Revisiting Mitochondrial pH with an Improved Algorithm for Calibration of the Ratiometric 5(6)-carboxy-SNARF-1 Probe Reveals Anticooperative Reaction with H+ Ions and Warrants Further Studies of Organellar pH

Organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH for biosensing, bioimaging and biotherapeutics applications

In recent years, organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH (DFR-MPs-pH) have been attracting much interest in fundamental application research fields. More and more scientific publications have reported the exploration of various DFR-MPs-pH systems that have unique dual-fluorescence ratiometry as the signal output, in-built and signal self-calibration functions to improve precise detection of targets. DFR-MPs-pH systems possess high-performance applications in biosensing, bioimaging and biomedicine fields. This review has comprehensively summarized recent advances of DFR-MPs-pH for the first time. First of all, the compositions and types of DFR-MPs-pH are introduced by summarizing different organic fluorophores-based molecule systems. Then, construction strategies are analyzed based on specific components, structures, properties and functions of DFR-MPs-pH. Afterward, biosensing and bioimaging applications are discussed in detail, primarily referring to pH sensing and imaging detection at the levels of living cells and small animals. Finally, biomedicine applications are fully summarized, majorly involving bio-toxicity evaluation, bio-distribution, biomedical diagnosis and therapeutics. Meanwhile, the current status, challenges and perspectives are rationally commented after detailed discussions of representative and state-of-the-art studies. Overall, this present review is comprehensive, in-time and in-depth, and can facilitate the following further exploration of new and versatile DFR-MPs-pH systems toward rational design, facile preparation, superior properties, adjustable functions and highly efficient applications in promising fields.

Harnessing elastic instabilities for enhanced mixing and reaction kinetics in porous media

Turbulent flows have been used for millennia to mix solutes; a familiar example is stirring cream into coffee. However, many energy, environmental, and industrial processes rely on the mixing of solutes in porous media where confinement suppresses inertial turbulence. As a result, mixing is drastically hindered, requiring fluid to permeate long distances for appreciable mixing and introducing additional steps to drive mixing that can be expensive and environmentally harmful. Here, we demonstrate that this limitation can be overcome just by adding dilute amounts of flexible polymers to the fluid. Flow-driven stretching of the polymers generates an elastic instability, driving turbulent-like chaotic flow fluctuations, despite the pore-scale confinement that prohibits typical inertial turbulence. Using in situ imaging, we show that these fluctuations stretch and fold the fluid within the pores along thin layers ("lamellae") characterized by sharp solute concentration gradients, driving mixing by diffusion in the pores. This process results in a [Formula: see text] reduction in the required mixing length, a [Formula: see text] increase in solute transverse dispersivity, and can be harnessed to increase the rate at which chemical compounds react by [Formula: see text]-enhancements that we rationalize using turbulence-inspired modeling of the underlying transport processes. Our work thereby establishes a simple, robust, versatile, and predictive way to mix solutes in porous media, with potential applications ranging from large-scale chemical production to environmental remediation.

Super-Resolution Imaging of Voltages in the Interior of Individual, Vital Mitochondria

We present super-resolution microscopy of isolated functional mitochondria, enabling real-time studies of structure and function (voltages) in response to pharmacological manipulation. Changes in mitochondrial membrane potential as a function of time and position can be imaged in different metabolic states (not possible in whole cells), created by the addition of substrates and inhibitors of the electron transport chain, enabled by the isolation of vital mitochondria. By careful analysis of structure dyes and voltage dyes (lipophilic cations), we demonstrate that most of the fluorescent signal seen from voltage dyes is due to membrane bound dyes, and develop a model for the membrane potential dependence of the fluorescence contrast for the case of super-resolution imaging, and how it relates to membrane potential. This permits direct analysis of mitochondrial structure and function (voltage) of isolated, individual mitochondria as well as submitochondrial structures in the functional, intact state, a major advance in super-resolution studies of living organelles.

Driving electrochemical reactions at the microscale using CMOS microelectrode arrays

Precise control of pH values at electrode interfaces enables the systematic investigation of pH-dependent processes by electrochemical means. In this work, we employed high-density complementary metal-oxide-semiconductor (CMOS) microelectrode arrays (MEAs) as miniaturized systems to induce and confine electrochemical reactions in areas corresponding to the pitch of single electrodes (17.5 μm). First, we present a strategy for generating localized pH patterns on the surface of the CMOS MEA with unprecedented spatial resolution. Leveraging the versatile routing capabilities of the switch matrix beneath the CMOS MEA, we created arbitrary combinations of anodic and cathodic electrodes and hence pH patterns. Moreover, we utilized the system to produce polymeric surface patterns by additive and subtractive methods. For additive patterning, we controlled the in situ formation of polydopamine at the microelectrode surface through oxidation of free dopamine above a threshold pH > 8.5. For subtractive patterning, we removed cell-adhesive poly-L-lysine from the electrode surface and backfilled the voids with antifouling polymers. Such polymers were chosen to provide a proof-of-concept application of controlling neuronal growth via electrochemically-induced patterns on the CMOS MEA surface. Importantly, our platform is compatible with commercially available high-density MEAs and requires no custom equipment, rendering the findings generalizable and accessible.

Ni(II) Ions May Target the Entire Melatonin Biosynthesis Pathway—A Plausible Mechanism of Nickel Toxicity

Nickel is toxic to humans. Its compounds are carcinogenic. Furthermore, nickel allergy is a severe health problem that affects approximately 10–20% of humans. The mechanism by which these conditions develop remains unclear, but it may involve the cleavage of specific proteins by nickel ions. Ni(II) ions cleave the peptide bond preceding the Ser/Thr-Xaa-His sequence. Such sequences are present in all four enzymes of the melatonin biosynthesis pathway, i.e., tryptophan 5-hydroxylase 1, aromatic-l-amino-acid decarboxylase, serotonin N-acetyltransferase, and acetylserotonin O-methyltransferase. Moreover, fragments prone to Ni(II) are exposed on surfaces of these proteins. Our results indicate that all four studied fragments undergo cleavage within tens of hours at pH 8.2 and 37 °C, corresponding with the conditions in the mitochondrial matrix. Since melatonin, a potent antioxidant and anti-inflammatory agent, is synthesized within the mitochondria of virtually all human cells, depleting its supply may be detrimental, e.g., by raising the oxidative stress level. Intriguingly, Ni(II) ions have been shown to mimic hypoxia through the stabilization of HIF-1α protein, but melatonin prevents the action of HIF-1α. Considering all this, the enzymes of the melatonin biosynthesis pathway seem to be a toxicological target for Ni(II) ions.

Long-range transport and directed assembly of charged colloids under aperiodic electrodiffusiophoresis

Faradaic reactions often lead to undesirable side effects during the application of electric fields. Therefore, experimental designs often avoid faradaic reactions by working at low voltages or at high frequencies, where the electrodes behave as ideally polarizable. In this work, we show how faradaic processes under ac fields can be used advantageously to effect long-range transport, focusing and assembly of charged colloids. Herein, we use confocal microscopy and ratiometric analysis to confirm that ac fields applied in media of low conductivity induce significant pH gradients below and above the electrode charging frequency of the system. At voltages above 1 V_pp, and frequencies below 1.7 kHz, the pH profile becomes highly nonlinear. Charged particles respond to such conditions by migrating towards the point of highest pH, thereby focusing tens of microns away from both electrodes. Under the combination of oscillating electric fields and concentration gradients of electroactive species, particles experience aperiodic electrodiffusiophoresis (EDP). The theory of EDP, along with a mass transport model, describes the dynamics of particles. Furthermore, the high local concentration of particles near the focusing point leads to disorder-order transitions, whereby particles form crystals. The position and order within the levitating crystalline sheet can be readily tuned by adjusting the voltage and frequency. These results not only have significant implications for the fundamental understanding of ac colloidal electrokinetics, but also provide new possibilities for the manipulation and directed assembly of charged colloids.

Visualization of Concentration Gradients and Colloidal Dynamics under Electrodiffusiophoresis

In this work, we present an experimental study of the dynamics of charged colloids under direct currents and gradients of chemical species (electrodiffusiophoresis). In our approach, we simultaneously visualize the development of concentration polarization and the ensuing dynamics of charged colloids near electrodes. With the aid of confocal microscopy and fluorescent probes, we show that the passage of current through water confined between electrodes, separated about a hundred microns, results in significant pH gradients. Depending on the current density and initial conditions, steep pH gradients develop, thus becoming a significant factor in the behavior of charged colloids. Furthermore, we show that steep pH gradients induce the focusing of charged colloids away from both electrodes. Our results provide the experimental basis for further development of models of electrodiffusiophoresis and the design of non-equilibrium strategies for the fabrication of advanced materials.

The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry

The proton is the smallest atomic particle, and in aqueous solution it is the smallest hydrated ion, having only two waters in its first hydration shell. In this article we survey key aspects of the proton in chemistry and biochemistry, starting with the definitions of pH and pK _a and their application inside biological cells. This includes an exploration of pH in nanoscale spaces, distinguishing between bulk and interfacial phases. We survey the Eigen and Zundel models of the structure of the hydrated proton, and how these can be used to explain: a) the behavior of protons at the water-hydrophobic interface, and b) the extraordinarily high mobility of protons in bulk water via Grotthuss hopping, and inside proteins via proton wires. Lastly, we survey key aspects of the effect of proton concentration and proton transfer on biochemical reactions including ligand binding and enzyme catalysis, as well as pH effects on biochemical thermodynamics, including the Chemiosmotic Theory. We find, for example, that the spontaneity of ATP hydrolysis at pH ≥ 7 is not due to any inherent property of ATP (or ADP or phosphate), but rather to the low concentration of H⁺. Additionally, we show that acidification due to fermentation does not derive from the organic acid waste products, but rather from the proton produced by ATP hydrolysis.

Energy landscapes and dynamics of ion translocation through membrane transporters: a meeting ground for physics, chemistry, and biology

The dynamics of ion translocation through membrane transporters is visualized from a comprehensive point of view by a Gibbs energy landscape approach. The ΔG calculations have been performed with the Kirkwood-Tanford-Warshel (KTW) electrostatic theory that properly takes into account the self-energies of the ions. The Gibbs energy landscapes for translocation of a single charge and an ion pair are calculated, compared, and contrasted as a function of the order parameter, and the characteristics of the frustrated system with bistability for the ion pair are described and quantified in considerable detail. These calculations have been compared with experimental data on the ΔG of ion pairs in proteins. It is shown that, under suitable conditions, the adverse Gibbs energy barrier can be almost completely compensated by the sum of the electrostatic energy of the charge-charge interactions and the solvation energy of the ion pair. The maxima in ΔG_KTW with interionic distance in the bound H⁺ - A^- charge pair on the enzyme is interpreted in thermodynamic and molecular mechanistic terms, and biological implications for molecular mechanisms of ATP synthesis are discussed. The timescale at which the order parameter moves between two stable states has been estimated by solving the dynamical equations of motion, and a wealth of novel insights into energy transduction during ATP synthesis by the membrane-bound F_OF₁-ATP synthase transporter is offered. In summary, a unifying analytical framework that integrates physics, chemistry, and biology has been developed for ion translocation by membrane transporters for the first time by means of a Gibbs energy landscape approach.

A modern, simple, and economical accessory for continuous L-format measurement of steady-state fluorescence anisotropy

In this study, the pros and cons of the most relevant L-format devices reported in the literature for measuring steady-state fluorescence polarization/anisotropy are identified. Combining all this information, and with the use of modern elements for the acquisition, treatment, and recording of signals, a modern, simple, and economical L-format accessory is implemented to rapidly and continuously record steady-state fluorescence anisotropy. This device can be adapted to the majority of the commercial spectrofluorometers (or fluorometers). During the measurement, the emission polarizer is in permanent rotation by means of a Gimbal brushless DC motor, and as a result the recorded fluorescence signal is sinusoidal. The maximums and minimums of this signal, which are obtained with the help of LabVIEW tools, allow recording the fluorescence anisotropy. The LabVIEW applications developed for this investigation are freely available, so it is not necessary to have LabVIEW software.

Mitochondrial energetics with transmembrane electrostatically localized protons: do we have a thermotrophic feature?

Transmembrane electrostatically localized protons (TELP) theory has been recently recognized as an important addition over the classic Mitchell's chemiosmosis; thus, the proton motive force (pmf) is largely contributed from TELP near the membrane. As an extension to this theory, a novel phenomenon of mitochondrial thermotrophic function is now characterized by biophysical analyses of pmf in relation to the TELP concentrations at the liquid-membrane interface. This leads to the conclusion that the oxidative phosphorylation also utilizes environmental heat energy associated with the thermal kinetic energy (kBT) of TELP in mitochondria. The local pmf is now calculated to be in a range from 300 to 340 mV while the classic pmf (which underestimates the total pmf) is in a range from 60 to 210 mV in relation to a range of membrane potentials from 50 to 200 mV. Depending on TELP concentrations in mitochondria, this thermotrophic function raises pmf significantly by a factor of 2.6 to sixfold over the classic pmf. Therefore, mitochondria are capable of effectively utilizing the environmental heat energy with TELP for the synthesis of ATP, i.e., it can lock heat energy into the chemical form of energy for cellular functions.

Energy Renewal: Isothermal Utilization of Environmental Heat Energy with Asymmetric Structures

Through the research presented herein, it is quite clear that there are two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth. Type A, such as glycolysis and the tricarboxylic acid cycle, apparently follows the second law well; Type B, as exemplified by the thermotrophic function with transmembrane electrostatically localized protons presented here, does not necessarily have to be constrained by the second law, owing to its special asymmetric function. This study now, for the first time, numerically shows that transmembrane electrostatic proton localization (Type-B process) represents a negative entropy event with a local protonic entropy change (ΔSL) in a range from -95 to -110 J/K∙mol. This explains the relationship between both the local protonic entropy change (ΔSL) and the mitochondrial environmental temperature (T) and the local protonic Gibbs free energy (ΔGL=TΔSL) in isothermal environmental heat utilization. The energy efficiency for the utilization of total protonic Gibbs free energy (ΔGT including ΔGL=TΔSL) in driving the synthesis of ATP is estimated to be about 60%, indicating that a significant fraction of the environmental heat energy associated with the thermal motion kinetic energy (kBT) of transmembrane electrostatically localized protons is locked into the chemical form of energy in ATP molecules. Fundamentally, it is the combination of water as a protonic conductor, and thus the formation of protonic membrane capacitor, with asymmetric structures of mitochondrial membrane and cristae that makes this amazing thermotrophic feature possible. The discovery of energy Type-B processes has inspired an invention (WO 2019/136037 A1) for energy renewal through isothermal environmental heat energy utilization with an asymmetric electron-gated function to generate electricity, which has the potential to power electronic devices forever, including mobile phones and laptops. This invention, as an innovative Type-B mimic, may have many possible industrial applications and is likely to be transformative in energy science and technologies for sustainability on Earth.

Coupling mechanisms in ATP synthesis: Rejoinder to "Response to molecular-level understanding of biological energy coupling and transduction"

Recently, an exchange of views on key fundamental aspects of biological energy coupling and ATP synthesis in the vital process of oxidative phosphorylation appeared in the pages of this journal. The very difficult scientific problems are analyzed and clarified. Errors in the mathematical/thermodynamic equations of a previous analysis have been identified that invalidate previous assertions, and the correct equations are derived. The major differences between the two competing models - localized versus delocalized - for biological energy coupling and transduction are discussed from physical, chemical, and mathematical perspectives. The opposing views are summarized, so that the reader can assess for himself or herself the merits of the two coupling mechanisms. A fresh attempt has been made to go to the root of bioenergetics by calculating the desolvation free energy barrier, ∆G_desolvation for ion transport across biomembranes. Several constructive suggestions are made that have the power to resolve the basic contradictions and the areas of fundamental conflict, and reach a consensus by catalyzing the progress of future research in this interdisciplinary field.

Regulating Mitochondrial pH with Light and Implications for Chemoresistance

Chemoresistance is one of the major challenges for cancer treatment, more recently ascribed to defective mitochondrial outer membrane permeabilization (MOMP), significantly diminishing chemotherapeutic agent-induced apoptosis. A boron-dipyrromethene (BODIPY) chromophore-based triarylsulfonium photoacid generator (BD-PAG) was used to target mitochondria with the aim to regulate mitochondrial pH and further depolarize the mitochondrial membrane. Cell viability assays demonstrated the relative biocompatibility of BD-PAG in the dark while live cell imaging suggested high accumulation in mitochondria. Specific assays indicated that BD-PAG is capable of regulating mitochondrial pH with significant effects on mitochondrial membrane depolarization. Therapeutic tests using chlorambucil in combination with BD-PAG revealed a new strategy in chemoresistance suppression.

Simultaneous Single-Particle Tracking and Dynamic pH Sensing Reveal Lysosome-Targetable Mesoporous Silica Nanoparticle Pathways

Nanoparticle (NP)-based targeted drug delivery is intended to transport therapeutically active molecules to specific cells and particular intracellular compartments. However, there is limited knowledge regarding the complete route of NPs in this targeting scenario. In this study, simultaneously performing motion and dynamic pH sensing using single-particle tracking (SPT) leads to an alternative method of gaining insights into the mesoporous silica nanoparticle's (MSN) journey in targeting lysosome. Two different pH-sensitive dyes and a reference dye are incorporated into mesoporous silica nanoparticles (MSNs) via co-condensation to broaden the measurable pH range (pH 4-7.5) of the nanoprobe. The phosphonate, amine, and lysosomal sorting peptides (YQRLGC) are conjugated onto the MSN's surface to study intracellular nano-biointeractions of two oppositely charged and lysosome-targetable MSNs. The brightness and stability of these MSNs allow their movement and dynamic pH evolution during their journey to be simultaneously monitored in real time. Importantly, a multidimensional analysis of MSN's movement and local pH has revealed new model intracellular dynamic states and distributions of MSNs, previously inaccessible when using single parameters alone. A key result is that YQRLGC-conjugated MSNs took an alternative route to target lysosomes apart from the traditional one, which sped up to 4 h and enhanced their targeting efficiency (up to 32%). The findings enrich our understanding of the intracellular journey of MSNs. This study offers complementary information on correlating the surface design with the full pathway of nanoparticles to achieve targeted delivery of therapeutic payload.

Development of photo- and chemo-stable near-infrared-emitting dyes: linear-shape benzo-rosol and its derivatives as unique ratiometric bioimaging platforms

Microscopic imaging aided with fluorescent probes has revolutionized our understanding of biological systems. Organic fluorophores and probes thus continue to evolve for bioimaging applications. Fluorophores such as cyanines and hemicyanines emit in the near-infrared (NIR) region and thus allow deeper imaging with minimal autofluorescence; however, they show limited photo- and chemo-stability, demanding new robust NIR fluorophores. Such photo- and chemo-stable NIR fluorophores, linear-shape π-extended rosol and rosamine analogues, are disclosed here which provide bright fluorescence images in cells as well as in tissues by confocal laser-scanning microscopy. Furthermore, they offer unique ratiometric imaging platforms for activatable probes with dual excitation and dual emission capability, as demonstrated with a 2,4-dinitrophenyl ether derivative of benzo-rosol.

NIR-emitting benzo-rosol and -rosamine dyes offer novel ratiometric imaging platforms with high pohoto- and chemo-stability.

An update of the chemiosmotic theory as suggested by possible proton currents inside the coupling membrane

Understanding how biological systems convert and store energy is a primary purpose of basic research. However, despite Mitchell's chemiosmotic theory, we are far from the complete description of basic processes such as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory may need updating, thanks to the latest structural data on respiratory chain complexes. In particular, up-to date technologies, such as those using fluorescence indicators following proton displacements, have shown that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still an unresolved issue, even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. Moreover, F_oF₁-ATP synthase ubiquitous motor enzyme has the peculiarity (unlike most enzymes) of affecting the thermodynamic equilibrium of ATP synthesis. It seems that the concept of diffusion of the proton charge expressed more than two centuries ago by Theodor von Grotthuss is to be taken into consideration to resolve these issues. All these uncertainties remind us that also in biology it is necessary to consider the Heisenberg indeterminacy principle, which sets limits to analytical questions.

Extramitochondrial energy production in platelets

BACKGROUND INFORMATION

Energy demand in human platelets is very high, to carry out their functions. As for most human cells, the aerobic metabolism represents the primary energy source in platelets, even though mitochondria are negligibly represented. Following the hypothesis that other structures could be involved in chemical energy production, in this work, we have investigated the functional expression of an extramitochondrial aerobic metabolism in platelets.

RESULTS

Oximetric and luminometric analyses showed that platelets consume large amounts of oxygen and produce ATP in the presence of common respiring substrates, such as pyruvate + malate or succinate, although morphological electron microscopy analysis showed that these contain few mitochondria. However, evaluation of the anaerobic glycolytic metabolism showed that only 13% of consumed glucose was converted to lactate. Interestingly, the highest OXPHOS activity was observed in the presence of NADH, not a readily permeant respiring substrate for mitochondria. Also, oxygen consumption and ATP synthesis fuelled by NADH were not affected by atractyloside, an inhibitor of the adenine nucleotide translocase, suggesting that these processes may not be ascribed to mitochondria. Functional data were confirmed by immunofluorescence microscopy and Western blot analyses, showing a consistent expression of the β subunit of F₁ F_o -ATP synthase and COXII, a subunit of Complex IV, but a low signal of translocase of the inner mitochondrial membrane (a protein not involved in OXPHOS metabolism). Interestingly, the NADH-stimulated oxygen consumption and ATP synthesis increased in the presence of the physiological platelets agonists, thrombin or collagen.

CONCLUSIONS

Data suggest that in platelets, aerobic energy production is mainly driven by an extramitochondrial OXPHOS machinery, originated inside the megakaryocyte, and that this metabolism plays a pivotal role in platelet activation.

SIGNIFICANCE

This work represents a further example of the existence of an extramitochondrial aerobic metabolism, which can contribute to the cellular energy balance.