M.Sc., 1982, Chemistry Faculty, Moscow State University, Russia
Ph.D, 1986, Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia

I currently teach Biochemical and Biophysical Methods, Ion Transport and Immunochemistry courses to third and fourth year science students. An outline of this course and all courses taught by staff in the Department of Biochemistry are available at UCC Book of Modules.

I am Principal Investigator in the UCC Analytical and Biological Chemistry Research Facility (ABCRF), Principal Investigator of the Science Foundation of Ireland Program Grant, and a co-founder of Luxcel Biosciences Ltd. - Irish biotech company established in 2002.

• Molecular Oxygen (O₂) in Biological Systems: Cell Metabolism, Mitochondrial Function, Bioenergetics, Responses to Hypoxia.
• Sensing and Imaging of O₂ in Live Cells and Tissues, Microrespirometry.
• O₂ as a Marker of Cellular (Dys)function and Toxicity: Application to Cancer, Neuroscience Research, Environmental Toxicology.
• Porphyrins, Sensors and Probes on their Basis. Phosphorescent Materials.
• Fluorescent Spectroscopy and BioImaging, Advanced (Bio)Materials, Bioconjugate Chemistry, Analytical Method Development.  

Members of the Lab:

• Alexander Zhdanov, PhD  - Postdoctoral Researcher  (SFI Project)
• Ruslan Dmitriev, PhD – Postdoctoral Researchers (SFI Project)
• Alice Zitova, MSc – PhD3 Student (EPA Scholarship) 
• Greg Jasionek, MSc – PhD3 Student (EI Project)
• Andreas Fercher, MSc – PhD2 Student (SFI Project)
• Nicolas Borchert, BSc – PhD1 Student (FIRM Project) – joint with Food Science Dept. 
• Maud Cross, MSc - Research Assistant (SFI Project)
• Natalia Papkovskaia, MSc – Research Assistant (FIRM project)

(102 KB)

O'Hagan KA, Cocchiglia S, Zhdanov AV, Tambawala MM, Cummins EP, Monfared M, Agbor TA, Garvey JF, Papkovsky DB, Taylor CT, Allan BB, PGC-1a is coupled to HIF-1a-dependent gene expression by increasing mitochondrial oxygen consumption in skeletal muscle cells, Proc Natl Acad Sci U S A,  2009 Jan 28. [Epub ahead of print]

Hynes J., O’Riordan T.C., Papkovsky D.B., The use of oxygen-sensitive fluorescent probes for the assessment of mitochondrial function, In: Mitochondrial Dysfunction in Drug-induced Toxicity, Eds. Y.Will, J.Dykins, John Wiley & Sons, 2008, Ch. 13.

Zhdanov A.V., Ward M., Prehn J.H. Papkovsky D.B., Dynamics of intracellular oxygen in PC12 cells upon stimulation of neurotransmission, J. Biol. Chem., 2008; 283(9):5650-61.

O’Riordan T. C., Zhdanov A. V., Ponomarev G. V., Papkovsky D.B. Analysis of intracellular oxygen and metabolic responses of mammalian cells by time-resolved fluorometry, Anal. Chem., 2007; 79(24):9414-9.

O’Riordan T.C., et al., Sensing intracellular oxygen using NIR phosphorescent probes and live-cell fluorescence imaging, Am. J. Cell Physiol., 2007 v.292(4): R1613-20.

Will Y., et al., Analysis of mitochondrial function using phosphorescent oxygen-sensitive probes, Nature Protocols, 2006, v.1(6), p.2563-2572.

O’Donovan C. et al., Development of a respirometric biochip for embryo assessment, Lab-on-a-Chip, 2006, v.6, 1438-1444.

Burke, M., et al., Analysis of close proximity quenching of phosphorescent metalloporphyrin labels in oligonucleotide structures, Anal. Chim. Acta, 2007, v. 585(1), 139-146.

O’Shea D.J., et al., Homogeneous TR-F assays for the detection of activity and inhibition of phosphatase enzymes employing phosphorescently labelled peptide substrates, Anal. Chim. Acta, 2007, v. 583(2), 349-356.

Hynes J., et al., Investigation of Drug-induced Mitochondrial Toxicity using Fluorescence-based Oxygen-sensitive Probes, Toxicol. Sci., 2006, 92 :186-200.

Papkovsky D.B., Hynes J., Will Y., Respirometric Screening Technology for ADME-Tox studies, Expert Opin. Drug Metab. Toxicol., 2006, 2: 313-323.

O'Mahony F.C., Papkovsky D.B., Rapid high throughput assessment of aerobic bacteria in complex samples by fluorescence-based oxygen respirometry, Appl. Environm. Microbiol., 2006, 72 :1279-1287.

Hynes, J., O'Riordan, T., Curtin, J., Cotter, T.G., Papkovsky, D.B. Fluorescence based oxygen uptake analysis in the study of metabolic responses to apoptosis induction, J. Immunol. Methods, 2005, 306: 193-201.

Papkovsky D.B., O'Riordan T.C. Emerging applications of the phosphorescent porphyrins. (Review), J. Fluoresc., 2005, 15: 569-584.

Ogurtsov, V.I., Papkovsky, D. B. Frequency spectroscopy of quenched-fluorescence oxygen sensors, Sensors Actuators B., 2006, 113: 608-616.

O' Donovan C., Hynes J., Yashunsky D.V., Papkovsky D. B. Phosphorescent oxygen-sensitive materials for biological applications, J. Mater. Chem., 2005, 15: 2946 – 2951.

O'Mahony F.C., et al., Optical oxygen micro-respirometry as a platform for animal model studies and toxicity screening, Env. Sci. Technol., 2005, 39: 5010-5014.

O'Riordan T.C., Ponomarev G.V., Yashunsky D.V., Papkovsky D.B., Homogeneous assays for cellular proteases employing the platinum(II)-coproporphyrin label and time-resolved phosphorescence, Anal. Biochem., 2005, 342 : 111-119.

Papkovsky D.B., Methods in optical oxygen sensing: protocols and critical analyses, In: Methods Enzymol. , Ed., C.K. Sen, G.L. Semenza, 2004, v.383, p.715-734.

Alderman J., Hynes J., Floyd S., Kruger J., O'Connor R., Papkovsky D.B. A low-volume platform for cell-respirometric screening based on quenched-luminescence oxygen sensing, Biosens. Bioelectronics, 2004, 19: 1529-1535.

Full publication list:
Search PubMed and Science Citation Index for Papkovsky DP and Papkovskii DB

Our lab has a range of modern spectroscopic and biochemical equipment including:

• Custom-built live-cell fluorescence imaging system with FLIM capabilities (Carl Zeiss - LaVision)
• Multi-label readers: Victor V (PerkinElmer), Genios Pro (Tecan)
• Phosphorescence lifetime spectrometer/plate readers ArcDia (Luxcel)
• Spectrofluorometers: LS-50B (PerkinElmer), Cary Eclipse (Varian)
• Two-photon excitation fluorescence reader ArcDia-TPX (Arctic Diagnostics)
• UV-VIS diode-array spec HP8453 (Agilent)
• Hypoxia Chamber (Coy Scientific) and related equipment.  
• HPLC system HP1100 Series (Agilent) with UV-VIS and fluorescence detectors
• Real-time PCR system LightCycler® (Roche)
• Phase-fluorimetric oxygen sensors (2)
• DNA amplification and detection equipment
• Precision gas mixing and gas delivery equipment for sensor characterization
• Tissue culture equipment

We also have access to centralised facilities such as tissue culture room, animal house, large pieces of equipment within the Biochemistry Department, ABCRF and UCC, and to microfabrication facilities at the Tyndall National Institute.

• Within UCC: Biochemistry (Prof. T. McCarthy, Prof. R. O'Connor); ZEPS (Prof. J.Davenport); Food Science (Dr. J.P. Kerry).
• Institute of Biomedical Chemistry, Moscow, Russia (Prof. G.V. Ponomarev) (http://www.ibmh.msk.su/)
• Conway Institute of Biomedical Sciences, University College Dublin (Prof. Cormac Taylor)
• Royal College of Surgeons in Ireland (Prof. Jochen Prehn)
• Technical University Graz, Austria (Prof. I. Klimant)
• Moscow State University
• Luxcel Biosciences, Cork , Ireland
• Arctic Diagnostics, Turku, Finland
• Tyndall National Institute