Dmitri B Papkovsky

Summary

Affiliation: University College Cork
Country: Ireland

Publications

  1. ncbi request reprint Emerging applications of phosphorescent metalloporphyrins
    Dmitri B Papkovsky
    Biochemistry Department ABCRF, University College Cork, College Road, Cork, Ireland
    J Fluoresc 15:569-84. 2005
  2. doi request reprint Availability of the key metabolic substrates dictates the respiratory response of cancer cells to the mitochondrial uncoupling
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland Electronic address
    Biochim Biophys Acta 1837:51-62. 2014
  3. doi request reprint Intracellular oxygen-sensitive phosphorescent probes based on cell-penetrating peptides
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, Cork, Ireland
    Anal Biochem 398:24-33. 2010
  4. ncbi request reprint Sensing intracellular oxygen using near-infrared phosphorescent probes and live-cell fluorescence imaging
    Kathleen Fitzgerald
    Luxcel Biosciences, BioInnovation Centre, University College Cork, Cork, Ireland
    Am J Physiol Regul Integr Comp Physiol 292:R1613-20. 2007
  5. doi request reprint Intracellular O2 sensing probe based on cell-penetrating phosphorescent nanoparticles
    Andreas Fercher
    Biochemistry Department, University College Cork, Cavanagh Building, College Road, Cork, Ireland
    ACS Nano 5:5499-508. 2011
  6. doi request reprint Toxicological profiling of chemical and environmental samples using panels of test organisms and optical oxygen respirometry
    Alice Zitova
    Biochemistry Department and ABCRF, University College Cork, Cavanagh Pharmacy Building, Cork, Ireland
    Environ Toxicol 24:116-27. 2009
  7. doi request reprint In vitro analysis of cell metabolism using a long-decay pH-sensitive lanthanide probe and extracellular acidification assay
    James Hynes
    Luxcel Biosciences, BioInnovation Center, University College Cork, Ireland
    Anal Biochem 390:21-8. 2009
  8. doi request reprint Assessment of cellular oxygen gradients with a panel of phosphorescent oxygen-sensitive probes
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cork, Ireland
    Anal Chem 84:2930-8. 2012
  9. doi request reprint Cell-penetrating conjugates of coproporphyrins with oligoarginine peptides: rational design and application for sensing intracellular O2
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cork, Ireland
    Bioconjug Chem 22:2507-18. 2011
  10. doi request reprint Imaging of cellular oxygen and analysis of metabolic responses of mammalian cells
    Andreas Fercher
    Biochemistry Department, University College Cork, Cork, Ireland
    Methods Mol Biol 591:257-73. 2010

Collaborators

  • Cormac T Taylor
  • Alexander V Zhdanov
  • Ruslan I Dmitriev
  • Aleksi E Soini
  • Jochen H M Prehn
  • Manus W Ward
  • Fergal O'Gara
  • Thomas G Cotter
  • Yvonne M Nolan
  • Ekaterina A Souslova
  • Tom Moore
  • James Hynes
  • Tomas C O'Riordan
  • Andreas Fercher
  • Fiach C O'Mahony
  • Alice Zitova
  • Yvonne Will
  • Joe P Kerry
  • Gelii V Ponomarev
  • Claudio Toncelli
  • Danielle M Troppens
  • Alina V Kondrashina
  • Nikolai F Bakeev
  • Alla Dolgova
  • Olga V Arzhakova
  • Nicolas B Borchert
  • Sergey M Borisov
  • Ingo Klimant
  • Ross N Gillanders
  • Martina Burke
  • Paul J O'Sullivan
  • Kathleen Fitzgerald
  • John Davenport
  • Vladimir I Ogurtsov
  • John Alderman
  • Rosemary O'Connor
  • Aleksandr L Volynskii
  • John P Morrissey
  • Alexander L Volynskii
  • Julien Kollar
  • Andreas Hempel
  • Larisa M Yarysheva
  • Georg Uray
  • Maud Cross
  • John Mackrill
  • Lisa D Marroquin
  • Roger Hill
  • Gregory J Stevens
  • Katerina N Christiansen
  • James Curtin
  • Dmitri Yashunski
  • Ciara O'Donovan
  • Jan Kr├╝ger
  • Suzanne M Floyd
  • Helen Berney
  • Suzanne Floyd
  • Juhani T Soini

Detail Information

Publications44

  1. ncbi request reprint Emerging applications of phosphorescent metalloporphyrins
    Dmitri B Papkovsky
    Biochemistry Department ABCRF, University College Cork, College Road, Cork, Ireland
    J Fluoresc 15:569-84. 2005
    ..The potential of phosphorescent porphyrin label methodology is discussed and compared to that of the long-decay fluorescent lanthanide chelates and other common fluorophores...
  2. doi request reprint Availability of the key metabolic substrates dictates the respiratory response of cancer cells to the mitochondrial uncoupling
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland Electronic address
    Biochim Biophys Acta 1837:51-62. 2014
    ....
  3. doi request reprint Intracellular oxygen-sensitive phosphorescent probes based on cell-penetrating peptides
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, Cork, Ireland
    Anal Biochem 398:24-33. 2010
    ..They provide a simple and versatile tool for O(2) monitoring in live cells and in tissue, and an alternative to the existing O(2) probes which require facilitated transport into the cell...
  4. ncbi request reprint Sensing intracellular oxygen using near-infrared phosphorescent probes and live-cell fluorescence imaging
    Kathleen Fitzgerald
    Luxcel Biosciences, BioInnovation Centre, University College Cork, Cork, Ireland
    Am J Physiol Regul Integr Comp Physiol 292:R1613-20. 2007
    ....
  5. doi request reprint Intracellular O2 sensing probe based on cell-penetrating phosphorescent nanoparticles
    Andreas Fercher
    Biochemistry Department, University College Cork, Cavanagh Building, College Road, Cork, Ireland
    ACS Nano 5:5499-508. 2011
    ..High brightness and photostability allow its use in screening experiments with cell populations on a commercial TR-F reader, and for single cell analysis on a fluorescent microscope...
  6. doi request reprint Toxicological profiling of chemical and environmental samples using panels of test organisms and optical oxygen respirometry
    Alice Zitova
    Biochemistry Department and ABCRF, University College Cork, Cavanagh Pharmacy Building, Cork, Ireland
    Environ Toxicol 24:116-27. 2009
    ..It allows ranking and profiling of samples, compares favorably with alternative methods such as MicroTox and mortality tests with animal models, and is well suited for large-scale monitoring programs such as CWA and WFD...
  7. doi request reprint In vitro analysis of cell metabolism using a long-decay pH-sensitive lanthanide probe and extracellular acidification assay
    James Hynes
    Luxcel Biosciences, BioInnovation Center, University College Cork, Ireland
    Anal Biochem 390:21-8. 2009
    ..More complex metabolic stimuli, such as G protein-coupled receptor (GPCR) activation and perturbed ion homeostasis, are also examined...
  8. doi request reprint Assessment of cellular oxygen gradients with a panel of phosphorescent oxygen-sensitive probes
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cork, Ireland
    Anal Chem 84:2930-8. 2012
    ..The new method facilitates the assessment of such gradients...
  9. doi request reprint Cell-penetrating conjugates of coproporphyrins with oligoarginine peptides: rational design and application for sensing intracellular O2
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cork, Ireland
    Bioconjug Chem 22:2507-18. 2011
    ..The results produced and the structure-activity relationships determined can facilitate the rational design of new bioconjugates of porphyrin dyes tailored to specific applications...
  10. doi request reprint Imaging of cellular oxygen and analysis of metabolic responses of mammalian cells
    Andreas Fercher
    Biochemistry Department, University College Cork, Cork, Ireland
    Methods Mol Biol 591:257-73. 2010
    ..Step by step procedures of typical experiments for each of these applications and troubleshooting guide are given...
  11. doi request reprint Imaging of neurosphere oxygenation with phosphorescent probes
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cork, Ireland Electronic address
    Biomaterials 34:9307-17. 2013
    ..The O2 imaging method allows multiplexing with many conventional fluorescent probes to perform multi-parametric imaging analysis of cells in 3D microenvironment. It can be applied to other types of spheroids and 3D tissue models...
  12. pmc Bafilomycin A1 activates HIF-dependent signalling in human colon cancer cells via mitochondrial uncoupling
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cork, Ireland
    Biosci Rep 32:587-95. 2012
    ..Altogether, by activating HIF signalling under moderate hypoxia, mitochondrial uncoupling can play an important regulatory role in colon cancer metabolism and modulate adaptation of cancer cells to natural hypoxic environments...
  13. doi request reprint Extracellular calcium depletion transiently elevates oxygen consumption in neurosecretory PC12 cells through activation of mitochondrial Na+/Ca2+ exchange
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, College Road, Cork, Ireland
    Biochim Biophys Acta 1797:1627-37. 2010
    ....
  14. ncbi request reprint A low-volume platform for cell-respirometric screening based on quenched-luminescence oxygen sensing
    John Alderman
    National Microelectronics Research Centre, Lee Maltings, Prospect Row, Cork, Ireland
    Biosens Bioelectron 19:1529-35. 2004
    ..Monitoring of as little as 300 mammalian cells in 3 microl volume has been demonstrated...
  15. ncbi request reprint Fluorescence based oxygen uptake analysis in the study of metabolic responses to apoptosis induction
    James Hynes
    Biochemistry Department, University College Cork, Lee Maltings, Cork, Ireland
    J Immunol Methods 306:193-201. 2005
    ..These reductions were observed earlier than detectable caspase-3 activity and were unaffected by pre-treatment with the caspase-3 inhibitor benzyloxycarbonyl-Val-Ala-Asp-fluoro-methylketone (zVADfmk)...
  16. ncbi request reprint Respirometric Screening Technology for ADME-Tox studies
    Dmitri B Papkovsky
    Luxcel Biosciences Ltd, G 17, Lee Maltings, Prospect Row, Cork, Ireland
    Expert Opin Drug Metab Toxicol 2:313-23. 2006
    ..Various RST assay formats are described and specific applications are discussed. Consideration is also given to the future potential of this analytical approach...
  17. ncbi request reprint Dynamics of intracellular oxygen in PC12 Cells upon stimulation of neurotransmission
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, Cork, Ireland
    J Biol Chem 283:5650-61. 2008
    ..Cleavage of synaptobrevin 2 by tetanus toxin, known to reduce neurotransmission, did not affect the respiratory response to K+, whereas the general excitability of d PC12 cells increased...
  18. ncbi request reprint Analysis of intracellular oxygen and metabolic responses of mammalian cells by time-resolved fluorometry
    Alexander V Zhdanov
    Luxcel Biosciences Ltd, BioInnovation Centre, UCC, Cork, Ireland
    Anal Chem 79:9414-9. 2007
    ..The assay provides relevant, information-rich data on cellular function and metabolism. It allows monitoring of small, rapid, and transient changes in cell respiration and screening of new chemical entities...
  19. doi request reprint Chronic hypoxia leads to a glycolytic phenotype and suppressed HIF-2 signaling in PC12 cells
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cork, Ireland
    Biochim Biophys Acta 1830:3553-69. 2013
    ..Along with other regulators of cell metabolism, hypoxia-inducible factors HIF-1 and HIF-2 differentially regulate cell adaptation to hypoxia. Switches in HIF-1/HIF-2 signaling in chronic hypoxia have not been fully investigated...
  20. doi request reprint Bactenecin 7 peptide fragment as a tool for intracellular delivery of a phosphorescent oxygen sensor
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Cork, Ireland
    FEBS J 277:4651-61. 2010
    ..In addition, the responses to metabolic stimuli can be assessed in a wide range of cells, as can the levels of relative cell oxygenation under external hypoxia...
  21. pmc Bafilomycin A1 activates respiration of neuronal cells via uncoupling associated with flickering depolarization of mitochondria
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Republic of Ireland
    Cell Mol Life Sci 68:903-17. 2011
    ..Cells treated with Baf become more susceptible to excitation with KCl. Such mitochondrial uncoupling may play a role in a number of (patho)physiological conditions induced by Baf...
  22. doi request reprint Monitoring of cell oxygenation and responses to metabolic stimulation by intracellular oxygen sensing technique
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cork, Ireland
    Integr Biol (Camb) 2:443-51. 2010
    ..This technique, which provides simple and reliable monitoring of cell oxygenation, is therefore important for hypoxia research, metabolic studies and experiments with respiring cells...
  23. ncbi request reprint The use of a fluorescence-based oxygen uptake assay in the analysis of cytotoxicity
    James Hynes
    Biochemistry Department, University College Cork, Lee Maltings, Cork, Ireland
    Toxicol In Vitro 20:785-92. 2006
    ..In conjunction with assays analysing other biomarkers of cytotoxicity, a more detailed picture of cell response to drug treatment can be obtained...
  24. ncbi request reprint Homogeneous assays for cellular proteases employing the platinum(II)-coproporphyrin label and time-resolved phosphorescence
    Tomas C O'Riordan
    Laboratory of Biophysics and Bioanalysis, Department of Biochemistry, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland
    Anal Biochem 342:111-9. 2005
    ..Dose-response and time course assays for the drug camptothecin were obtained for comparison with conventional fluorometric detection...
  25. ncbi request reprint Investigation of drug-induced mitochondrial toxicity using fluorescence-based oxygen-sensitive probes
    James Hynes
    Luxcel Biosciences Ltd, G 17, Lee Maltings, Cork, Ireland
    Toxicol Sci 92:186-200. 2006
    ..Throughput may be increased by moving to a 384-well plate format...
  26. doi request reprint Oxygen-sensitive phosphorescent nanomaterials produced from high-density polyethylene films by local solvent-crazing
    Claudio Toncelli
    University College Cork, Biochemistry Department, Cavanagh Pharmacy Building, Cork, Ireland
    Anal Chem 86:1917-23. 2014
    ..The high degree of lateral and in-depth homogeneity of these O2-sensitive materials was confirmed by high-resolution atomic force and wide-field optical microscopy, including 2D and 3D phosphorescence lifetime imaging. ..
  27. ncbi request reprint Biological detection by optical oxygen sensing
    Dmitri B Papkovsky
    Biochemistry Department, University College Cork, College Road, Cork, Ireland
    Chem Soc Rev 42:8700-32. 2013
    ..An outlook of future scientific and technological developments in the field is also provided. ..
  28. doi request reprint Measurement of cell respiration and oxygenation in standard multichannel biochips using phosphorescent O2-sensitive probes
    Alina V Kondrashina
    Biochemistry Department, University College Cork, Cork, Ireland
    Analyst 138:4915-21. 2013
    ..It also allows re-perfusion and multiple treatments of cells and multi-parametric analyses in conjunction with other probes. Optical measurements are conducted on standard fluorescence readers and microscopes. ..
  29. doi request reprint Genome-wide investigation of cellular targets and mode of action of the antifungal bacterial metabolite 2,4-diacetylphloroglucinol in Saccharomyces cerevisiae
    Danielle M Troppens
    Microbiology Department, University College Cork, Cork, Ireland
    FEMS Yeast Res 13:322-34. 2013
    ..Sphingolipids and their derivatives are important eukaryotic signal molecules, and the observation that altering homoeostasis may affect yeast response to metabolic uncoupling agents raises some intriguing questions for future studies...
  30. pmc Rapid high-throughput assessment of aerobic bacteria in complex samples by fluorescence-based oxygen respirometry
    Fiach C O'Mahony
    Biochemistry Department ABCRF, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland
    Appl Environ Microbiol 72:1279-87. 2006
    ....
  31. pmc Optical probes and techniques for O2 measurement in live cells and tissue
    Ruslan I Dmitriev
    Biochemistry Department, University College Cork, Ireland
    Cell Mol Life Sci 69:2025-39. 2012
    ..Altogether, this gives the potential user a comprehensive guide for the proper selection of the appropriate optical probe(s) and detection platform to suit their particular biological applications and measurement requirements...
  32. ncbi request reprint Optical oxygen microrespirometry as a platform for environmental toxicology and animal model studies
    Fiach C O'Mahony
    Biochemistry Department ABCRF, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland
    Environ Sci Technol 39:5010-4. 2005
    ..Applications include screening for acute toxicity of compound libraries and environmental samples, and the study of animal physiology and metabolism...
  33. ncbi request reprint Kinetic analysis of local oxygenation and respiratory responses of mammalian cells using intracellular oxygen-sensitive probes and time-resolved fluorometry
    Alexander V Zhdanov
    Biochemistry Department, University College Cork, Cork, Ireland
    Methods Enzymol 542:183-207. 2014
    ....
  34. ncbi request reprint Fluorescence-based cell viability screening assays using water-soluble oxygen probes
    James Hynes
    Biochemistry Department, University College Cork, Ireland
    J Biomol Screen 8:264-72. 2003
    ..The assay is cell noninvasive, more simple, robust, and cost-effective than existing microplate-based cell viability assays; is compatible with existing instrumentation; and allows for high-throughput analysis of cell viability...
  35. ncbi request reprint Homogeneous time-resolved fluorescence assays for the detection of activity and inhibition of phosphatase enzymes employing phosphorescently labeled peptide substrates
    Dmitri B Papkovsky
    Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland
    Anal Chim Acta 583:349-56. 2007
    ..Parameters of these enzymatic reactions such as Km's, limits of detection (L.O.D's) and IC50 values for the non-specific inhibitor sodium orthovanadate were also determined...
  36. ncbi request reprint Evaluation of the phosphorescent palladium(II)-coproporphyrin labels in separation-free hybridization assays
    Martina Burke
    Biochemistry Department ABCRF, University College Cork, Lee Maltings, Cork, Ireland
    Anal Biochem 320:273-80. 2003
    ..Intensity and lifetime changes of the phosphorescence, distance, and temperature dependences were investigated in detail. The potential of the new label and probes for sensitive and separation-free hybridization assays was discussed...
  37. doi request reprint Phosphorescent oxygen sensors based on nanostructured polyolefin substrates
    Ross N Gillanders
    Biochemistry Department, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
    Anal Chem 82:466-8. 2010
    ..They are well suited for large-scale applications such as nondestructive control of residual oxygen and "smart" packaging...
  38. doi request reprint Analysis of activity and inhibition of oxygen-dependent enzymes by optical respirometry on the LightCycler system
    Alice Zitova
    Department of Biochemistry, University College Cork, Cavanagh Pharmacy Building, Cork, Ireland
    Anal Biochem 397:144-51. 2010
    ..It is also applicable to other O(2)-dependent enzymes and enzymatic systems...
  39. ncbi request reprint O(2)/pH Multisensor Based on One Phosphorescent Dye
    Nicolas B Borchert
    Department of Food Science and Technology, University College Cork, College Road, Cork, Ireland, Institute of Biomedical Chemistry, Moscow, Russia, and Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, College Road, Ireland
    Anal Chem 83:18-22. 2011
    ..This approach can be extended to sensing of some other analytes...
  40. ncbi request reprint Performance evaluation of the phosphorescent porphyrin label: solid-phase immunoassay of alpha-fetoprotein
    Tomas C O'Riordan
    Biochemistry Department, National University of Ireland, Cork, Lee Maltings, Prospect Row, Cork, Ireland
    Anal Chem 74:5845-50. 2002
    ..The performance of metalloporphyrin labels, instrumentation, and solid-phase immunoassays as an alternative to the established detection platforms is discussed...
  41. pmc Synthesis and evaluation of phosphorescent oligonucleotide probes for hybridisation assays
    Paul J O'Sullivan
    Biochemistry Department, University College Cork, Lee Maltings, Cork, Ireland
    Nucleic Acids Res 30:e114. 2002
    ..The potential applications of PtCP-labelled probes in hybridisation assays were discussed...
  42. ncbi request reprint Methods in optical oxygen sensing: protocols and critical analyses
    Dmitri B Papkovsky
    Biochemistry Department, University College of Cork, Ireland
    Methods Enzymol 381:715-35. 2004
  43. ncbi request reprint Phosphorescent metalloporphyrins as labels in time-resolved luminescence microscopy: effect of mounting on emission intensity
    Aleksi E Soini
    Laboratory of Biophysics, Institute of Biomedicine, University of Turku, P O Box 123, FIN 20521 Turku, Finland
    Microsc Res Tech 58:125-31. 2002
    ..The results indicate that microscopy samples stained with PtCP exhibit the brightest phosphorescence emission in non-mounted form or when mounted in non-aqueous permanent mounting media...
  44. ncbi request reprint Analysis of mitochondrial function using phosphorescent oxygen-sensitive probes
    Yvonne Will
    Pfizer Drug Safety Research and Development, San Diego, USA
    Nat Protoc 1:2563-72. 2006
    ..It allows dozens of compounds (or hundreds of assay points) to be analyzed in a single day, and can be further up-scaled, automated and adapted for other enzyme- and cell-based screening applications...