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Papkovsky group

About the Papkovsky research group

The Papkovsky Biophysics and Bioanalysis lab, established in 1997, focuses its research on the following areas:

• Roles of molecular oxygen (O₂) in biological systems. Cell and tissue respiration, metabolism, bioenergetics, mitochondrial function. Hypoxia research and signalling. O₂ as a marker of cellular (dys)function and toxicity,  applications to cancer, neuroscience and stem cell research.
• Imaging of cell and tissue O₂. Live cell confocal FLIM and PLIM (Fluorescence / Phosphorescence Lifetime Imaging Microscopy). New O₂ sensors, imaging probes and their bioanalytical applications.
• Advanced (bio)materials, phosphorescent porphyrins, bioconjugate chemistry, analytical method development. Fluorescent spectroscopy, time-resolved fluorescence. 

Current research projects in the Papkovsky research group

Current research projects

1. Development of tissue O₂ imaging PLIM-TCSPC method and imaging instrumentation.
2. Development of advanced phosphorescent probes for imaging tissue O₂ in vitro, ex-vivo and in vivo.
3. 3D tissue models: spheroids, tissue explants, organoids.
4. Effects of hypoxia on cell and tissue function, metabolic switching, hypoxia signalling.
5. Multi-parametric imaging studies with various cells and disease models.

 

Funded projects

1. ‘Advanced optical oxygen imaging platform for in vivo use’ – Enterprise Ireland Commercialisation Fund project (jointly with Anatomy Department (Prof. J. Cryan), 2013-2015.
2. Development of new probes and systems for measuring cellular oxygen and respiration EU FP7 Project Chemical Bioanalysis (‘Chebana’), 2010-2014.
3. Photonic Integration for Cell and Tissue Analysis – Science Foundation Ireland Research Center project grant ‘Irish Photonics Integration Centre, IPIC’, 2013 – 2016.
4. Smart Packaging systems containing novel optochemical O₂ and CO₂ sensors for the food industry – Irish Department of Agriculture FIRM project, 2012-2016.
5. Development of Bionic Sensor materials for metabolic imaging in regenerative medicine –Science Foundation Ireland Starting Investigator Research Grant of Dr. Ruslan Dmitriev.

 

People in the Papkovsky research group

Current lab members

Dr Ruslan Dmitriev

James Jenkins, BSc  

Caroline Kelly, BSc

Neil O’Donnell, MSc 

Dr Irina Okkelman  

Dr Alexander Zhdanov

 

Past lab members

 Dr Swagata Banerjee

Publications

Full list of publications

Professor Dmitri B. Papkovsky 

 

Selected publications

Phosphorescent O₂ sensing and imaging probes

Versatile conjugated polymer nanoparticle probes for high-resolution O₂ imaging in 3D cell and tissue models.

Dmitriev RI, Borisov SM, Dussmann H, Sun S, Müller BJ, Prehn J, Baklaushev VP, Klimant I, Papkovsky DB (2015).

ACS Nano (in press).

 

Small molecule phosphorescent probes for O₂ imaging in 3D tissue models.

Dmitriev RI, Kondrashina AV, Koren K, Klimant I, Pakan J, McDermott K, Zhdanov AV, Papkovsky DB (2014).

Biomaterials Science 2(6): 853-866.

DOI: 10.1039/C3bm60272a. 

 

Intracellular O₂ sensing probe based on cell-penetrating phosphorescent nanoparticles.

Fercher A, Borisov SM, Zhdanov AV, Klimant I, Papkovsky DB (2011).

ACS Nano 5(7): 5499-5508.

DOI: 10.1021/nn200807g.

 

A phosphorescent nanoparticle based probe for sensing and imaging of (intra)cellular oxygen in multiple detection modalities.

Kondrashina AV, Dmitriev RI, Borisov SM, Klimant I, O’Brian I, Nolan YM, Zhdanov AV, Papkovsky DB (2012).

Advanced Functional Materials 22(23): 4931-4939.

DOI: 10.1002/adfm.201201387.      

 

Imaging cell and tissue oxygen

Imaging oxygen in neural cell and tissue models by means of anionic cell-permeable phosphorescent nanoparticles.

Dmitriev RI, Borisov SM, Kondrashina AV, Pakan JMP, Anilkumar U,  Prehn JHM, Zhdanov AV, McDermott KW, Klimant I, Papkovsky DB (2015).

Cellular and Molecular Life Sciences 72(2): 367-381.

DOI: 10.1007/s00018-014-1673-5.

 

Imaging of neurosphere oxygenation with phosphorescent probes.

Dmitriev, R. I., A. V. Zhdanov, Y. M. Nolan and D. B. Papkovsky (2013).

Biomaterials 34(37): 9307-9317.

DOI: 10.1016/j.biomaterials.2013.08.065.

 

Oxygen-sensing scaffolds for 3-dimensional cell and tissue culture.

Jenkins, J., R. I. Dmitriev, K. Morten, K. W. McDermott and D. B. Papkovsky (2015).

Acta Biomater 16: 126-135.

DOI: 10.1016/j.actbio.2015.01.032.

 

In vivo imaging of brain metabolism activity using a phosphorescent oxygen-sensitive probe.

Tsytsarev, V., H. Arakawa, S. Borisov, E. Pumbo, R. S. Erzurumlu and D. B. Papkovsky (2013).

Journal of Neuroscience Methods 216(2): 146-151.

DOI: 10.1016/j.jneumeth.2013.04.005.

 

Cellular respiration and metabolism

Cell energy budget platform for assessment of cell metabolism.

Papkovsky, D. B. and A. V. Zhdanov (2015).

Methods Mol Biol 1265: 333-348.

DOI: 10.1007/978-1-4939-2288-8_23.

 

Comparison of the three optical platforms for measurement of cellular respiration.

Kondrashina, A. V., V. I. Ogurtsov and D. B. Papkovsky (2015).

Analytical Biochemistry 468: 1-3. DOI: Doi 10.1016/J.Ab.2014.09.001.

 

Kinetic analysis of local oxygenation and respiratory responses of mammalian cells using intracellular oxygen-sensitive probes and time-resolved fluorometry.

Zhdanov, A. V., R. I. Dmitriev, J. Hynes and D. B. Papkovsky (2014).

Methods Enzymol 542: 183-207.

DOI: 10.1016/B978-0-12-416618-9.00010-8.

 

Availability of the key metabolic substrates dictates the respiratory response of cancer cells to the mitochondrial uncoupling.

Zhdanov, A. V., A. H. C. Waters, A. V. Golubeva, R. I. Dmitriev and D. B. Papkovsky (2014).

Biochimica Et Biophysica Acta-Bioenergetics 1837(1): 51-62.

DOI: 10.1016/j.bbabio.2013.07.008.

 

Comparative bioenergetic assessment of transformed cells using a cell energy budget platform.

Zhdanov, A. V., C. Favre, L. O'Flaherty, J. Adam, R. O'Connor, P. J. Pollard and D. B. Papkovsky (2011).

Integr Biol (Camb) 3(11): 1135-1142.

DOI: 10.1039/c1ib00050k.

 

Hypoxia research

Oxygen and glucose deprivation induces both global and gene-specific alterations in mRNA translation within 20 minutes.

Andreev DE, O’Connor PBF, Zhdanov AV, Dmitriev RI, Shatsky IN, Papkovsky DB,  Baranov PV (2015).

Genome Biology (in press).

 

Chronic hypoxia leads to a glycolytic phenotype and suppressed HIF-2 signaling in PC12 cells.

Zhdanov, A. V., R. I. Dmitriev, A. V. Golubeva, S. A. Gavrilova and D. B. Papkovsky (2013).

Biochimica Et Biophysica Acta-Bioenergetics 1830(6): 3553-3569.

DOI: 10.1016/j.bbagen.2013.02.016.

 

Metabolic profiling of hypoxic cells revealed a catabolic signature required for cell survival.

Frezza, C., L. Zheng, D. A. Tennant, D. B. Papkovsky, B. A. Hedley, G. Kalna, D. G. Watson and E. Gottlieb (2011).

PLoS One 6(9): e24411.

DOI: 10.1371/journal.pone.0024411.

 

Solid-state oxygen sensors and applications

Oxygen-sensitive phosphorescent nanomaterials produced from high-density polyethylene films by local solvent-crazing.

Toncelli, C., O. V. Arzhakova, A. Dolgova, A. L. Volynskii, N. F. Bakeev, J. P. Kerry and D. B. Papkovsky (2014).

Analytical Chemistry 86(3): 1917-1923.

DOI: 10.1021/ac404072z.

 

Phosphorescent oxygen sensors produced by spot-crazing of polyphenylenesulfide films.

Toncelli, C., O. V. Arzhakova, A. Dolgova, A. L. Volynskii, J. P. Kerry and D. B. Papkovsky (2014).

Journal of Materials Chemistry C 2(38): 8035-8041.

DOI: 10.1039/C4tc01390e.

 

Application of gas sensing technologies for non-destructive monitoring of headspace gases (O₂ and CO₂) during chilled storage of packaged mushrooms (Agaricus bisporus) and their correlation with product quality parameters.

Borchert, N. B., M. C. Cruz-Romero, P. V. Mahajan, M. Ren, D. B. Papkovsky and J. P. Kerry (2014).

Food Packaging Shelf Life(2): 17-29.

 

O(2)/pH Multisensor Based on One Phosphorescent Dye.

Borchert, N. B., G. V. Ponomarev, J. P. Kerry and D. B. Papkovsky (2011).

Analytical Chemistry 83(1): 18-22.

DOI: 10.1021/Ac1025754.

 

Reviews

Intracellular probes for imaging oxygen concentration: how good are they?

Dmitriev RI and Papkovsky DB (2015).

Methods Appl Fluoresc (in press).  

 

Biological detection by optical oxygen sensing.

Papkovsky, D. B. and R. I. Dmitriev (2013).

Chem Soc Rev 42(22): 8700-8732.

DOI: 10.1039/c3cs60131e.

 

Optical probes and techniques for O₂ measurement in live cells and tissue.

Dmitriev, R. I. and D. B. Papkovsky (2012).

Cellular and Molecular Life Sciences 69(12): 2025-2039.

DOI: 10.1007/s00018-011-0914-0.

 

Phosphorescent Oxygen-sensitive Probes

Papkovsky DB, Zhdanov AV, Fercher A, Dmitriev RI, Hynes J.

Springer Briefs in Biochemistry and Molecular Biology, 2012.

ISBN 978-3-0348-0524-7.

Links and professional activities

Links

Professor Dmitri Papkovsky’s UCC research profile

Papkovsky lab blog

 

Professor Dmitri Papkovsky’s Professional Activities

PI and Member of Executive Management Committee of the Irish Photonics Integration Centre.

Management Team Member of the Analytical and Biological Research Facility at UCC.

Member of HypoxiaNet consortium (EU Cost Action).

Committee member of the Microscopy Society of Ireland.

Member of Permanent Steering Committee of Europtrode conference series.

Associated Editor of Sensors & Actuators, Part B journal.

Co-Founder and Chief Scientific Officer of Luxcel Biosciences Ltd.

Member of the Royal Society of Chemistry.