Dmitri B Papkovsky

Dmitri B Papkovsky
University College Cork | UCC · Department of Biochemistry

About

315
Publications
44,767
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9,773
Citations
Additional affiliations
January 2006 - present
University College Cork
Position
  • Tyndall National Institute
January 1999 - December 2012
University College Cork

Publications

Publications (315)
Conference Paper
We introduce a new biosensor platform based on oxygen respirometry, for rapid and simple quantification of total aerobic viable counts of bacteria (TVC) on surfaces. This system adopts a convenient swab sachet format, with an integrated phosphorescent O₂ sensor and a handheld reader for seamless signal readout. In our approach, surface swab samples...
Article
Full-text available
Respirometric microbial assays are gaining popularity, but their uptake is limited by the availability of optimal O2 sensing materials and the challenge of validating assays with complex real samples. We conducted a comparative evaluation of four different O2-sensing probes based on Pt-porphyrin phosphors in respirometric bacterial assays performed...
Article
Full-text available
Monitoring of tissue O2 is essential for cancer development and treatment, as hypoxic tumour regions develop resistance to radio- and chemotherapy. We describe a minimally invasive technique for the monitoring of tissue oxygenation in developing grafted tumours, which uses the new phosphorescence lifetime based Tpx3Cam imager. CT26 cells stained wi...
Article
Full-text available
We describe a new sensor platform for simple on-site analysis of total aerobic viable counts (TVCs) in food samples, which uses disposable sealable plastic sachets with phosphorescent oxygen sensor inserts and liquid growth media. Food samples are collected, placed directly in the sachets, which are then sealed and incubated at 30 °C while monitori...
Article
Full-text available
In this study, rapid respirometric microbial testing was combined with 16S rRNA amplicon sequencing, to assess the composition of microbiota in a total of 64 samples of commercial beef, turkey, lamb and pork mince. The O2 sensor-based respirometry system, while producing the anticipated total aerobic viable counts (TVC) data and patterns for most s...
Article
Full-text available
The current status of microbiological testing methods for the determination of viable bacteria in complex sample matrices, such as food samples, is the focus of this review. Established methods for the enumeration of microorganisms, particularly, the ‘gold standard’ agar plating method for the determination of total aerobic viable counts (TVC), bio...
Article
Two common platforms currently used in respirometric microbial assays were evaluated comparatively with a panel of selective and differential media specific for E. coli, including the MacConkey (MC), M-Lauryl Sulfate (MLS), Minerals Modified Glutamate (MMG) and Rapid Coliform ChromoSelect (RCC) broths. The first automated platform is based on a sol...
Article
Full-text available
Biological applications of phosphorescent probes for sensing molecular oxygen (O 2) and bioimaging have gained popularity, but their choice is rather limited. We describe a family of new heterosubstituted phosphorescent bioprobes based on the Pt(II)-tetrakis(pentafluorophenyl)porphyrin (PtPFPP) dye. The probes are produced by simple click modificat...
Article
Optochemical sensors are actively used in cell analysis, however existing systems have limitations with respect to their robustness and analytical performance. We have developed advanced multimodal and multi-parametric solid-state pH sensors for cell analysis based on hydrophobic protonable metal-free porphyrins, such as octaethylporphine (OEP), an...
Article
Using several types of Pt-porphyrin based oxygen sensing materials and conditions, we evaluated comparatively four different detection platforms that perform phosphorescence lifetime (PLT) measurements in the microsecond time domain. The time-resolved fluorescence reader Victor 2, which utilises Rapid Lifetime Determination method and Xe-flash lamp...
Article
Full-text available
Activated ghrelin receptor GHS-R1α triggers cell signalling pathways that modulate energy homeostasis and biosynthetic processes. However, the effects of ghrelin on mRNA translation are unknown. Using various reporter assays, here we demonstrate a rapid elevation of protein synthesis in cells within 15–30 min upon stimulation of GHS-R1α by ghrelin....
Article
Full-text available
Mutations in genes encoding cytochrome c oxidase (COX; mitochondrial complex IV) subunits and assembly factors (e.g., SCO1, SCO2, COA6) are linked to severe metabolic syndromes. Notwithstanding that SCO2 is under transcriptional control of tumour suppressor p53, the role of mitochondrial complex IV dysfunction in cancer metabolism remains obscure....
Article
Full-text available
Aims: To develop an oxygen sensor based method for testing total aerobic viable counts (TVC) in raw meat samples and cattle carcass swabs, which is rapid, simple, affordable, provides good sensitivity and analytical performance and allows on-site use. Methods and results: The test uses the same sample preparation procedure as the established pla...
Conference Paper
Full-text available
Microbial swab testing is a fundamental component of surface sampling and process monitoring, especially in the food, pharmaceutical and biotech industries. Environmental and microbiological surveillance is currently conducted through routine sampling of contact surfaces with dedicated swabs: brush swabs, sponge swabs or integrated swabbing devices...
Article
Full-text available
Vacuum packaging (VP) is used to reduce exposure of retail meat samples to ambient oxygen (O2) and preserve their quality. A simple sensor system produced from commercial components is described, which allows for non-destructive monitoring of the O2 concentration in VP raw meat samples. Disposable O2 sensor inserts were produced by spotting small a...
Chapter
Specific bioenergetic signature reports on the current metabolic state of the cell, which may be affected by metabolic rearrangement, dysfunction or dysregulation of relevant signaling pathways, altered physiological condition or energy stress. A combined analysis of respiration, glycolytic flux, Krebs cycle activity, ATP levels, and total biomass...
Article
Full-text available
We describe a new biosensor platform for rapid and simple quantification of total aerobic viable counts of bacteria (TVC) in food and environmental swabs by oxygen respirometry. The system uses disposable swab vials with phosphorescent oxygen sensors integrated in the bottom part, a small block heater/incubator and a handheld sensor reader. In the...
Article
Full-text available
O2 PLIM microscopy was employed in various studies, however current platforms have limitations in sensitivity, image acquisition speed, accuracy and general usability. We describe a new PLIM imager based on the Timepix3 camera (Tpx3cam) and its application for imaging of O2 concentration in various tissue samples stained with a nanoparticle based p...
Article
Full-text available
Purpose: The lamina cribrosa (LC) is a key site of damage in glaucomatous optic neuropathy. We previously found that glaucoma LC cells have an increased profibrotic gene expression, with mitochondrial dysfunction in the form of decreased mitochondrial membrane potential. Altered cell bioenergetics have recently been reported in organ fibrosis and...
Conference Paper
SCO2 (synthesis of cytochrome c oxidase 2) is essential for the assembly and functioning of mitochondrial cytochrome c oxidase (COX) complex (IV). Mutations in the SCO2 gene have been reported to cause COX deficiency and result in fatal infantile cardioencephalomyopathy. Furthermore, the tumor suppressor protein p53 has been shown to mediate its ef...
Article
Full-text available
Significance In this study, we describe a previously unknown mechanism of de novo protein-coding gene evolution. We show that the POLG gene, which encodes the catalytic subunit of mitochondrial DNA polymerase, is in fact a dual coding gene. Ribosome profiling, phylogenetic conservation, and reporter construct analyses all demonstrate that POLG mRNA...
Conference Paper
Cancer cells alter the metabolism in their microenvironment to sustain their survival, growth and rogression. Heat is an essential factor that can affect metabolism. However, it is unclear whether cancer cells can alter their temerature by regulating heat roduction. Non-shivering thermogenesis is known to takes lace in inducible beige adiocytes exr...
Chapter
Fluorescence lifetime imaging microscopy (FLIM), enabling live quantitative multiparametric analyses, is an emerging bioimaging approach in tissue engineering and regenerative medicine. When combined with stem cell-derived intestinal organoid models, FLIM allows for tracing stem cells and monitoring of their proliferation, metabolic fluxes, and oxy...
Article
Full-text available
Eukaryotic translation initiation involves preinitiation ribosomal complex 5′-to-3′ directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak (i.e., nonoptimal), leaky scann...
Article
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Background: Humans produce heat through non-shivering thermogenesis, a metabolic process that occurs in inducible beige adipocytes expressing uncoupling protein 1 (UCP1). UCP1 dissipates the proton gradient of the mitochondrial inner membrane and converts that energy into heat. It is unclear whether cancer cells can exhibit autonomous thermogenesi...
Article
Full-text available
Microbial spoilage and foodborne diseases cause significant economic and productivity losses. There is a need for novel approaches and antimicrobial treatments to extend shelf life of products, improve quality and microbial safety, and reduce spoilage and waste, and new assessment methods. Traditional assays for testing the toxicity of antimicrobia...
Article
Full-text available
A set of phosphorescent materials were evaluated using a new macro-imager based on fast time-stamping Tpx3Cam camera with phosphorescent lifetime imaging (PLIM) capabilities. The near-infrared emitting O2-sensitive dye PtBP was embedded in several polymers having different permeability for O2 and applied as solid-state coatings on polyester film su...
Preprint
Full-text available
While near cognate codons are frequently used for translation initiation in eukaryotes, their efficiencies are usually low (<10% compared to an AUG in optimal context). Here we describe a rare case of highly efficient near cognate initiation. A CUG triplet located in the 5’ leader of POLG mRNA initiates almost as efficiently (~60-70%) as an AUG in...
Article
Full-text available
The properties of a novel ultra-fast optical imager, Tpx3Cam, were investigated for macroscopic wide-field phosphorescent lifetime imaging (PLIM) applications. The camera is based on a novel optical sensor and Timepix3 readout chip with a time resolution of 1.6 ns, recording of photon arrival time and time over threshold for each pixel, and readout...
Article
Full-text available
Stem cells and the niche in which they reside feature a complex microenvironment with tightly regulated homeostasis, cell-cell interactions and dynamic regulation of metabolism. A significant number of organoid models has been described over the last decade, yet few methodologies can enable single cell level resolution analysis of the stem cell nic...
Article
Extruded phosphorescent O2-sensitive composite materials comprising cross-linked polystyrene-divinylbenzene (PS-DVB) microspheres impregnated with Pt-benzoporphyrin dye and dispersed in low-density polyethylene (LDPE) or polylactic acid (PLA) carrier polymer are described. The sensors produced by hot melt extrusion method are specifically tailored...
Preprint
Full-text available
Stem cells and the niche in which they reside feature a complex microenvironment with tightly regulated homeostasis, cell-cell interactions and dynamic regulation of metabolism. A significant number of organoid models has been described over the last decade, yet few methodologies can enable single cell level resolution analysis of the stem cell nic...
Article
Monitoring of cell metabolism represents an important application area for fluorescence lifetime imaging microscopy (FLIM). In particular, assessment of mitochondrial membrane potential (MMP) in complex three‐dimensional multicellular in vitro, ex vivo, and in vivo models would enable improved segmentation and functional discrimination of cell type...
Chapter
Consumer demand for high quality foods and environmental concerns about food waste production has driven the demand for innovative food packaging systems to guarantee food safety, quality, traceability and food waste reduction. Factors such as O2 concentration, loss of packaging containment, seal integrity, inadequate gas mixes used in modified atm...
Article
Oxygenation of stem cell niche is important metabolic activity indicator for the intestine in normal and diseased states. In vivo , it can be affected by such factors as diet, drugs, metabolites produced by microbiota, and inflammation. We hypothesized that O 2 must be also very important for adequate development of organoids and organs‐on‐chip, gr...
Article
Quantitative measurement of pH and metabolite gradients by microscopy is one of the challenges in the production of scaffold-grown organoids and multicellular aggregates. Herein, we used the cellulose-binding domain (CBD) of the Cellulomonas fimi CenA protein for designing biosensor scaffolds that allow measurement of pH and Ca2+ gradients by fluor...
Article
Full-text available
Five types of new solid-state oxygen sensors, four based on microporous polypropylene fabric materials and one on polyphenylene sulphide films impregnated with phosphorescent platinum(II)-benzoporphyrin dye, were tested for their stability and safety in food packaging applications. All these sensors exhibit useful optical signals (phosphorescence l...
Article
Full-text available
Molecular oxygen (O2) is a key player in cell mitochondrial function, redox balance and oxidative stress, normal tissue function and many common disease states. Various chemical, physical and biological methods have been proposed for measurement, real-time monitoring and imaging of O2 concentration, state of decreased O2 (hypoxia) and related param...
Chapter
Advances in materials science, chemistry, sensor design, bioconjugation and nanotechnology helped to develop a new class of phosphorescent cell-penetrating O2-sensitive materials, enabling non-invasive sensing of intracellular O2 and its gradients in live cells. Cell-penetrating O2 probes compatible with live cell and tissue imaging are available t...
Chapter
Rational design of oxygen sensing materials, optimal integration of reporter phosphor chemistry with the other sensor components (encapsulation matrix, support material, additives) and simple fabrication procedures are the main bottlenecks and challenges in producing simple and affordable O2 sensors with stable and predictable working characteristi...
Article
Full-text available
The commercially-available optical oxygen-sensing system Optech-O2 Platinum was applied to nondestructively assess the in situ performance of bulk, vacuum-packaged raw beef in three ~300 kg containers. Twenty sensors were attached to the inner surface of the standard bin-contained laminate bag (10 on the front and back sides), such that after filli...
Article
Full-text available
The imaging of real-time fluxes of K+ ions in live cell with high dynamic range (5–150 × 10−3 m) is of paramount importance for neuroscience and physiology of the gastrointestinal tract, kidney, and other tissues. In particular, the research on high-performance deep-red fluorescent nanoparticle-based biosensors is highly anticipated. It is found th...
Article
Full-text available
Purpose: Optic nerve cupping in glaucoma is characterized by remodeling of the extracellular matrix (ECM) and fibrosis in the lamina cribrosa (LC). We have previously shown that glaucoma LC cells express raised levels of ECM genes and have elevated intracellular calcium ([Ca2+]i). Raised [Ca2+]i is known to promote proliferation, activation, and c...
Article
Full-text available
In addition to acting as template for protein synthesis, messenger RNA (mRNA) often contains sensory sequence elements that regulate this process. Here we report a new mechanism that limits the number of complete protein molecules that can be synthesized from a single mRNA molecule of the human AMD1 gene encoding adenosylmethionine decarboxylase 1...
Chapter
Over the last two decades brain optical imaging methods have yielded a number of revolutionary results when applied to the functional mapping of the cerebral cortex. The purpose of this review is to analyze research capabilities and limitations of the different optical imaging techniques based on the visualization of oxygenation and deoxygenation p...
Chapter
Consumer demand for high quality food products has driven the packaging industry to look for new solutions to enhance food safety. In packaged food products, seal integrity is essential to the physical, chemical and biological quality of the packaged product as seal integrity failure will not only compromise product safety and containment, but also...
Chapter
In the last decade considerable progress has been achieved in the design of various fluorescent and phosphorescent oxygen sensing probes, their delivery to live animal tissue and subsequent imaging of tissue oxygenation. A significant number of publications reflect the growing interests in O2 imaging technologies. The in vivo O2 imaging platforms,...
Article
Full-text available
Background During early treatment of haemorrhagic shock, cerebral perfusion pressure can be restored by small-volume resuscitation with vasopressors. Whether this therapy is improved with additional fluid remains unknown. We assessed the value of terlipressin and lactated Ringer’s solution (LR) on the early recovery of the microcirculation, tissue...
Chapter
Dynamics of oxygenation of tissue and stem cell niches are important for understanding physiological function of the intestine in normal and diseased states. Only a few techniques allow live visualization of tissue hypoxia at cellular level and in three dimensions. We describe an optimized protocol, which uses cell-penetrating O2-sensitive probe, P...
Article
Scope: Enteroendocrine cell lines are routinely assayed in simple buffers at ∼20% oxygen to screen foods for bioactives that boost satiety hormone levels. However, in vivo, enteroendocrine cells are exposed to different phases of food digestion and function at low oxygen concentration ranging from 7.5% in the stomach to 0.5% in the colon-rectal ju...
Article
Intestinal organoids are widely applied in stem cell research, regenerative medicine, toxicology, pharmacology, and host-microbe interactions research. The variability of oxidative metabolism for stem and differentiated cell types constituting organoid is known to be important but so far it has not been studied in details. Here, we report the use o...
Article
Full-text available
Mitochondrial activity and metabolic reprogramming influence the phenotype of cancer cells and resistance to targeted therapy. We previously established that an Insulin-like Growth Factor 1 (IGF-1)-inducible mitochondrial UTP carrier (PNC1/SLC25A33) promotes cell growth. This prompted us to investigate whether IGF signaling is essential for mitocho...
Conference Paper
Mitochondrial membrane potential (DYm) is one of the key drivers of free radical production. Changes in DYm strongly affect free radical turnover in both mitochondria and cytosol. We found that in cytochrome c oxidase deficient HCT116 cells F1Fo ATP synthase (mATPase) is reversed in order to maintain DYm polarisation. For small energy costs, mATPas...
Article
Full-text available
The detection of intracellular molecular oxygen (O2) levels is important for understanding cell physiology, cell death, and drug effects, and has recently been improved with the development of oxygen-sensitive probes that are compatible with live cell time-lapse microscopy. We here provide a protocol for the use of the nanoparticle probe MitoImage-...
Article
It is well known that sensitivity of quenched-phosphorescence O2 sensors can be tuned by changing the nature of indicator dye and host polymer acting as encapsulation and quenching medium. Here we describe a new type of sensor materials based on nanostructured hard elastic polymeric substrates. With the example of hard elastic polypropylene films i...
Article
Full-text available
A profound understanding of how to tailor surface topographies of electrospun fibers is of great importance for surface sensitive applications including optical sensing, catalysis, drug delivery and tissue engineering. Hereby, a novel approach to comprehend the driving forces for fiber surface topography formation is introduced through inclusion...
Article
Mitochondrial polarisation is paramount for a variety of cellular functions. Under ischemia, mitochondrial membrane potential (ΔΨm) and proton gradient (ΔpH) are maintained via a reversal of mitochondrial F1Fo ATP synthase (mATPase), which can rapidly deplete ATP and drive cells into energy crisis. We found that under normal conditions in cells wit...