Ruslan Dmitriev lab

Prof. dr. Ruslan Dmitriev


Research topic

One of the current challenges faced by the organoid technology is their high variability and lack of tools for single cell real-time analysis. My team focuses on combining innovations in biosensors, fluorescence lifetime imaging microscopy (FLIM) and biofabrication fields to controllably produce intestinal organoid cultures with known and controllable growth and metabolic characteristics. To solve this challenge, we develop multi-parametric 3D live imaging methodologies addressing analysis of organoid oxygenation, visualization of stem cell niche, labelling of specific cell types, their proliferation and metabolism. Using this approach we aim to design ‘active’ biosensors scaffold materials, understand gut-microbiota interactions and physiological role of O2 gradients in the intestine, in health and disease.

Areas of expertise

  • Intestinal organoids
  • Tissue engineering and biofabrication
  • 3D tissue models
  • FLIM, PLIM and hypoxia imaging
  • Biosensors and microscopy

Selected publications

  1. Okkelman IA, McGarrigle R, O'Carroll S, Carvajal Berrio D, Schenke-Layland K, Hynes J, Dmitriev RI: Extracellular Ca2+-sensing fluorescent protein biosensor based on a collagen-binding domain.
    ACS Applied Bio Materials 2020. DOI: 10.1021/acsabm.0c00649
  2. Okkelman IA, Neto N, Papkovsky DB, Monaghan M, Dmitriev RI: A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (FLIM) and extracellular flux analyses.
    Redox Biology 2019:101420.
  3. O'Donnell N, Okkelman IA, Timashev P, Gromovykh TI, Papkovsky DB, Dmitriev RI: Cellulose-based scaffolds for fluorescence lifetime imaging-assisted tissue engineering.
    Acta Biomaterialia 2018, 80, 85-96.
  4. Müller BJ, Zhdanov AV, Borisov SM, Foley T, Okkelman IA, Tsytsarev V, Tang Q, Erzurumlu RS, Chen Y, Zhang H, Toncelli C, Klimant I, Papkovsky DB, Dmitriev RI: Nanoparticle-Based Fluoroionophore for Analysis of Potassium Ion Dynamics in 3D Tissue Models and In Vivo.
    Advanced Functional Materials 2018. DOI: 10.1002/adfm.201704598
  5. Okkelman I.A., Foley T., Papkovsky DB, Dmitriev RI: Live cell imaging of mouse intestinal organoids reveals heterogeneity in their oxygenation.
    Biomaterials 2017, 146, 86-96.
  6. Okkelman I. A., Dmitriev R. I., Foley T., Papkovsky, D. B.: Use of Fluorescence Lifetime Imaging Microscopy (FLIM) as a Timer of Cell Cycle S Phase.
    PLOS ONE 2016, 11, e0167385.
  7. Dmitriev RI, Borisov SM, Düssmann H, Sun S, Müller BJ, Prehn J, Baklaushev VP, Klimant I, Papkovsky DB: Versatile Conjugated Polymer Nanoparticles for High-Resolution O2 Imaging in Cells and 3D Tissue Models.
    ACS Nano 2015,9(5), 5275-5288.

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