Enhanced-contrast two-photon optogenetic pH sensing and pH-resolved brain imaging

Acidification on the plasma membrane

The pH balance between extracellular and intracellular space is crucial for a multitude of cellular processes. Real-time observation of pH fluctuations in the range 4-9 in live cells and tissues in a sensitive, non-invasive manner has become feasible with advances in pH quantification by organic dyes, genetically encoded fluorescent proteins, and DNA-based probes. We discuss mechanisms through which pH affects cell cycle, transcription, senescence, neurotransmission, glycolipid-lectin driven endocytosis, tissue remodelling, immune responses, and GPCR signalling. Growth factor-stimulated acidification of the extracellular space notably triggers enzymatic reactions like desialylation at the plasma membrane that control processes involving cell migration and bone resorption. Research into the role of pH in cellular physiology continues to be a fertile ground for discovery that underscores its fundamental importance.

Thermal and Quantum Barrier Passage as Potential-Driven Markovian Dynamics

Rapidly progressing laser technologies provide powerful tools to study potential barrier-passage dynamics in physical, chemical, and biological systems with unprecedented temporal and spatial resolution and a remarkable chemical and structural specificity. The available theories of barrier passage, however, operate with equations, potentials, and parameters that are best suited for a specific area of research and a specific class of systems and processes. Making connections among these theories is often anything but easy. Here, we address this problem by presenting a unified framework for the description of a vast variety of classical and quantum barrier-passage phenomena, revealing an innate connection between various types of barrier-passage dynamics and providing closed-form equations showing how the signature exponentials in classical and quantum barrier-passage rates relate to and translate into each other. In this framework, the Arrhenius-law kinetics, the emergence of the Gibbs distribution, Hund's molecular wave-packet well-to-well oscillatory dynamics, Keldysh photoionization, and Kramers' escape over a potential barrier are all understood as manifestations of a potential-driven Markovian dynamics whereby a system evolves from a state of local stability. Key to the irreducibility of quantum tunneling to thermally activated barrier passage is the difference in the ways the diffusion-driving potentials emerge in these two tunneling settings, giving rise to stationary states with a distinctly different structure.

Real-time fiber-optic recording of acute-ischemic-stroke signatures

We present an experimental framework and methodology for in vivo studies on rat stroke models that enable a real-time fiber-optic recording of stroke-induced hydrogen peroxide and pH transients in ischemia-affected brain areas. Arrays of reconnectable implantable fiber probes combined with advanced optogenetic fluorescent protein sensors are shown to enable a quantitative multisite time-resolved study of oxidative-stress and acidosis buildup dynamics as the key markers, correlates and possible drivers of ischemic stroke. The fiber probes designed for this work provide a wavelength-multiplex forward-propagation channel for a spatially localized, dual-pathway excitation of genetically encoded fluorescence-protein sensors along with a back-propagation channel for the fluorescence return from optically driven fluorescence sensors. We show that the spectral analysis of the fiber-probe-collected fluorescence return provides means for a high-fidelity autofluorescence background subtraction, thus enhancing the sensitivity of real-time detection of stroke-induced transients and significantly reducing measurement uncertainties in in vivo acute-stroke studies as inherently statistical experiments operating with outcomes of multiply repeated measurements on large populations of individually variable animal stroke models.

Genetically Encoded Fluorescent Biosensors for Biomedical Applications

One of the challenges of modern biology and medicine is to visualize biomolecules in their natural environment, in real-time and in a non-invasive fashion, so as to gain insight into their physiological behavior and highlight alterations in pathological settings, which will enable to devise appropriate therapeutic strategies. Genetically encoded fluorescent biosensors constitute a class of imaging agents that enable visualization of biological processes and events directly in situ, preserving the native biological context and providing detailed insight into their localization and dynamics in cells. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the obvious benefits of using genetically encoded fluorescent biosensors in drug screening. This review summarizes results of the studies that have been conducted in the last years toward the fabrication of genetically encoded fluorescent biosensors for biomedical applications with a comprehensive discussion on the challenges, future trends, and potential inputs needed for improving them.