• An annual profile of the impacts of simulated oil spills on the Northeast Arctic cod and haddock fisherie 

      Carroll, JoLynn; Frøysa, Håvard Guldbrandsen; Vikebø, Frode Bendiksen; Broch, Ole Jacob; Nepstad, Raymond; Augustine, Starrlight; Skeie, Geir Morten; Bockwoldt, Mathias; Howell, Daniel (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-10-10)
      We simulate the combined natural and pollutant-induced survival of early life stages of NEA cod and haddock, and the impact on the adult populations in response to the time of a major oil spill in a single year. Our simulations reveal how dynamic ocean processes, controlling both oil transport and fate and the frequency of interactions of oil with drifting fish eggs and larvae, mediate the magnitude ...
    • An annual profile of the impacts of simulated oil spills on the Northeast Arctic cod and haddock fisheries 

      Carroll, JoLynn; Frøysa, Håvard Guldbrandsen; Vikebø, Frode Bendiksen; Broch, Ole Jacob; Howell, Daniel; Nepstad, Raymond; Augustine, Starrlight; Skeie, Geir Morten; Bockwoldt, Mathias (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-10-10)
      We simulate the combined natural and pollutant-induced survival of early life stages of NEA cod and haddock, and the impact on the adult populations in response to the time of a major oil spill in a single year. Our simulations reveal how dynamic ocean processes, controlling both oil transport and fate and the frequency of interactions of oil with drifting fish eggs and larvae, mediate the magnitude ...
    • Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria 

      Sharma, Suraj; Hsieh, Yin-Chen; Dietze, Jørn; Bockwoldt, Mathias; Strømland, Øyvind; Ziegler, Mathias; Heiland, Ines (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-06-21)
      Bacteria use two alternative pathways to synthesize nicotinamide adenine dinucleotide (NAD) from nicotinamide (Nam). A short, two-step route proceeds through nicotinamide mononucleotide (NMN) formation, whereas the other pathway, a four-step route, includes the deamidation of Nam and the reamidation of nicotinic acid adenine dinucleotide (NAAD) to NAD. In addition to having twice as many enzymatic ...
    • Evidence for Strong Fixation Bias at 4-fold Degenerate Sites Across Genes in the Great Tit Genome 

      Gossmann, Toni Ingolf; Bockwoldt, Mathias; Diringer, Lilith; Schwarz, Friedrich; Schumann, Vic-Fabienne (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-11-29)
      It is well established that GC content varies across the genome in many species and that GC biased gene conversion, one form of meiotic recombination, is likely to contribute to this heterogeneity. Bird genomes provide an extraordinary system to study the impact of GC biased gene conversion owed to their specific genomic features. They are characterized by a high karyotype conservation with ...
    • A first insight into the fecal microbiota of the high Arctic muskoxen (Ovibos moschatus) 

      Salgado, Alejandro Flores; Bockwoldt, Mathias; Hagen, Live Heldal; Pope, Phillip; Sundset, Monica Alterskjær (Journal article; Tidsskriftartikkel, 2016-07-11)
      The faecal microbiota of muskoxen (n=3) pasturing on Ryøya (69° 33′ N 18° 43′ E), Norway, in late September was characterized using high-throughput sequencing of partial 16S rRNA gene regions. A total of 16 209 high-quality sequence reads from bacterial domains and 19 462 from archaea were generated. Preliminary taxonomic classifications of 806 bacterial operational taxonomic units (OTUs) resulted ...
    • G3BPs tether the TSC complex to lysosomes and suppress mTORC1 signaling 

      Prentzell, Mirja Tamara; Rehbein, Ulrike; Sandoval, Marti Cadena; De Meulemeester, Ann-Sofie; Baumeister, Ralf; Brohée, Laura; Berdel, Bianca; Bockwoldt, Mathias; Carroll, Bernadette; Chowdhury, Suvagata Roy; von Deimling, Andreas; Demetriades, Constantinos; Figlia, Gianluca; de Arauj, Mariana Eca Guimaraes; Heberle, Alexander Martin; Heiland, Ines; Holzwarth, Birgit; Huber, Lukas A; Jaworski, Jacek; Kedra, Magdalena; Kern, Katharina; Kopach, Andrii; Korolchuk, Viktor I; van't Land-Kuper, Ineke; Macias, Matylda; Nellist, Mark; Palm, Wilhelm; Pusch, Stefan; Ramos Pittol, Jose Miguel; Reil, Michèle; Reintjes, Anja; Reuter, Friederike; Sampson, Julian R.; Scheldeman, Chloë; Siekierska, Aleksandra; Stefan, Eduard; Teleman, Aurelio A; Thomas, Laura E; Torres-Quesada, Omar; Trump, Saskia; West, Hannah D; de Witte, Peter; Woltering, Sandra; Yordanov, Teodor E; Zmorzynska, Justyna; Opitz, Christiane A.; Thedieck, Kathrin (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-01-25)
      Ras GTPase-activating protein-binding proteins 1 and 2 (G3BP1 and G3BP2, respectively) are widely recognized as core components of stress granules (SGs). We report that G3BPs reside at the cytoplasmic surface of lysosomes. They act in a non-redundant manner to anchor the tuberous sclerosis complex (TSC) protein complex to lysosomes and suppress activation of the metabolic master regulator mechanistic ...
    • Human long intrinsically disordered protein regions are frequent targets of positive selection 

      Afanasyeva, Arina; Bockwoldt, Mathias; Cooney, Christopher; Heiland, Ines; Gossmann, Toni Ingolf (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-06-01)
      Intrinsically disordered regions occur frequently in proteins and are characterized by a lack of a well-defined three-dimensional structure. Although these regions do not show a higher order of structural organization, they are known to be functionally important. Disordered regions are rapidly evolving, largely attributed to relaxed purifying selection and an increased role of genetic drift. It has ...
    • Identification of evolutionary and kinetic drivers of NAD-dependent signaling 

      Bockwoldt, Mathias; Houry, Dorothee; Niere, Marc; Gossmann, Toni I.; Reinartz, Ines; Schug, Alexander; Ziegler, Mathias; Heiland, Ines (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-07-24)
      Nicotinamide adenine dinucleotide (NAD) is best known as an essential cofactor of biochemical reactions. In addition, it is involved in the regulation of virtually all major cellular events. These NAD-dependent regulatory functions are mediated by enzymes (e.g., sirtuins, poly–adenosine -diphosphate [ADP] ribose polymerases, ADP-ribosyl cyclases) that cleave the molecule to liberate nicotinamide ...
    • Mind the gap – Relevant design for laboratory oil exposure of fish as informed by a numerical impact assessment model 

      Frøysa, Håvard Guldbrandsen; Nepstad, Raymond; Meier, Sonnich; Donald, Carey; Sørhus, Elin; Bockwoldt, Mathias; Carroll, JoLynn; Vikebø, Frode Bendiksen (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-09-09)
      Laboratory experiments provide knowledge of species-specific effects thresholds that are used to parameterize impact assessment models of oil contamination on marine ecosystems. Such experiments typically place individuals of species and life stages in tanks with different contaminant concentrations. Exposure concentrations are usually fixed, and the individuals experience a shock treatment being ...
    • SBMLmod: a Python-based web application and web service for efficient data integration and model simulation 

      Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-06-24)
      BACKGROUND: Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. <br>RESULTS: We present ...
    • Sequence-Based Analysis of Eukaryotic Protein Evolution 

      Bockwoldt, Mathias (Doctoral thesis; Doktorgradsavhandling, 2018-10-12)
      The goal of this thesis was to comprehend evolutionary patterns in different contexts. To get a broad spectrum of methods, three projects were included of which one is published and two are in preparation. In the first project, we looked into the fate of new mutations in protein regions that do not have a defined three-dimensional structure. Generally, the fate of a new mutation is governed by ...