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Now showing items 14-27 of 27
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Kahlke, Tim; Thorvaldsen, Steinar (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: Cold-adaptation strategies have been studied in multiple psychrophilic organisms, especially for psychrophilic enzymes. Decreased enzyme activity caused by low temperatures as well as a higher viscosity of the aqueous environment require certain adaptations to the metabolic machinery of the cell. In addition to this, low temperature has deleterious effects on the lipid bilayer of bacterial membranes and therefore might also affect the embedded membrane proteins. Little is known about the adaptation of membrane proteins to stresses of the cold. In this study we investigate a set of 66 membrane proteins from the core genome of the bacterial family Vibrionaceae to identify general characteristics that discern psychrophilic and mesophilic membrane proteins. Bioinformatical and statistical methods were used to analyze the alignments of the three temperature groups mesophilic, intermediate and psychrophilic. Surprisingly, our results show little or no adaptation to low temperature for those parts of the proteins that are predicted to be inside the membrane. However, changes in amino acid composition and hydrophobicity are found for complete sequences and sequence parts outside the lipid bilayer. Among others, the results presented here indicate a preference for helix-breaking and destabilizing amino acids Ile, Asp and Thr and an avoidance of the helix-forming amino acid Ala in the amino acid composition of psychrophilic membrane proteins. Furthermore, we identified a lower overall hydrophobicity of psychrophilic membrane proteins in comparison to their mesophilic homologs. These results support the stability-flexibility hypothesis and link the cold-adaptation strategies of membrane proteins to those of loop regions of psychrophilic enzymes. URI: http://hdl.handle.net/10037/4922 File(s) in this item: 1
article.pdf (231.9Kb) -
Kahlke, Tim; Goesmann, Alexander; Hjerde, Erik; Willassen, Nils Peder; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups. The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin. The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development. URI: http://hdl.handle.net/10037/4905 File(s) in this item: 1
article.pdf (709.4Kb) -
Kostenko, Nataliya; Gottfriedsen, Jochen; Hilfert, Liane; Edelmann, Frank T (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: A synthetic route to potentially biocidal silsesquioxanes functionalized by quaternary pyridinium functionalities has been developed. N-Alkylation reactions of the precursor compounds 4-(2-(trimethoxysilyl)ethyl)-pyridine (5) and 4-(2-trichloro-silylethyl)pyridine (6) with iodomethane, n-hexylbromide, and n-hexadecylbromide cleanly afforded the corresponding N-alkylpyridinium salts (7–10). The synthesis of a 4-(2-ethyl)pyridine POSS derivative (2) was achieved by capping of the silsesquioxane trisilanol Cy7Si7O9(OH)3 (1) via two different preparative routes. Attempts to use compound 2 as precursor for quaternary pyridinium salt-functionalized POSS derivatives were met with only partial success. Only the reaction with iodomethane cleanly afforded the new N-methylpyridinium salt 12 in high yield, whereas n-hexylbromide and n-hexadecylbromide failed to react with 2 even under forcing conditions. URI: http://hdl.handle.net/10037/4923 File(s) in this item: 1
article.pdf (919.7Kb) -
Langner, J.; Engardt, M.; Baklanov, A.; Christensen, J. H.; Gauss, Michael; Geels, Camila; Hedegaard, G.B.; Nuterman, R.; Simpson, D.; Soares, J; Sofiev, M; Wind, Peter; Zakey, A. (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: The impact of climate change on surface ozone over Europe was studied using four offline regional chemistry transport models (CTMs) and one online regional integrated climate-chemistry model (CCM), driven by the same global projection of future climate under the SRES A1B scenario. Anthropogenic emissions of ozone precursors from RCP4.5 for year 2000 were used for simulations of both present and future periods in order to isolate the impact of climate change and to assess the robustness of the results across the different models. The sensitivity of the simulated surface ozone to changes in climate between the periods 2000–2009 and 2040–2049 differs by a factor of two between the models, but the general pattern of change with an increase in southern Europe is similar across different models. Emissions of isoprene differ substantially between different CTMs ranging from 1.6 to 8.0 Tg yr−1 for the current climate, partly due to differences in horizontal resolution of meteorological input data. Also the simulated change in total isoprene emissions varies substantially across models explaining part of the different climate response on surface ozone. Ensemble mean changes in summer mean ozone and mean of daily maximum ozone are close to 1 ppb(v) in parts of the land area in southern Europe. Corresponding changes of 95-percentiles of hourly ozone are close to 2 ppb(v) in the same region. In northern Europe ensemble mean for mean and daily maximum show negative changes while there are no negative changes for the higher percentiles indicating that climate impacts on O3 could be especially important in connection with extreme summer events. URI: http://hdl.handle.net/10037/4913 File(s) in this item: 1
article.pdf (1.600Mb) -
Leiros, Hanna-Kirsti S. (Conference object; Konferansebidrag, 02-Sep-2010)[+][-]
Description: Innlegg på seminaret "Science - who cares?" ved NT-fak, Universitetet i Tromsø. URI: http://hdl.handle.net/10037/2697 File(s) in this item: 1
article.pdf (2.376Mb) -
Lejon, Tore; Gozhina, Olga Vladimirovna; Khrustalev, Victor N. (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: The molecule of the title compound, C16H21BO2, comprises a chiral fused tricyclic system containing five-membered (1,3,2-dioxaborolane), six-membered (cyclohexane) and four-membered (cyclobutane) rings. The 1,3,2-dioxaborolane ring is almost planar (r.m.s. deviation = 0.035 Å), and the syn H and Me substituents at this ring are in an eclipsed conformation. The cyclohexane and cyclobutane rings adopt sofa and butterfly conformations, respectively. The B atom has a trigonal-planar configuration (sum of the bond angles = 360.0°). The phenyl ring is practically coplanar with the 1,3,2-dioxaborolane ring [dihedral angle between the ring planes = 1.96 (8)°]. The absolute structure was determined from the known configuration of (+)-pinanediol which was used in the synthesis. In the crystal, weak C-H...[pi](Ph) interactions occur. URI: http://hdl.handle.net/10037/4635 File(s) in this item: 1
article.pdf (396.8Kb) -
Lejon, Tore; Gorovoy, Alexey Sergeevich; Khrustalev, Victor N. (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: The title compound, K+·C8H8BF3N3-, is a salt containing the chiral organic trifluoridoborate anion. The organic anions and potassium cations are tightly bound to each other by the coordination K-F [2.654 (3)-3.102 (3) Å] and K-N [2.951 (4)-3.338 (4) Å] interactions. Thus, the potassium cation adopts a nine-vertex coordination polyhedron, which can be described as a distorted monocapped tetragonal antiprism. In the crystal, the organic anions and potassium cations form layers parallel to (001). Weak C-H...[pi] interactions between neighbouring phenyl rings further stabilize the crystal. Description: This article is part of Alexey S. Gorovoy's doctoral thesis. Available in Munin at http://hdl.handle.net/10037/4653 URI: http://hdl.handle.net/10037/4734 File(s) in this item: 1
article.pdf (2.213Mb) -
Lejon, Tore Sigvard; Ingebrigtsen, Truls Erik; Hansen, Lars Kr (Journal article; Tidsskriftartikkel; Peer reviewed, 2006)[+][-]
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Lindell, Kristoffer; Fahlgren, Anna; Hjerde, Erik; Willassen, Nils Peder; Fällman, Maria; Milton, Debra L (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: Colonization of host tissues is a first step taken by many pathogens during the initial stages of infection. Despite the impact of bacterial disease on wild and farmed fish, only a few direct studies have characterized bacterial factors required for colonization of fish tissues. In this study, using live-cell and confocal microscopy, rainbow trout skin epithelial cells, the main structural component of the skin epidermis, were demonstrated to phagocytize bacteria. Mutant analyses showed that the fish pathogen Vibrio anguillarum required the lipopolysaccharide O-antigen to evade phagocytosis and that O-antigen transport required the putative wzm-wzt-wbhA operon, which encodes two ABC polysaccharide transporter proteins and a methyltransferase. Pretreatment of the epithelial cells with mannose prevented phagocytosis of V. anguillarum suggesting that a mannose receptor is involved in the uptake process. In addition, the O-antigen transport mutants could not colonize the skin but they did colonize the intestines of rainbow trout. The O-antigen polysaccharides were also shown to aid resistance to the antimicrobial factors, lysozyme and polymyxin B. In summary, rainbow trout skin epithelial cells play a role in the fish innate immunity by clearing bacteria from the skin epidermis. In defense, V. anguillarum utilizes O-antigen polysaccharides to evade phagocytosis by the epithelial cells allowing it to colonize rapidly fish skin tissues. URI: http://hdl.handle.net/10037/4914 File(s) in this item: 1
article.pdf (1.446Mb) -
Pecul, Magdalena; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2011)[+][-]
Abstract: The circularly polarized luminescence (CPL) and electronic circular dichroism (CD) spectroscopic parameters corresponding to the n ← π* and n → π* transitions, respectively, have been calculated for selected β,γ-enones using density functional theory. For the smallest β,γ-enone, (1R,4R)-bicyclo[2.2.1]hept-5-en-2-one (norbornenone), coupled-cluster calculations have also been carried out. The excited-state potential energy surface for three of the five enones studied reveals two minima with different C[double bond, length as m-dash]OC[double bond, length as m-dash]C dihedral angles, and with rotatory strengths of opposite sign. The relative energies of the minima determine the sign of the CPL intensity, which may be the same or opposite as in the CD spectrum, in agreement with experimental data. The results obtained in this first computational study of CPL demonstrate its usefulness as an indicator of excited-state structures of chiral species. URI: http://hdl.handle.net/10037/4069 File(s) in this item: 1
article.pdf (420.8Kb) -
Pflug, Alexander; Johnson, Kenneth; Engh, Richard Alan (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: With its ability to show the interactions between drug-target proteins and small-molecule ligands, X-ray crystallography is an essential tool in drug-discovery programmes. However, its usefulness can be limited by crystallization artifacts or by the data resolution, and in particular when assumptions of unimodal binding (and isotropic motion) do not apply. Discrepancies between the modelled crystal structure and the physiological range of structures generally prevent quantitative estimation of binding energies. Improved crystal structure resolution will often not aid energy estimation because the conditions which provide the highest rigidity and resolution are not likely to reflect physiological conditions. Instead, strategies must be employed to measure and model flexibility and multiple binding modes to supplement crystallographic information. One useful tool is the use of anomalous dispersion for small molecules that contain suitable atoms. Here, an analysis of the binding of the kinase inhibitor H-89 to protein kinase A (PKA) is presented. H-89 contains a bromobenzene moiety that apparently binds with multiple conformations in the kinase ATP pocket. Using anomalous dispersion methods, it was possible to resolve these conformations into two distinct binding geometries. Description: This article is part of Alexander Pflugs' doctoral thesis, available in Munin at http://hdl.handle.net/10037/4145 URI: http://hdl.handle.net/10037/4645 File(s) in this item: 1
article.pdf (1.012Mb) -
Shcherbin, Dmitri; Thorvaldsen, Andreas johan; Jonsson, Dan Johan; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2011)[+][-]
Abstract: We present the first gauge-origin independent formulation of Jones birefringence at the Hartree–Fock level of theory. Gauge-origin independence is achieved through the use of London atomic orbitals. The implementation is based on a recently proposed atomic orbital-based response theory formulation that allows for the use of both time- and perturbation-dependent basis sets [Thorvaldsen, Ruud, Kristensen, Jørgensen, and Coriani, J. Chem. Phys. 129, 214108 (2008)]. We present the detailed expressions for the response functions entering the Jones birefringence when London atomic orbitals are used. The implementation is tested on a set of polar and dipolar molecules at the Hartree–Fock level of theory. It is demonstrated that London orbitals lead to much improved basis-set convergence, and that the use of small, conventional basis sets may lead to the wrong sign for the calculated birefringence. For large basis sets, London orbitals and conventional basis sets converge to the same results. URI: http://hdl.handle.net/10037/3909 File(s) in this item: 1
article.pdf (843.4Kb) -
Simpson, David; Benedictow, Anna; Berge, Halldis; Bergström, Robert; Emberson, Lisa D.; Fagerli, Hilde; Flechard, Chris R.; Hayman, Garry D.; Gauss, Michael; Jonson, Jan Eiof; Jenkin, Michael E.; Nyiri, Agnes; Richter, Cornelia; Semeena, Valiyavetil S.; Tsyro, Svetlana; Tuovinen, Juha Pekka; Valdebenito, Alvaro; Wind, Peter (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: The Meteorological Synthesizing Centre-West (MSC-W) of the European Monitoring and Evaluation Programme (EMEP) has been performing model calculations in support of the Convention on Long Range Transboundary Air Pollution (CLRTAP) for more than 30 years. The EMEP MSC-W chemical transport model is still one of the key tools within European air pollution policy assessments. Traditionally, the model has covered all of Europe with a resolution of about 50 km × 50 km, and extending vertically from ground level to the tropopause (100 hPa). The model has changed extensively over the last ten years, however, with flexible processing of chemical schemes, meteorological inputs, and with nesting capability: the code is now applied on scales ranging from local (ca. 5 km grid size) to global (with 1 degree resolution). The model is used to simulate photo-oxidants and both inorganic and organic aerosols. In 2008 the EMEP model was released for the first time as public domain code, along with all required input data for model runs for one year. The second release of the EMEP MSC-W model became available in mid 2011, and a new release is targeted for summer 2012. This publication is intended to document this third release of the EMEP MSC-W model. The model formulations are given, along with details of input data-sets which are used, and a brief background on some of the choices made in the formulation is presented. The model code itself is available at www.emep.int, along with the data required to run for a full year over Europe. URI: http://hdl.handle.net/10037/4915 File(s) in this item: 1
article.pdf (953.1Kb) -
The Methylococcus capsulatus (Bath) secreted protein, MopE*, binds both reduced and oxidized copper.Ve, Thomas; Mathisen, Karina; Helland, Ronny; Karlsen, Odd Andre; Fjellbirkeland, Anne; Røhr, Åsmund Kjendseth; Andersson, K. Kristoffer; Pedersen, Rolf B.; Lillehaug, Johan R.; Jensen, Harald B (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)[+][-]
Abstract: Under copper limiting growth conditions the methanotrophic bacterium Methylococcus capsulatus (Bath) secrets essentially only one protein, MopE*, to the medium. MopE* is a copper-binding protein whose structure has been determined by X-ray crystallography. The structure of MopE* revealed a unique high affinity copper binding site consisting of two histidine imidazoles and one kynurenine, the latter an oxidation product of Trp130. In this study, we demonstrate that the copper ion coordinated by this strong binding site is in the Cu(I) state when MopE* is isolated from the growth medium of M. capsulatus. The conclusion is based on X-ray Near Edge Absorption spectroscopy (XANES), and Electron Paramagnetic Resonance (EPR) studies. EPR analyses demonstrated that MopE*, in addition to the strong copper-binding site, also binds Cu(II) at two weaker binding sites. Both Cu(II) binding sites have properties typical of non-blue type II Cu (II) centres, and the strongest of the two Cu(II) sites is characterised by a relative high hyperfine coupling of copper (A|| = 20 mT). Immobilized metal affinity chromatography binding studies suggests that residues in the N-terminal part of MopE* are involved in forming binding site(s) for Cu(II) ions. Our results support the hypothesis that MopE plays an important role in copper uptake, possibly making use of both its high (Cu(I) and low Cu(II) affinity properties. URI: http://hdl.handle.net/10037/4450 File(s) in this item: 1
article.pdf (557.2Kb)
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