Recent developments in the area of biological detection by optical sensing of molecular oxygen (O2) are reviewed, with particular emphasis on the quenched-phosphorescence O2 sensing technique. Following a brief introduction to the main principles, materials and formats of sensor technology, the main groups of applications targeted to biological detection using an O2 transducer are described. These groups include: enzymatic assays; analysis of respiration of mammalian and microbial cells, small organisms and plants; food and microbial safety; monitoring of oxygenation in cell cultures, 3D models of live tissue, bioreactors and fluidic chips; ex vivo and in vivo O2 measurements; trace O2 analysis. For these systems, which enable a range of new bioanalytical tasks with different samples and models in a minimally invasive, contact-less manner, with high sensitivity, flexibility and imaging capabilities in 2D and 3D, relevant practical examples are presented and their merits and limitations discussed. An outlook of future scientific and technological developments in the field is also provided.

In recent years, significant progress has been achieved in the sensing and imaging of molecular oxygen (O2) in biological samples containing live cells and tissue. We review recent developments in the measurement of O2 in such samples by optical means, particularly using the phosphorescence quenching technique. The main types of soluble O2 sensors are assessed, including small molecule, supramolecular and particle-based structures used as extracellular or intracellular probes in conjunction with different detection modalities and measurement formats. For the different O2 sensing systems, particular attention is paid to their merits and limitations, analytical performance, general convenience and applicability in specific biological applications. The latter include measurement of O2 consumption rate, sample oxygenation, sensing of intracellular O2, metabolic assessment of cells, and O2 imaging of tissue, vasculature and individual cells. 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.

BackgroundOxygen and glucose metabolism play pivotal roles in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) during ischemia and stroke results in extensive tissue injury and cell death.ResultsUsing time-resolved ribosome profiling, we assess gene expression levels in a neural cell line, PC12, during the first hour of OGD. The most substantial alterations are seen to occur within the first 20 minutes of OGD. While transcription of only 100 genes is significantly altered during one hour of OGD, the translation response affects approximately 3,000 genes. This response involves reprogramming of initiation and elongation rates, as well as the stringency of start codon recognition. Genes involved in oxidative phosphorylation are most affected. Detailed analysis of ribosome profiles reveals salient alterations of ribosome densities on individual mRNAs. The mRNA-specific alterations include increased translation of upstream open reading frames, site-specific ribosome pauses, and production of alternative protein isoforms with amino-terminal extensions. Detailed analysis of ribosomal profiles also reveals six mRNAs with translated ORFs occurring downstream of annotated coding regions and two examples of dual coding mRNAs, where two protein products are translated from the same long segment of mRNA, but in two different frames.ConclusionsThese findings uncover novel regulatory mechanisms of translational response to OGD in mammalian cells that are different from the classical pathways such as hypoxia inducible factor (HIF) signaling, while also revealing sophisticated organization of protein coding information in certain genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0651-z) contains supplementary material, which is available to authorized users.

High brightness, chemical and photostability, tunable characteristics, and spectral and surface properties are important attributes for nanoparticle probes designed for live cell imaging. We describe a class of nanoparticles for high-resolution imaging of O2 that consists of a substituted conjugated polymer (polyfluorene or poly(fluorene-alt-benzothiadiazole)) acting as a FRET antenna and a fluorescent reference with covalently bound phosphorescent metalloporphyrin (PtTFPP, PtTPTBPF). The nanoparticles prepared from such copolymers by precipitation method display stability, enhanced (>5-10 times) brightness under one- and two-photon excitation, compatibility with ratiometric and lifetime-based imaging modes, and low toxicity for cells. Their cell-staining properties can be modulated with positively and negatively charged groups grafted to the backbone. The "zwitter-ionic" nanoparticles show high cell-staining efficiency, while their cell entry mechanisms differ for the different 3D models. When injected in the bloodstream, the cationic and anionic nanoparticles show similar distribution in vivo. These features and tunable properties make the conjugated polymer based phosphorescent nanoparticles a versatile tool for quantitative O2 imaging with a broad range of cell and 3D tissue models.

PtPFPP-carbohydrate conjugates are promising O2probes for 3D PLIM imaging of live spheroids and brain explants.

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Monitoring cell and tissue oxygenation is important for the analysis of cell development and differentiation, mitochondrial function, and common (patho)physiological conditions such as ischemia, cancer, neurodegenerative disorders. A number of materials for sensing cellular oxygen (O2) by optical means have been described in recent years, but the diverse range of biological models and measurement tasks demands more versatile, flexible, and simple O2 sensors. A new cell‐penetrating phosphorescent nanosensor material called MM2 probe is presented. In it, the highly photostable phosphorescent reporter dye Pt(II)‐5,10,15,20‐tetrakis‐(2,3,4,5,6‐pentafluorophenyl)‐porphyrin (PtTFPP; emission at 650 nm) and poly(9,9‐dioctylfluorene) (PFO) fluorophore act as Förster resonance energy transfer (FRET) donor and two‐photon antennae are embedded in cationic hydrogel nanoparticles. Such probe formulation provides efficient delivery into the cell and subsequent sensing and high‐resolution imaging of cellular O2 in different detection modalities, including ratiometric intensity and phosphorescence lifetime‐based sensing under one‐photon and two photon excitation. MM2 probe combines high brightness, photo‐ and chemical stability, low toxicity, and ease of fabrication and use. Its versatility and analytical performance are demonstrated in physiological experiments with adherent cells and neurospheres representing 2D and 3D respiring objects and detection on time‐resolved fluorescent readers, confocal and multiphoton microscopes, and customized microsecond fluorescence/phosphorescence lifetime imaging microscopy (FLIM) systems.

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