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  • 301.
    Cavka, Adnan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Stagge, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jönsson, Leif J.
    Identification of Small Aliphatic Aldehydes in Pretreated Lignocellulosic Feedstocks and Evaluation of Their Inhibitory Effects on Yeast2015Inngår i: Journal of Agricultural and Food Chemistry, ISSN 0021-8561, E-ISSN 1520-5118, Vol. 63, nr 44, s. 9747-9754Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Six lignocellulosic hydrolysates produced through acid pretreatment were analyzed for the occurrence of formaldehyde, acetaldehyde, and glycolaldehyde. Acetaldehyde was found in all six (0.3-1.6 mM) and formaldehyde in four (<= 4.4 mM), whereas glycolaldehyde was not detected. To assess the relevance of these findings, fermentations with yeast and formaldehyde or acetaldehyde were performed in the concentration interval 0.5-10 mM. Formaldehyde already inhibited at 1.0 mM, whereas 5.0 mM acetaldehyde was needed to obtain a clear inhibitory effect. After 24 h of fermentation, 1.5 mM formaldehyde reduced the glucose consumption by 85%, the balanced ethanol yield by 92%, and the volumetric productivity by 91%. The results show that formaldehyde and acetaldehyde are prevalent in pretreated lignocellulose and that formaldehyde in some cases could explain a large part of the inhibitory effects on yeast by lignocellulosic hydrolysates, as three of six hydrolysates contained >= 1.9 mM formaldehyde, which was shown to be strongly inhibitory.

  • 302.
    Cedergren, Anders
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Nordmark, Ulrika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Determination of water in NIST reference material for mineral oils2000Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 72, nr 14, s. 3392-3395Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The accuracy of the reference concentrations of moisture in electrical insulating oil RM 8506 and lubricating oil RM 8507 (both of mineral type) and specified by the National institute of Standards and Technology (NIST) as containing 39.7 and 76.8 ppm (w/w) water, respectively, has recently been the subject of debate in this journal. To shed some further light on this controversy, we report in this correspondence results for these oils obtained by two additional methods, one based on specially designed reagents for diaphragm-free Karl Fischer (KF) coulometry and the other based on the concept of stripping at elevated temperature/continuous KF coulometry. A positive interference effect was shown to take place for RM 8506 when the direct coulometric method was used. If the results are corrected for this, the values including six different procedures varied in the range 13.5-15.6 ppm (w/w). For RM 8507, all values were between 42.5 and 47.2 ppm (w/w), which means that the values recommended by NIST for both reference oils using volumetric titration are about twice as high as those obtained with the other techniques. A possible explanation for this discrepancy is presented.

  • 303. Chaintreau, Alain
    et al.
    Fieber, Wolfgang
    Sommer, Horst
    Gilbert, Alexis
    Yamada, Keita
    Yoshida, Naohiro
    Pagelot, Alain
    Moskau, Detlef
    Moreno, Aitor
    Schleucher, Jürgen
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Reniero, Fabiano
    Holland, Margaret
    Guillou, Claude
    Silvestre, Virginie
    Akoka, Serge
    Remaud, Gerald S
    Site-specific C-13 content by quantitative isotopic C-13 nuclear magnetic resonance spectrometry: a pilot inter-laboratory study2013Inngår i: Analytica Chimica Acta, ISSN 0003-2670, E-ISSN 1873-4324, Vol. 788, s. 108-113Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Isotopic C-13 NMR spectrometry, which is able to measure intra-molecular C-13 composition, is of emerging demand because of the new information provided by the C-13 site-specific content of a given molecule. A systematic evaluation of instrumental behaviour is of importance to envisage isotopic C-13 NMR as a routine tool. This paper describes the first collaborative study of intra-molecular C-13 composition by NMR. The main goals of the ring test were to establish intra-and inter-variability of the spectrometer response. Eight instruments with different configuration were retained for the exercise on the basis of a qualification test. Reproducibility at the natural abundance of isotopic C-13 NMR was then assessed on vanillin from three different origins associated with specific delta C-13(i) profiles. The standard deviation was, on average, between 0.9 and 1.2 parts per thousand for intra-variability. The highest standard deviation for inter-variability was 2.1%. This is significantly higher than the internal precision but could be considered good in respect of a first ring test on a new analytical method. The standard deviation of delta C-13(i) in vanillin was not homogeneous over the eight carbons, with no trend either for the carbon position or for the configuration of the spectrometer. However, since the repeatability for each instrument was satisfactory, correction factors for each carbon in vanillin could be calculated to harmonize the results.

    (C) 2013 Elsevier B.V. All rights reserved.

  • 304.
    Charlson, Alexandra
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Removal of pharmaceuticalcontainingwastewater by bioandhydrochar adsorbents: Adsorption capacity and surface functionalities2017Independent thesis Advanced level (degree of Master (Two Years)), 40 poäng / 60 hpOppgave
  • 305. Chartrand, Michelle
    et al.
    Passeport, Elodie
    Rose, Carla
    Lacrampe-Couloume, Georges
    Bidleman, Terry F.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Liisa M. Jantunen, Liisa M.
    Sherwood Lollar, Barbara
    Compound specific isotope analysis of hexachlorocyclohexane isomers: a method for source fingerprinting and field investigation of in situ biodegradation2015Inngår i: Rapid Communications in Mass Spectrometry, ISSN 0951-4198, E-ISSN 1097-0231, Vol. 29, nr 6, s. 505-514Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    RATIONALE: The manufacturing and uses of hexachlorocyclohexane (HCH) have resulted in a serious environmentalchallenge and legacy. This study highlights the ability of compound specific isotope analysis (CSIA) to distinguishamong various HCH sources and to support the evaluation of the potential for in situ biodegradation in contaminatedgroundwater.

    METHODS: Tests were conducted to verify the absence of significant isotope fractionation during HCH sample preconcentrationincluding dichloromethane extraction, solvent exchange into iso-octane, and H2SO4 clean-up, and analysisby gas chromatography/combustion-isotope ratio mass spectrometry (GC/C-IRMS). The method was then applied tofour Technical Grade (TG) HCH mixtures procured from different sources and to groundwater samples from acontaminated site.

    RESULTS: The pre-concentration method enabled determination of carbon isotope ratios (δ13C values) of HCH isomerswith no significant isotopic fractionation. The TG-HCH mixtures had significantly different δ13C values. Moreover, forany given TG-HCH, all isomers had δ13C values within 1.1‰ of each other – a distinctly uniform fingerprint. At theHCH-contaminated field site, compared with source wells, downgradient wells showed significant (up to 5.1‰)enrichment in 13C and the δ13C values of the HCH isomers were significantly different from each other.

    CONCLUSIONS: A method was successfully developed for the CSIA of HCH isomers that showed potential for HCHsource differentiation and identification of HCH in situ biodegradation. At the HCH-contaminated site, the observedpreferential isotopic enrichment of certain isomers relative to others for a given source allows differentiation betweenbiodegraded and non-biodegraded HCH.

  • 306.
    Chateau, Denis
    et al.
    Laboratoire de Chimie, Université de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, CNRS UMR5182, Lyon 69364, France.
    Chaput, Frederic
    Laboratoire de Chimie, Université de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, CNRS UMR5182, Lyon 69364, France.
    Lopes, Cesar
    Information Systems, Swedish Defence Research Agency (FOI), Linköping SE-581 11, Sweden.
    Lindgren, Mikael
    Department of Physics, Norwegian University of Science and Technology, Trondheim NO-7491, Norway.
    Brännlund, Carl
    Information Systems, Swedish Defence Research Agency (FOI), Linköping SE-581 11, Sweden.
    Öhgren, Johan
    Information Systems, Swedish Defence Research Agency (FOI), Linköping SE-581 11, Sweden.
    Djourelov, Nikolay
    Institut de Physique Nucléaire, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, France.
    Nedelec, Patrick
    Institut de Physique Nucléaire, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, France.
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kindahl, Tomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Lerouge, Frederic
    Laboratoire de Chimie, Université de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, CNRS UMR5182, Lyon 69364, France.
    Andraud, Chantal
    Laboratoire de Chimie, Université de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, CNRS UMR5182, Lyon 69364, France.
    Parola, Stephane
    Laboratoire de Chimie, Université de Lyon, Université Claude Bernard Lyon 1, ENS Lyon, CNRS UMR5182, Lyon 69364, France.
    Silica hybrid sol-gel materials with unusually high concentration of Pt-organic molecular guests: Studies of luminescence and nonlinear absorption of light2012Inngår i: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 4, nr 5, s. 2369-2377Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The development of new photonic materials is a key step towards improvement of existing optical devices and for the preparation of a new generation of systems. Therefore synthesis of photonic hybrid materials with a thorough understanding and control of the microstructure-to-properties relationships is crucial. In this perspective, a new preparation method based on fast gelation reactions using simple dispersion of dyes without strong covalent bonding between dye and matrix has been developed. This new sol-gel method is demonstrated through synthesis of monolithic siloxane-based hybrid materials highly doped by various platinum(II) acetylide derivatives. Concentrations of the chromophores as high as 400 mM were obtained and resulted in unprecedented optical power limiting (OPL) performance at 532 nm of the surface-polished solids. Static and time-resolved photoluminescence of the prepared hybrid materials were consistent with both OPL data and previous studies of similar Pt(II) compounds in solution. The impacts of the microstructure and the chemical composition of the matrix on the spectroscopic properties, are discussed.

  • 307.
    Chatterjee, Robin
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johansson, Kristin
    Department of Chemical Engineering, Karlstad University, SE-651 88 Karlstad, Sweden.
    Järnström, Lars
    Department of Chemical Engineering, Karlstad University, SE-651 88 Karlstad, Sweden.
    Jönsson, Leif J
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Evaluation of the potential of fungal and plant laccases for active-packaging applications2011Inngår i: Journal of Agricultural and Food Chemistry, ISSN 0021-8561, E-ISSN 1520-5118, Vol. 59, nr 10, s. 5390-5395Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Laccases from Trametes versicolor (TvL), Myceliophthora thermophila (MtL), and Rhus vernicifera (RvL) were investigated with regard to their potential utilization as oxygen scavengers in active packages containing food susceptible to oxidation reactions. The substrate selectivity of the laccases was investigated with a set of 17 reducing substrates, mainly phenolic compounds. The temperature dependence of reactions performed at low temperatures (4-31 °C) was studied. Furthermore, the laccases were subjected to immobilization in a latex/clay matrix and drying procedures performed at temperatures up to 105 °C. The results show that it is possible to immobilize the laccases with retained activity after dispersion coating, drying at 75-105 °C, and subsequent storage of the enzyme-containing films at 4 °C. TvL and, to some extent, MtL were promiscuous with regard to their reducing substrate, in the sense that the difference in activity with the 17 substrates tested was relatively small. RvL, on the other hand, showed high selectivity, primarily toward substrates resembling its natural substrate urushiol. When tested at 7 °C, all three laccases retained >20% of the activity they had at 25 °C, which suggests that it would be possible to utilize the laccases also in refrigerated food packages. Coating and drying resulted in a remaining enzymatic activity ranging from 18 to 53%, depending on the drying conditions used. The results indicate that laccases are useful for active-packaging applications and that the selectivity for reducing substrates is an important characteristic of laccases from different sources.

  • 308. Chatterjee, Ruchira
    et al.
    Lassalle, Louise
    Gul, Sheraz
    Fuller, Franklin D.
    Young, Iris D.
    Ibrahim, Mohamed
    de Lichtenberg, Casper
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemistry – Ångström, Molecular Biomimetics, Uppsala University, Uppsala 75237, Sweden.
    Cheah, Mun Hon
    Zouni, Athina
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemistry – Ångström, Molecular Biomimetics, Uppsala University, Uppsala 75237, Sweden.
    Yachandra, Vittal K.
    Kern, Jan
    Yano, Junko
    Structural isomers of the S-2 state in photosystem II: do they exist at room temperature and are they important for function?2019Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 166, nr 1, s. 60-72Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In nature, an oxo‐bridged Mn4CaO5 cluster embedded in photosystem II (PSII), a membrane‐bound multi‐subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light‐induced charge separations in the reaction center of PSII. The Mn4CaO5 cluster accumulates four oxidizing equivalents to enable the four‐electron four‐proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S‐states, S0 – S4 in the Kok cycle. One important question related to the catalytic mechanism of the oxygen‐evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S‐states and if such equilibria are essential for the mechanism of the O‐O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X‐ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S2state of PSII with structural data collected of the S1, S2 and S3 states by serial crystallography at neutral pH (∼6.5) using an X‐ray free electron laser at room temperature. While the cryogenic data show the presence of at least two structural forms of the S2 state, the room temperature crystallography data can be well‐described by just one S2 structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.

  • 309.
    Chee, Pui Shan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ammonium and Acetate Ion Uptake on Stationary Phases in Hydrophilic Interaction Chromatography by the Minor Disturbance Method2015Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
  • 310.
    Chen, Genqiang
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Donghua University, College of Chemistry, Chemical Engineering & Biotechnology, Shanghai, Peoples Republic of China.
    Wu, Guochao
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hong, Feng
    Jönsson, Leif
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Production of bacterial nanocellulose from waste fiber sludge and its use in papermaking2017Inngår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 254Artikkel i tidsskrift (Annet vitenskapelig)
  • 311. Chen, Xi
    et al.
    Venkatachalapathy, Muthukumaran
    Dehmelt, Leif
    Wu, Yao-Wen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Multidirectional Activity Control of Cellular Processes by a Versatile Chemo-optogenetic Approach2018Inngår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 57, nr 37, s. 11993-11997Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The spatiotemporal dynamics of proteins or organelles plays a vital role in controlling diverse cellular processes. However, acute control of activity at distinct locations within a cell is challenging. A versatile multidirectional activity control (MAC) approach is presented, which employs a photoactivatable system that may be dimerized upon chemical inducement. The system comprises second-generation SLF*-TMP (S*T) and photocaged NvocTMP-Cl dimerizers; where, SLF*-TMP features a synthetic ligand of the FKBP(F36V) binding protein, Nvoc is a caging group, and TMP is the antibiotic trimethoprim. Two MAC strategies are demonstrated to spatiotemporally control cellular signaling and intracellular cargo transport. The novel platform enables tunable, reversible, and rapid control of activity at multiple compartments in living cells.

  • 312. Chen, Xi
    et al.
    Venkatachalapathy, Muthukumaran
    Kamps, Dominic
    Weigel, Simone
    Kumar, Ravi
    Orlich, Michael
    Garrecht, Ruben
    Hirtz, Michael
    Niemeyer, Christof M.
    Wu, Yao-Wen
    Chemical Genomics Centre of the Max-Planck Society, Dortmund, Germany.
    Dehmelt, Leif
    “Molecular Activity Painting”: Switch-like, light-controlled perturbations inside living cells2017Inngår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, nr 21, s. 5916-5920Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Acute subcellular protein targeting is a powerful tool to study biological networks. However, signaling at the plasma membrane is highly dynamic, making it difficult to study in space and time. In particular, sustained local control of molecular function is challenging due to lateral diffusion of plasma membrane targeted molecules. Here we present “Molecular Activity Painting” (MAP), a novel technology which combines photoactivatable chemically induced dimerization (pCID) with immobilized artificial receptors. The immobilization of artificial receptors by surface-immobilized antibodies blocks lateral diffusion, enabling rapid and stable “painting” of signaling molecules and their activity at the plasma membrane with micrometer precision. Using this method, we show that painting of the RhoA-myosin activator GEF-H1 induces patterned acto-myosin contraction inside living cells.

  • 313. Chen, Xiao-Jia
    et al.
    Dinh, Ngoc Phuoc
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Zhao, Jing
    Wang, Yi-Tao
    Li, Shao-Ping
    Svec, Frantisek
    Effect of ion adsorption on CEC separation of small molecules using hypercrosslinked porous polymer monolithic capillary columns2012Inngår i: Journal of Separation Science, ISSN 1615-9306, E-ISSN 1615-9314, Vol. 35, nr 12, s. 1502-1505Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Both poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) and poly(4-methylstyrene-co-vinylbenzyl chloride-co-divinylbenzene) monolithic columns have been hypercrosslinked and for the first time used to achieve capillary electrochromatographic separations. Although these columns do not contain ionizable functionalities, electroosmotic flow was observed due to adsorption of ions from a buffer solution contained in the mobile phase on the surface of the hydrophobic polymer. An increase of more than one order of magnitude was observed with the use of both monolithic polymers. The hypercrosslinking reaction creates a large surface area thus enabling adsorption of a much larger number of ions. Alkylbenzenes were successfully separated using the hypercrosslinked monolithic columns.

  • 314.
    Chen, Yang-Er
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. College of Life Sciences, Sichuan Agricultural University, Ya'an, China.
    Yuan, Shu
    Schröder, Wolfgang P.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Comparison of methods for extracting thylakoid membranes of Arabidopsis plants2016Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 156, nr 1, s. 3-12Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Robust and reproducible methods for extracting thylakoid membranes are required for the analysis of photosynthetic processes in higher plants such as Arabidopsis. Here, we compare three methods for thylakoid extraction using two different buffers. Method I involves homogenizing the plant material witha metal/glass blender; method II involves manually grinding the plant materialin ice-cold grinding buffer with a mortar and method III entails snap-freezing followed by manual grinding with a mortar, after which the frozen powder is thawed in isolation buffer. Thylakoid membrane samples extracted using each method were analyzed with respect to protein and chlorophyll content, yields relative to starting material, oxygen-evolving activity, protein complex content and phosphorylation. We also examined how the use of fresh and frozen thylakoid material affected the extracts’ contents of protein complexes. The use of different extraction buffers did not significantly alter the protein contentof the extracts in any case. Method I yielded thylakoid membranes with the highest purity and oxygen-evolving activity. Method III used low amounts of starting material and was capable of capturing rapid phosphorylation changes in the sample at the cost of higher levels of contamination. Method II yielded thylakoid membrane extracts with properties intermediate between those obtained with the other two methods. Finally, frozen and freshly isolated thylakoid membranes performed identically in blue native-polyacrylamide gel electrophoresis experiments conducted in order to separate multimeric protein supracomplexes.

  • 315.
    Cheregi, Otilia
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Antibiotic Disc Assay for Measuring Cell Wall Function in Synechocystis sp. PCC68032016Inngår i: Bio-protocol, E-ISSN 2331-8325, Vol. 6, nr 24Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This protocol describes how to investigate the integrity of the outer cell wall in thecyanobacterium Synechocystis sp. PCC6803 using antibiotics. It is adapted to the agar diffusion test(Bauer et al., 1966), in which filter paper discs impregnated with specified concentrations of antibioticswere placed on agar plates inoculated with bacteria. The antibiotics we tested, interfering with thebiosynthesis/function of bacterial cell walls, will diffuse into the agar and produce a zone ofcyanobacterial growth inhibition around the disc(s). The size of the inhibition zone reflects the sensitivityof the strain to the action of antibiotics, e.g., a mutation in a protein functioning within the cell wall or itsconstruction would render the mutant strain more sensitive to the respective antibiotic. The method hasproven to be useful for phenotyping a mutant of Synechocystis sp. PCC6803 lacking all three genesencoding Deg proteases. Deletion of these ATP-independent serine proteases was shown to haveimpact on the outer cell layers of Synechocystis cells.

  • 316.
    Cheregi, Otilia
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Regulation of the scp Genes in the Cyanobacterium Synechocystis sp PCC 6803-What is New?2015Inngår i: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 20, nr 8, s. 14621-14637Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5' GGCGATCGCC 3', was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.

  • 317.
    Cheregi, Otilia
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kotabová, Eva
    Prášil, Ondřej
    Schröder, Wolfgang P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kaňa, Radek
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Presence of state transitions in the cryptophyte alga Guillardia theta2015Inngår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, nr 20, s. 6461-6470Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plants and algae have developed various regulatory mechanisms for optimal delivery of excitation energy to the photosystems even during fluctuating light conditions; these include state transitions as well as non-photochemical quenching. The former process maintains the balance by redistributing antennae excitation between the photosys-tems, meanwhile the latter by dissipating excessive excitation inside the antennae. In the present study, these mecha-nisms have been analysed in the cryptophyte alga Guillardia theta. Photoprotective non-photochemical quenching was observed in cultures only after they had entered the stationary growth phase. These cells displayed a diminished overall photosynthetic efficiency, measured as CO2 assimilation rate and electron transport rate. However, in the logarithmic growth phase G. theta cells redistributed excitation energy via a mechanism similar to state transitions. These state transitions were triggered by blue light absorbed by the membrane integrated chlorophyll a/c antennae, and green light absorbed by the lumenal biliproteins was ineffective. It is proposed that state transitions in G. thetaare induced by small re-arrangements of the intrinsic antennae proteins, resulting in their coupling/uncoupling to the photosystems in state 1 or state 2, respectively. G. theta therefore represents a chromalveolate algae able to perform state transitions.

  • 318.
    Cheregi, Otilia
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Miranda, Hélder
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gröbner, Gerhard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Inactivation of the Deg protease family in the cyanobacterium Synechocystis sp. PCC 6803 has impact on the outer cell layers2015Inngår i: Journal of Photochemistry and Photobiology. B: Biology, ISSN 1011-1344, E-ISSN 1873-2682, s. 383-394Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The serine type Deg/HtrA proteases are distributed in a wide range of organisms from Escherichia coli to humans. The cyanobacterium Synechocystis sp. PCC 6803 possesses three Deg protease orthologues: HtrA, HhoA and HhoB. Previously we compared Synechocystis 6803 wild type cells exposed to mild or severe stress conditions with a mutant lacking all three Deg proteases and demonstrated that stress had strong impact on the proteomes and metabolomes [1]. To identify the biochemical processes, which this protease family is involved in, here we compared Synechocystis sp. PCC 6803 wild type cells with a mutant lacking all three Deg proteases grown under normal growth conditions (30 °C and 40 μmol photons m−2 s−1). Deletion of the Deg proteases lead to the down-regulation of proteins related to the biosynthesis of outer cell layers (e.g. the GDP mannose 4,6-dehydratase) and affected protein secretion. During the late growth phase of the culture Deg proteases were found to be secreted to the extracellular medium of the Synechocystis sp. PCC 6803 wild type strain. While cyanobacterial Deg proteases seem to act mainly in the periplasmic space, deletion of the three proteases influences the proteome and metabolome of the whole cell. Impairments in the outer cell layers of the triple mutant might explain the higher sensitivity toward light and oxidative stress, which was observed earlier by Barker and coworkers [2].

  • 319.
    Cheregi, Otilia
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Vermaas, Wim
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    The search for new chlorophyll-binding proteins in the cyanobacterium Synechocystis sp. PCC 68032012Inngår i: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 162, nr 1, s. 124-133Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Light harvesting provides a major challenge in the production of biofuels from microorganisms; while sunlight provides the energy necessary for biomass/biofuel production, at the same time it damages the cells. The genome of Synechocystis sp. PCC 6803 was searched for open reading frames that might code for yet unidentified chlorophyll-binding proteins with low molecular mass that could be involved in stress-adaptation. Amongst 9,167 hypothetical ORFs corresponding to potential polypeptides of 100 amino acids or less, two were identified that had the potential to be pigment-binding, because they i) encoded a potential transmembrane region, ii) showed sequence similarity with known chlorophyll-binding domains, iii) were conserved in other cyanobacterial species, and iv) their codon adaptation index indicated significant translation probability. The two ORFs were located complementary (antisense) and internal to the ferrochelatase (hemH) and the pyruvate dehydrogenase (pdh) genes and therefore were named a-fch and a-pdh, respectively. Transcription of both genes was confirmed; however, no translated proteins could be detected immunologically. Whereas mutations within a-pdh or a-fch did not lead to any obvious phenotype, it is clear that transcripts and proteins over and above the currently known set may play a role in defining the physiology of cyanobacteria and other organisms.

     

     

  • 320.
    Cheregi, Otilia
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wagner, Raik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Insights into the Cyanobacterial Deg/HtrA Proteases2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 694Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serinetype ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.

  • 321. Chilkoor, Govinda
    et al.
    Karanam, Sushma Priyanka
    Star, Shane
    Shrestha, Namita
    Sani, Rajesh K.
    Upadhyayula, Venkata K. K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ghoshal, Debjit
    Koratkar, Nikhil A.
    Meyyappan, M.
    Gadhamshetty, Venkataramana
    Hexagonal Boron Nitride: The Thinnest Insulating Barrier to Microbial Corrosion2018Inngår i: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 12, nr 3, s. 2242-2252Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report the use of a single layer of two-dimensional hexagonal boron nitride (SL-hBN) as the thinnest insulating barrier to microbial corrosion induced by the sulfate-reducing bacteria Desulfovibrio alaskensis G20. We used electrochemical methods to assess the corrosion resistance of SL-hBN on copper against the effects of both the planktonic and sessile forms of the sulfate-reducing bacteria. Cyclic voltammetry results show that SL-hBN-Cu is effective in suppressing corrosion effects of the planktonic cells at potentials as high as 0.2 V (vs Ag/AgCl). The peak anodic current for the SL-hBN coatings is ∼36 times lower than that of bare Cu. Linear polarization resistance tests confirm that the SL-hBN coatings serve as a barrier against corrosive effects of the G20 biofilm when compared to bare Cu. The SL-hBN serves as an impermeable barrier to aggressive metabolites and offers ∼91% corrosion inhibition efficiency, which is comparable to much thicker commercial coatings such as polyaniline. In addition to impermeability, the insulating nature of SL-hBN suppresses galvanic effects and improves its ability to combat microbial corrosion.

  • 322.
    Chorell, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pilicides and Curlicides: Design, synthesis, and evaluation of novel antibacterial agents targeting bacterial virulence2010Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    New strategies are needed to counter the growing problem of bacterial resistance to antibiotics. One such strategy is to design compounds that target bacterial virulence, which could work separately or in concert with conventional bacteriostatic or bactericidal antibiotics. Pilicides are a class of compounds based on a ring-fused 2-pyridone scaffold that target bacterial virulence by blocking the chaperone/usher pathway in E. coli and thereby inhibit the assembly of pili. This thesis describes the design, synthesis, and biological evaluation of compounds based on the pilicide scaffold with the goal of improving the pilicides and expanding their utility. Synthetic pathways have been developed to enable the introduction of substituents at the C-2 position of the pilicide scaffold. Biological evaluation of these compounds demonstrated that some C-2 substituents give rise to significant increases in potency. X-ray crystallography was used to elucidate the structural basis of this improved biological activity. Furthermore, improved methods for the preparation of oxygen-analogues and C-7 substituted derivatives of the pilicide scaffold have been developed. These new methods were used in combination with existing strategies to decorate the pilicide scaffold as part of a multivariate design approach to improve the pilicides and generate structure activity relationships (SARs).

    Fluorescent pilicides were prepared using a strategy where selected substituents were replaced with fluorophores having similar physicochemical properties as the original substituents. Many of the synthesized fluorescent compounds displayed potent pilicide activities and can thus be used to study the complex interactions between pilicide and bacteria. For example, when E. coli was treated with fluorescent pilicides, it was found that the compounds were not uniformly distributed throughout the bacterial population, suggesting that the compounds are primarily associated to bacteria with specific properties.

    Finally, by studying compounds designed to inhibit the aggregation of Aβ, it was found that some compounds based on the pilicide scaffold inhibit the formation of the functional bacterial amyloid fibers known as curli; these compounds are referred to as 'curlicides'. Some of the curlicides also prevent the formation of pili and thus exhibit dual pilicide-curlicide activity. The potential utility of such 'dual-action' compounds was highlighted by a study of one of the more potent dual pilicide-curlicides in a murine UTI model were the compound was found to significantly attenuate virulence in vivo.

  • 323.
    Chorell, Erik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Andersson, Emma
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Evans, Margery L.
    Jain, Neha
    Götheson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Åden, Jörgen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Chapman, Matthew R.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Wittung-Stafshede, Pernilla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bacterial Chaperones CsgE and CsgC Differentially Modulate Human α-Synuclein Amyloid Formation via Transient Contacts2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 10, s. 1-11, artikkel-id e0140194Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Amyloid formation is historically associated with cytotoxicity, but many organisms produce functional amyloid fibers (e.g., curli) as a normal part of cell biology. Two E. coli genes in the curli operon encode the chaperone-like proteins CsgC and CsgE that both can reduce in vitro amyloid formation by CsgA. CsgC was also found to arrest amyloid formation of the human amyloidogenic protein α-synuclein, which is involved in Parkinson’s disease. Here, we report that the inhibitory effects of CsgC arise due to transient interactions that promote the formation of spherical α-synuclein oligomers. We find that CsgE also modulates α-synuclein amyloid formation through transient contacts but, in contrast to CsgC, CsgE accelerates α-synuclein amyloid formation. Our results demonstrate the significance of transient protein interactions in amyloid regulation and emphasize that the same protein may inhibit one type of amyloid while accelerating another.

  • 324.
    Chorell, Erik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bengtsson, Christoffer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sainte-Luce Banchelin, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Das, Pralay
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Uvell, Hanna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sinha, Arun K
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pinkner, Jerome S
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Hultgren, Scott J
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Synthesis and application of a bromomethyl substituted scaffold to be used for efficient optimization of anti-virulence activity2011Inngår i: European Journal of Medicinal Chemistry, ISSN 0223-5234, E-ISSN 1768-3254, Vol. 46, nr 4, s. 1103-1116Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pilicides are a class of compounds that attenuate virulence in Gram negative bacteria by blocking the chaperone/usher pathway in Escherichia coli. It has also been shown that compounds derived from the peptidomimetic scaffold that the pilicides are based on can prevent both Aβ aggregation and curli formation. To facilitate optimizations towards the different targets, a new synthetic platform has been developed that enables fast and simple introduction of various substituents in position C-7 on the peptidomimetic scaffold. Importantly, this strategy also enables introduction of previously unattainable heteroatoms in this position. Pivotal to the synthetic strategy is the synthesis of a C-7 bromomethyl substituted derivative of the ring-fused dihydrothiazolo 2-pyridone pilicide scaffold. From this versatile and reactive intermediate various heteroatom-linked substituents could be introduced on the scaffold including amines, ethers, amides and sulfonamides. In addition, carbon-carbon bonds could be introduced to the sp(3)-hybridized bromomethyl substituted scaffold by Suzuki-Miyaura cross couplings. Evaluation of the 24 C-7 substituted compounds in whole-bacterial assays provided important structure-activity data and resulted in the identification of a number of new pilicides with activity as good or better than those developed previously.

  • 325.
    Chorell, Erik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Chorell, Elin
    Umeå universitet, Medicinska fakulteten, Institutionen för folkhälsa och klinisk medicin, Medicin.
    Efficient Synthesis of 2-Substituted Phthalimides from Phthalic Acids in One Step2013Inngår i: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 2013, nr 33, s. 7512-7516Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Efficient procedures for synthesizing 2-substituted phthalimide (isoindole-1,3-dione) analogues starting from phthalic acids have been developed by using experimental design. The phthalimide central fragment frequently appears in biologically active compounds, materials, catalysts, and fluorescent probes, and therefore the development of general, fast, and convenient synthetic methods to this scaffold under neutral, acidic, and basic conditions would be attractive. After an initial screening, the use of acetonitrile, acetic acid, or pyridine in combination with microwave heating proved most promising. Experimental design was applied to these conditions to optimize the time, temperature, and concentration. This strategy has successfully generated synthetic methods that have been used to synthesize a series of phthalimides from phthalic acids and various amines or anilines in excellent yields. The developed methods have proven to be general, fast, convenient, and economic, and thus are expected to have broad utility to efficiently construct novel compounds for future biological and chemical applications.

  • 326.
    Chorell, Erik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pinkner, Jerome S
    Bengtsson, Christoffer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Banchelin, Thomas Sainte-Luce
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Edvinsson, Sofie
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Linusson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hultgren, Scott J
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mapping pilicide anti-virulence effect in Escherichia coli, a comprehensive structure-activity study2012Inngår i: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 20, nr 9, s. 3128-3142Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pilicides prevent pili formation and thereby the development of bacterial biofilms in Escherichia coli. We have performed a comprehensive structure activity relationship (SAR) study of the dihydrothiazolo ring-fused 2-pyridone pilicide central fragment by varying all open positions. Orthogonal projections to latent structures discriminant analysis (OPLS-DA) was used to distinguish active from inactive compounds in which polarity proved to be the most important factor for discrimination. A quantitative SAR (QSAR) partial least squares (PLS) model was calculated on the active compounds for prediction of biofilm inhibition activity. In this model, compounds with high inhibitory activity were generally larger, more lipophilic, more flexible and had a lower HOMO. Overall, this resulted in both highly valuable SAR information and potent inhibitors of type 1 pili dependent biofilm formation. The most potent biofilm inhibitor had an EC(50) of 400nM.

  • 327.
    Chorell, Erik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pinkner, Jerome S
    Bengtsson, Christoffer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Edvinsson, Sofie
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Cusumano, Corinne K
    Rosenbaum, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johansson, Lennart B-Å
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hultgren, Scott J
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Design and Synthesis of Fluorescent Pilicides and Curlicides: Bioactive Tools to Study Bacterial Virulence Mechanisms2012Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 18, nr 15, s. 4522-4532Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pilicides and curlicides are compounds that block the formation of the virulence factors pili and curli, respectively. To facilitate studies of the interaction between these compounds and the pili and curli assembly systems, fluorescent pilicides and curlicides have been synthesized. This was achieved by using a strategy based on structure-activity knowledge, in which key pilicide and curlicide substituents on the ring-fused dihydrothiazolo 2-pyridone central fragment were replaced by fluorophores. Several of the resulting fluorescent compounds had improved activities as measured in pili- and curli-dependent biofilm assays. We created fluorescent pilicides and curlicides by introducing coumarin and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) fluorophores at two positions on the peptidomimetic pilicide and curlicide central fragment. Fluorescence images of the uropathogenic Escherichia coli (UPEC) strain UTI89 grown in the presence of these compounds shows that the compounds are strongly associated with the bacteria with a heterogeneous distribution.

  • 328.
    Chorell, Erik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pinkner, Jerome S.
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Bengtsson, Christoffer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Edvinsson, Sofie
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Cusumano, Corinne K.
    Rosenbaum, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johansson, Lennart B-Å
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hultgren, Scott J.
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Design and synthesis of fluorescently labeled pilicides and curlicides: bioactive tools to study bacterial virulence mechanismsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Pilicides and curlicides block formation of the E. coli virulence factors pili and curli. To facilitate studies of the interaction between these compounds and the pili and curli assembly systems, fluorescent pilicides and curlicides have been synthesized. This was achieved using a strategy where key pilicide and curlicide substituents were replaced by fluorophores having similar physicochemical properties. The resulting fluorescent compounds had improved anti-virulence activities as measured in pili- and curli-dependent biofilm assays. We created fluorescent pilicides and curlicides by introducing both coumarin and 4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) fluorophores at two positions on the peptidomimetic pilicide and curlicide scaffold. Fluorescence images of the uropathogenic Escherichia coli (UPEC) strain UTI89 grown in the presence of these compounds shows that the compounds are strongly associated to the bacteria and seem to discriminate between different bacteria in a population.

  • 329.
    Christiansen, Alexander
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Effects of Macromolecular Crowding on Protein Folding: - in-vitro equilibrium and kinetic studies on selected model systems2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Protein folding is the process during which an extended and unstructured polypeptide converts to its compact folded structure that is most often the functional state. The process has been characterized extensively in dilute buffer in-vitro during the last decades but the actual biological place for this process is the inside of living cells. The cytoplasm of a cell is filled with a plethora of different macromolecules that together occupy up to 40% of the total volume. This large amount of macromolecules restricts the available space to each individual molecule, which has been termed macromolecular crowding. Macromolecular crowding results in excluded volume effects and also increases chances for non-specific interactions. Macromolecular crowding should favor reactions that lead to a decrease in the total occupied volume by all molecules, such as folding reactions. Theoretical models have predicted that the stability of protein folded states should increase in presence of macromolecular crowding due to unfavorable effects on the extended unfolded state. To understand protein folding and function in living systems, we need to have a defined quantitative link between in-vitro dilute conditions (where most biophysical experiments are made) and in-vivo crowded conditions. An important question is thus how macromolecular crowding modifies the biophysical properties of a protein.

    The work underlying this thesis focused on how macromolecular crowding tunes protein equilibrium stability and kinetic folding processes. To mimic the crowded cellular environment, synthetic sugar-based polymers (Dextrans of different sizes and Ficoll 70) were used as crowding agents (crowders) in controlled in-vitro experiments. In contrast to previous studies which often have focused on one protein and one crowder at a time, the goal here was to make systematic analyses of how size, shape and concentration of the crowders affect both equilibrium and kinetic properties of structurally-different proteins. Three model proteins (cytochrome c, apoazurin and apoflavodoxin) were investigated under crowding by Ficoll 70 and different-size Dextrans, using various spectroscopic techniques such as far-UV circular dichroism and intrinsic tryptophan fluorescence. Thermodynamic models were applied to explain the experimental results.

    It was discovered that equilibrium stability of all three proteins increased in presence of crowding agents in a crowder concentration dependent manner. The stabilization effect was around 2-3 kJ/mol, larger for the various Dextrans than for Ficoll 70 at the same g/l, but independent of Dextran size (in the range 20 to 70 kDa). To further investigate the cause for the stabilization a theoretical crowding model was applied. In this model, Dextran and Ficoll were modeled as elongated rods and the protein was represented as a sphere, where the folded sphere representation was smaller than the unfolded sphere representation. It is notable that the observed stability changes could be reproduced by this model taking only steric interactions into account. This correlation showed that when using sugar-based crowding agents, excluded volume effects could be studied in isolation and there were no contributions from nonspecific interactions.

    Time-resolved experiments with apoazurin and apoflavodoxin revealed an increase in the folding rate constants while the unfolding rates were invariant in the presence of crowding agents. For apoflavodoxin and cytochrome c, the presence of crowding agents also altered the folding pathway such that it became more homogeneous (cytochrome c) and it gave less misfolding (apoflavodoxin). These results showed that macromolecular crowding restricts the conformational space of the unfolded polypeptide chain, makes the conformations more compact which, in turn, eliminates access to certain pathways.

    The results from kinetic and equilibrium measurements on three model proteins, together with available data from the literature, demonstrate that macromolecular crowding effects due to volume exclusion are in the order of a few kJ/mol. Considering the numerous concentration balances and cross-dependent reactions of the cellular machinery, small changes in energetics/kinetics of the magnitudes found here can still have dramatic consequences for cellular fitness. In fact local and transient changes in macromolecular crowding levels may be a way to tune biochemical reactions without invoking gene expression. 

  • 330.
    Christiansen, Alexander
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wang, Qian
    Department of Physics, University of Houston, Houston, Texas, USA .
    Samiotakis, Antonios
    Department of Physics, University of Houston, Houston, Texas, USA .
    Cheung, Margaret S
    Department of Physics, University of Houston, Houston, Texas, USA .
    Wittung-Stafshede, Pernilla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Factors defining effects of Macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c2010Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 49, nr 31, s. 6519-6530Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Previous experiments with two single-domain proteins showed that macromolecular crowding can stabilize dramatically toward heat perturbation and modulate native-state structure and shape. To assess the generality of this, we here tested the effects of the synthetic crowding agents on cytochrome c, a small single-domain protein. Using far-UV circular dichroism (CD), we discovered that there is no effect on cytochrome c's secondary structure upon addition of Ficoll or dextran (0-400 mg/mL, pH 7). Thermal experiments revealed stabilizing effects (5-10 degrees C) of Ficoll 70 and dextran 70; this effect was enhanced by the presence of low levels of guanidine hydrochloride (GuHCl) that destabilize the protein. When using a smaller dextran, dextran 40, the thermal effects were larger (10-20 degrees C). In silico analysis, using structure-based (Go-like) interactions for cytochrome c, is in excellent agreement with the in vitro thermodynamic data and also agrees with scaled particle theory. Simulations of a range of crowder size and shape demonstrated that the smaller the crowder the larger the favorable effect on cytochrome c's folded-state stability. Together with previous data, we conclude that protein size, stability, conformational malleability, and folding routes, as well as crowder size and shape, are key factors that modulate the net effect of macromolecular crowding on proteins.

  • 331.
    Christiansen, Alexander
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wittung-Stafshede, Pernilla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Synthetic crowding agent dextran causes excluded volume interactions exclusively to tracer protein apoazurin2014Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 588, nr 5, s. 811-814Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To understand protein biophysics in crowded cellular environments, researchers often use synthetic polymers as 'crowding agents' in vitro. The idea is that these agents will occupy space and reproduce the in vivo scenario in terms of excluded volume. However, recent work has challenged this concept and pointed out that attractive interactions between protein and crowding agent will provide an enthalpic contribution to the overall effect on protein thermodynamics. Here we use a typical synthetic crowding agent and a well-studied model protein to demonstrate in a window of 50 K that the presence of dextran 20 affects apoazurin by steric repulsion. (C) 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  • 332. Chrysina, Maria
    et al.
    Heyno, Eiri
    Kutin, Yury
    Reus, Michael
    Nilsson, Håkan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Nowaczyk, Marc M.
    DeBeer, Serena
    Neese, Frank
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemistry–Ångström Laboratorium, Uppsala University, 75120 Uppsala, Sweden.
    Lubitz, Wolfgang
    Cox, Nicholas
    Five-coordinate Mn-IV intermediate in the activation of nature's water splitting cofactor2019Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, nr 34, s. 16841-16846Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Nature's water splitting cofactor passes through a series of catalytic intermediates (S-0-S-4) before O-O bond formation and O-2 release. In the second last transition (S-2 to S-3) cofactor oxidation is coupled to water molecule binding to Mn1. It is this activated, water-enriched all Mn-IV form of the cofactor that goes on to form the O-O bond, after the next light-induced oxidation to S-4. How cofactor activation proceeds remains an open question. Here, we report a so far not described intermediate (S-3') in which cofactor oxidation has occurred without water insertion. This intermediate can be trapped in a significant fraction of centers (> 50%) in (i) chemical-modified cofactors in which Ca2+ is exchanged with Sr2+; the Mn4O5Sr cofactor remains active, but the S-2-S-3 and S-3-S-0 transitions are slower than for the Mn4O5Ca cofactor; and (ii) upon addition of 3% vol/vol methanol; methanol is thought to act as a substrate water analog. The S-3' electron paramagnetic resonance (EPR) signal is significantly broader than the untreated S-3 signal (2.5 T vs. 1.5 T), indicating the cofactor still contains a 5-coordinate Mn ion, as seen in the preceding S-2 state. Magnetic double resonance data extend these findings revealing the electronic connectivity of the S-3' cofactor is similar to the high spin form of the preceding S-2 state, which contains a cuboidal Mn3O4Ca unit tethered to an external, 5-coordinate Mn ion (Mn-4). These results demonstrate that cofactor oxidation regulates water molecule insertion via binding to Mn-4. The interaction of ammonia with the cofactor is also discussed.

  • 333. Chumakova, Natalia A.
    et al.
    Rebrikova, Anastasya T.
    Talyzin, Aleksandr V.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Paramonov, Nikita A.
    Vorobiev, Andrey Kh
    Korobov, Mikhail, V
    Properties of Graphite Oxide Powders and Membranes as Revealed by Electron Paramagnetic Resonance Spectroscopy2018Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, nr 39, s. 22750-22759Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The spin probe technique was used to study graphite oxide (GO) powders swelled in polar liquids (CH3CN, CH3OH, and H2O) and liquid-free GO membranes (GOM). The nitroxide radicals TEMPO (2,2,6,6-tetramethylpiperidine-N-oxyl) and TEMPOL (4-hydroxy-2,2,6,6-tetramethylpiperidine-N-oxyl) readily penetrated into the interplane space of GO from the solution. Electron paramagnetic resonance (EPR) spectra of these radical probes were sensitive to molecular mobility and orientation ordering within the internal space of GO. The radicals embedded in swelled GO were in two states with different rotational mobilities. The small fraction of radicals located in the interplane space of GO and detected in the broad range of temperatures was in the state of fast rotation, similar to the same radicals dissolved in bulk liquids, thus providing experimental evidence of formation of a liquid-like media within the interplane space of GO. Such mobile media may be responsible for the unusual permeation properties of GOM, which is reported in the literature. Second, less-mobile fraction of radicals was found to be immobilized at the internal surface of GO and was sensitive to phase transformations in the swelled GO structures. The transformations were detected as anomalies at temperature dependences of rotational mobility of radicals. The detected dependence of EPR spectra of probe radicals on orientation of GOM, relative to the direction of magnetic field in the EPR spectrometer, was used for quantitative characterization of orientation alignment of GO planes within the membranes. Such an approach may serve as an elegant method to estimate the relative quality of membranes and other GO-layered structures.

  • 334. Chung, Jade C. S.
    et al.
    Rzhepishevska, Olena
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ramstedt, Madeleine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Welch, Martin
    Type III secretion system expression in oxygen-limited Pseudomonas aeruginosa cultures is stimulated by isocitrate lyase activity2013Inngår i: Open Biology, ISSN 2046-2441, E-ISSN 2046-2441, Vol. 3, artikkel-id 120131Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pseudomonas aeruginosa is an opportunistic human pathogen and a common cause of chronic infections in individuals with cystic fibrosis (CF). Oxygen limitation was recently reported to regulate the expression of a major virulence determinant in P. aeruginosa, the type III secretion system (T3SS). Here, we show that expression of the T3SS in oxygen-limited growth conditions is strongly dependent on the glyoxylate shunt enzyme, isocitrate lyase (ICL; encoded by aceA), which was previously shown to be highly expressed in CF isolates. ICL-dependent regulation of the T3SS did not alter the expression level of the master transcriptional regulator, ExsA, but did affect expression of the T3 structural proteins, effectors and regulators (ExsC, ExsD and ExsE). An aceA mutant displayed enhanced biofilm formation during anaerobic growth, which suggested that AceA-dependent modulation of type III secretion might impinge upon the RetS/LadS signalling pathways. Indeed, our data suggest that RetS is able to mediate some of its effects through AceA, as expression of aceA in trans partially restored T3SS expression in a retS mutant. Our findings indicate that AceA is a key player in the metabolic regulation of T3SS expression during oxygen-limited growth of P. aeruginosa. To the best of our knowledge, this is the first demonstration that the T3SS can be regulated by factors that do not affect ExsA expression levels.

  • 335.
    Claeson, Anna-Sara
    et al.
    Umeå universitet, Samhällsvetenskapliga fakulteten, Institutionen för psykologi.
    Gouveia-Figueira, Sandra C.
    Swedish Metabolomics Centre (SMC), Umeå, Sweden.
    Stenlund, Hans
    Swedish Metabolomics Centre (SMC), Umeå, Sweden.
    Johansson, Annika I.
    Swedish Metabolomics Centre (SMC), Umeå, Sweden.
    A standardized protocol for comparable analysis of GSH/GSSG by UHPLC-ESI-MSMS for human plasma2019Inngår i: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 1104, s. 67-72Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Variability in the levels of GSH and GSSG in plasma is suggested to derive from inadequate pre-processing methods. The aim of this study was to develop a protocol for comparable and reliable measurements of GSH/GSSG. Venous blood from 8 healthy individuals were collected and divided into 7 different pre-processing procedures. For three of the samples an extraction mixture was added after 0 (baseline), 4 and 8 min and for three of the samples the extraction mixture was added at different times during defrost. A worst case scenario where a sample was left in a cool box during 6 h was also included. The samples were analyzed with UHPLC-ESIMSMS. A large difference in the levels of GSH and GSSG were identified and it was clearly associated with the sample handling procedures. A sample left untreated for 4 min will have significantly reduced amount of GSH. Stability tests showed that the level of GSH was reduced after 3 months in -80 degrees C.

  • 336.
    Claesson, Ola
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten.
    An investigation of the radiation chemistry of a hydrocarbon system and simulation of ESR spectra of triplet state molecules1980Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis can be divided into two parts.The aim of the studies described in the first part of the thesis isto make clear the dominating processes in the selective decorrpositionof certain solutes that follow low-terrperature radiolysis of crystalline hydrocarbons.

    1. The isotope effect in the production of radicals has been studiedby Electron Spin Resonance and Gas Chromatography/MassSpectrometry in the C10H22/C10D22 system. Two independent methodshave never been used on the same system in this contextbefore. The methods gave the same ratio of protiated to deuteratedradicals.

    2. The isotope effect in the production of hydrogen gas has beenstudied with Mass Spectrometry in the C10H22/C10D22 system.

    3. The amount of reactive D-atoms has been measured in C10D22 using an olefin, C10H20, as a scavanger.

    4. The effect of an electron scavenger, C8H16Cl2, in C10H22 has been investigated.

    Two processes for the explanation of the isotope effects are discussed.

    a. transfer of excitation energy

    b. selective abstraction.

    The results show that reactive D-atoms are present in the C10D22 system and suggest that the isotope effects can be explained by selectiveabstraction. The effect of the electron scavenger can beexplained by energy transfer, but not entirely by selective abstraction.

    In the second part of the thesis, a method to simulate Electron SpinResonance spectra for the case of a Hamiltonian containing nuclearinteractions is described. The method has been applied to the S = 1 case. It is suggested that the method can be generalized to an arbitraryelectronic spin state, and to include second order nuclear corrections.

  • 337. Colak, Burcu
    et al.
    Da Silva, Julio C. S.
    Soares, Thereza A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Departament of Fundamental Chemistry, CCEN, Federal University of Pernambuco, Cidade Universitaria, Brazil.
    Gautrot, Julien E.
    Impact of the Molecular Environment on Thiol-Ene Coupling For Biofunctionalization and Conjugation2016Inngår i: Bioconjugate chemistry, ISSN 1043-1802, E-ISSN 1520-4812, Vol. 27, nr 9, s. 2111-2123Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Thiol-ene radical coupling is increasingly used for the biofunctionalization of biomaterials and the formation of 3D hydrogels enabling cell encapsulation. Indeed, thiol-ene chemistry presents interesting features that are particularly attractive for platforms requiring specific reactions of peptides or proteins, in particular, in situ, during cell culture or encapsulation. Despite such interest, little is known about the factors impacting thiol-ene chemistry in situ, under biologically relevant conditions. Here we explore some of the molecular parameters controlling photoinitiated thiol-ene couplings with a series of alkenes and thiols, including peptides, in buffered conditions. H-1 NMR and HPLC were used to quantify the efficiency of couplings and the impact of the pH of the buffer, as well as the molecular structure and local microenvironment close to alkenes and thiols to be coupled. Some of these observations are supported by molecular dynamics and quantum mechanics calculations. An important finding of our work is that the plc of thiols (and its variation upon changes in molecular structure) have a striking impact on coupling efficiencies. Similarly, positively charged and aromatic amino acids are found to have some impact on thiol-ene couplings. Hence, our study demonstrates that molecular design should be carefully selected in order to achieve high biofunctionalization levels in biomaterials with peptides or promote the efficient formation of peptide-based hydrogels.

  • 338.
    Conlan, Brendon
    et al.
    Australian National University, Canberra, Australia.
    Cox, Nicholas
    Australian National University, Canberra, Australia.
    Su, Ji-Hu
    Max Planck Institute for Bioinorganic Chemistry, Mülheim an der Ruhr, Germany.
    Hillier, Warwick
    Australian National University, Canberra, Australia.
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Lubitz, Wolfgang
    Max Planck Institute for Bioinorganic Chemistry, Mülheim an der Ruhr, Germany.
    Dutton, P Leslie
    University of Pennsylvania, Philadelphia, USA.
    Wydrzynski, Tom
    Australian National University, Canberra, Australia.
    Photo-catalytic oxidation of a di-nuclear manganese centre in an engineered bacterioferritin 'reaction centre'2009Inngår i: Biochimica et Biophysica Acta, ISSN 0006-3002, E-ISSN 1878-2434, Vol. 1787, nr 9, s. 1112-1121Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Photosynthesis involves the conversion of light into chemical energy through a series of electron transfer reactions within membrane-bound pigment/protein complexes. The Photosystem II (PSII) complex in plants, algae and cyanobacteria catalyse the oxidation of water to molecular O(2). The complexity of PSII has thus far limited attempts to chemically replicate its function. Here we introduce a reverse engineering approach to build a simple, light-driven photo-catalyst based on the organization and function of the donor side of the PSII reaction centre. We have used bacterioferritin (BFR) (cytochrome b1) from Escherichia coli as the protein scaffold since it has several, inherently useful design features for engineering light-driven electron transport. Among these are: (i.) a di-iron binding site; (ii.) a potentially redox-active tyrosine residue; and (iii.) the ability to dimerise and form an inter-protein heme binding pocket within electron tunnelling distance of the di-iron binding site. Upon replacing the heme with the photoactive zinc-chlorin e(6) (ZnCe(6)) molecule and the di-iron binding site with two manganese ions, we show that the two Mn ions bind as a weakly coupled di-nuclear Mn(2)(II,II) centre, and that ZnCe(6) binds in stoichiometric amounts of 1:2 with respect to the dimeric form of BFR. Upon illumination the bound ZnCe(6) initiates electron transfer, followed by oxidation of the di-nuclear Mn centre possibly via one of the inherent tyrosine residues in the vicinity of the Mn cluster. The light dependent loss of the Mn(II) EPR signals and the formation of low field parallel mode Mn EPR signals are attributed to the formation of Mn(III) species. The formation of the Mn(III) is concomitant with consumption of oxygen. Our model is the first artificial reaction centre developed for the photo-catalytic oxidation of a di-metal site within a protein matrix which potentially mimics WOC photo-assembly.

  • 339.
    Cornea, Flavia
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Evaluation of an alternative extraction method of PCDD/Fs from flue gas samples2016Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
  • 340.
    Cornelissen, Gerard
    et al.
    Norwegian Geotechnical Institute (NGI), Oslo, Norway.
    Wiberg, Karin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Broman, Dag
    Department of Applied Environmental Sciences (ITM), Stockholm University, Stockholm, Sweden.
    Arp, Hans Peter
    Norwegian Geotechnical Institute (NGI), Oslo, Norway.
    Persson, Ylva
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sundqvist, Kristina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jonsson, Per
    Department of Applied Environmental Sciences (ITM), Stockholm University, Stockholm, Sweden.
    Freely dissolved concentrations and sediment-water activity ratios of PCDD/Fs and PCBs in the open Baltic Sea2008Inngår i: Environmental Science & Technology, Vol. 42, nr 23, s. 8733-8739Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aqueous concentrations of polychlorinated dibenzo-p-dioxins and -furans (PCDD/Fs) as well as polychlorinated biphenyls (PCBs) in the open sea have heretofore been measured by filtering and extracting large amounts of water. Measurement of freely dissolved concentrations with this technique is difficult because of corrections for sorption to dissolved organic matter. In this study we use a novel, more economic technique using equilibrium passive samplers consisting of 17-μm thin polyoxymethylene (POM-17), capable of measuring freely dissolved aqueous concentrations (CW) in pristine (i.e., background) locations. POM-17 was employed in an extensive field campaign at five stations in the open Baltic sea to obtain CW at two depths (1 m above the seafloor and 25 m below the surface). Median CW in the overlying water was 2.3 pg toxic equivalents (TEQ)/m3 PCDD/Fs and 15 pg/L sum 7-PCB, with generally less than a factor two variation among sites and depths. Also freely dissolved concentrations of native compounds in the surface sediment porewater (CPW) were determined in laboratory batch experiments. The data were used to derive sediment-water activity ratios, which indicate the diffusive flux direction. It was found that the PCDD/Fs and PCBs were in close equilibrium between the sediment porewater and the overlying water. Comparison of CPW with total sediment concentrations indicated that more than 90% of the compounds were sorbed to sedimentary black carbon.

  • 341.
    Cornelissen, Gerard
    et al.
    Department of Applied Environmental Sciences (ITM), Stockholm University, Stockholm, Sweden.
    Wiberg, Karin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Broman, Dag
    Department of Applied Environmental Sciences (ITM), Stockholm University, Stockholm, Sweden.
    Breedveld, G
    Jonsson, Per
    Department of Applied Environmental Sciences (ITM), Stockholm University, Stockholm, Sweden.
    Freely dissolved concentrations and sediment-water activity ratios of PCDD/Fs and PCBs in the open Baltic Sea2008Inngår i: Abstract to SETAC North America conference, Nov. 16-20, 2008, Tampa, FA, USA, 2008Konferansepaper (Annet vitenskapelig)
  • 342. Cortinez, V
    et al.
    Hyvärinen, S
    Reunanen, M
    Hemming, J
    Lienqueo, M E
    Murzin, D Yu
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Evaluation of ionic liquid mediated pretreatment for the enzymatic hydrolysis of forest residues to obtain bioethanol2009Konferansepaper (Annet vitenskapelig)
  • 343. Cortinez, V
    et al.
    Hyvärinen, S
    Reunanen, M
    Hemming, J
    Murzin, D Yu
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Lienqueo, ME
     Pretreatment with ionic líquids of Lenga (Nothofagus pumilio) and Eucalyptus (Eucalyptus nitens) residues for producción of second generation bioethanol2009Konferansepaper (Annet vitenskapelig)
  • 344.
    Courtois, Julien
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Monolithic separation media synthesized in capillaries and their applications for molecularly imprinted networks2006Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The thesis describes the synthesis of chromatographic media using several different approaches, their characterizations and applications in liquid chromatography. The steps to achieve a separation column for a specific analyte are presented. The main focus of the study was the design of novel molecularly imprinted polymers.

    Attachment of monolithic polymeric substrates to the walls of fused silica capillaries was studied in Paper I. With a broad literature survey, a set of common methods were tested by four techniques and ranked by their ability to improve anchoring of polymers. The best procedure was thus used for all further studies.

    Synthesis of monoliths in capillary columns was studied in Paper II. With the goal of separating proteins without denaturation, various monoliths were polymerized in situ using a set of common monomers and cross-linkers mixed with poly(ethylene glycol) as porogen. The resulting network was expected to present “protein-friendly pores”. Chemometrics were used to find and describe a set of co-porogens added to the polymerization cocktails in order to get good porosity and flow-through properties.

    Assessment of the macroporous structure of a monolith was described in Paper III. An alternative method to mercury intrusion porosimetry was proposed. The capillaries were embedded in a stained resin and observed under transmission electron microscope. Images were then computed to determine the pore sizes.

    Synthesis of molecularly imprinted polymers grafted to a core mono-lith in a capillary was described in Paper IV. The resulting material, imprinted with local anaesthetics, was tested for its chromatographic performance. Similar imprinted polymers were characterized by microcalorimetry in Paper V. Finally, imprinted monoliths were also synthesized in a glass tube and further introduced in a NMR rotor to describe the interactions between stationary phase and template in Paper VI.

  • 345.
    Courtois, Julien
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Byström, Emil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Irgum, Knut
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Novel monolithic materials using poly(ethylene glycol) as porogen for protein separation2006Inngår i: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 47, nr 8, s. 2603-2611Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Several recipes are described for the preparation of porous polymeric monoliths in the capillary format, using poly(ethylene glycol) (PEG) as porogen as well as constituent in the monomer mixture. Acrylic or methacrylic monomers with a variety of terminal groups, with and without ethylene glycol links of differing lengths in the side chains, have been used in combination with triethylene glycol dimethacrylate (TEGDMA) and trimethylol-propane trimethacrylate (TRIM) as cross-linkers. PEGs of 4–20 kDa molecular weight dissolved in 2-methoxy-ethanol were used as porogens to yield large, biocompatible pores. A number of common solvents have been used as co-porogens for the PEGs, and the surface areas, median pore diameters, and back pressures of the resulting monoliths have been correlated with a number of molecular descriptors by means of chemometrics to describe the results. Photopolymerizations induced by either continuous or pulsed UV light were furthermore compared. Pore size distribution and surface area characterization have been assessed by nitrogen adsorption–desorption and mercury intrusion porosimetry, and scanning electron microscopy (SEM) was used to evaluate the differences in macroporous morphology obtained with the different porogen solutions. Mixtures selected from screening syntheses carried out in vials have been implemented in 100 μm fused silica capillaries and the back pressures measured and cross-validated with the pore information. Some of these capillary columns were finally tested for the separation of proteins using micro-HPLC.

  • 346. Cox, Nicholas
    et al.
    Ames, William
    Epel, Boris
    Kulik, Leonid V
    Rapatskiy, Leonid
    Neese, Frank
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wieghardt, Karl
    Lubitz, Wolfgang
    Electronic Structure of a Weakly Antiferromagnetically Coupled Mn(II)Mn(III) Model Relevant to Manganese Proteins: A Combined EPR, (55)Mn-ENDOR, and DFT Study2011Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 50, nr 17, s. 8238-8251Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An analysis of the electronic structure of the [Mn(II)Mn(III)(μ-OH)-(μ-piv)(2)(Me(3)tacn)(2)](ClO(4))(2) (PivOH) complex is reported. It displays features that include: (i) a ground 1/2 spin state; (ii) a small exchange (J) coupling between the two Mn ions; (iii) a mono-μ-hydroxo bridge, bis-μ-carboxylato motif; and (iv) a strongly coupled, terminally bound N ligand to the Mn(III). All of these features are observed in structural models of the oxygen evolving complex (OEC). Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) measurements were performed on this complex, and the resultant spectra simulated using the Spin Hamiltonian formalism. The strong field dependence of the (55)Mn-ENDOR constrains the (55)Mn hyperfine tensors such that a unique solution for the electronic structure can be deduced. Large hyperfine anisotropy is required to reproduce the EPR/ENDOR spectra for both the Mn(II) and Mn(III) ions. The large effective hyperfine tensor anisotropy of the Mn(II), a d(5) ion which usually exhibits small anisotropy, is interpreted within a formalism in which the fine structure tensor of the Mn(III) ion strongly perturbs the zero-field energy levels of the Mn(II)Mn(III) complex. An estimate of the fine structure parameter (d) for the Mn(III) of -4 cm(-1) was made, by assuming the intrinsic anisotropy of the Mn(II) ion is small. The magnitude of the fine structure and intrinsic (onsite) hyperfine tensor of the Mn(III) is consistent with the known coordination environment of the Mn(III) ion as seen from its crystal structure. Broken symmetry density functional theory (DFT) calculations were performed on the crystal structure geometry. DFT values for both the isotropic and the anisotropic components of the onsite (intrinsic) hyperfine tensors match those inferred from the EPR/ENDOR simulations described above, to within 5%. This study demonstrates that DFT calculations provide reliable estimates for spectroscopic observables of mixed valence Mn complexes, even in the limit where the description of a well isolated S = 1/2 ground state begins to break down.

  • 347.
    Cox, Nicholas
    et al.
    Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, Germany.
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Reflections on substrate water and dioxygen formation2013Inngår i: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1827, nr 8-9, s. 1020-1030Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    This brief article aims at presenting a concise summary of all experimental findings regarding substrate water-binding to the Mn4CaO5 cluster in photosystem II. Mass spectrometric and spectroscopic results are interpreted in light of recent structural information of the water oxidizing complex (WOC) obtained by x-ray crystallography, spectroscopy and theoretical modeling. Within this framework current proposals for the mechanism of photosynthetic water-oxidation are evaluated.

  • 348. Cox, Nicholas
    et al.
    Rapatskiy, Leonid
    Su, Ji-Hu
    Pantazis, Dimitrios A
    Sugiura, Miwa
    Kulik, Leonid
    Dorlet, Pierre
    Rutherford, A William
    Neese, Frank
    Boussac, Alain
    Lubitz, Wolfgang
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Effect of Ca(2+)/Sr(2+) substitution on the electronic structure of the oxygen-evolving complex of photosystem II: a combined multifrequency EPR, (55)Mn-ENDOR, and DFT study of the S(2) State2011Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, nr 10, s. 3635-3648Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The electronic structures of the native Mn(4)O(x)Ca cluster and the biosynthetically substituted Mn(4)O(x)Sr cluster of the oxygen evolving complex (OEC) of photosystem II (PSII) core complexes isolated from Thermosynechococcus elongatus, poised in the S(2) state, were studied by X- and Q-band CW-EPR and by pulsed Q-band (55)Mn-ENDOR spectroscopy. Both wild type and tyrosine D less mutants grown photoautotrophically in either CaCl(2) or SrCl(2) containing media were measured. The obtained CW-EPR spectra of the S(2) state displayed the characteristic, clearly noticeable differences in the hyperfine pattern of the multiline EPR signal [Boussac et al. J. Biol. Chem.2004, 279, 22809-22819]. In sharp contrast, the manganese ((55)Mn) ENDOR spectra of the Ca and Sr forms of the OEC were remarkably similar. Multifrequency simulations of the X- and Q-band CW-EPR and (55)Mn-pulsed ENDOR spectra using the Spin Hamiltonian formalism were performed to investigate this surprising result. It is shown that (i) all four manganese ions contribute to the (55)Mn-ENDOR spectra; (ii) only small changes are seen in the fitted isotropic hyperfine values for the Ca(2+) and Sr(2+) containing OEC, suggesting that there is no change in the overall spin distribution (electronic coupling scheme) upon Ca(2+)/Sr(2+) substitution; (iii) the changes in the CW-EPR hyperfine pattern can be explained by a small decrease in the anisotropy of at least two hyperfine tensors. It is proposed that modifications at the Ca(2+) site may modulate the fine structure tensor of the Mn(III) ion. DFT calculations support the above conclusions. Our data analysis also provides strong support for the notion that in the S(2) state the coordination of the Mn(III) ion is square-pyramidal (5-coordinate) or octahedral (6-coordinate) with tetragonal elongation. In addition, it is shown that only one of the currently published OEC models, the Siegbahn structure [Siegbahn, P. E. M. Acc. Chem. Res.2009, 42, 1871-1880, Pantazis, D. A. et al. Phys. Chem. Chem. Phys.2009, 11, 6788-6798], is consistent with all data presented here. These results provide important information for the structure of the OEC and the water-splitting mechanism. In particular, the 5-coordinate Mn(III) is a potential site for substrate 'water' (H(2)O, OH(-)) binding. Its location within the cuboidal structural unit, as opposed to the external 'dangler' position, may have important consequences for the mechanism of O-O bond formation.

  • 349. Cui, Wen
    et al.
    Yao, Mingguang
    Yao, Zhen
    Ma, Fengxian
    Li, Quanjun
    Liu, Ran
    Liu, Bo
    Zou, Bo
    Cui, Tian
    Liu, Bingbing
    Sundqvist, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Reversible pressure-induced polymerization of Fe(C5H5)(2) doped C-702013Inngår i: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 62, s. 447-454Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    High pressure Raman, IR and X-ray diffraction (XRD) studies have been carried out on C-70(Fe(C5H5)(2))(2) (hereafter, "C-70(Fc)(2)") sheets. Theoretical calculation is further used to analyze the Electron Localization Function (ELF) and charge transfer in the crystal and thus to understand the transformation of C-70(Fc)(2) under pressure. Our results show that even at room temperature dimeric phase and one dimensional (1D) polymer phase of C-70 molecules can be formed at about 3 and 8 GPa, respectively. The polymerization is found to be reversible Upon decompression and the reversibility is related to the pressure-tuned charge transfer, as well as the overridden steric repulsion of counter ions. According to the layered structure of the intercalated ferrocene molecules formed in the crystal, we suggest that ferrocene acts as not only a spacer to restrict the polymerization of C-70 molecules within a layer, but also as charge reservoir to tune the polymerization process. This supplies a possible way for us to design the polymerization of fullerenes at suitable conditions.

  • 350. Cuklev, Filip
    et al.
    Fick, Jerker
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Cvijovic, Marija
    Kristiansson, Erik
    Förlin, Lars
    Larsson, D G Joakim
    Does ketoprofen or diclofenac pose the lowest risk to fish?2012Inngår i: Journal of Hazardous Materials, ISSN 0304-3894, E-ISSN 1873-3336, Vol. 229-230, s. 100-106Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ketoprofen and diclofenac are non-steroidal anti-inflammatory drugs (NSAIDs) often used for similar indications, and both are frequently found in surface waters. Diclofenac affects organ histology and gene expression in fish at around 1μg/L. Here, we exposed rainbow trout to ketoprofen (1, 10 and 100μg/L) to investigate if this alternative causes less risk for pharmacological responses in fish. The bioconcentration factor from water to fish blood plasma was <0.05 (4 for diclofenac based on previous studies). Ketoprofen only reached up to 0.6‰ of the human therapeutic plasma concentration, thus the probability of target-related effects was estimated to be fairly low. Accordingly, a comprehensive analysis of hepatic gene expression revealed no consistent responses. In some contrast, trout exposed to undiluted, treated sewage effluents bioconcentrated ketoprofen and other NSAIDs much more efficiently, according to a meta-analysis of recent studies. Neither of the setups is however an ideal representation of the field situation. If a controlled exposure system with a single chemical in pure water is a reasonable representation of the environment, then the use of ketoprofen is likely to pose a lower risk for wild fish than diclofenac, but if bioconcentration factors from effluent-exposed fish are applied, the risks may be more similar.

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