Roles
NHM research coordinator. Main areas of responsibility:
- Support researchers in finding and writing proposals for external funding (both national and international sources)
- Draft consortium agreements and contracts
- Advise and assist on reporting to funding bodies
- Project management
- Conference and event planning for NHM researchers and leadership
- Support writing up of scientific publications
Background
Publications
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Weiland, Claus; Bauer, Daniel; Chala, Desalegn; Endresen, Dag; Grieb, Jonas & Kehel, Zakaria
[Show all 9 contributors for this article]
(2025).
FAIRification and AI-Readiness for Biodiversity Digital Twins.
Biodiversity Information Science and Standards (BISS).
9.
doi:
10.3897/biss.9.181439.
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The European Green Deal addresses a wide array of critical topics regarding the interaction and exchange between society and ecosystems involving human-induced climate change, biodiversity loss, and deforestation. To support the development of appropriate and sustainable mitigation strategies, both political frameworks as well as large-scale scenario forecast and simulation infrastructures such as Destination Earth Data Lake (DEDL, Puechmaille et al. 2025) and the Green Deal Data Space (Penninga et al. 2021) are currently implemented. Setting up these data spaces requires the consolidation and harmonization of vast amounts of data, among them data from long-term biodiversity monitoring (e.g. eDNA, Abarenkov et al. 2023), near real-time data captured by IoT devices (e.g. camera traps, Grieb et al. (2025)) and large-scale Earth observation data (e.g. ERA5 global reanalysis, Hersbach et al. (2020)). Key tools and research methodologies for integration of such data have been developed in the Destination Earth-linked Biodiversity Digital Twin project (BioDT). Biodiversity digital twins provide digital replicas of biodiversity patterns and processes (Khan et al. 2025), for FAIR-compliant reuse and cross-platform portability, they are packaged in BioDT using the RO-Crate specification. Resulting datasets as well as computational workflows are bundled as digital objects and annotated with rich machine-interpretable metadata using schema.org and its extensions Bioschemas and Croissant (high-level metadata specification supporting AI-Readiness, Bolleman et al. 2025). The workflow.earth pilot was developed to migrate and functionally integrate BioDT's digital twin for crop wild relatives (BioDT CWR) into DEDL. BioDT CWR is designed to identify genetic resources in crop wild relatives (CWR) and aid in creating strategies to mitigate food-related crises linked to climate change (Chala et al. 2024). CWR are crucial sources of untapped genetic diversity, offering greater adaptability to extreme weather events such as droughts, cold waves, and heavy precipitation. They are therefore of particular importance to ensure food security with regard to Sustainable Development Goals (notably Goal 2 “End hunger, achieve food security and improved nutrition and promote sustainable agriculture”, United Nations 2023). Major objectives for workflow.earth are to enhance visibility and long-term availability of the BioDT CWR, to improve its prediction capabilities using DEDL’s near data processing services, and to facilitate (in perspective) the orchestrated interplay with other digital twins such as the Climate Change Adaptation DT (Weiland et al. 2024). to enhance visibility and long-term availability of the BioDT CWR, to improve its prediction capabilities using DEDL’s near data processing services, and to facilitate (in perspective) the orchestrated interplay with other digital twins such as the Climate Change Adaptation DT (Weiland et al. 2024). On top of RO-Crate, workflow.earth employs FAIR Signposting to add machine-interpretable links to human-readable digital objects using link relation types (RFC8288, Fig. 1) to present the web topology of a resource (Soiland-Reyes et al. 2024). In this presentation, we will demonstrate the deployment of agrobiodiversity workflows in DEDL using workflow.earth and the publication of model and results as webby FDOs.
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Yarava, Jayasubba Reddy; Rydmark, Marcella Christine Orwick; Ryoo, David; Hofstetter, Albert; Gumbart, James C. & Habeck, Michael
[Show all 9 contributors for this article]
(2025).
Probing the Dynamics of Yersinia Adhesin A (YadA) in Outer Membranes Hints at Requirements for β-Barrel Membrane Insertion.
Journal of the American Chemical Society.
ISSN 0002-7863.
147(10),
p. 8618–8628.
doi:
10.1021/jacs.4c17726.
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The vast majority of cells are protected and functionalized by a dense surface layer of glycans, proteoglycans, and glycolipids. This surface represents an underexplored space in structural biology that is exceedingly challenging to recreate in vitro. Here, we investigate β-barrel protein dynamics within an asymmetric outer membrane environment, with the trimeric autotransporter Yersinia adhesin A (YadA) as an example. Magic-angle spinning NMR relaxation data and a model-free approach reveal increased mobility in the second half of strand β2 after the conserved G72, which is responsible for membrane insertion and autotransport, and in the subsequent loop toward β3. In contrast, the protomer–protomer interaction sites (β1i–β4i–1) are rigid. Intriguingly, the mobility in the β-strand section following G72 is substantially elevated in the outer membrane and less so in the detergent environment of microcrystals. A possible source is revealed by molecular dynamics simulations that show the formation of a salt bridge involving E79 and R76 in competition with a dynamic interplay of calcium binding by E79 and the phosphate groups of the lipids. An estimation of overall barrel motion in the outer membrane and detergent-containing crystals yields values of around 41 ns for both. The global motion of YadA in the outer membrane has a stronger rotational component orthogonal to the symmetry axis of the trimeric porin than in the detergent-containing crystal. In summary, our investigation shows that the mobility in the second half of β2 and the loop to β3 required for membrane insertion and autotransport is maintained in the final folded form of YadA.
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Hermansen, Simen; Ryoo, David; Rydmark, Marcella Christine Orwick; Saragliadis, Athanasios; Gumbart, James C & Linke, Dirk
(2022).
The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of Escherichia coli.
Frontiers in Molecular Biosciences.
9.
doi:
10.3389/fmolb.2022.918480.
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The outer membrane of Gram-negative bacteria acts as an additional diffusion barrier for solutes and nutrients. It is perforated by outer membrane proteins (OMPs) that function most often as diffusion pores, but sometimes also as parts of larger cellular transport complexes, structural components of the cell wall, or even as enzymes. These OMPs often have large loops that protrude into the extracellular environment, which have promise for biotechnological applications and as therapeutic targets. Thus, understanding how modifications to these loops affect OMP stability and folding is critical for their efficient application. In this work, the small outer membrane protein OmpX was used as a model system to quantify the effects of loop insertions on OMP folding and stability. The insertions were varied according to both hydrophobicity and size, and their effects were determined by assaying folding into detergent micelles in vitro by SDS-PAGE and in vivo by isolating the outer membrane of cells expressing the constructs. The different insertions were also examined in molecular dynamics simulations to resolve how they affect OmpX dynamics in its native outer membrane. The results indicate that folding of OMPs is affected by both the insert length and by its hydrophobic character. Small insertions sometimes even improved the folding efficiency of OmpX, while large hydrophilic inserts reduced it. All the constructs that were found to fold in vitro could also do so in their native environment. One construct that could not fold in vitro was transported to the OM in vivo , but remained unfolded. Our results will help to improve the design and efficiency of recombinant OMPs used for surface display.
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Bjørnestad, Victoria Ariel; Rydmark, Marcella Christine Orwick & Lund, Reidar
(2021).
Understanding the Structural Pathways for Lipid Nanodisc Formation: How Styrene Maleic Acid Copolymers Induce Membrane Fracture and Disc Formation.
Langmuir.
ISSN 0743-7463.
37(20),
p. 6178–6188.
doi:
10.1021/acs.langmuir.1c00304.
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Lipid nanodiscs formed by mixtures of styrene maleic acid (SMA) copolymers and lipid membranes are important tools for studying membrane proteins in many biotechnological applications. However, molecular interactions leading up to their formation are not well understood. Here, we elucidate the nanodisc formation pathways for SMA/lipid vesicle mixtures using small-angle X-ray scattering (SAXS) that allows detailed in situ nanostructural information. SMA copolymer that is initially aggregated in solution inserts its styrene units into the lipid bilayer hydrocarbon region, leading to fractures in the membrane. The initial copolymer–lipid interactions observed in the vesicles are also present in the formed discs, with excess copolymer distributed along the normal of the bilayer. The size and SMA distribution in the resulting discs strongly depend on the temperature, lipid/copolymer ratio, and lipid type. We find that the solubilization limit increases for membranes above the melting point, suggesting that defects in gel-like lipid membranes play a significant role in membrane fracturing and nanodisc formation. These findings provide unique insights into the formation of nanodiscs as well as into the microscopic mechanism of solubilization, which plays an important role in many applications and products ranging from household goods to biotechnology and medicine.
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Ryoo, David; Rydmark, Marcella Orwick; Pang, Yui Tik; Lundquist, Karl P; Linke, Dirk & Gumbart, James C
(2020).
BamA is required for autotransporter secretion.
Biochimica et Biophysica Acta - General Subjects.
ISSN 0304-4165.
1864(7),
p. 1–8.
doi:
10.1016/j.bbagen.2020.129581.
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Background In Gram-negative bacteria, type Va and Vc autotransporters are proteins that contain both a secreted virulence factor (the “passenger” domain) and a β-barrel that aids its export. While it is known that the folding and insertion of the β-barrel domain utilize the β-barrel assembly machinery (BAM) complex, how the passenger domain is secreted and folded across the membrane remains to be determined. The hairpin model states that passenger domain secretion occurs independently through the fully-formed and membrane-inserted β-barrel domain via a hairpin folding intermediate. In contrast, the BamA-assisted model states that the passenger domain is secreted through a hybrid of BamA, the essential subunit of the BAM complex, and the β-barrel domain of the autotransporter. Methods To ascertain the models' plausibility, we have used molecular dynamics to simulate passenger domain secretion for two autotransporters, EspP and YadA. Results We observed that each protein's β-barrel is unable to accommodate the secreting passenger domain in a hairpin configuration without major structural distortions. Additionally, the force required for secretion through EspP's β-barrel is more than that through the BamA β-barrel. Conclusions Secretion of autotransporters most likely occurs through an incompletely formed β-barrel domain of the autotransporter in conjunction with BamA. General significance Secretion of virulence factors is a process used by practically all pathogenic Gram-negative bacteria. Understanding this process is a necessary step towards limiting their infectious capacity.
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Chauhan, Nandini; Hatlem, Daniel; Rydmark, Marcella Orwick; Schneider, Kenneth; Flötenmeyer, Matthias & Rossum, Barth-J Van
[Show all 8 contributors for this article]
(2019).
Insights into the autotransport process of a trimeric autotransporter, Yersinia Adhesin A (YadA).
Molecular Microbiology.
ISSN 0950-382X.
111(3),
p. 844–862.
doi:
10.1111/mmi.14195.
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Trimeric autotransporter adhesins (TAAs) are a subset of a larger protein family called the type V secretion systems. They are localized on the cell surface of Gram‐negative bacteria, function as mediators of attachment to inorganic surfaces and host cells, and thus include important virulence factors. Yersinia adhesin A (YadA) from Yersinia enterocolitica is a prototypical TAA that is used extensively to study the structure and function of the type Vc secretion system. A solid‐state NMR study of the membrane anchor domain of YadA previously revealed a flexible stretch of small residues, termed the ASSA region, that links the membrane anchor to the stalk domain. In this study, we present evidence that single amino acid proline substitutions produce two different conformers of the membrane anchor domain of YadA; one with the N‐termini facing the extracellular surface, and a second with the N‐termini located in the periplasm. We propose that TAAs adopt a hairpin intermediate during secretion, as has been shown before for other subtypes of the type V secretion system. As the YadA transition state intermediate can be isolated from the outer membrane, future structural studies should be possible to further unravel details of the autotransport process.
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Rydmark, Marcella Orwick; Christensen, Mikkel; Köksal, Elif; Kantarci, Ilayda; Kustanovich, Kiryl & Yantchev, Ventsislav
[Show all 8 contributors for this article]
(2019).
Styrene maleic acid copolymer induces pores in biomembranes.
Soft Matter.
ISSN 1744-683X.
15(39),
p. 7934–7944.
doi:
10.1039/C9SM01407A.
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We investigated the interactions between styrene–maleic acid (SMA) copolymers and phospholipid bilayers, using confocal microscopy and surface acoustic wave resonance (SAR) sensing. For the first time we experimentally observed and followed pore formation by SMA copolymers in intact supported bilayers and unilamellar vesicles, showing that fluorescein, a water-soluble organic compound with a mean diameter of 6.9 Å, can traverse the membrane. Our findings are in agreement with recent theoretical predictions, which suggested that SMA copolymers may insert along the plane of the bilayer to form stable toroidal pores.
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Michalik, Marcin; Rydmark, Marcella Orwick; Habeck, Michael; Alva, Vikram; Arnold, Thomas & Linke, Dirk
(2017).
An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins.
PLOS ONE.
12(8).
doi:
10.1371/journal.pone.0182016.
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An intimate interaction between a pair of amino acids, a tyrosine and glycine on neighboring β-strands, has been previously reported to be important for the structural stability of autotransporters. Here, we show that the conservation of this interacting pair extends to nearly all major families of outer membrane β-barrel proteins, which are thought to have originated through duplication events involving an ancestral ββ hairpin. We analyzed the function of this motif using the prototypical outer membrane protein OmpX. Stopped-flow fluorescence shows that two folding processes occur in the millisecond time regime, the rates of which are reduced in the tyrosine mutant. Folding assays further demonstrate a reduction in the yield of folded protein for the mutant compared to the wild-type, as well as a reduction in thermal stability. Taken together, our data support the idea of an evolutionarily conserved ‘folding core’ that affects the folding, membrane insertion, and thermal stability of outer membrane protein β-barrels.
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Rydmark, Marcella Christine Orwick & Woudstra, Yannick
(2022).
Chapter 9. Sequencing platforms.
In Boer, Hugo de; Rydmark, Marcella Christine Orwick; Verstraete, Brecht & Gravendeel, Barbara (Ed.),
Molecular identification of plants: from sequence to species.
Pensoft Publishers.
ISSN 9786192480912.
doi:
10.3897/ab.e98875.
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Boer, Hugo de; Endresen, Dag; Schigel, Dmitry; Russell, Laura Anne; Rydmark, Marcella Christine Orwick & Abrahamyan, Armine
[Show all 9 contributors for this article]
(2022).
BioDATA final symposium for partner universities, ForBio, and GBIF at Tøyen in Oslo in November 2022.
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Typically, established researchers, museum curators, and collection managers are involved in data management and data publishing to national and global biodiversity data facilities. By training early career (student) biodiversity scholars, we will efficiently turn the current academic and education landscape into a more open-data-friendly one. The closing event will focus on addressing students from the University of Oslo. Two students from each BioDATA partner country will be able to participate and present their studies and data activities as dataset publications through GBIF.org and/or as data papers, an emerging and student-friendly publication type. GBIF Norway with the support from the GBIF Secretariat will act as a data publishing facilitator.
BioDATA final symposium for partner universities, ForBio, and GBIF. Venue in Oslo (11-12 November 2022).
https://www.nhm.uio.no/english/research/projects/biodata/activities/2022-final-seminar.html
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Blakeney, Rebecca Angelica; Rydmark, Marcella Christine Orwick; Ulriksen, Emilie Steinbakk; Heien, Greta Karoline; Butt, Hussain Shakeel & Kool, Anneleen
[Show all 8 contributors for this article]
(2021).
Exhibition: Pharmaceutical Time Travels: From Ancient Plant Remedies to Modern Medicines / Utstilling: Farmasøytisk tidsreise: Fra historiske planteremedier til moderne medisiner.
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Rydmark, Marcella Orwick; Chauhan, Nandini & Linke, Dirk
(2016).
Structure and Dynamics of The Yersinia Adhesin A
Membrane-Anchor Domain by NMR.
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Bjerregaard-Andersen, Kaare; Rydmark, Marcella Orwick & Krengel, Ute
(2015).
Structure determination of a bacterial adhesin.
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Published
July 31, 2020 10:20 AM
- Last modified
Aug. 14, 2026 2:04 PM
