Dmitri B. Papkovsky

School of Biochemistry and Cell Biology, University College Cork

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title	2023

Other Publications

Article	Year
Spectral-luminescent study of the porphyrin-diketones and their complexes. Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy\| PubMed ID: 11506042	2001
Synthesis and evaluation of phosphorescent oligonucleotide probes for hybridisation assays. Nucleic acids research\| PubMed ID: 12409473	2002
Fluorescence-based cell viability screening assays using water-soluble oxygen probes. Journal of biomolecular screening\| PubMed ID: 12857380	2003
Evaluation of the phosphorescent palladium(II)-coproporphyrin labels in separation-free hybridization assays. Analytical biochemistry\| PubMed ID: 12927834	2003
Homogeneous assays for cellular proteases employing the platinum(II)-coproporphyrin label and time-resolved phosphorescence. Analytical biochemistry\| PubMed ID: 15958187	2005
Optical oxygen microrespirometry as a platform for environmental toxicology and animal model studies. Environmental science & technology\| PubMed ID: 16053104	2005
Emerging applications of phosphorescent metalloporphyrins. Journal of fluorescence\| PubMed ID: 16167215	2005
Fluorescence based oxygen uptake analysis in the study of metabolic responses to apoptosis induction. Journal of immunological methods\| PubMed ID: 16212976	2005
The use of a fluorescence-based oxygen uptake assay in the analysis of cytotoxicity. Toxicology in vitro : an international journal published in association with BIBRA\| PubMed ID: 16386874	2006
Rapid high-throughput assessment of aerobic bacteria in complex samples by fluorescence-based oxygen respirometry. Applied and environmental microbiology\| PubMed ID: 16461677	2006
Sensing intracellular oxygen using near-infrared phosphorescent probes and live-cell fluorescence imaging. American journal of physiology. Regulatory, integrative and comparative physiology\| PubMed ID: 17170232	2007
Homogeneous time-resolved fluorescence assays for the detection of activity and inhibition of phosphatase enzymes employing phosphorescently labeled peptide substrates. Analytica chimica acta\| PubMed ID: 17386566	2007
Dynamics of intracellular oxygen in PC12 Cells upon stimulation of neurotransmission. The Journal of biological chemistry\| PubMed ID: 18086678	2008
Toxicological profiling of chemical and environmental samples using panels of test organisms and optical oxygen respirometry. Environmental toxicology\| PubMed ID: 18442072	2009
PGC-1alpha is coupled to HIF-1alpha-dependent gene expression by increasing mitochondrial oxygen consumption in skeletal muscle cells. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19179292	2009
In vitro analysis of cell metabolism using a long-decay pH-sensitive lanthanide probe and extracellular acidification assay. Analytical biochemistry\| PubMed ID: 19379702	2009
Analysis of activity and inhibition of oxygen-dependent enzymes by optical respirometry on the LightCycler system. Analytical biochemistry\| PubMed ID: 19849999	2010
Intracellular oxygen-sensitive phosphorescent probes based on cell-penetrating peptides. Analytical biochemistry\| PubMed ID: 19931212	2010
Imaging of cellular oxygen and analysis of metabolic responses of mammalian cells. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 19957136	2010
Phosphorescent oxygen sensors based on nanostructured polyolefin substrates. Analytical chemistry\| PubMed ID: 20038091	2010
Extracellular calcium depletion transiently elevates oxygen consumption in neurosecretory PC12 cells through activation of mitochondrial Na+/Ca2+ exchange. Biochimica et biophysica acta\| PubMed ID: 20550942	2010
Monitoring of cell oxygenation and responses to metabolic stimulation by intracellular oxygen sensing technique. Integrative biology : quantitative biosciences from nano to macro\| PubMed ID: 20657921	2010
Bafilomycin A1 activates respiration of neuronal cells via uncoupling associated with flickering depolarization of mitochondria. Cellular and molecular life sciences : CMLS\| PubMed ID: 20820851	2011
Bactenecin 7 peptide fragment as a tool for intracellular delivery of a phosphorescent oxygen sensor. The FEBS journal\| PubMed ID: 20883447	2010
Intracellular O2 sensing probe based on cell-penetrating phosphorescent nanoparticles. ACS nano\| PubMed ID: 21671589	2011
Metabolic profiling of hypoxic cells revealed a catabolic signature required for cell survival. PloS one\| PubMed ID: 21912692	2011
Cell-penetrating conjugates of coproporphyrins with oligoarginine peptides: rational design and application for sensing intracellular O2. Bioconjugate chemistry\| PubMed ID: 22035070	2011
Optical probes and techniques for O2 measurement in live cells and tissue. Cellular and molecular life sciences : CMLS\| PubMed ID: 22249195	2012
Assessment of cellular oxygen gradients with a panel of phosphorescent oxygen-sensitive probes. Analytical chemistry\| PubMed ID: 22380020	2012
G2019S leucine-rich repeat kinase 2 causes uncoupling protein-mediated mitochondrial depolarization. Human molecular genetics\| PubMed ID: 22736029	2012
Bafilomycin A1 activates HIF-dependent signalling in human colon cancer cells via mitochondrial uncoupling. Bioscience reports\| PubMed ID: 22943412	2012
Genome-wide investigation of cellular targets and mode of action of the antifungal bacterial metabolite 2,4-diacetylphloroglucinol in Saccharomyces cerevisiae. FEMS yeast research\| PubMed ID: 23445507	2013
Chronic hypoxia leads to a glycolytic phenotype and suppressed HIF-2 signaling in PC12 cells. Biochimica et biophysica acta\| PubMed ID: 23462283	2013
In vivo imaging of brain metabolism activity using a phosphorescent oxygen-sensitive probe. Journal of neuroscience methods\| PubMed ID: 23624034	2013
Biological detection by optical oxygen sensing. Chemical Society reviews\| PubMed ID: 23775387	2013
Measurement of cell respiration and oxygenation in standard multichannel biochips using phosphorescent O2-sensitive probes. The Analyst\| PubMed ID: 23803790	2013
Availability of the key metabolic substrates dictates the respiratory response of cancer cells to the mitochondrial uncoupling. Biochimica et biophysica acta\| PubMed ID: 23891695	2014
Imaging of neurosphere oxygenation with phosphorescent probes. Biomaterials\| PubMed ID: 24016849	2013
Oxygen-sensitive phosphorescent nanomaterials produced from high-density polyethylene films by local solvent-crazing. Analytical chemistry\| PubMed ID: 24422456	2014
Kinetic analysis of local oxygenation and respiratory responses of mammalian cells using intracellular oxygen-sensitive probes and time-resolved fluorometry. Methods in enzymology\| PubMed ID: 24862267	2014
Imaging oxygen in neural cell and tissue models by means of anionic cell-permeable phosphorescent nanoparticles. Cellular and molecular life sciences : CMLS\| PubMed ID: 25006059	2015
Comparison of the three optical platforms for measurement of cellular respiration. Analytical biochemistry\| PubMed ID: 25233002	2015
Multi-parametric O₂ imaging in three-dimensional neural cell models with the phosphorescent probes. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 25431057	2015
Differential contribution of key metabolic substrates and cellular oxygen in HIF signalling. Experimental cell research\| PubMed ID: 25447307	2015
In vitro ischemia decreases histone H4K16 acetylation in neural cells. FEBS letters\| PubMed ID: 25479088	2015
Cell energy budget platform for assessment of cell metabolism. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 25634285	2015
Oxygen-sensing scaffolds for 3-dimensional cell and tissue culture. Acta biomaterialia\| PubMed ID: 25653216	2015
Versatile Conjugated Polymer Nanoparticles for High-Resolution O2 Imaging in Cells and 3D Tissue Models. ACS nano\| PubMed ID: 25858428	2015
Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes. Genome biology\| PubMed ID: 25943107	2015
A novel effect of DMOG on cell metabolism: direct inhibition of mitochondrial function precedes HIF target gene expression. Biochimica et biophysica acta\| PubMed ID: 26143176	2015
Hypothermia protects brain mitochondrial function from hypoxemia in a murine model of sepsis. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism\| PubMed ID: 26661160	2016
Metallochelate Coupling of Phosphorescent Pt-Porphyrins to Peptides, Proteins, and Self-Assembling Protein Nanoparticles. Bioconjugate chemistry\| PubMed ID: 26704593	2016
The Ca2+/Mn2+-transporting SPCA2 pump is regulated by oxygen and cell density in colon cancer cells. The Biochemical journal\| PubMed ID: 27316461	2016
An Assessment of the Influence of the Industry Distribution Chain on the Oxygen Levels in Commercial Modified Atmosphere Packaged Cheddar Cheese Using Non-Destructive Oxygen Sensor Technolog... Sensors (Basel, Switzerland)\| PubMed ID: 27331815	2016
Quantitative analysis of mucosal oxygenation using ex vivo imaging of healthy and inflamed mammalian colon tissue. Cellular and molecular life sciences : CMLS\| PubMed ID: 27510419	2017
Sulforhodamine Nanothermometer for Multiparametric Fluorescence Lifetime Imaging Microscopy. Analytical chemistry\| PubMed ID: 27696826	2016
Phosphorescence based O sensors - Essential tools for monitoring cell and tissue oxygenation and its impact on metabolism. Free radical biology & medicine\| PubMed ID: 27789291	2016
Cellular ROS imaging with hydro-Cy3 dye is strongly influenced by mitochondrial membrane potential. Biochimica et biophysica acta. General subjects\| PubMed ID: 27818165	2017
Use of Fluorescence Lifetime Imaging Microscopy (FLIM) as a Timer of Cell Cycle S Phase. PloS one\| PubMed ID: 27973570	2016
Low energy costs of F1Fo ATP synthase reversal in colon carcinoma cells deficient in mitochondrial complex IV. Free radical biology & medicine\| PubMed ID: 28189850	2017
Planar implantable sensor for in vivo measurement of cellular oxygen metabolism in brain tissue. Journal of neuroscience methods\| PubMed ID: 28219725	2017
Assessment and Use of Optical Oxygen Sensors as Tools to Assist in Optimal Product Component Selection for the Development of Packs of Ready-to-Eat Mixed Salads and for the Non-Destructive M... Foods (Basel, Switzerland)\| PubMed ID: 28239110	2013
Use of Optical Oxygen Sensors in Non-Destructively Determining the Levels of Oxygen Present in Combined Vacuum and Modified Atmosphere Packaged Pre-Cooked Convenience-Style Foods and the Use... Foods (Basel, Switzerland)\| PubMed ID: 28239134	2013
Steering surface topographies of electrospun fibers: understanding the mechanisms. Scientific reports\| PubMed ID: 28279011	2017
Phosphorescent Oxygen and Mechanosensitive Nanostructured Materials Based on Hard Elastic Polypropylene Films. ACS applied materials & interfaces\| PubMed ID: 28367617	2017
Single-cell time-lapse imaging of intracellular O in response to metabolic inhibition and mitochondrial cytochrome-c release. Cell death & disease\| PubMed ID: 28569778	2017
Insulin-like growth factor 1 signaling is essential for mitochondrial biogenesis and mitophagy in cancer cells. The Journal of biological chemistry\| PubMed ID: 28821609	2017
Live cell imaging of mouse intestinal organoids reveals heterogeneity in their oxygenation. Biomaterials\| PubMed ID: 28898760	2017
Multi-Parametric Imaging of Hypoxia and Cell Cycle in Intestinal Organoid Culture. Advances in experimental medicine and biology\| PubMed ID: 29080132	2017
Intracellular probes for imaging oxygen concentration: how good are they? Methods and applications in fluorescence\| PubMed ID: 29148495	2015
Assessment of Performance of the Industrial Process of Bulk Vacuum Packaging of Raw Meat with Nondestructive Optical Oxygen Sensing Systems. Sensors (Basel, Switzerland)\| PubMed ID: 29724024	2018
Imaging of oxygen and hypoxia in cell and tissue samples. Cellular and molecular life sciences : CMLS\| PubMed ID: 29761206	2018
Cellulose-based scaffolds for fluorescence lifetime imaging-assisted tissue engineering. Acta biomaterialia\| PubMed ID: 30261339	2018
Nanoparticle-based fluoroionophore for analysis of potassium ion dynamics in 3D tissue models and . Advanced functional materials\| PubMed ID: 30271316	2018
Estimation of the Mitochondrial Membrane Potential Using Fluorescence Lifetime Imaging Microscopy. Cytometry. Part A : the journal of the International Society for Analytical Cytology\| PubMed ID: 31486581	2020
A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (FLIM) and extracellular flux analyses. Redox biology\| PubMed ID: 31935648	2020
Small molecule phosphorescent probes for O imaging in 3D tissue models. Biomaterials science\| PubMed ID: 32481818	2014
Disruption of hypoxia-inducible fatty acid binding protein 7 induces beige fat-like differentiation and thermogenesis in breast cancer cells. Cancer & metabolism\| PubMed ID: 32647572	2020
Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context. Genome research\| PubMed ID: 32669370	2020
Visualization of Stem Cell Niche by Fluorescence Lifetime Imaging Microscopy. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 32705636	2020
Correction to: Disruption of hypoxia-inducible fatty acid binding protein 7 induces beige fat-like differentiation and thermogenesis in breast cancer cells. Cancer & metabolism\| PubMed ID: 32789015	2020
Unusually efficient CUG initiation of an overlapping reading frame in mRNA yields novel protein POLGARF. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 32958672	2020
Reduced Oxidative Phosphorylation and Increased Glycolysis in Human Glaucoma Lamina Cribrosa Cells. Investigative ophthalmology & visual science\| PubMed ID: 33137197	2020
Mapping O concentration in ex-vivo tissue samples on a fast PLIM macro-imager. Scientific reports\| PubMed ID: 33149165	2020
Facile biosensor-based system for on-site quantification of total viable counts in food and environmental swabs. Biosensors & bioelectronics\| PubMed ID: 33395568	2021
Cell Energy Budget Platform for Multiparametric Assessment of Cell and Tissue Metabolism. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34060051	2021
A Simple Sensor System for Onsite Monitoring of O in Vacuum-Packed Meats during the Shelf Life. Sensors (Basel, Switzerland)\| PubMed ID: 34206251	2021
A sensor-based system for rapid on-site testing of microbial contamination in meat samples and carcasses. Journal of applied microbiology\| PubMed ID: 34464989	2022
Mitochondrial complex IV defects induce metabolic and signaling perturbations that expose potential vulnerabilities in HCT116 cells. FEBS open bio\| PubMed ID: 35302710	2022
Ghrelin rapidly elevates protein synthesis in vitro by employing the rpS6K-eEF2K-eEF2 signalling axis. Cellular and molecular life sciences : CMLS\| PubMed ID: 35841486	2022
Heterosubstituted Derivatives of PtPFPP for O Sensing and Cell Analysis: Structure-Activity Relationships. Bioconjugate chemistry\| PubMed ID: 36289566	2022