Metabolic Imaging & Tissue Engineering: publications of Prof. Dmitriev group

2015:

1.    Dmitriev R, Papkovsky D: Multi-parametric O2 Imaging in Three-Dimensional Neural Cell Models with the Phosphorescent Probes. In: Neuronal Cell Death. Edited by Lossi L, Merighi A, vol. 1254: Springer New York; 2015: 55-71. Book chapter

2.    Jenkins J, Dmitriev R, Papkovsky D: Imaging Cell and Tissue O2 by TCSPC-PLIM. In: Advanced Time-Correlated Single Photon Counting Applications. Edited by Becker W, vol. 111: Springer International Publishing; 2015: 225-247. Book chapter

3.    Dmitriev RI, Borisov SM, Jenkins J, Papkovsky DB: Multi-parametric imaging of tumor spheroids with ultra-bright and tunable nanoparticle O2 probes. In: Photonics West 2015: 2015. 932806-932806-932808. Published Conference proceedings (Photonics SPIE)

4.    Jenkins J, Dmitriev RI, Morten K, McDermott KW, Papkovsky DB: Oxygen-sensing scaffolds for 3-dimensional cell and tissue culture. Acta Biomaterialia 2015, 16(0):126-135.

5.    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.

6.    Andreev D, O'Connor P, Zhdanov A, Dmitriev R, Shatsky I, Papkovsky D, Baranov P: Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20minutes. Genome Biology 2015, 16(1):90.

7.    Dmitriev RI, Papkovsky DB: Intracellular probes for imaging oxygen concentration: How good are they? Methods and Applications in Fluorescence 2015, 3(3):034001. (review)

2016:

1.    Dmitriev RI, O’Donnell N, Papkovsky DB: Metallochelate Coupling of Phosphorescent Pt-Porphyrins to Peptides, Proteins, and Self-Assembling Protein Nanoparticles. Bioconjugate Chemistry 2016, 27(2):439-445.

2.    Fomin M, Dmitriev RI, Jenkins J, Papkovsky DB, Heindl D, König B: A Two-Acceptor Cyanine-Based Fluorescent Indicator for NAD(P)H in Tumor Cell Models. ACS Sensors 2016, 1(6):702-709.

3.    Jenkins J, Borisov SM, Papkovsky DB, Dmitriev RI: Sulforhodamine nanothermometer for multi-parametric Fluorescence Lifetime Imaging Microscopy. Analytical Chemistry 2016, 88(21):10566-10572.

4.    Jenkins J, Papkovsky DB, Dmitriev RI: The Ca2+/Mn2+ -transporting SPCA2 pump is regulated by oxygen and cell density in colon cancer cells. Biochemical Journal 2016, 473(16):2507-2518.

5.    Korneenko TV, Pestov NB, Ahmad N, Okkelman IA, Dmitriev RI, Shakhparonov MI, Modyanov NN: Evolutionary diversification of the BetaM interactome acquired through co-option of the ATP1B4 gene in placental mammals. Scientific Reports 2016, 6:22395.

6.    Okkelman IA, Dmitriev RI, Foley T, Papkovsky DB: Use of Fluorescence Lifetime Imaging Microscopy (FLIM) as a Timer of Cell Cycle S Phase. PLOS ONE 2016, 11(12):e0167385.

7.    Tzani I, Ivanov IP, Andreev DE, Dmitriev RI, Dean KA, Baranov PV, Atkins JF, Loughran G: Systematic analysis of the PTEN 5′ leader identifies a major AUU initiated proteoform. Open Biology 2016, 6(5):150203.

2017:

1.    Dmitriev RI (ed.): Multi-Parametric Live Cell Microscopy of 3D Tissue Models: Springer International Publishing AG 2017; 2017. Book

2.    O’Donnell N, Dmitriev RI: Three-Dimensional Tissue Models and Available Probes for Multi-Parametric Live Cell Microscopy: A Brief Overview. In: Multi-Parametric Live Cell Microscopy of 3D Tissue Models. Springer; 2017: 49-67. Book chapter

3.    Okkelman IA, Foley T, Papkovsky DB, Dmitriev RI: Multi-Parametric Imaging of Hypoxia and Cell Cycle in Intestinal Organoid Culture. In: Multi-Parametric Live Cell Microscopy of 3D Tissue Models.Springer; 2017: 85-103. Book chapter

4.    Shpichka A, Koroleva A, Kuznetsova D, Dmitriev RI, Timashev P: Fabrication and Handling of 3D Scaffolds Based on Polymers and Decellularized Tissues. In: Multi-Parametric Live Cell Microscopy of 3D Tissue Models. Springer; 2017: 71-81. Book chapter

5.    Okkelman IA, Foley T, Papkovsky DB, Dmitriev RI: Live cell imaging of mouse intestinal organoids reveals heterogeneity in their oxygenation. Biomaterials 2017, 146:86-96.

6.    Yazgan G, Dmitriev RI, Tyagi V, Jenkins J, Rotaru G-M, Rottmar M, Rossi RM, Toncelli C, Papkovsky DB, Maniura-Weber K et al: Steering surface topographies of electrospun fibers: understanding the mechanisms. Scientific Reports 2017, 7(1):158.

2018:

1.    Papkovsky D, Dmitriev R: Quenched-phosphorescence Detection of Molecular Oxygen: Applications in Life Sciences: The Royal Society of Chemistry; 2018. Book

2.    Papkovsky DB, Dmitriev RI: CHAPTER 3 Evolution of Cell-penetrating Phosphorescent O2 Probes. In: Quenched-phosphorescence Detection of Molecular Oxygen: Applications in Life Sciences. Edited by Papkovsky DB, Dmitriev RI: The Royal Society of Chemistry; 2018: 50-70. Book chapter

3.    Kornev VA, Grebenik EA, Solovieva AB, Dmitriev RI, Timashev PS: Hydrogel-assisted neuroregeneration approaches towards brain injury therapy: A state-of-the-art review. Computational and Structural Biotechnology Journal 2018, 16:488-502. Review

4.    Papkovsky DB, Dmitriev RI: Imaging of oxygen and hypoxia in cell and tissue samples. Cell Mol Life Sci 2018, 75(16):2963-2980. Review

5.    Müller BJ, Zhdanov AV, Borisov SM, Foley T, Okkelman IA, Tsytsarev V, Tang Q, Erzurumlu RS, Chen Y, Zhang H et al: Nanoparticle-Based Fluoroionophore for Analysis of Potassium Ion Dynamics in 3D Tissue Models and In Vivo. Advanced Functional Materials 2018, 28(9):1704598.

6.    Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF: Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. Journal of Biological Chemistry 2018, 293:4434-4444.

7.    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.

2019:

1.    Dalfen I, Dmitriev RI, Holst G, Klimant I, Borisov SM: Background-Free Fluorescence-Decay-Time Sensing and Imaging of pH with Highly Photostable Diazaoxotriangulenium Dyes. Analytical Chemistry 2019, 91(1):808-816.

2.    Grebenik EA, Istranov LP, Istranova EV, Churbanov SN, Shavkuta BS, Dmitriev RI, Veryasova NN, Kotova SL, Kurkov AV, Shekhter AB et al: Chemical cross-linking of xenopericardial biomeshes: A bottom-up study of structural and functional correlations. Xenotransplantation 2019, 0(0):e12506.

3.    Koren K, Gravesen Salinas NK, Santella M, Moßhammer M, Müller M-C, Dmitriev RI, Borisov SM, Kühl M, Laursen BW: Evaluation of Ebselen-azadioxatriangulenium as redox-sensitive fluorescent intracellular probe and as indicator within a planar redox optode. Dyes and Pigments 2019:107866.

4.    Okkelman IA, Papkovsky DB, Dmitriev RI: Estimation of the Mitochondrial Membrane Potential Using Fluorescence Lifetime Imaging Microscopy. Cytometry Part A 2019, 0(0).

2020

1. Okkelman IA, Neto N, Papkovsky DB, Monaghan MG, Dmitriev RI: A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (FLIM) and extracellular flux analyses. Redox Biology 2020, 30:101420.

2. Elagin V, Kuznetsova D, Grebenik E, Zolotov DA, Istranov L, Zharikova T, Istranova E, Polozova A, Reunov D, Kurkov A et al: Multiparametric Optical Bioimaging Reveals the Fate of Epoxy Crosslinked Biomeshes in the Mouse Subcutaneous Implantation Model. Frontiers in Bioengineering and Biotechnology 2020, 8(107).

3. Neto N, Dmitriev RI, Monaghan MG: Seeing Is Believing: Noninvasive Microscopic Imaging Modalities for Tissue Engineering and Regenerative Medicine. In: Cell Engineering and Regeneration. Edited by Gimble JM, Marolt Presen D, Oreffo R, Redl H, Wolbank S. Cham: Springer International Publishing; 2020: 1-41.

4. Kawashima M, Bensaad K, Zois CE, Barberis A, Bridges E, Wigfield S, Lagerholm C, Dmitriev RI, Tokiwa M, Toi M et al: Disruption of hypoxia-inducible fatty acid binding protein 7 induces beige fat-like differentiation and thermogenesis in breast cancer cells. Cancer & Metabolism 2020, 8(1):13.

5. Okkelman IA, Puschhof J, Papkovsky DB, Dmitriev RI: Visualization of Stem Cell Niche by Fluorescence Lifetime Imaging Microscopy. In: Intestinal Stem Cells: Methods and Protocols. Edited by Ordóñez-Morán P. New York, NY: Springer US; 2020: 65-97.

After joining Ghent University:

6. Okkelman I, 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. 

2021

1. Perottoni S, Neto NGB, Di Nitto C, Dmitriev RI, Raimondi MT, Monaghan MG: Intracellular label-free detection of mesenchymal stem cell metabolism within a perivascular niche-on-a-chip. Lab on a Chip 2021, 21(7):1395-1408.

2. Dmitriev RI, Intes X, Barroso M: Luminescence lifetime imaging of three-dimensional biological objects. Review. Journal of Cell Science 2021, 134(9): 1-17.

3. Peirsman A, Blondeel E, Ahmed T, Anckaert J, Audenaert D, Boterberg T, Buzas K, Carragher N, Castellani G, Castro F: MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity. Nature methods 2021:1-10.

2022

1. Okkelman IA, Vercruysse C, Kondrashina AV, Borisov SM, Dmitriev RI: Affordable Oxygen Microscopy-Assisted Biofabrication of Multicellular Spheroids. JoVE 2022:e63403.

2. Van de Voorde B, Sensu B, De Vos L, Colenbier R, Baskan H, Geltmeyer J, Parmentier L, Van Daele L, Dmitriev RI, Pyl L et al: Electrospinning of poly(decamethylene terephthalate) to support vascular graft applications. European Polymer Journal 2022:111003.

3. Debruyne AC, Okkelman IA, Dmitriev RI: Balance between the cell viability and death in 3D (review). Seminars in Cell & Developmental Biology 2022. https://doi.org/10.1016/j.semcdb.2022.09.005

2023

1. Russegger A, Debruyne AC, Berrio DC, Fuchs S, Marzi J, Schenke-Layland K, Dmitriev RI, Borisov SM: Bright and Photostable TADF-Emitting Zirconium(IV) Pyridinedipyrrolide Complexes: Efficient Dyes for Decay Time-Based Temperature Sensing and Imaging. Advanced Optical Materials 2023, n/a(n/a):2202720.

2. Okkelman IA, Dmitriev RI: Fluorescence Intensity and Fluorescence Lifetime Imaging Microscopies (FLIM) of Cell Differentiation in the Small Intestinal Organoids Using Cholera Toxin. In: Intestinal Differentiated Cells: Methods and Protocols. Edited by Ordóñez-Morán P. New York, NY: Springer US; 2023: 171-195.

3. Van Daele L, Van de Voorde B, Colenbier R, De Vos L, Parmentier L, Van der Meeren L, Skirtach A, Dmitriev RI, Dubruel P, Van Vlierberghe S: Effect of molar mass and alkyl chain length on the surface properties and biocompatibility of poly(alkylene terephthalate)s for potential cardiovascular applications. Journal of Materials Chemistry B 2023.

4. Parmentier L, D'Haese S, Carpentier N, Dmitriev RI, Van Vlierberghe S: Bottom-up Extrusion-Based Biofabrication of the Osteoid Niche. Macromolecular Bioscience 2023, n/a(n/a):2300395.

5. Parmentier L, D'Haese S, Duquesne J, Bray F, Van der Meeren L, Skirtach AG, Rolando C, Dmitriev RI, Van Vlierberghe S: 2D fibrillar osteoid niche mimicry through inclusion of visco-elastic and topographical cues in gelatin-based networks. International Journal of Biological Macromolecules 2023:127619.

6. Barroso M, Monaghan MG, Niesner R, Dmitriev RI: Probing organoid metabolism using fluorescence lifetime imaging microscopy (FLIM): The next frontier of drug discovery and disease understanding. Advanced Drug Delivery Reviews 2023, 201:115081.

7. Cruyssen RVd, Devan J, Heggli I, Burri D, Gaublomme D, Josipovic I, Dumas E, Vlieghe C, Raimondo MG, Zakharov P et al: GDF15 mediates inflammation-associated bone loss through a brain-bone axis. bioRxiv 2023:2023.2011.2022.568290. (PREPRINT)

8. Debruyne AC, Okkelman IA, Heymans N, Nobis M, Borisov SM, Dmitriev RI: Live microscopy of multicellular spheroids with the multi-modal near-infrared nanoparticles reveals differences in oxygenation gradients. bioRxiv 2023:2023.2012.2011.571110. (PREPRINT)

2024

1. Barra J, Crosbourne I, Roberge CL, Bossardi-Ramos R, Warren JSA, Matteson K, Wang L, Jourd’heuil F, Borisov SM, Bresnahan E et al: DMT1-dependent endosome-mitochondria interactions regulate mitochondrial iron translocation and metastatic outgrowth. Oncogene 2024. https://www.nature.com/articles/s41388-023-02933-x