Recent additions

  • Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis 

    Klemetsen, Terje; Willassen, Nils Peder; Karlsen, Christian René (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-07-04)
    Understanding fish‐microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, ...
  • Improved CRISPR/Cas9 gene editing by fluorescence activated cell sorting of green fluorescence protein tagged protoplasts 

    Petersen, Bent Larsen; Möller, Svenning Rune; Mravec, Jozef; Jørgensen, Bodil; Christensen, Mikkel; Liu, Ying; Wandall, Hans H.; Bennett, Eric Paul; Yang, Zhang (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-06-17)
    <i>Background</i>: CRISPR/Cas9 is widely used for precise genetic editing in various organisms. CRISPR/Cas9 editing may in many plants be hampered by the presence of complex and high ploidy genomes and inefficient or poorly controlled delivery of the CRISPR/Cas9 components to gamete cells or cells with regenerative potential. Optimized strategies and methods to overcome these challenges are ...
  • Fully Polarizable QM/Fluctuating Charge Approach to Two-Photon Absorption of Aqueous Solutions 

    Di Remigio, Roberto; Giovannini, Tommaso; Ambrosetti, Matteo; Cappelli, Chiara; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-06-05)
    We present the extension of the quantum/classical polarizable fluctuating charge model to the calculation of single residues of quadratic response functions, as required for the computational modeling of two-photon absorption cross sections. By virtue of a variational formulation of the quantum/classical polarizable coupling, we are able to exploit an atomic orbital-based quasienergy formalism to ...
  • All-electron fully relativistic Kohn-Sham theory for solids based on the Dirac-Coulomb Hamiltonian and Gaussian-type functions 

    Kadek, Marius; Repisky, Michal; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-05-03)
    We present the first full-potential method that solves the fully relativistic four-component Dirac-Kohn-Sham equation for materials in the solid state within the framework of atom-centered Gaussian-type orbitals (GTOs). Our GTO-based method treats one-, two-, and three-dimensional periodic systems on an equal footing, and allows for a seamless transition to the methodology commonly used in studies ...
  • Response properties of embedded molecules through the polarizable embedding model 

    Steinmann, Casper; Reinholdt, Peter; Nørby, Morten Steen; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-04)
    The polarizable embedding (PE) model is a fragment‐based quantum‐classical approach aimed at accurate inclusion of environment effects in quantum‐mechanical response property calculations. The aim of this tutorial review is to give insight into the practical use of the PE model. Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to ...
  • MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry 

    Olsen, Jógvan Magnus Haugaard; Bolnykh, Viacheslav; Meloni, Simone; Ippoliti, Emiliano; Bircher, Martin Peter; Carloni, Paolo; Rothlisberger, Ursula (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-04-18)
    We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the existing parallelization strategies used by the coupled programs while maintaining a ...
  • Features and structure of a cold active N-acetylneuraminic acid lyase 

    Gurung, Man Kumari; Altermark, Bjørn; Helland, Ronny; Smalås, Arne O.; Ræder, Inger Lin Uttakleiv (Journal article; Peer reviewed, 2019-06-11)
    N-acetylneuraminate lyases (NALs) are enzymes that catalyze the reversible cleavage and synthesis of sialic acids. They are therefore commonly used for the production of these high-value sugars. This study presents the recombinant production, together with biochemical and structural data, of the NAL from the psychrophilic bacterium Aliivibrio salmonicida LFI1238 (AsNAL). Our characterization shows ...
  • Design and Biological Evaluation of Antifouling Dihydrostilbene Oxime Hybrids 

    Moodie, Lindon W. K.; Cervin, Gunnar; Trepos, Rozenn; Labriere, Christophe; Hellio, Claire; Pavia, Henrik; Svenson, Johan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-03-13)
    By combining the recently reported repelling natural dihydrostilbene scaffold with an oxime moiety found in many marine antifoulants, a library of nine antifouling hybrid compounds was developed and biologically evaluated. The prepared compounds were shown to display a low antifouling effect against marine bacteria but a high potency against the attachment and growth of microalgae down to MIC ...
  • Exploring the transcriptome of luxI- and ΔainS mutants and the impact of N-3-oxo-hexanoyl-L- and N-3-hydroxy- decanoyl-L-homoserine lactones on biofilm formation in Aliivibrio salmonicida 

    Khider, Miriam; Hansen, Hilde; Hjerde, Erik; Johansen, Jostein A; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-04-30)
    <i>Background</i>: Bacterial communication through quorum sensing (QS) systems has been reported to be important in coordinating several traits such as biofilm formation. In <i>Aliivibrio salmonicida</i> two QS systems the LuxI/R and AinS/R, have been shown to be responsible for the production of eight acyl-homoserine lactones (AHLs) in a cell density dependent manner. We have previously ...
  • Innføring av studentaktive arbeidsformer i seminarundervisningen. Hvilken betydning har dette på læringsutbyttet og klassemiljøet? 

    Netland, Kjell Øystein; Sivertsen, Annfrid; Olufsen, Magne (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-03-08)
    I denne studien ønsket vi å undersøke hvordan innføring av studentaktive læringsformer i seminarundervisningen påvirket det faglige læringsutbyttet og klassemiljøet i STEM-fag (science, technology, engineering and mathematics). Et randomisert kontrollert studie ble gjennomført i seminarundervisningen i to innføringsemner i fysikk og kjemi ved UiT Norges arktiske universitet. I emnene fulgte ...
  • Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat 

    Juhasz, Angela; Belova, Tatiana; Florides, Chris G; Maulis, Csaba; Fischer, Iris; Gell, Gyongyver; Birinyi, Zsofia; Ong, Jamie; Keeble-Gagnere, Gabriel; Maharajan, Amudha Deepalakshmi; Ma, Wujun; Gibson, Peter; Jia, Jizeng; Lang, Daniel; Mayer, Klaus F X; Spannagl, Manuel; Tye-Din, Jason A.; Appels, Rudi; Olsen, Odd-Arne (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-08-17)
    Wheat is an important staple grain for humankind globally because of its end-use quality and nutritional properties and its adaptability to diverse climates. For a small proportion of the population, specific wheat proteins can trigger adverse immune responses and clinical manifestations such as celiac disease, wheat allergy, baker’s asthma, and wheat-dependent exercise-induced anaphylaxis (WDEIA). ...
  • OXA-48-Mediated Ceftazidime-Avibactam Resistance Is Associated with Evolutionary Trade-Offs 

    Frøhlich, Christopher; Sørum, Vidar; Thomassen, Ane Molden; Johnsen, Pål Jarle; Samuelsen, Ørjan (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-03-27)
    Infections due to carbapenemase-producing Gram-negative pathogens are associated with limited treatment options and consequently lead to increased mortality and morbidity. In response, combinations of existing β-lactams and novel β-lactamase inhibitors, such as ceftazidime-avibactam (CAZ-AVI), have been developed as alternative treatment options. To understand the development of resistance and ...
  • Magnetic Diversity in Heteroisocorroles: Aromatic Pathways in 10-Heteroatom-Substituted Isocorroles 

    Foroutan-Nejad, Cina; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-11-21)
    A recent study on magnetically induced currents in 10-isocorrole derivatives indicated that both the free-base and metal-complexed forms of the unsubstituted macrocycle are homoaromatic. Furthermore, depending on the substituents at the 10-position, the aromatic character was found to swing between substantially homoaromatic to substantially antihomoaromatic. Heteroisocorroles, in which the saturated ...
  • Differential expression profiling of ΔlitR and ΔrpoQ mutants reveals insight into QS regulation of motility, adhesion and biofilm formation in Aliivibrio salmonicida 

    Khider, Miriam; Hjerde, Erik; Hansen, Hilde; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-03-15)
    <i>Background</i>: The coordination of group behaviors in bacteria is achieved by a cell-cell signaling process called quorum sensing (QS). QS is an intercellular communication system, which synchronously controls expression of a vast range of genes in response to changes in cell density and is mediated by autoinducers that act as extracellular signals. <i>Aliivibrio salmonicida</i>, the causative ...
  • The alternative sigma factor RpoQ regulates colony morphology, biofilm formation and motility in the fish pathogen Aliivibrio salmonicida 

    Khider, Miriam; Willassen, Nils Peder; Hansen, Hilde (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-12)
    <i>Background</i>: Quorum sensing (QS) is a cell-to cell communication system that bacteria use to synchronize activities as a group. LitR, the master regulator of QS in <i>Aliivibrio salmonicida</i>, was recently shown to regulate activities such as motility, rugosity and biofilm formation in a temperature dependent manner. LitR was also found to be a positive regulator of <i>rpoQ</i>. RpoQ ...
  • Stable Platinum(IV) Corroles: Synthesis, Molecular Structure, and Room-Temperature Near-IR Phosphorescence 

    Alemayehu, Abraham; McCormick, Laura J; Gagnon, Kevin J.; Borisov, Sergey M.; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-08-17)
    A series of stable Pt(IV) corrole complexes with the general formula Pt<sup>IV</sup>[TpXPC](<i>m/p</i>-C<sub>6</sub>H<sub>4</sub>CN)(py), where TpXPC<sup>3–</sup> is the trianion of a tris(<i>p</i>-X-phenyl)corrole and X = CF<sub>3</sub>, H, and CH<sub>3</sub>, has been synthesized, affording key physicochemical data on a rare and elusive class of metallocorroles. Single-crystal X-ray structures of ...
  • Synthesis and Molecular Structure of a Copper Octaiodocorrole 

    Thomassen, Ivar Kristian; McCormick, Laura J.; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-09)
    Although rather delicate on account of their propensity to undergo deiodination, β-octaiodoporphyrinoids are of considerable interest as potential precursors to novel β-octasubstituted macrocycles. Presented herein are early results of our efforts to synthesize β-octaiodocorrole derivatives. Oxidative condensation of 3,4-diiodopyrrole and aromatic aldehydes failed to yield free-base octaiodocorroles. ...
  • DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases 

    Williamson, Adele Kim; Grgic, Miriam; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-07-11)
    DNA ligases join breaks in the phosphodiester backbone of DNA by catalysing the formation of bonds between opposing 5′P and 3′OH ends in an adenylation-dependent manner. Catalysis is accompanied by reorientation of two core domains to provide access to the active site for cofactor utilization and enable substrate binding and product release. The general paradigm is that DNA ligases engage their DNA ...
  • Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives 

    Thode, Sunniva Katharina; Rojek, Ewelina; Kozlowski, Mikolaj; Ahmad, Rafi; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02-14)
    Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from <i>Vibrionaceae</i> representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster ...
  • Diagrammatic Coupled Cluster Monte Carlo 

    Scott, Charles J. C.; Di Remigio, Roberto; Crawford, T. Daniel; Thom, Alex J. W. (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-02-09)
    We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker–Campbell–Hausdorff expansion of the similarity-transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach—diagCCMC—allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, ...

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