemical composition of organic matter and the temperature response of decomposition differed between litter and SOM. The temperature response of soil decomposition processes can thus be described by the chemical composition of its constituent organic matter, this paves the way for improved ecosystem modelling of biosphere feedbacks under a changing climate.

  • 14.
    Fernández-Domínguez, David
    et al.
    INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, Narbonne, France.
    Yekta, Sepehr Shakeri
    Department of Thematic Studies-Environmental Change and Biogas Research Center, Linköping University, Linköping, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Patureau, Dominique
    INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, Narbonne, France.
    Jimenez, Julie
    INRAE, Univ. Montpellier, LBE, 102 Avenue des étangs, Narbonne, France.
    Deciphering the contribution of microbial biomass to the properties of dissolved and particulate organic matter in anaerobic digestates2023In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 877, article id 162882Article in journal (Refereed)
    Abstract [en]

    The recalcitrant structures either from substrate or microbial biomass contained in digestates after anaerobic digestion (AD) highly influence digestate valorization. To properly assess the microbial biomass contribution to the digested organic matter (OM), a combination of characterization methods and the use of various substrate types in anaerobic continuous reactors was required. The use of totally biodegradable substrates allowed detecting soluble microbial products via fluorescence spectroscopy at emission wavelengths of 420 and 460 nm while the protein-like signature was enhanced by the whey protein. During reactors' operation, a transfer of complex compounds to the dissolved OM from the particulate OM was observed through fluorescence applied on biochemical fractionation. Consequently, the fluorescence complexity index of the dissolved OM increased from 0.59–0.60 to 1.06–1.07, whereas it decreased inversely for the extractable soluble from the particulate OM from 1.16–1.19 to 0.42–0.54. Accordingly, fluorescence regional integration showed differences among reactors based on visual inspection and orthogonal partial latent structures (OPLS) analysis. Similarly, the impact of the substrate type and operation time on the particulate OM was revealed by 13C nuclear magnetic resonance using OPLS, providing a good model (R2X = 0.93 and Q2 = 0.8) with a clear time-trend. A high signal resonated at ∼30 ppm attributed to CH2-groups in the aliphatic chain of lipid-like structure besides carbohydrates intensities at 60–110 ppm distinguished the reactor fed with whey protein from the other, which was mostly biomass related. Indeed, this latter displayed a higher presence of peptidoglycan (δH/C: 1.6–2.0/20–25 ppm) derived from microbial biomass by 1H-13C heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance. Interestingly, the sample distribution obtained by non-metric multidimensional scaling of bacterial communities resembled the attained using 13C NMR properties, opening new research perspectives. Overall, this study discloses the microbial biomass contribution to digestates composition to improve the OM transformation mechanism knowledge.

  • 15.
    Gillgren, Thomas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Comparison of laccase-catalyzed cross-linking of organosolv lignin and lignosulfonates2017In: International Journal of Biological Macromolecules, ISSN 0141-8130, E-ISSN 1879-0003, Vol. 105, no 1, p. 438-446Article in journal (Refereed)
    Abstract [en]

    Lignin, an underutilized by-product from chemical pulping of wood, can be modified enzymatically through oxidation by laccase. However, little is known about the molecular details surrounding the cross linking which is a result of the oxidation. To reduce this lack of knowledge, we used oxygen consumption rate data, phenolic content data and molecular weight data together with data from NMR and FTIR spectroscopy to.characterize laccase-catalyzed cross-linking of the industrial lignin preparations organosolv lignin and lignosulfonate. The organosolv lignin preparation had a M-n of 780 g/mol, a M-w of 5200 g/mol, and a phenolic content of 1.8 mmol/g. The lignosulfonate preparation had a M-n of 6000 g/mol, a M-w of 19800 g/mol, and a phenolic content of 1.1 mmol/g. Laccase-catalyzed oxidation of organosolv lignin was characterized by a relatively slow increase in molecular weight, decreased intensities for aromatic signals and p-hydroxycinnamyl groups, and increased intensity for beta-O-4' signals, whereas oxidation of lignosulfonates resulted in a very rapid increase in molecular weight, and strongly decreased intensities for aromatic signals. The data suggest that lignosulfonates cross-linked by couplings to the aromatic ring (e.g. 5-5' and 4-O-5'), whereas beta-O-4' coupling characterized cross-linking of organosolv lignin, probably involving cinnamyl alcohol end-groups. (C) 2017 Published by Elsevier B.V.

  • 16.
    Gustafsson, Tomas
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Chemistry.
    Synthesis of a C-Glycoside Analogue of -D-Galactosyl Hydroxylysine and Incorporation in a Glycopeptide from Type II Collagen2006In: Journal of Organic Chemistry, Vol. 71, no 5, p. 1911-9Article in journal (Refereed)
    Abstract [en]

    A stereoselective synthesis of the C-glycoside analogue of -D-galactosyl-(5R,2S)-hydroxylysine (1) has been achieved starting from tetra-O-benzyl-D-galactopyranosyl lactone. The synthesis involved establishment of three stereogenic centers in an unambiguous manner. A facially selective Grignard reaction followed by a silane reduction was used for the anomeric position of the C-galactose residue. An Evans allylation established the configuration of the -aminomethylene group of the hydroxylysine moiety, whereas an asymmetric hydrogenation utilizing Burk's catalyst was used for the -amino acid moiety itself. The synthesis was completed in 17 steps with an overall yield of 18%, resulting in the most complex and functionalized C-glycoside analogue of a naturally occurring glycosylated amino acid prepared to date. In addition, amino acid 1 was incorporated in a glycopeptide from type II collagen known to be crucial for the response of autoimmune T cells obtained in models of rheumatoid arthritis. A preliminary immunological study revealed that four out of five members in a panel of T cell hybridomas were able to recognize this C-linked glycopeptide when presented by Aq class II MHC molecules.

  • 17.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Chemistry.
    NMR as a tool in drug research: Structure elucidation of peptidomimetics and pilicide-chaperone complexes2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the last decades NMR spectroscopy has become an invaluable tool both in academic research and in the pharmaceutical industry. This thesis describes applications of NMR spectroscopy in biomedicinal research for structure elucidation of biologically active peptides and peptidomimetics as well as in studies of ligand-protein interactions.

    The first part of this thesis describes the theory and methodology of structure calculations of peptides using experimental restraints derived from NMR spectroscopy. This methodology has been applied to novel mimetics of the peptide hormones desmopressin and Leu-enkephalin. The results of these studies highlight the complicating issue of conformational exchange often encountered in structural determination of peptides and how careful analysis of experimental data as well as optimization of experimental conditions can enable structure determinations in such instances. Although the mimetics of both desmopressin and Leu-enkephalin were found to adopt the wanted conformations, they exhibited no or very poor biological activity. These results demonstrate the difficulties in designing peptidomimetics without detailed structural information of the receptors. A stereoselective synthetic route towards XxxΨ[CH2O]Ala pseudodipeptides is also presented. Such pseudodipeptides can be used as isosteric amide bond replacements in peptides in order to increase their resistance towards proteolytic degradation.

    The second part of this thesis describes the study of the interaction between compounds that inhibit pilius assembly, pilicides, and periplasmic chaperones from uropathogenic Escherichia coli. Periplasmic chaperones are key components in assembly of pili, i.e. hair-like protein complexes located on the surface of Escherichia coli that cause urinary tract infections. Detailed knowledge about this interaction is important in understanding how pilicides can inhibit pilus assembly by binding to chaperones. Relaxation-edited NMR experiments were used to confirm the affinity of the pilicides for the chaperones and chemical shift mapping was used to study the pilicide-chaperone interaction surface. These studies show that at least two interaction sites are present on the chaperone surface and consequently that two different mechanisms resulting in inhibition of pilus assembly may exist.

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  • 18.
    Hedenström, Mattias
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Emtenäs, Hans
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pemberton, Nils
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Åberg, Veronica
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hultgren, Scott J.
    Pinkner, Jerome S.
    Tegman, Viola
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sethson, Ingmar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    NMR studies of interactions between periplasmic chaperones from uropathogenic E-coli and pilicides that interfere with chaperone function and pilus assembly2005In: ORGANIC & BIOMOLECULAR CHEMISTRY, ISSN 1477-0520, Vol. 3, no 23, p. 4193-4200Article in journal (Refereed)
    Abstract [en]

    Adherence of uropathogenic Escherichia coli to host tissue is mediated by pili, which are hair-like protein structures extending from the outer cell membrane of the bacterium. The chaperones FimC and PapD are key components in pilus assembly since they catalyse folding of subunits that are incorporated in type 1 and P pili, respectively, and also transport the subunits across the periplasmic space. Recently, compounds that inhibit pilus biogenesis and interfere with chaperone-subunit interactions have been discovered and termed pilicides. In this paper NMR spectroscopy was used to study the interaction of different pilicides with PapD and FimC in order to gain structural knowledge that would explain the effect that some pilicides have on pilus assembly. First relaxation-edited NMR experiments revealed that the pilicides bound to the PapD chaperone with mM affinity. Then the pilicide-chaperone interaction surface was investigated through chemical shift mapping using N-15-labelled FimC. Principal component analysis performed on the chemical shift perturbation data revealed the presence of three binding sites on the surface of FimC, which interacted with three different classes of pilicides. Analysis of structure-activity relationships suggested that pilicides reduce pilus assembly in E. coli either by binding in the cleft of the chaperone, or by influencing the orientation of the flexible F1-G1 loop, both of which are part of the surface by which the chaperone forms complexes with pilus subunits. It is suggested that binding to either of these sites interferes with folding of the pilus subunits, which occurs during formation of the chaperone-subunit complexes. In addition, pilicides that influence the F1-G1 loop also appear to reduce pilus formation by their ability to dissociate chaperone-subunit complexes.

  • 19.
    Hedenström, Mattias
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Holm, Lotta
    Umeå University, Faculty of Science and Technology, Chemistry.
    Yuan, ZhongQing
    Umeå University, Faculty of Science and Technology, Chemistry.
    Emtenäs, Hans
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Chemistry.
    Stereoselective Synthesis of Ψ[CH2O] Pseudodipeptides and Conformational Analysis of a PheΨ[CH2O]Ala Containing Analogue of the Drug Desmopressin2002In: Bioorganic & Medicinal Chemistry Letters, Vol. 12, no 6, p. 841-4Article in journal (Refereed)
    Abstract [en]

    A method for synthesis of XaaΨ[CH2O]Ala/Gly pseudodipeptides in good yields and excellent diastereoselectivity from azido alcohols and (R)-2-chloropropionic acid or tert-butyl bromoacetate has been developed. Insertion of one of the pseudodipeptide building blocks in the peptide drug desmopressin revealed that methylene ether isosteres may have only a minor influence on the secondary structure of peptides.

  • 20.
    Hedenström, Mattias
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wiklund, Susanne
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sundberg, Björn
    Edlund, Ulf
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Visualization and interpretation of OPLS models based on 2D NMR Data2008In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 92, no 2, p. 110-117Article in journal (Refereed)
    Abstract [en]

    Multivariate analysis on spectroscopic 1H NMR data is well established in metabolomics and other fields where the composition of complex samples is studied. However, biomarker identification can be hampered by overlapping resonances. 2D NMR data provides a more detailed “fingerprint” of the chemical structure and composition of the sample with greatly improved spectral resolution compared to 1H NMR data. In this report, we demonstrate a procedure for the construction of multivariate models based on frequency domain 2D NMR data where the loadings can be visualized as highly informative 2D loading spectra. This method is based on the analysis of raw spectral data without any need for peak picking or integration prior to analysis. Spectral features such as line widths and peak positions are thus retained. Hence, the loadings can be visualized and interpreted on a molecular level as pseudo 2D spectra in order to identify potential biomarkers. To demonstrate this strategy we have analyzed HSQC spectra acquired from populus phloem plant extracts originating from a set of designed experiments with OPLS regression.

  • 21.
    Hedenström, Mattias
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wiklund-Lindström, Susanne
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Öman, Tommy
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lu, Fachuang
    Gerber, Lorenz
    Schatz, Paul
    Sundberg, Björn
    Ralph, John
    Identification of lignin and polysaccharide modifications in Populus wood by chemometric analysis of 2D NMR spectra from dissolved cell walls2009In: Molecular Plant, ISSN 1674-2052, Vol. 2, no 5, p. 933-942Article in journal (Refereed)
    Abstract [en]

    2D (13)C-(1)H HSQC NMR spectroscopy of acetylated cell walls in solution gives a detailed fingerprint that can be used to assess the chemical composition of the complete wall without extensive degradation. We demonstrate how multivariate analysis of such spectra can be used to visualize cell wall changes between sample types as high-resolution 2D NMR loading spectra. Changes in composition and structure for both lignin and polysaccharides can subsequently be interpreted on a molecular level. The multivariate approach alleviates problems associated with peak picking of overlapping peaks, and it allows the deduction of the relative importance of each peak for sample discrimination. As a first proof of concept, we compare Populus tension wood to normal wood. All well established differences in cellulose, hemicellulose, and lignin compositions between these wood types were readily detected, confirming the reliability of the multivariate approach. In a second example, wood from transgenic Populus modified in their degree of pectin methylesterification was compared to that of wild-type trees. We show that differences in both lignin and polysaccharide composition that are difficult to detect with traditional spectral analysis and that could not be a priori predicted were revealed by the multivariate approach. 2D NMR of dissolved cell wall samples combined with multivariate analysis constitutes a novel approach in cell wall analysis and provides a new tool that will benefit cell wall research.

  • 22.
    Hedenström, Mattias
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johnels, Dan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Characterization of Hydrogenated Fullerenes by NMR Spectroscopy2010In: Fulleranes: The Hydrogenated Fullerenes / [ed] Franco Cataldo, Susana Iglesias-Groth, Dordrecht: Springer Netherlands, 2010, Vol. 2, p. 171-202Chapter in book (Other academic)
    Abstract [en]

    NMR spectroscopy is so far the only analytical technique that has been used to get a detailed structural characterization of hydrogenated fullerenes. A substantial amount of information derived from different NMR experiments can thus be found in the literature for a number of fullerenes hydrogenated to various degrees. These studies have benefitted from the fact that chemical shifts of H-1 and C-13 and in some cases also He-3 can be used to obtain structural information of these compounds. Such results, together with discussions about different NMR experiments and general considerations regarding sample preparations, are summarized in this chapter. The unique information, both structural and physicochemical, that can be derived from different NMR experiments ensures that this technique will continue to be of central importance in characterization of hydrogenated fullerenes.

  • 23.
    Hedenström, Mattias
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Yuan, ZhongQing
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brickmann, Kay
    Carlsson, Jolanta
    Ekholm, Kjell
    Johansson, Birgitta
    Kreutz, Eva
    Nilsson, Anders
    Sethson, Ingmar
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Conformations and Receptor Activity of Desmopressin Analogues, Which Contain -Turn Mimetics or a [CH2O] Isostere2002In: Journal of Medicinal Chemistry, Vol. 45, no 12, p. 2501-11Article in journal (Refereed)
    Abstract [en]

    Three analogues of the antidiuretic drug desmopressin ([1-desamino,8-D-arginine]vasopressin) have been prepared. In two of these, -turn mimetics based on a morpholin-3-one framework have been inserted instead of residues Phe3-Asn5, whereas the third analogue has a methylene ether isostere in place of the amide bond between residues 3 and 4. The three analogues were used to probe if the structure determined for desmopressin in aqueous solution, which contains an inverse -turn centered around Gln4, is important in interactions with the vasopressin V2 receptor. Conformational studies revealed that the analogues that contain either an inverse -turn mimetic or a methylene ether isostere mimicked the conformation of desmopressin fairly well and very well, respectively. Despite this, the analogues displayed only very low agonistic activities at the vasopressin V2 receptor. Consequently, an inverse -turn involving residues Phe3-Asn5 does not appear to be important when desmopressin is bound to the V2 receptor. In addition, it was concluded that the amide bond between Phe3 and Gln4 in desmopressin is crucial for interactions with the antidiuretic V2 receptor.

  • 24.
    Jamroskovic, Jan
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Doimo, Mara
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Chand, Karam
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Obi, Ikenna
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Kumar, Rajendra
    Umeå University, Faculty of Science and Technology, Department of Physics. Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Das, Rabindra Nath
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Akhunzianov, Almaz
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia.
    Deiana, Marco
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Kasho, Kazutoshi
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Sulis Sato, Sebastian
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Pourbozorgi-Langroudi, Parham
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Mason, James E.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
    Medini, Paolo
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Öhlund, Daniel
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
    Wanrooij, Sjoerd
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sabouri, Nasim
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization2020In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 142, no 6, p. 2876-2888Article in journal (Refereed)
    Abstract [en]

    The signal transducer and activator of transcription 3 (STAT3) protein is a master regulator of most key hallmarks and enablers of cancer, including cell proliferation and the response to DNA damage. G-Quadruplex (G4) structures are four-stranded noncanonical DNA structures enriched at telomeres and oncogenes' promoters. In cancer cells, stabilization of G4 DNAs leads to replication stress and DNA damage accumulation and is therefore considered a promising target for oncotherapy. Here, we designed and synthesized novel quinazoline-based compounds that simultaneously and selectively affect these two well-recognized cancer targets, G4 DNA structures and the STAT3 protein. Using a combination of in vitro assays, NMR, and molecular dynamics simulations, we show that these small, uncharged compounds not only bind to the STAT3 protein but also stabilize G4 structures. In human cultured cells, the compounds inhibit phosphorylation-dependent activation of STAT3 without affecting the antiapoptotic factor STAT1 and cause increased formation of G4 structures, as revealed by the use of a G4 DNA-specific antibody. As a result, treated cells show slower DNA replication, DNA damage checkpoint activation, and an increased apoptotic rate. Importantly, cancer cells are more sensitive to these molecules compared to noncancerous cell lines. This is the first report of a promising class of compounds that not only targets the DNA damage cancer response machinery but also simultaneously inhibits the STAT3-induced cancer cell proliferation, demonstrating a novel approach in cancer therapy.

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  • 25.
    Jogunola, Olatunde
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Eta, Valerie
    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, 20500 Åbo/Turku, Finland.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sundman, Ola
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Salmi, Tapio
    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, 20500 Åbo/Turku, Finland.
    Ionic liquid mediated technology for synthesis of cellulose acetates using different co-solvents2016In: Carbohydrate Polymers, ISSN 0144-8617, E-ISSN 1879-1344, Vol. 135, p. 341-348Article in journal (Refereed)
    Abstract [en]

    In this work, cellulose acetate was synthesized under homogeneous conditions. Cellulose was first dispersed in acetone, acetonitrile, 1,5-diazabicyclo(4.3.0)non-5-ene (DBN) or dimethyl sulphoxide (DMSO) and the resulting suspension was dissolved in an ionic liquid, 1,5-diazabicyclo(4.3.0)non-5-enium acetate [HDBN][OAc] at 70 °C for 0.5 h. It was possible to dissolve more than 12 wt% cellulose with a degree of polymerization in the range of 1000–1100. The dissolved cellulose was derivatized with acetic anhydride (Ac2O) to yield acetylated cellulose. As expected, the use of the co-solvents improved the acetylation process significantly. In fact, cellulose acetates with different properties could be obtained in half an hour, thus facilitating rapid processing. When DBN was used as the dispersing agent (the precursor of the ionic liquid), the problems associated with recycling of the ionic liquid were significantly reduced. In fact, additional [HDBN][OAc] was obtained from the interaction of the DBN and the by-product, acetic acid (from Ac2O). However, the cellulose acetate obtained in this manner had the lowest DS. Consequently, the native cellulose and acetylated celluloses were characterized by means of 1H- and 13C-NMR, FT-IR, GPC/SEC and by titration. The cellulose acetates produced were soluble in organic solvents such as acetone, chloroform, dichloromethane and DMSO which is essential for their further processing. It was demonstrated that the ionic liquid can be recovered from the system by distillation and re-used in consecutive acetylation batches.

  • 26.
    Karlsson, Göran
    et al.
    Swedish NMR Centre at the University of Gothenburg.
    Persson, Cecilia
    Swedish NMR Centre at the University of Gothenburg.
    Mayzel, Maxim
    Swedish NMR Centre at the University of Gothenburg.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Backman, Lars
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Solution structure of the calmodulin-like C-terminal domain of Entamoeba α-actinin22016In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 84, no 4, p. 461-466Article in journal (Refereed)
    Abstract [en]

    Cell motility is dependent on a dynamic meshwork of actin filaments that is remodelled continuously. A large number of associated proteins that are severs, cross-links, or caps the filament ends have been identified and the actin cross-linker α-actinin has been implied in several important cellular processes. In Entamoeba histolytica, the etiological agent of human amoebiasis, α-actinin is believed to be required for infection. To better understand the role of α-actinin in the infectious process we have determined the solution structure of the C-terminal calmodulin-like domain using NMR. The final stru-ture ensemble of the apo form shows two lobes, that both resemble other pairs of calcium-binding EF-hand motifs, connected with a mobile linker.

  • 27.
    Kumar, Rajendra
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chand, Karam
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bhowmik, Sudipta
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, India.
    Das, Rabindra Nath
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bhattacharjee, Snehasish
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes2020In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 48, no 3, p. 1108-1119Article in journal (Refereed)
    Abstract [en]

    G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. However, the development of these types of specific compounds remain as a great challenge. In here, we have developed a compound with ability to specifically signal a certain c-MYC G4 DNA structure through a fluorescence light-up mechanism. Despite the compound's two binding sites on the G4 DNA structure, only one of them result in the fluorescence light-up effect. This G-tetrad selectivity proved to originate from a difference in flexibility that affected the binding affinity and tilt the compound out of the planar conformation required for the fluorescence light-up mechanism. The intertwined relation between the presented factors is likely the reason for the lack of examples using rational design to develop compounds with turn-on emission that specifically target certain G4 DNA structures. However, this study shows that it is indeed possible to develop such compounds and present insights into the molecular details of specific G4 DNA recognition and signaling to advance future studies of G4 biology.

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  • 28. Laera, Andreina
    et al.
    Yekta, Sepehr Shakeri
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Buzier, Remy
    Guibaud, Gilles
    Dario, Mårten
    Esposito, Giovanni
    van Hullebusch, Eric D.
    A simultaneous assessment of organic matter and trace elements bio-accessibility in substrate and digestate from an anaerobic digestion plant2019In: Bioresource Technology, ISSN 0960-8524, E-ISSN 1873-2976, Vol. 288, article id 121587Article in journal (Refereed)
    Abstract [en]

    This study evaluates a simultaneous assessment of organic matter (OM) and trace elements (TE) bio-accessibility in substrate and digestate from a full-scale anaerobic digester by a sequential OM extraction method. Simultaneous release of TE was determined along with the extraction of different OM fractions and the effects of extracting reagents on characteristics of OM were evaluated by nuclear magnetic resonance (NMR) spectroscopy. The reagents used for sequential extraction of OM were not enough selective. However, proteins were particularly removed by 0.1 M NaOH, while 72% H2SO4 mainly extracted hemicellulose and cellulose. The OM fractionation allowed for simultaneous extraction of > 60% of total As, Cd, Co, Fe, Mn, Ni and Zn, while the extraction was limited for Al, Cr, Cu, Mo, and Pb. In substrate, > 50% of total As, Co, Mn and Ni and < 40% of total Fe, Zn and Mo were identified in bio-accessible fractions. In digestate, all elements demonstrated poor bio-accessibility except for As.

  • 29.
    Livendahl, Madeleine
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jamroskovic, Jan
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Görlich, T.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sabouri, Nasim
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Synthesis of phenanthridine spiropyrans and studies of their effects on G-quadruplex DNA2017In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 15, no 15, p. 3265-3275Article in journal (Refereed)
    Abstract [en]

    G-quadruplex (G4) DNA structures are involved in many important biological processes and can be linked to several human diseases. Drug-like low molecular weight compounds that target G4 structures are therefore interesting not only for their potential therapeutic properties but also for their potential use as chemical research tools. We report here on the development of methods to synthesize spiropyrans using a condensation-cyclisation reaction of quaternary salts of [small alpha]-methyl quinoline or phenanthridine with salicylaldehydes. Evaluation of the synthesized phenanthridine spiropyrans' interactions with G4 DNA was performed with a Thioflavin T displacement assay, circular dichroism, Taq DNA polymerase stop assay, and NMR. This revealed that the substitution pattern on the phenanthridine spiropyrans was very important for their ability to bind and stabilize G4 structures. Some of the synthesized low molecular weight spirocyclic compounds efficiently stabilized G4 structures without inducing structural changes by binding the first G-tetrad in the G4 structure.

  • 30.
    Lundstedt, Torbjörn
    et al.
    AcurePharma AB, Uppsala, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Soeria-Atmadja, D
    Division of Toxicology, National Food Administration, Uppsala, Sweden.
    Hammerling, U
    Division of Toxicology, National Food Administration, Uppsala, Sweden.
    Gabrielsson, Jon
    AcureOmics AB, Umeå, Sweden.
    Olsson, J
    KPL Good Food Practice AB, Uppsala, Sweden.
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dynamic modelling of time series data in nutritional metabonomics: A powerful complement to randomized clinical trials in functional food studies2010In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 104, no 1, p. 112-120Article in journal (Refereed)
    Abstract [en]

    Functional foods are foods or dietary ingredients that provide a health benefit beyond basic nutrition. A new legislation, known as the Nutrition and Health Claims Regulation, defines the legal framework for such claims within the European Union. Any claim about the nutritional or physiological effects of a product must be scientifically demonstrated. In this study, we have focused on the exploration of metabonomics as a complementary profiling technology to establish monitoring/data analysis procedures of randomized nutritional trials. More specifically, a combined intake of soybean and grapefruit in a human intervention study was analyzed with respect to both pharmacological and physiological effects. Resulting multivariate models showed a diet-induced decrease of lactate, cholesterols and triglycerides. The most drastically elevated metabolite, myo-inositol, was found to accompany a marked reduction of triglyceride levels. Suggestively, this is due to the biotransformation of myo-inositol to phosphatidylinositol, which results in a decrease of available precursors to form triglycerides. Strong inter-subject variation was present that required special attention. Dynamic modelling of collected time series data that provided the opportunity to identify slow, medium or fast responders as well as groups of subjects showing different response profiles, was also highlighted in the study. The applied strategy of time series data has proven to be a powerful complement to randomized nutritional studies adopting a clinical trial design.

  • 31. Mahboubi, Amir
    et al.
    Linden, Pernilla
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Moritz, Thomas
    Niittyla, Totte
    C-13 Tracking after (CO2)-C-13 Supply Revealed Diurnal Patterns of Wood Formation in Aspen2015In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 168, no 2, p. 478-489Article in journal (Refereed)
    Abstract [en]

    Wood of trees is formed from carbon assimilated in the photosynthetic tissues. Determining the temporal dynamics of carbon assimilation, subsequent transport into developing wood, and incorporation to cell walls would further our understanding of wood formation in particular and tree growth in general. To investigate these questions, we designed a (CO2)-C-13 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula 3 tremuloides). Tracking of C-13 incorporation to wood over a time course using nuclear magnetic resonance spectroscopy revealed diurnal patterns in wood cell wall biosynthesis. The dark period had a differential effect on C-13 incorporation to lignin and cell wall carbohydrates. No C-13 was incorporated into aromatic amino acids of cell wall proteins in the dark, suggesting that cell wall protein biosynthesis ceased during the night. The results show previously unrecognized temporal patterns in wood cell wall biosynthesis, suggest diurnal cycle as a possible cue in the regulation of carbon incorporation to wood, and establish a unique C-13 labeling method for the analysis of wood formation and secondary growth in trees.

  • 32.
    Mercier, Guillaume
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Klechikov, Alexey
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Hedenstrom, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Johnels, Dan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Baburin, Igor A.
    Seifert, Gotthard
    Mysyk, Roman
    Talyzin, Alexandr V.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Porous Graphene Oxide/Diboronic Acid Materials: Structure and Hydrogen Sorption2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 49, p. 27179-27191Article in journal (Refereed)
    Abstract [en]

    Solvothermal reaction of graphite oxide (GO) with benzene-1,4-diboronic acid (DBA) was reported previously to result in formation of graphene oxide framework (GOP) materials. The theoretical structure of GOFs consists of graphene layers separated by benzene-diboronic "pillars" with similar to 1 nm slit pores thus providing the opportunity to use it as a model material to verify the effect of a small pore size on hydrogen adsorption. A set of samples with specific surface area (SSA) in the range of similar to 50-1000 m(2)/g were prepared using variations of synthesis conditions and GO/DBA proportions. Hydrogen storage properties of GOF samples evaluated at 293 and 77 K were found to be similar to other nanocarbon trends in relation to SSA values. Structural characterization of GO/DBA samples showed all typical features reported as evidence for formation of a framework structure such as expanded interlayer distance, increased temperature of thermal exfoliation, typical features in FTIR spectra, etc. However, the samples also exhibited reversible swelling in polar solvents which is not compatible with the idealized GOF structure linked by benzenediboronic molecular pillars. Therefore, possible alternative nonframework models of structures with pillars parallel and perpendicular to GO planes are considered.

  • 33. Michel, Maurice
    et al.
    Visnes, Torkild
    Homan, Evert J.
    Seashore-Ludlow, Brinton
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wiita, Elisee
    Vallin, Karl
    Paulin, Cynthia B. J.
    Zhang, Jiaxi
    Wallner, Olov
    Scobie, Martin
    Schmidt, Andreas
    Jenmalm-Jensen, Annika
    Berglund, Ulrika Warpman
    Helleday, Thomas
    Computational and Experimental Druggability Assessment of Human DNA Glycosylases2019In: ACS Omega, E-ISSN 2470-1343, Vol. 4, no 7, p. 11642-11656Article in journal (Refereed)
    Abstract [en]

    Due to a polar or even charged binding interface, DNA-binding proteins are considered extraordinarily difficult targets for development of small-molecule ligands and only a handful of proteins have been targeted successfully to date. Recently, however, it has been shown that development of selective and efficient inhibitors of 8-oxoguanine DNA glycosylase is possible. Here, we describe the initial druggability assessment of DNA glycosylases in a computational setting and experimentally investigate several methods to target endonuclease VIII-like 1 (NEIL1) with small-molecule inhibitors. We find that DNA glycosylases exhibit good predicted druggability in both DNA-bound and -unbound states. Furthermore, we find catalytic sites to be highly flexible, allowing for a range of interactions and binding partners. One flexible catalytic site was rationalized for NEIL1 and further investigated experimentally using both a biochemical assay in the presence of DNA and a thermal shift assay in the absence of DNA.

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  • 34.
    Miranda, Diego A.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Instituto de Investigación y Desarrollo de Procesos Químicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andrés, La Paz, Bolivia.
    Marín, Katherine
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Instituto de Investigación y Desarrollo de Procesos Químicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andrés, La Paz, Bolivia.
    Sundman, Ola
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Quillaguaman, Jorge
    Planta Piloto de Bioprocesos, Facultad de Ciencias y Tecnología, Universidad Mayor de San Simón, Cochabamba, Bolivia.
    Gorzsás, András
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Broström, Markus
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Carlborg, Markus
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Lundqvist, Jenny
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Romero-Soto, Luis
    Instituto de Investigación y Desarrollo de Procesos Químicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andrés, La Paz, Bolivia.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Carrasco, Cristhian
    Instituto de Investigación y Desarrollo de Procesos Químicos, Chemical Engineering, Faculty of Engineering, Universidad Mayor de San Andrés, La Paz, Bolivia.
    Martin, Carlos
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.
    Production and characterization of poly(3-hydroxybutyrate) from Halomonas boliviensis LC1 cultivated in hydrolysates of quinoa stalks2023In: Fermentation, E-ISSN 2311-5637, Vol. 9, no 6, article id 556Article in journal (Refereed)
    Abstract [en]

    The global production of fossil-based plastics has reached critical levels, and their substitution with bio-based polymers is an urgent requirement. Poly(3-hydroxybutyrate) (PHB) is a biopolymer that can be produced via microbial cultivation, but efficient microorganisms and low-cost substrates are required. Halomonas boliviensis LC1, a moderately halophilic bacterium, is an effective PHB producer, and hydrolysates of the residual stalks of quinoa (Chenopodium quinoa Willd.) can be considered a cheap source of sugars for microbial fermentation processes in quinoa-producing countries. In this study, H. boliviensis LC1 was adapted to a cellulosic hydrolysate of quinoa stalks obtained via acid-catalyzed hydrothermal pretreatment and enzymatic saccharification. The adapted strain was cultivated in hydrolysates and synthetic media, each of them with two different initial concentrations of glucose. Cell growth, glucose consumption, and PHB formation during cultivation were assessed. The cultivation results showed an initial lag in microbial growth and glucose consumption in the quinoa hydrolysates compared to cultivation in synthetic medium, but after 33 h, the values were comparable for all media. Cultivation in hydrolysates with an initial glucose concentration of 15 g/L resulted in a higher glucose consumption rate (0.15 g/(L h) vs. 0.14 g/(L h)) and volumetric productivity of PHB (14.02 mg/(L h) vs. 10.89 mg/(L h)) than cultivation in hydrolysates with 20 g/L as the initial glucose concentration. During most of the cultivation time, the PHB yield on initial glucose was higher for cultivation in synthetic medium than in hydrolysates. The produced PHBs were characterized using advanced analytical techniques, such as high-performance size-exclusion chromatography (HPSEC), Fourier transform infrared (FTIR) spectroscopy, 1H nuclear magnetic resonance (NMR) spectroscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD), and thermogravimetric analysis (TGA). HPSEC revealed that the molecular weight of PHB produced in the cellulosic hydrolysate was lower than that of PHB produced in synthetic medium. TGA showed higher thermal stability for PHB produced in synthetic medium than for that produced in the hydrolysate. The results of the other characterization techniques displayed comparable features for both PHB samples. The presented results show the feasibility of producing PHB from quinoa stalks with H. boliviensis.

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  • 35.
    Mojica, Sergio A.
    et al.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Salin, Olli
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Bastidas, Robert J.
    Sunduru, Naresh
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Andersson, C. David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Núñez-Otero, Carlos
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Engström, Patrik
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Valdivia, Raphael H.
    Elofsson, Mikael
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Gylfe, Åsa
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    N-acylated derivatives of sulfamethoxazole block Chlamydia fatty acid synthesis and interact with FabF2017In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 61, no 10, article id e00716-17Article in journal (Refereed)
    Abstract [en]

    The type II fatty acid synthesis (FASII) pathway is essential for bacterial lipid biosynthesis and continues to be a promising target for novel antibacterial compounds. Recently, it has been demonstrated that Chlamydia is capable of FASII and this pathway is indispensable for Chlamydia growth. Previously, a high-content screen with Chlamydia trachomatis-infected cells was performed, and acylated sulfonamides were identified to be potent growth inhibitors of the bacteria. C. trachomatis strains resistant to acylated sulfonamides were isolated by serial passage of a wild-type strain in the presence of low compound concentrations. Results from whole-genome sequencing of 10 isolates from two independent drug-resistant populations revealed that mutations that accumulated in fabF were predominant. Studies of the interaction between the FabF protein and small molecules showed that acylated sulfonamides directly bind to recombinant FabF in vitro and treatment of C. trachomatis-infected HeLa cells with the compounds leads to a decrease in the synthesis of Chlamydia fatty acids. This work demonstrates the importance of FASII for Chlamydia development and may lead to the development of new antimicrobials.

  • 36.
    Momayez, Forough
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Stagge, Stefan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Martin, Carlos
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Inland Norway University of Applied Sciences, Department of Biotechnology, Hamar, Norway.
    Valorization of hydrolysis lignin from a spruce-based biorefinery by applying y-valerolactone treatment2022In: Bioresource Technology, ISSN 0960-8524, E-ISSN 1873-2976, Vol. 359, article id 127466Article in journal (Refereed)
    Abstract [en]

    Hydrolysis lignin, i.e., the hydrolysis residue of cellulosic ethanol plants, was extracted with the green solvent γ-valerolactone (GVL). Treatments at 170–210 °C were performed with either non-acidified GVL/water mixtures (NA-GVL) or with mixtures containing sulfuric acid (SA-GVL). SA-GVL treatment at 210 °C resulted in the highest lignin solubilization (64% (w/w) of initial content), and 76% of the solubilized mass was regenerated by water-induced precipitation. Regenerated lignins were characterized through compositional analysis with sulfuric acid, as well as using pyrolysis–gas chromatography/mass spectrometry (Py-GC/MS), high-performance size-exclusion chromatography (HPSEC), solid-state cross-polarization/magic angle spinning 13C nuclear magnetic resonance (CP/MAS 13C NMR) spectroscopy, 1H–13C heteronuclear single-quantum coherence NMR (HSQC NMR), and Fourier-transform infrared (FTIR) spectroscopy. The characterization revealed that the main difference between regenerated lignins was their molecular weight. Molecular weight averages increased with treatment temperature, and they were higher and had broader distribution for SA-GVL lignins than for NA-GVL lignins.

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  • 37.
    Nilsson, Emma C
    et al.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Storm, Rickard J
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Bauer, Johannes
    University of Tübingen.
    Johansson, Susanne M C
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Lookene, Aivar
    Tallinn University of Technology, Tallinn, Estonia..
    Ångström, Jonas
    University of Göteborg.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Eriksson, Therese L
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Frängsmyr, Lars
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Rinaldi, Simon
    University of Glasgow.
    Willison, Hugh J
    University of Glasgow.
    Domellöf, Fatima Pedrosa
    Umeå University, Faculty of Medicine, Department of Clinical Sciences, Ophthalmology. Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB), Anatomy.
    Stehle, Thilo
    University of Tübingen, Vanderbilt University School of Medicine.
    Arnberg, Niklas
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    The GD1a glycan is a cellular receptor for adenoviruses causing epidemic keratoconjunctivitis (Letter)2011In: Nature Medicine, ISSN 1078-8956, E-ISSN 1546-170X, Vol. 17, no 1, p. 105-109Article in journal (Refereed)
    Abstract [en]

    Adenovirus type 37 (Ad37) is a leading cause of epidemic keratoconjunctivitis (EKC), a severe and highly contagious ocular disease. Whereas most other adenoviruses infect cells by engaging CD46 or the coxsackie and adenovirus receptor (CAR), Ad37 binds previously unknown sialic acid-containing cell surface molecules. By glycan array screening, we show here that the receptor-recognizing knob domain of the Ad37 fiber protein specifically binds a branched hexasaccharide that is present in the GD1a ganglioside and that features two terminal sialic acids. Soluble GD1a glycan and GD1a-binding antibodies efficiently prevented Ad37 virions from binding and infecting corneal cells. Unexpectedly, the receptor is constituted by one or more glycoproteins containing the GD1a glycan motif rather than the ganglioside itself, as shown by binding, infection and flow cytometry experiments. Molecular modeling, nuclear magnetic resonance and X-ray crystallography reveal that the two terminal sialic acids dock into two of three previously established sialic acid-binding sites in the trimeric Ad37 knob. Surface plasmon resonance analysis shows that the knob-GD1a glycan interaction has high affinity. Our findings therefore form a basis for the design and development of sialic acid-containing antiviral drugs for topical treatment of EKC.

  • 38.
    Normark, Monica
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pommer, Linda
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Gräsvik, John
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gorzsas, Andras
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Winestrand, Sandra
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Biochemical Conversion of Torrefied Norway Spruce After Pretreatment with Acid or Ionic Liquid2016In: Bioenergy Research, ISSN 1939-1234, E-ISSN 1939-1242, Vol. 9, no 1, p. 355-368Article in journal (Refereed)
    Abstract [en]

    The chemical effects of torrefaction and the possibility to combine torrefaction with biochemical conversion were explored in experiments with five preparations of wood of Norway spruce that had been torrefied using different degrees of severity. Compositional analysis and analyses using solid-state CP/MAS C-13 NMR, Fourier-transform infrared (FTIR) spectroscopy, and Py-GC/MS showed small gradual changes, such as decreased hemicellulosic content and increased Klason lignin value, for torrefaction conditions in the range from 260 A degrees C and 8 min up to 310 A degrees C and 8 min. The most severe torrefaction conditions (310 A degrees C, 25 min) resulted in substantial loss of glucan and further increase of the Klason lignin value, which was attributed to conversion of carbohydrate to pseudo-lignin. Even mild torrefaction conditions led to decreased susceptibility to enzymatic hydrolysis of cellulose, a state which was not changed by pretreatment with sulfuric acid. Pretreatment with the ionic liquid (IL) 1-butyl-3-methylimidazolium acetate overcame the additional recalcitrance caused by torrefaction, and the glucose yields after 72 h of enzymatic hydrolysis of wood torrefied at 260 A degrees C for 8 min and at 285 A degrees C for 16.5 min were as high as that of IL-pretreated non-torrefied spruce wood. Compared to IL-pretreated non-torrefied reference wood, the glucose production rates after 2 h of enzymatic hydrolysis of IL-pretreated wood torrefied at 260 A degrees C for 8 min and at 285 A degrees C for 16.5 min were 63 and 40 % higher, respectively. The findings offer increased understanding of the effects of torrefaction and indicate that mild torrefaction is compatible with biochemical conversion after pretreatment with alternative solvents that disrupt pseudo-lignin-containing lignocellulose.

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  • 39. Pawar, Prashant Mohan-Anupama
    et al.
    Derba-Maceluch, Marta
    Chong, Sun-Li
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bashar, Shamrat Shafiul
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ahvenainen, Patrik
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ozparpucu, Merve
    Ruggeberg, Markus
    Serimaa, Ritva
    Lawoko, Martin
    Tenkanen, Maija
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    In muro deacetylation of xylan affects lignin properties and improves saccharification of aspen wood2017In: Biotechnology for Biofuels, ISSN 1754-6834, E-ISSN 1754-6834, Vol. 10, article id 98Article in journal (Refereed)
    Abstract [en]

    Background: Lignocellulose from fast growing hardwood species is a preferred source of polysaccharides for advanced biofuels and “green” chemicals. However, the extensive acetylation of hardwood xylan hinders lignocellulose saccharification by obstructing enzymatic xylan hydrolysis and causing inhibitory acetic acid concentrations during microbial sugar fermentation. To optimize lignocellulose for cost-effective saccharification and biofuel production, an acetyl xylan esterase AnAXE1 from Aspergillus niger was introduced into aspen and targeted to cell walls.

    Results: AnAXE1-expressing plants exhibited reduced xylan acetylation and grew normally. Without pretreatment, their lignocellulose yielded over 25% more glucose per unit mass of wood (dry weight) than wild-type plants. Glucose yields were less improved (+7%) after acid pretreatment, which hydrolyses xylan. The results indicate that AnAXE1 expression also reduced the molecular weight of xylan, and xylan–lignin complexes and/or lignin co-extracted with xylan, increased cellulose crystallinity, altered the lignin composition, reducing its syringyl to guaiacyl ratio, and increased lignin solubility in dioxane and hot water. Lignin-associated carbohydrates became enriched in xylose residues, indicating a higher content of xylo-oligosaccharides.

    Conclusions: This work revealed several changes in plant cell walls caused by deacetylation of xylan. We propose that deacetylated xylan is partially hydrolyzed in the cell walls, liberating xylo-oligosaccharides and their associated lignin oligomers from the cell wall network. Deacetylating xylan thus not only increases its susceptibility to hydrolytic enzymes during saccharification but also changes the cell wall architecture, increasing the extractability of lignin and xylan and facilitating saccharification.

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  • 40. Pawar, Prashant Mohan-Anupama
    et al.
    Ratke, Christine
    Balasubramanian, Vimal K.
    Chong, Sun-Li
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Adriasola, Mathilda
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenstrom, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Szwaj, Klaudia
    Derba-Maceluch, Marta
    Gaertner, Cyril
    Mouille, Gregory
    Ezcurra, Ines
    Tenkanen, Maija
    Jonsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, p. 1491-1505Article in journal (Refereed)
    Abstract [en]

    High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter:: GUS lines in hybrid aspen (Populus tremula x tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.

  • 41. Pinkner, Jerome S.
    et al.
    Remaut, Han
    Buelens, Floris
    Miller, Eric
    Åberg, Veronica
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pemberton, Nils
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, Andreas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Seed, Patrick
    Waksman, Gabriel
    Hultgren, Scott J.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Rationally designed small compounds inhibit pilus biogenesis in uropathogenic bacteria2006In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 103, no 47, p. 17897-17902Article in journal (Refereed)
    Abstract [en]

    A chemical synthesis platform with broad applications and flexibility was rationally designed to inhibit biogenesis of adhesive pili assembled by the chaperone–usher pathway in Gram-negative pathogens. The activity of a family of bicyclic 2-pyridones, termed pilicides, was evaluated in two different pilus biogenesis systems in uropathogenic Escherichia coli. Hemagglutination mediated by either type 1 or P pili, adherence to bladder cells, and biofilm formation mediated by type 1 pili were all reduced by 90% in laboratory and clinical E. coli strains. The structure of the pilicide bound to the P pilus chaperone PapD revealed that the pilicide bound to the surface of the chaperone known to interact with the usher, the outer-membrane assembly platform where pili are assembled. Point mutations in the pilicide-binding site dramatically reduced pilus formation but did not block the ability of PapD to bind subunits and mediate their folding. Surface plasmon resonance experiments confirmed that the pilicide interfered with the binding of chaperone–subunit complexes to the usher. These pilicides thus target key virulence factors in pathogenic bacteria and represent a promising proof of concept for developing drugs that function by targeting virulence factors.

  • 42.
    Prasad, Bagineni
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Das, Rabindra Nath
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jamroskovic, Jan
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Kumar, Rajendra
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sabouri, Nasim
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The Relation Between Position and Chemical Composition of Bis-Indole Substituents Determines Their Interactions With G-Quadruplex DNA2020In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 26, no 43, p. 9561-9572Article in journal (Refereed)
    Abstract [en]

    G‐quadruplex (G4) DNA structures are linked to fundamental biological processes and human diseases, which has triggered the development of compounds that affect these DNA structures. However, more knowledge is needed about how small molecules interact with G4 DNA structures. This study describes the development of a new class of bis‐indoles (3,3‐diindolyl‐methyl derivatives) and detailed studies of how they interact with G4 DNA using orthogonal assays, biophysical techniques, and computational studies. This revealed compounds that strongly bind and stabilize G4 DNA structures, and detailed binding interactions which e.g. show that charge variance can play a key role in G4 DNA binding. Furthermore, the structure‐activity relationships generated opened the possibilities to replace or introduce new substituents on the core structure, which is of key importance to optimize compound properties or introduce probes to further expand the possibilities of these compounds as tailored research tools to study G4 biology.

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  • 43.
    Renström, Anna
    et al.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Choudhary, Shruti
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jämtgård, Sandra
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden; Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Tuominen, Hannele
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation2024In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 176, no 1, article id e14219Article in journal (Refereed)
    Abstract [en]

    Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR <0.01) respond to added NO3- , the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.

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  • 44.
    Roach, Melissa
    et al.
    Swedish University of Agricultural Sciences.
    Gerber, Lorenz
    Swedish University of Agricultural Sciences.
    Sandquist, David
    Gorzsás, András
    Swedish University of Agricultural Sciences.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kumar, Manoj
    Swedish University of Agricultural Sciences.
    Steinhauser, Marie Caroline
    Feil, Regina
    Daniel, Geoffrey
    Stitt, Mark
    Sundberg, Björn
    Swedish University of Agricultural Sciences.
    Niittylä, Totte
    Swedish University of Agricultural Sciences.
    Fructokinase is required for carbon partitioning to cellulose in aspen wood2012In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 70, no 6, p. 967-977Article in journal (Refereed)
    Abstract [en]

    Sucrose is the main transported form of carbon in several plant species, including Populus species. Sucrose metabolism in developing wood has therefore a central role in carbon partitioning to stem biomass. Half of the sucrose-derived carbon is in the form of fructose, but metabolism of fructose has received little attention as a factor in carbon partitioning to walls of wood cells. We show that RNAi-mediated reduction of FRK2 activity in developing wood of hybrid aspen (Populus tremula × tremuloides) led to the accumulation of soluble neutral sugars and a decrease in hexose phosphates and UDP-glucose, indicating that carbon flux to cell-wall polysaccharide precursors is decreased. Reduced FRK2 activity also led to thinner fiber cell walls with a reduction in the proportion of cellulose. No pleiotropic effects on stem height or diameter were observed. The results establish a central role for FRK2 activity in carbon flux to wood cellulose.

  • 45.
    Semenchuk, Philipp R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Climate Impacts Research Centre, Umeå University, Abisko, Sweden; Department of Arctic and Marine Biology, Faculty of Biosciences Fisheries and Economics, UiT-The Arctic University of Norway, Tromsø, Norway; Division of Conservation Biology, Vegetation Ecology and Landscape Ecology, Department of Botany and Biodiversity Research, Vienna University, Vienna, Austria.
    Krab, Eveline J
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Climate Impacts Research Centre, Umeå University, Abisko, Sweden; Swedish University of Agricultural Sciences, Department of Soil and Environment, Uppsala, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Phillips, Carly A.
    Ancin-Murguzur, Francisco J.
    Cooper, Elisabeth J.
    Soil organic carbon depletion and degradation in surface soil after long-term non-growing season warming in High Arctic Svalbard2019In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 646, p. 158-167Article in journal (Refereed)
    Abstract [en]

    Arctic tundra active-layer soils are at risk of soil organic carbon (SOC) depletion and degradation upon global climate warming because they are in a stage of relatively early decomposition. Non-growing season (NGS) warming is particularly pronounced, and observed increases of CO2 emissions during experimentally warmed NGSs give concern for great SOC losses to the atmosphere. Here, we used snow fences in Arctic Spitsbergen dwarf shrub tundra to simulate 1.86 degrees C NGS warming for 9 consecutive years, while growing season temperatures remained unchanged. In the snow fence treatment, the 4-11 cm thick A-horizon had a 2% lower SOC concentration and a 0.48 kg Cm-2 smaller pool size than the controls, indicating SOC pool depletion. The snow fence treatment's A-horizon's alkyl/O-alkyl ratio was also significantly increased, indicating an advance of SOC degradation. The underlying 5 cm of B/C-horizon did not show these effects. Our results support the hypothesis that SOC depletion and degradation are connected to the long-term transience of observed ecosystem respiration (ER) increases upon soil warming. We suggest that the bulk of warming induced ER increases may originate from surface and not deep active layer or permafrost horizons. The observed losses of SOC might be significant for the ecosystem in question, but are in magnitude comparatively small relative to anthropogenic greenhouse gas enrichment of the atmosphere. We conclude that a positive feedback of carbon losses from surface soils of Arctic dwarf shrub tundra to anthropogenic forcing will be minor, but not negligible.

  • 46.
    Shakeri Yekta, Sepehr
    et al.
    Department of Thematic Studies - Environmental Change, Linköping University, Linköping, Sweden; Biogas Research Center, Linköping University, Linköping, Sweden.
    Elreedy, Ahmed
    Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Tokyo, Japan; Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany.
    Liu, Tong
    Biogas Research Center, Linköping University, Linköping, Sweden; Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Uppsala, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Isaksson, Simon
    Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Uppsala, Sweden.
    Fujii, Manabu
    Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Tokyo, Japan.
    Schnürer, Anna
    Biogas Research Center, Linköping University, Linköping, Sweden; Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Uppsala, Sweden.
    Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane2022In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 817, article id 152967Article in journal (Refereed)
    Abstract [en]

    This study aims to elucidate the role of sulfide and its precursors in anaerobic digestion (i.e., cysteine, representing sulfur-containing amino acids, and sulfate) on microbial oleate conversion to methane. Serine, with a similar structure to cysteine but with a hydroxyl group instead of a thiol, was included as a control to assess potential effects on methane formation that were not related to sulfur functionalities. The results showed that copresence of sulfide and oleate in anaerobic batch assays accelerated the methane formation compared to assays with only oleate and mitigated negative effect on methane formation caused by increased sulfide level. Nuclear magnetic resonance spectroscopy of sulfide-exposed oleate suggested that sulfide reaction with oleate double bonds likely contributed to negation of the negative effect on the methanogenic activity. Methane formation from oleate was also accelerated in the presence of cysteine or serine, while sulfate decreased the cumulative methane formation from oleate. Neither cysteine nor serine was converted to methane, and their accelerating effects was associated to different mechanisms due to establishment of microbial communities with different structures, as evidenced by high-throughput sequencing of 16S rRNA gene. These outcomes contribute with new knowledge to develop strategies for optimum use of sulfur- and lipid-rich wastes in anaerobic digestion processes.

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  • 47.
    Strunk, Peter
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Öman, Tommy
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gorzsás, András
    Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Eliasson, Bertil
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Characterization of dissolving pulp by multivariate data analysis of FT-IR and NMR spectra2011In: Nordic Pulp & Paper Research Journal, ISSN 0283-2631, E-ISSN 2000-0669, Vol. 26, no 4, p. 398-409Article in journal (Refereed)
    Abstract [en]

    Several grades of dissolving pulps have been analyzed using FT-IR, solid state13C NMR and two dimensional1H-13C HSQC NMR spectroscopy to obtain an extensive data set for further characterization. The selection of the dissolving pulps with high cellulose purity was based on pulping process, wood type and, intrinsic pulp viscosity. Multivariate data analysis was used to investigate how information derived from the spectroscopic data correlate to each of the selection criterion: wood type, process type and viscosity. The spectroscopic methods were also compared with common dissolving pulp analyses to see to what extent spectroscopy can predict pulp analyses.

    Correlations were found between the spectroscopic data and the pulp characteristics process type and wood type, but not for intrinsic viscosity. A reason for a good correlation to wood type appears to be the hemicelluloses composition, expressed as the xylose:mannose ratio by 2D NMR spectroscopy. For process type, 2D NMR showed the most characteristic property to be the amount of reducing ends in the cellulosic samples, which in turn strongly correlates to lower molecular weight for the sulfite samples as determined by molecular weight distribution.

    Many common, yet expensive and time consuming, pulp analyses could also be predicted by the achieved models. It can be concluded that investigations of dissolving pulp characteristics, especially concerning different wood and process types, can take advantage of the methods and models presented in this study.

  • 48.
    Svensson, Anette
    et al.
    Organic Chemistry 2 Center for Chemistry and Chemical Engineering Lund Institute of Technology, Lund University P.O. Box 124, SE-221 00 Lund, Sweden.
    Larsson, Andreas
    Umeå University, Faculty of Science and Technology, Chemistry.
    Emtenäs, Hans
    Umeå University, Faculty of Science and Technology, Chemistry.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Chemistry.
    Fex, Tomas
    3Active Biotech, Lund Research Center P.O. Box 724, SE-220 07 Lund, Sweden.
    Hultgren, Scott J.
    Department of Molecular Microbiology Washington University School of Medicine 660 South Euclid Avenue, St. Louis, MO 63110, USA.
    Pinker, Jerome S.
    Department of Molecular Microbiology Washington University School of Medicine 660 South Euclid Avenue, St. Louis, MO 63110, USA.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Chemistry.
    Design and evaluation of Pilicides: Potential novel antibacterial agents directed against Uropathogenic Escherichia coli2001In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, ChemBioChem (Online), ISSN '1439-7633', Vol. 2, no 12, p. 915-918Article in journal (Refereed)
  • 49. Takahashi, Junko
    et al.
    Rudsander, Ulla J
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Banasiak, Alicja
    Harholt, Jesper
    Amelot, Nicolas
    Immerzeel, Peter
    Ryden, Peter
    Endo, Satoshi
    Ibatullin, Farid M
    Brumer, Harry
    del Campillo, Elena
    Master, Emma R.
    Scheller, Henrik Vibe
    Sundberg, Björn
    Teeri, Tuula T
    Mellerowicz, Ewa J
    KORRIGAN1 and its Aspen Homolog PttCel9A1 Decrease Cellulose Crystallinity in Arabidopsis Stems2009In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, no 6, p. 1099-1115Article in journal (Refereed)
    Abstract [en]

    KORRIGAN1 (KOR1) is a membrane-bound cellulase implicated incellulose biosynthesis. PttCel9A1 from hybrid aspen (Populustremula L. x tremuloides Michx.) has high sequence similarityto KOR1 and we demonstrate here that it complements kor1-1 mutants,indicating that it is a KOR1 ortholog. We investigated the functionof PttCel9A1/KOR1 in Arabidopsis secondary growth using transgeniclines expressing 35S::PttCel9A1 and the KOR1 mutant line irx2-2.The presence of elevated levels of PttCel9A1/KOR1 in secondarywalls of 35S::PttCel9A1 lines was confirmed by in muro visualizationof cellulase activity. Compared with the wild type, 35S::PttCel9A1lines had higher trifluoroacetic acid (TFA)-hydrolyzable glucancontents, similar Updegraff cellulose contents and lower cellulosecrystallinity indices, as determined by 13C solid-state nuclearmagnetic resonance (NMR) spectroscopy. irx2-2 mutants had wild-typeTFA-hydrolyzable glucan contents, but reduced Updegraff cellulosecontents and higher than wild-type cellulose crystallinity indices.The data support the hypothesis that PttCel9A1/KOR1 activityis present in cell walls, where it facilitates cellulose biosynthesisin a way that increases the amount of non-crystalline cellulose.

  • 50.
    Talyzin, Alexandr
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Mercier, Guillaume
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Klechikov, Alexey
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Johnels, Dan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wei, Di
    Cotton, Darryl
    Opitz, Andreas
    Moons, Ellen
    Brodie vs Hummers graphite oxides for preparation of multi-layered materials2017In: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 115, p. 430-440Article in journal (Refereed)
    Abstract [en]

    Graphite oxides synthesized by one and two step Brodie oxidation (BGO) and Hummers (HGO) methods were analyzed by a variety of characterization methods in order to evaluate the reasons behind the difference in their properties. It is found that the Brodie method results in a higher relative amount of hydroxyl groups and a more homogeneous overall distribution of functional groups over the planar surface of the graphene oxide flakes. The higher number of carbonyl and carboxyl groups in HGO, detected by several methods, including XPS, NMR and FTIR, unavoidably results in defects of the graphene "skeleton", holes and overall disruption of the carbon-carbon bond network, stronger deviation from planar flake shape and poor ordering of the graphene oxide layers. It is also suggested that functional groups in HGO are less homogeneously distributed over the flake surface, forming some nanometer-sized graphene areas. The presence of differently oxidized areas on the GO surface results in inhomogeneous solvation and hydration of HGO and effects of inter- and intra-stratification. The proposed interpretation of the data explains the higher mechanical strength of multi-layered BGO membranes/papers, which are also less affected by humidity changes, thus providing an example of a membrane property superior to that of HGO.

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