Resolving subcellular pH with a quantitative fluorescent lifetime biosensor

Smart on-demand drug release strategies for cancer combination therapy

In cancer therapy, enhancing therapeutic indices and patient compliance has been a central focus in recent drug delivery technology development. However, achieving a delicate balance between improving anti-tumor efficacy and minimizing toxicity to normal tissues remains a significant challenge. With the advent of smart on-demand drug release strategies, new opportunities have emerged. These strategies represent a promising approach to drug delivery, enabling precise control over the release of therapeutic agents in a programmed and spatiotemporal manner. Recent studies have focused on designing delivery systems capable of releasing multiple therapeutic agents sequentially, while achieving spatial resolution in vivo. Smart on-demand drug release strategies have demonstrated considerable potential in tumor combination therapy for achieving precision drug delivery and controlled release by responding to specific physiological signals or external physical stimuli in the tumor microenvironment. These strategies not only improve tumor targeting and reduce toxicity to healthy tissues but also enable sequential release in combination therapy, allowing multiple drugs to be released in a specific spatiotemporal order to enhance synergistic treatment effects. In this paper, we systematically reviewed the current research progress of smart on-demand drug release drug delivery strategies in anti-tumor combination therapy. We highlighted representative integrated drug delivery systems and discussed the challenges associated with their clinical application. Additionally, potential future research directions are proposed to further advance this promising field.

GSLab: open-source platform for advanced phasor analysis in fluorescence microscopy

SUMMARY

GSLab addresses the need for effective image analysis tools in fluorescence microscopy by providing an open-source platform that enhances traditional phasor analysis with advanced features. Key capabilities include machine learning-based clustering, real-time monitoring, and quantitative unmixing of fluorescent species. Designed for both commercial and custom systems, GSLab provides researchers with comprehensive lifetime and spectral phasor image analysis tools to tackle complex biological problems.

AVAILABILITY AND IMPLEMENTATION

The software is written as a MATLAB app. It is available for download at: https://doi.org/10.6084/m9.figshare.27921966. Example files and tutorials are also available: https://doi.org/10.6084/m9.figshare.28067108. For developers who wish to contribute please use: https://github.com/AlexVallmitjana/GSLab. A compiled Windows installer (does not require MATLAB) is available at: https://doi.org/10.6084/m9.figshare.28655276.

Fluorescence lifetime imaging in drug delivery research

Once an exotic add-on to fluorescence microscopy for life science research, fluorescence lifetime imaging (FLIm) has become a powerful and increasingly utilised technique owing to its self-calibration nature, which affords superior quantification over conventional steady-state fluorescence imaging. This review focuses on the state-of-the-art implementation of FLIm related to the formulation, release, dosage, and mechanism of action of drugs aimed for innovative diagnostics and therapy. Quantitative measurements using FLIm have appeared instrumental for encapsulated drug delivery design, pharmacokinetics and pharmacodynamics, pathological investigations, early disease diagnosis, and evaluation of therapeutic efficacy. Attention is paid to the latest advances in lifetime-engineered nanomaterials and practical instrumentation, which begin to show preclinical and clinical translation potential beyond in vitro samples of cells and tissues. Finally, major challenges that need to be overcome in order to facilitate future perspectives are discussed.

Quantitative profiling pH heterogeneity of acidic endolysosomal compartments using fluorescence lifetime imaging microscopy

The endolysosomal system plays a crucial role in maintaining cellular homeostasis and promoting organism fitness. The pH of its acidic compartments is a crucial parameter for proper function, and it is dynamically influenced by both intracellular and environmental factors. Here, we present a method based on fluorescence lifetime imaging microscopy (FLIM) for quantitatively analyzing the pH profiles of acidic endolysosomal compartments in diverse types of primary mammalian cells and in live organism Caenorhabditis elegans. This FLIM-based method exhibits high sensitivity in resolving subtle pH differences, thereby revealing heterogeneity within a cell and across cell types. This method enables rapid measurement of pH changes in the acidic endolysosomal system in response to various environmental stimuli. Furthermore, the fast FLIM measurement of pH-sensitive dyes circumvents the need for transgenic reporters and mitigates potential confounding factors associated with varying dye concentrations or excitation light intensity. This FLIM approach offers absolute pH quantification and highlights the significance of pH heterogeneity and dynamics, offering a valuable tool for investigating lysosomal functions and their regulation in various physiological and pathological contexts.

GSLab: Open-Source Platform for Advanced Phasor Analysis in Fluorescence Microscopy

GSLab addresses the need for effective image analysis tools in fluorescence microscopy by providing an open-source platform that enhances traditional phasor analysis with advanced features. Key capabilities include machine learning-based clustering, real-time monitoring, and quantitative unmixing of fluorescent species. Designed for both commercial and custom systems, GSLab provides researchers with comprehensive lifetime and spectral phasor image analysis tools to tackle complex biological problems.

pH Measurements Using Leaky Waveguides with Synthetic Hydrogel Films

Leaky waveguides (LWs) are low-refractive-index films deposited on glass substrates. In these, light can travel in the film while leaking out at the film-substrate interface. The angle at which light can travel in the film is dependent on its refractive index and thickness, which can change with pH when the film is made of pH-responsive materials. Herein, we report an LW comprising a waveguide film made of a synthetic hydrogel containing the monomers acrylamide and N-[3-(dimethylamino)propyl]methacrylamide (DMA) and a bisacrylamide crosslinker for pH measurements between 4 and 8. The response of the LW pH sensor was reversible and the response times were 0.90 ± 0.14 and 2.38 ± 0.22 min when pH was changed from low to high and high to low, respectively. The reported LW pH sensor was largely insensitive to typical concentrations of common interferents, including sodium chloride, urea, aluminum sulfate, calcium chloride, and humic acid. Compared to a glass pH electrode, the measurement range is smaller but is close to the range required for monitoring the pH of drinking water. The pH resolution of the hydrogel sensor was ~0.004, compared to ~0.01 for the glass electrode.

Using environment-sensitive tetramethylated thiophene-BODIPY fluorophores in DNA probes for studying effector-induced conformational changes of protein-DNA complexes

The LutR protein represses the transcription of genes encoding enzymes for the utilization of l-lactate in Bacillus subtilis through binding to a specific DNA region. In this study, we employed oligonucleotide probes modified by viscosity-sensitive tetramethylated thiophene-BODIPY fluorophores to investigate the impact of selected metabolites on the LutR-DNA complex. Our goal was to identify the effector molecule whose binding alters the protein-DNA affinity, thereby enabling gene transcription. The designed DNA probes exhibited distinctive responses to the binding and release of the protein, characterized by significant alterations in fluorescence lifetime. Through this method, we have identified l-lactate as the sole metabolite exerting a substantial modulating effect on the protein-DNA interaction and thus confirmed its role as an effector molecule. Moreover, we showed that our approach was able to follow conformation changes affecting affinity, which were not captured by other methods commonly used to study the protein-DNA interaction, such as electro-mobility shift assays and florescence anisotropy binding studies. This work underlines the potential of environment-sensitive fluorophore-linked nucleotide modifications, i.e. dCTBdp, for studying the dynamics and subtle changes of protein-DNA interactions.

Reversible addition-fragmentation chain transfer enhanced aggregation signal-on fluorescence detection of alkaline phosphatase

The instability of the signal intensity of fluorescent biosensors and the false signals have been significant factors affecting the performance of biosensors. Herein, a novel signaling system is devised through the application of reversible addition-fragmentation chain transfer (RAFT) polymerization with monomers containing the tetraphenylethylene (TPE) groups. TPE exhibits an aggregation-induced emission (AIE) phenomenon in certain solvents, mainly due to the blockage of the rotation of its four benzene rings, which also exist in the aggregated state. With this property, a series of molecules are modified based on click chemistry for RAFT polymerization using Fe3O4 magnetic beads as the carriers, and stable aggregated luminescent TPE polymers are formed on the surface of magnetic beads to realize the transformation of fluorescence signal from "0" to "1". In addition, the fluorescence signal demonstrates a positive correlation with alkaline phosphatase (ALP) activity, which can be quantified by measuring the fluorescence intensity. The biosensor exhibits high sensitivity and good linearity in the range of 0.1-5 U/L, with a LOD of 0.079 U/L. Furthermore, the designed strategy demonstrated satisfactory performance in the quantitative determination of ALP activity in serum samples, indicating that the signaling system developed by combining RAFT polymerization and AIE molecules has an important application in the field of fluorescent biosensors.

Exploring salinity induced adaptations in marine diatoms using advanced photonic techniques

Photonic-based methods are crucial in biology and medicine due to their non-invasive nature, allowing remote measurements without affecting biological specimens. The study of diatoms using advanced photonic methods remains a relatively underexplored area, presenting significant opportunities for pioneering discoveries. This research provides a comprehensive analysis of marine diatoms, specifically Nitzschia sp., across varying salinity levels, integrating fluorescence lifetime imaging microscopy (FLIM), combined photoacoustic and fluorescence tomographies (PAFT), and ultrastructural examinations using transmission electron microscopy. Key findings include a systematic shift in the mean fluorescence lifetime from 570 ps at 20‰ to 940 ps at 80‰, indicating functional adaptations in chlorophyll molecules within light-harvesting complexes. At 60‰ salinity, anomalies are observed in the development of silica valves and polysaccharide layers, suggesting abnormalities in valve morphogenesis. Lipid droplets within the cells display a minimum diameter at 40‰, indicating metabolic adjustments to osmotic stress. The intensity of both fluorescence and photoacoustic signals increases with increasing salinity levels. These insights enhance understanding of the ecological implications of salinity stress on diatom communities and pave the way for future research on leveraging the unique adaptive mechanisms of microalgae for environmental monitoring and sustainable biotechnological applications.

Diatoms exhibit dynamic chloroplast calcium signals in response to high light and oxidative stress

Diatoms are a group of silicified algae that play a major role in marine and freshwater ecosystems. Diatom chloroplasts were acquired by secondary endosymbiosis and exhibit important structural and functional differences from the primary plastids of land plants and green algae. Many functions of primary plastids, including photoacclimation and inorganic carbon acquisition, are regulated by calcium-dependent signaling processes. Calcium signaling has also been implicated in the photoprotective responses of diatoms; however, the nature of calcium elevations in diatom chloroplasts and their wider role in cell signaling remains unknown. Using genetically encoded calcium indicators, we find that the diatom Phaeodactylum tricornutum exhibits dynamic calcium elevations within the chloroplast stroma. Stromal calcium ([Ca2+]str) acts independently from the cytosol and is not elevated by stimuli that induce large cytosolic calcium ([Ca2+]cyt) elevations. In contrast, high light and exogenous hydrogen peroxide (H2O2) induce large, sustained [Ca2+]str elevations that are not replicated in the cytosol. Measurements using the fluorescent H2O2 sensor roGFP2-Oxidant Receptor Peroxidase 1 (Orp1) indicate that [Ca2+]str elevations induced by these stimuli correspond to the accumulation of H2O2 in the chloroplast. [Ca2+]str elevations were also induced by adding methyl viologen, which generates superoxide within the chloroplast, and by treatments that disrupt nonphotochemical quenching (NPQ). The findings indicate that diatoms generate specific [Ca2+]str elevations in response to high light and oxidative stress that likely modulate the activity of calcium-sensitive components in photoprotection and other regulatory pathways.

Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals

Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.

Naltrexone blocks alcohol-induced effects on kappa-opioid receptors in the plasma membrane

Naltrexone (NTX), a homolog of the opiate antidote naloxone, is an orally active long-acting general opioid receptor antagonist used in the treatment of opiate dependence. NTX is also found to relieve craving for alcohol and is one of few FDA-approved medications for treatment of alcohol use disorder (AUD). While it was early on established that NTX acts by blocking the binding of endogenous opioid peptide ligands released by alcohol, experimental evidence emerged that could not be fully accounted for by this explanation alone, suggesting that NTX may have additional modes of action. Mu- and kappa-opioid receptors (MOP and KOP, respectively) are structurally related G-protein-coupled receptors (GPCRs), but they are anatomically differently distributed and functionally distinct, often mediating opposite responses, with MOP typically promoting euphoria and reward, while KOP is associated with dysphoria and aversive states. While the actions of NTX on MOP are extensively characterized, the interactions with KOP are not. Here, we used sensitive fluorescence-based methods with single-molecule sensitivity to study in live cells the influence of alcohol (ethanol, EtOH) on KOP and the interaction between KOP and NTX. Our data show that alcohol, at relevant concentrations (10-40 mM), alters KOP interactions with the lipid environment in the plasma membrane. The counteracting effects of NTX are exerted by both its canonical action on KOP and its hitherto unrevealed effects on the lateral dynamics and organization of lipids in the plasma membrane. The KOP-specific antagonist LY2444296, in clinical trial for major depressive disorder (MDD), blocks KOP but does not show the full action profile of NTX. The therapeutic effect of NTX treatment in AUD may in part be due to direct actions on KOP and in part due to its effect on the surrounding lipid environment.

Legumain/asparaginyl endopeptidase-resistant tau fibril fold produces corticobasal degeneration-specific C-terminal tau fragment

Corticobasal degeneration (CBD) is a major four-repeat tauopathy along with progressive supranuclear palsy (PSP). Although detergent-insoluble 37-40-kDa carboxyl-terminal tau fragments (CTFs) are hallmarks of CBD pathology, the process of their formation is unknown. This study monitored the formation of CBD-type fibrils that exhibit astrocytic plaques, a characteristic CBD pathology, using its biochemical properties different from those of Alzheimer's disease/PSP-type fibrils. Tau fibrils from patients with CBD were amplified in non-astrocytic cultured cells, which maintained CBD-specific biochemical properties. We found that the lysosomal protease Legumain (LGMN) was involved in the generation of CBD-specific 37-40-kDa CTFs. While LGMN cleaved tau fibrils at Asn167 and Asn368 in the brain tissues of patients with Alzheimer's disease and PSP, tau fibrils from patients with CBD were predominantly resistant to cleavage at Asn368 by LGMN, resulting in the generation of CBD-specific CTFs. LGMN preference in tau fibrils was lost upon unraveling the tau fibril fold, suggesting that the CBD-specific tau fibril fold contributes to CBD-specific CTF production. From these findings, we found a way to differentiate astrocytic plaque from tufted astrocyte using the anti-Asn368 LGMN cleavage site-specific antibody. Inoculation of tau fibrils amplified in non-astrocytic cells into the mouse brain reproduced LGMN-resistant tau fibrils and recapitulated anti-Asn368-negative astrocytic plaques, which are characteristic of CBD pathology. This study supports the existence of disease-specific tau fibrils and contribute to further understanding of the tauopathy diagnosis. Our tau propagation mouse model using cellular tau seeds may contribute to uncovering disease mechanisms and screening for potential therapeutic compounds.

pH-Responsive Fluorescent Switches through Intramolecular Conjugate Addition Reactions and Application in Fluorogenic Bioimaging

We report new photoluminescent switching systems achieved through pH-induced intramolecular oxa-Michael conjugate addition reactions. Ratiometric absorbance and fluorescence emission were observed across conjugate acceptors triggered by pH, resulting in specific pseudo pKa values. The effect of substituents on the pseudo pKa's was investigated, showing increased values from electron-withdrawing to electron-donating groups. Inspired by the physiologically related pKa, a fluorescent probe was designed, successfully distinguishing cancer cells from normal cells through live cellular imaging.

Enhancing Targeted Drug Delivery through Cell-Specific Endosomal Escape

Endosome is a major barrier in the intracellular delivery of drugs, especially for biologics, such as proteins, peptides, and nucleic acids. After being endocytosed, these cargos will be trapped inside the endosomal compartments and finally degraded in the lysosomes. Thus, various strategies have been developed to facilitate the escape of cargos from the endosomes to improve the intracellular delivery efficiency. While the majority of the studies are focusing on strengthening the endosomal escape capability to maximize the delivery outcome, recent evidence suggests that a careful control of the endosomal escape process could provide opportunity for targeted drug delivery. In this concept review, we examined current delivery systems that can sense intra-endosomal factors or external stimuli for controlling endosomal escape toward a targeted intracellular delivery of cargos. Furthermore, the prospects and challenges of such strategies are discussed.

Nanoparticle Targeting Strategies for Lipid and Polymer-Based Gene Delivery to Immune Cells In Vivo

Lipid nanoparticles and polymeric nanoparticles are promising biomaterial platforms for robust intracellular DNA and mRNA delivery, highlighted by the widespread use of nanoparticle- (NP) based mRNA vaccines to help end the COVID-19 pandemic. Recent research has sought to adapt this nanotechnology to transfect and engineer immune cells in vivo. The immune system is an especially appealing target due to its involvement in many different diseases, and ex vivo-engineered immune cell therapies like chimeric antigen receptor (CAR) T therapy have already demonstrated remarkable clinical success in certain blood cancers. Although gene delivery can potentially address some of the cost and manufacturing concerns associated with current autologous immune cell therapies, transfecting immune cells in vivo is challenging. Not only is extrahepatic NP delivery to lymphoid organs difficult, but immune cells like T cells have demonstrated particular resistance to transfection. Despite these challenges, the modular nature of NPs allows researchers to examine critical structure-function relationships between a particle's properties and its ability to specifically engineer immune cells in vivo. Herein, several nanomaterial components are outlined, including targeting ligands, nucleic acid cargo, chemical properties, physical properties, and the route of administration to specifically target NPs to immune cells for optimal in vivo transfection.

Endolysosomal trapping of therapeutics and endosomal escape strategies

Internalizing therapeutic molecules or genes into cells and safely delivering them to the target tissue where they can perform the intended tasks is one of the key characteristics of the smart gene/drug delivery vector. Despite much research in this field, endosomal escape continues to be a significant obstacle to the development of effective gene/drug delivery systems. In this review, we discuss in depth the several types of endocytic pathways involved in the endolysosomal trapping of therapeutic agents. In addition, we describe numerous mechanisms involved in nanoparticle endosomal escape. Furthermore, many other techniques are employed to increase endosomal escape to minimize entrapment of therapeutic compounds within endolysosomes, which have been reviewed at length in this study.

pH-Assisted multichannel heat shock monitoring in the endoplasmic reticulum with a pyridinium fluorophore

Heat shock is a global health concern as it causes permanent damage to living cells and has a relatively high mortality rate. Therefore, diagnostic tools that facilitate a better understanding of heat shock damage and the defense mechanism at the sub-cellular level are of great importance. In this report, we have demonstrated the use of a pyridinium-based fluorescent molecule, PM-ER-OH, as a 'multichannel' imaging probe to monitor the pH change associated with a heat shock in the endoplasmic reticulum. Among the three pyridinium derivatives synthesized, PM-ER-OH was chosen for study due to its excellent biocompatibility, good localization in the endoplasmic reticulum, and intracellular pH response signaled by a yellow fluorescence (λ max = 556 nm) at acidic pH and a far red fluorescence (λ max = 660 nm) at basic pH. By changing the excitation wavelength, we could modulate the fluorescence signal in 'turn-ON', single excitation ratiometric and 'turn-OFF' modes, making the fluorophore a 'multichannel' probe for both ex vitro and in vitro pH monitoring in the endoplasmic reticulum. The probe could efficiently monitor the pH change when heat shock was applied to cells either directly or in a pre-heated manner, which gives insight on cellular acidification caused by heat stress.

Control of Inflammatory Response by Tissue Microenvironment

Inflammation is an essential defense response but operates at the cost of normal functions. Whether and how the negative impact of inflammation is monitored remains largely unknown. Acidification of the tissue microenvironment is associated with inflammation. Here we investigated whether macrophages sense tissue acidification to adjust inflammatory responses. We found that acidic pH restructured the inflammatory response of macrophages in a gene-specific manner. We identified mammalian BRD4 as a novel intracellular pH sensor. Acidic pH disrupts the transcription condensates containing BRD4 and MED1, via histidine-enriched intrinsically disordered regions. Crucially, decrease in macrophage intracellular pH is necessary and sufficient to regulate transcriptional condensates in vitro and in vivo, acting as negative feedback to regulate the inflammatory response. Collectively, these findings uncovered a pH-dependent switch in transcriptional condensates that enables environmental sensing to directly control inflammation, with a broader implication for calibrating the magnitude and quality of inflammation by the inflammatory cost.

Polymeric Nanoparticles for Drug Delivery

The recent emergence of nanomedicine has revolutionized the therapeutic landscape and necessitated the creation of more sophisticated drug delivery systems. Polymeric nanoparticles sit at the forefront of numerous promising drug delivery designs, due to their unmatched control over physiochemical properties such as size, shape, architecture, charge, and surface functionality. Furthermore, polymeric nanoparticles have the ability to navigate various biological barriers to precisely target specific sites within the body, encapsulate a diverse range of therapeutic cargo and efficiently release this cargo in response to internal and external stimuli. However, despite these remarkable advantages, the presence of polymeric nanoparticles in wider clinical application is minimal. This review will provide a comprehensive understanding of polymeric nanoparticles as drug delivery vehicles. The biological barriers affecting drug delivery will be outlined first, followed by a comprehensive description of the various nanoparticle designs and preparation methods, beginning with the polymers on which they are based. The review will meticulously explore the current performance of polymeric nanoparticles against a myriad of diseases including cancer, viral and bacterial infections, before finally evaluating the advantages and crucial challenges that will determine their wider clinical potential in the decades to come.

Reversible assembly and disassembly of V-ATPase during the lysosome regeneration cycle

Regulation of the luminal pH of late endocytic compartments in continuously fed mammalian cells is poorly understood. Using normal rat kidney fibroblasts, we investigated the reversible assembly/disassembly of the proton pumping V-ATPase when endolysosomes are formed by kissing and fusion of late endosomes with lysosomes and during the subsequent reformation of lysosomes. We took advantage of previous work showing that sucrosomes formed by the uptake of sucrose are swollen endolysosomes from which lysosomes are reformed after uptake of invertase. Using confocal microscopy and subcellular fractionation of NRK cells stably expressing fluorescently tagged proteins, we found net recruitment of the V1 subcomplex during sucrosome formation and loss during lysosome reformation, with a similar time course to RAB7a loss. Addition of invertase did not alter mTORC1 signalling, suggesting that the regulation of reversible V-ATPase assembly/disassembly in continuously fed cells differs from that in cells subject to amino acid depletion/refeeding. Using live cell microscopy, we demonstrated recruitment of a fluorescently tagged V1 subunit during endolysosome formation and a dynamic equilibrium and rapid exchange between the cytosolic and membrane bound pools of this subunit. We conclude that reversible V-ATPase assembly/disassembly plays a key role in regulating endolysosomal/lysosomal pH in continuously fed cells.

Recent Progress in the Endosomal Escape Mechanism and Chemical Structures of Polycations for Nucleic Acid Delivery

Nucleic acid-based therapies are seeing a spiralling surge. Stimuli-responsive polymers, especially pH-responsive ones, are gaining widespread attention because of their ability to efficiently deliver nucleic acids. These polymers can be synthesized and modified according to target requirements, such as delivery sites and the nature of nucleic acids. In this regard, the endosomal escape mechanism of polymer-nucleic acid complexes (polyplexes) remains a topic of considerable interest owing to various plausible escape mechanisms. This review describes current progress in the endosomal escape mechanism of polyplexes and state-of-the-art chemical designs for pH-responsive polymers. The importance is also discussed of the acid dissociation constant (i.e., pKa) in designing the new generation of pH-responsive polymers, along with assays to monitor and quantify the endosomal escape behavior. Further, the use of machine learning is addressed in pKa prediction and polymer design to find novel chemical structures for pH responsiveness. This review will facilitate the design of new pH-responsive polymers for advanced and efficient nucleic acid delivery.

Kinetics of RNA-LNP delivery and protein expression

Lipid nanoparticles (LNPs) employing ionizable lipids are the most advanced technology for delivery of RNA, most notably mRNA, to cells. LNPs represent well-defined core-shell particles with efficient nucleic acid encapsulation, low immunogenicity and enhanced efficacy. While much is known about the structure and activity of LNPs, less attention is given to the timing of LNP uptake, cytosolic transfer and protein expression. However, LNP kinetics is a key factor determining delivery efficiency. Hence quantitative insight into the multi-cascaded pathway of LNPs is of interest to elucidate the mechanism of delivery. Here, we review experiments as well as theoretical modeling of the timing of LNP uptake, mRNA-release and protein expression. We describe LNP delivery as a sequence of stochastic transfer processes and review a mathematical model of subsequent protein translation from mRNA. We compile probabilities and numbers obtained from time resolved microscopy. Specifically, live-cell imaging on single cell arrays (LISCA) allows for high-throughput acquisition of thousands of individual GFP reporter expression time courses. The traces yield the distribution of mRNA life-times, expression rates and expression onset. Correlation analysis reveals an inverse dependence of gene expression efficiency and transfection onset-times. Finally, we discuss why timing of mRNA release is critical in the context of codelivery of multiple nucleic acid species as in the case of mRNA co-expression or CRISPR/Cas gene editing.

Progress in pH-Sensitive sensors: essential tools for organelle pH detection, spotlighting mitochondrion and diverse applications

pH-sensitive fluorescent proteins have revolutionized the field of cellular imaging and physiology, offering insight into the dynamic pH changes that underlie fundamental cellular processes. This comprehensive review explores the diverse applications and recent advances in the use of pH-sensitive fluorescent proteins. These remarkable tools enable researchers to visualize and monitor pH variations within subcellular compartments, especially mitochondria, shedding light on organelle-specific pH regulation. They play pivotal roles in visualizing exocytosis and endocytosis events in synaptic transmission, monitoring cell death and apoptosis, and understanding drug effects and disease progression. Recent advancements have led to improved photostability, pH specificity, and subcellular targeting, enhancing their utility. Techniques for multiplexed imaging, three-dimensional visualization, and super-resolution microscopy are expanding the horizon of pH-sensitive protein applications. The future holds promise for their integration into optogenetics and drug discovery. With their ever-evolving capabilities, pH-sensitive fluorescent proteins remain indispensable tools for unravelling cellular dynamics and driving breakthroughs in biological research. This review serves as a comprehensive resource for researchers seeking to harness the potential of pH-sensitive fluorescent proteins.

Self-Immolative Polymer Nanoparticles with Precise and Controllable pH-Dependent Degradation

Polymer nanoparticles have generated significant interest as delivery systems for therapeutic cargo. Self-immolative polymers (SIPs) are an interesting category of materials for delivery applications, as the characteristic property of end-to-end depolymerization allows for the disintegration of the delivery system, facilitating a more effective release of the cargo and clearance from the body after use. In this work, nanoparticles based on a pH-responsive polymer poly(ethylene glycol)-b-(2-diisopropyl)amino ethyl methacrylate) and a self-immolative polymer poly[N,N-(diisopropylamino)ethyl glyoxylamide-r-N,N-(dibutylamino)ethyl glyoxylamide] (P(DPAEGAm-r-DBAEGAm)) were developed. Four particles were synthesized based on P(DPAEGAm-r-DBAEGAm) polymers with varied diisopropylamino to dibutylamino ratios of 4:1, 2:1, 2:3, and 0:1, termed 4:1, 2:1, 2:3, and 0:1 PGAm particles. The pH of particle disassembly was tuned from pH 7.0 to pH 5.0 by adjusting the ratio of diisopropylamino to dibutylamino substituents on the pendant tertiary amine. The P(DPAEGAm-r-DBAEGAm) polymers were observed to depolymerize (60-80%) below the particle disassembly pH after ∼2 h, compared to <10% at pH 7.4 and maintained reasonable stability at pH 7.4 (20-50% depolymerization) after 1 week. While all particles exhibited the ability to load a peptide cargo, only the 4:1 PGAm particles had higher endosomal escape efficiency (∼4%) compared to the 2:3 or 0:1 PGAm particles (<1%). The 4:1 PGAm particle is a promising candidate for further optimization as an intracellular drug delivery system with rapid and precisely controlled degradation.

Genetically encoded fluorescence lifetime biosensors: overview, advances, and opportunities

Genetically encoded biosensors based on fluorescent proteins (FPs) are powerful tools for tracking analytes and cellular events with high spatial and temporal resolution in living cells and organisms. Compared with intensiometric readout and ratiometric readout, fluorescence lifetime readout provides absolute measurements, independent of the biosensor expression level and instruments. Thus, genetically encoded fluorescence lifetime biosensors play a vital role in facilitating accurate quantitative assessments within intricate biological systems. In this review, we first provide a concise description of the categorization and working mechanism of genetically encoded fluorescence lifetime biosensors. Subsequently, we elaborate on the combination of the fluorescence lifetime imaging technique and lifetime analysis methods with fluorescence lifetime biosensors, followed by their application in monitoring the dynamics of environment parameters, analytes and cellular events. Finally, we discuss worthwhile considerations for the design, optimization and development of fluorescence lifetime-based biosensors from three representative cases.

Fluorescent dyes based on rhodamine derivatives for bioimaging and therapeutics: recent progress, challenges, and prospects

Since their inception, rhodamine dyes have been extensively applied in biotechnology as fluorescent markers or for the detection of biomolecules owing to their good optical physical properties. Accordingly, they have emerged as a powerful tool for the visualization of living systems. In addition to fluorescence bioimaging, the molecular design of rhodamine derivatives with disease therapeutic functions (e.g., cancer and bacterial infection) has recently attracted increased research attention, which is significantly important for the construction of molecular libraries for diagnostic and therapeutic integration. However, reviews focusing on integrated design strategies for rhodamine dye-based diagnosis and treatment and their wide application in disease treatment are extremely rare. In this review, first, a brief history of the development of rhodamine fluorescent dyes, the transformation of rhodamine fluorescent dyes from bioimaging to disease therapy, and the concept of optics-based diagnosis and treatment integration and its significance to human development are presented. Next, a systematic review of several excellent rhodamine-based derivatives for bioimaging, as well as for disease diagnosis and treatment, is presented. Finally, the challenges in practical integration of rhodamine-based diagnostic and treatment dyes and the future outlook of clinical translation are also discussed.

Macropinoscope: Real-Time Simultaneous Tracking of pH and Cathepsin B Activity in Individual Macropinosomes

A fluorescent sensor that allows simultaneous analysis of environmental factors in a limited cellular space is useful for understanding precise molecular interactions in live cells and their biological responses. Macropinocytosis is a ubiquitous endocytic pathway for massive uptake of extracellular fluids, resulting in the formation of macropinosomes. Although macropinocytosis may impact intracellular delivery and cancer proliferation, information on the intracellular behaviors of macropinosomes is limited. Here, we aimed to develop a macropinoscope, a sensor that simultaneously detects pH and cathepsin B activity in individual macropinosomes. A macropinosome-specific marker, dextran (70 kDa), was employed as a platform, onto which fluorescein, Oregon Green, and tetramethylrhodamine were loaded for ratiometric pH sensing and imaging. A cathepsin-B-cleavable peptide sequence bearing sulfo-Cy5 and the quencher BHQ-3 was also mounted; cleavage of the sequence was detected as an increase in sulfo-Cy5 fluorescence. A steep decrease in pH was observed 5-10 min after macropinosome formation, which was accompanied by an immediate increase in cathepsin B activity. Our design concept will lead to the development of other macropinoscopes for the simultaneous detection of other parameters in individual macropinosomes.

Aβ40 Aggregation under Changeable Conditions

Homeostasis is crucial for cell function, and disturbances in homeostasis can lead to health disorders. Under normal conditions, intracellular pH is maintained between 7.35 and 7.45. Altered endosomal and lysosomal pH together with a general drop in brain pH are associated with the aggregation of amyloid-β-peptide (Aβ) and the development of Alzheimer's disease. Under acidic conditions, close to the Aβ isoelectric point, the absence of charges favors the formation of intermolecular contacts and promotes aggregation. Here, we analyzed how pH levels affect the aggregation of Aβ40 considering the variations in brain pH and the coexistence of different aggregated conformations. Our results suggest that different macromolecular conformations can interact with each other and influence the aggregation process. In addition, we showed that neutral pH and physiological salt concentrations favor a slow aggregation, resulting in ordered, stable fibrils, with low cytotoxic effects. Overall, we highlight the complexity of the aggregation processes occurring in different physiological and pathological environments.