• Adaptive fluctuation imaging captures rapid subcellular dynamics 

      Opstad, Ida Sundvor; Ströhl, Florian; Birgisdottir, Åsa birna; Acuña Maldonado, Sebastian Andres; Kalstad, Trine; Myrmel, Truls; Agarwal, Krishna; Ahluwalia, Balpreet Singh (Journal article; Tidsskriftartikkel, 2019-07-22)
      In this work we have explored the live-cell friendly nanoscopy method Multiple Signal Classification Algorithm (MUSICAL) for multi-colour imaging of various organelles and sub-cellular structures in the cardiomyoblast cell line H2c9. We have tested MUSICAL for fast (up to 230Hz), multi-colour time-lapse sequences of various sub-cellular structures (mitochondria, endoplasmic reticulum, microtubules, ...
    • Adaptive fluctuation imaging captures rapid subcellular dynamics 

      Opstad, Ida Sundvor; Ströhl, Florian; Birgisdottir, Åsa birna; Maldonado, Sebastián Andrés Acuña; Kalstad, Trine; Myrmel, Truls; Agarwal, Krishna; Ahluwalia, Balpreet Singh (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-07-22)
      In this work we have explored the live-cell friendly nanoscopy method Multiple Signal Classification Algorithm (MUSICAL) for multi-colour imaging of various organelles and sub-cellular structures in the cardiomyoblast cell line H2c9. We have tested MUSICAL for fast (up to 230Hz), multi-colour time-lapse sequences of various sub-cellular structures (mitochondria, endoplasmic reticulum, microtubules, ...
    • Analyzing Mitochondrial Morphology Through Simulation Supervised Learning 

      Punnakkal, Abhinanda Ranjit; Godtliebsen, Gustav; Somani, Ayush; Acuna Maldonado, Sebastian Andres; Birgisdottir, Åsa birna; Prasad, Dilip K.; Horsch, Alexander; Agarwal, Krishna (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-03-03)
      The quantitative analysis of subcellular organelles such as mitochondria in cell fluorescence microscopy images is a demanding task because of the inherent challenges in the segmentation of these small and morphologically diverse structures. In this article, we demonstrate the use of a machine learning-aided segmentation and analysis pipeline for the quantification of mitochondrial morphology in ...
    • ATG8 Family Proteins Act as Scaffolds for Assembly of the ULK Complex SEQUENCE REQUIREMENTS FOR LC3-INTERACTING REGION (LIR) MOTIFS 

      Alemu, Endalkachew Ashenafi; Lamark, Trond; Torgersen, Knut Martin; Birgisdottir, Åsa birna; Larsen, Kenneth Bowitz; Jain, Ashish; Olsvik, Hallvard Lauritz; Øvervatn, Aud Karin; Kirkin, Vladimir; Johansen, Terje (Journal article; Tidsskriftartikkel; Peer reviewed, 2012-10-05)
      Autophagy is a lysosome-dependent degradation system conserved among eukaryotes. The mammalian Atg1 homologues, Unc-51 like kinase (ULK) 1 and 2, are multifunctional proteins with roles in autophagy, neurite outgrowth, and vesicle transport. The mammalian ULK complex involved in autophagy consists of ULK1, ULK2, ATG13, FIP200, and ATG101. We have used pulldown and peptide array overlay assays to ...
    • Autophagy and endocytosis – interconnections and interdependencies 

      Birgisdottir, Åsa birna; Johansen, Terje (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-05-22)
      Autophagy and endocytosis are membrane-vesicle-based cellular pathways for degradation and recycling of intracellular and extracellular components, respectively. These pathways have a common endpoint at the lysosome, where their cargo is degraded. In addition, the two pathways intersect at different stages during vesicle formation, fusion and trafficking, and share parts of the molecular machinery. ...
    • High-resolution visualization and assessment of basal and OXPHOS-induced mitophagy in H9c2 cardiomyoblasts 

      Godtliebsen, Gustav; Larsen, Kenneth Bowitz; Bhujabal, Zambarlal Babanrao; Opstad, Ida Sundvor; Nager Grifo, Mireia; Punnakkal, Abhinanda Ranjit; Kalstad, Trine; Olsen, Randi; Lund, trine; Prasad, Dilip K.; Agarwal, Krishna; Myrmel, Truls; Birgisdottir, Åsa birna (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-07-05)
      Mitochondria are susceptible to damage resulting from their activity as energy providers. Damaged mitochondria can cause harm to the cell and thus mitochondria are subjected to elaborate quality-control mechanisms including elimination via lysosomal degradation in a process termed mitophagy. Basal mitophagy is a house-keeping mechanism fine-tuning the number of mitochondria according to the metabolic ...
    • Multifocus microscopy with optical sectioning and high axial resolution 

      Ströhl, Florian; Hansen, Daniel Henry; Nàger, Mireia; Birgisdottir, Åsa birna (Journal article; Tidsskriftartikkel; Peer reviewed, 2022)
      Multifocus microscopy enables recording of entire volumes in a single camera 11 exposure. In dense samples, multifocus microscopy is severely hampered by background haze. 12 Here, we introduce a scalable multifocus method that incorporates optical sectioning and offers 13 improved axial resolution capabilities. In our method, a dithered oblique light-sheet scans the 14 sample volume during a ...
    • Structured Illumination Microscopy of Biological Structures 

      Wolfson, Deanna; Villegas, Luis; Opstad, Ida Sundvor; Birgisdottir, Åsa birna; Øie, Cristina Ionica; Ahluwalia, Balpreet Singh (Conference object; Konferansebidrag, 2018)
      <p>Resolution in optical microscopy has long been limited to the Abbe diffraction limit, i.e. about 250 nm laterally for visible wavelengths on a very good microscope. In the last two decades several techniques have been devised to circumvent this limit: an achievement which was recognized with the 2014 Nobel Prize in Chemistry. Structured Illumination Microscopy (SIM) was the first of these techniques ...
    • Three-dimensional structured illumination microscopy data of mitochondria and lysosomes in cardiomyoblasts under normal and galactose-adapted conditions 

      Opstad, Ida Sundvor; Godtliebsen, Gustav; Ströhl, Florian; Myrmel, Truls; Ahluwalia, Balpreet Singh; Agarwal, Krishna; Birgisdottir, Åsa birna (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-03-23)
      This three-dimensional structured illumination microscopy (3DSIM) dataset was generated to highlight the suitability of 3DSIM to investigate mitochondria-derived vesicles (MDVs) in H9c2 cardiomyoblasts in living or fxed cells. MDVs act as a mitochondria quality control mechanism. The cells were stably expressing the tandem-tag eGFP-mCherry-OMP25-TM (outer mitochondrial membrane) which can be used ...
    • Use of Peptide Arrays for Identification and Characterization of LIR Motifs 

      Rasmussen, Mads Skytte; Birgisdottir, Åsa birna; Johansen, Terje (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-01-05)
      The mammalian ATG8 proteins (LC3A-C/GABARAP, GABARAPL1, and GABARAPL2) are small ubiquitin-like proteins critically involved in macroautophagy. Their processed C-termini are posttranslationally conjugated to a phosphatidylethanolamine moiety, enabling their insertion into the lipid bilayers of both the inner and outer membranes of the forming autophagosomes. The ATG8s bind a diverse selection of ...
    • Virtual labeling of mitochondria in living cells using correlative imaging and physics-guided deep learning 

      Somani, Ayush; Sekh, Arif Ahmed; Opstad, Ida Sundvor; Birgisdottir, Åsa birna; Myrmel, Truls; Ahluwalia, Balpreet Singh; Horsch, Alexander; Agarwal, Krishna; Prasad, Dilip K. (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-09-28)
      Mitochondria play a crucial role in cellular metabolism. This paper presents a novel method to visualize mitochondria in living cells without the use of fluorescent markers. We propose a physics-guided deep learning approach for obtaining virtually labeled micrographs of mitochondria from bright-field images. We integrate a microscope’s point spread function in the learning of an adversarial neural ...