Determination of intracellular pH and compartmentation using diffusion-weighted NMR spectroscopy with pH-sensitive indicators

Ratiometric i-Motif-Based Sensor for Precise Long-Term Monitoring of pH Micro Alterations in the Nucleoplasm and Interchromatin Granules

DNA-intercalated motifs (iMs) are facile scaffolds for the design of various pH-responsive nanomachines, including biocompatible pH sensors. First, DNA pH sensors relied on complex intermolecular scaffolds. Here, we used a simple unimolecular dual-labeled iM scaffold and minimized it by replacing the redundant loop nucleosides with abasic or alkyl linkers. These modifications improved the thermal stability of the iM and increased the rates of its pH-induced conformational transitions. The best effects were obtained upon the replacement of all three native loops with short and flexible linkers, such as the propyl one. The resulting sensor showed a pH transition value equal to 6.9 ± 0.1 and responded rapidly to minor acidification (tau_1/2 <1 s for 7.2 → 6.6 pH jump). We demonstrated the applicability of this sensor for pH measurements in the nuclei of human lung adenocarcinoma cells (pH = 7.4 ± 0.2) and immortalized embryonic kidney cells (pH = 7.0 ± 0.2). The sensor stained diffusely the nucleoplasm and piled up in interchromatin granules. These findings highlight the prospects of iMs in the studies of normal and pathological pH-dependent processes in the nucleus, including the formation of biomolecular condensates.

Nano- and Microsensors for In Vivo Real-Time Electrochemical Analysis: Present and Future Perspectives

Electrochemical nano- and microsensors have been a useful tool for measuring different analytes because of their small size, sensitivity, and favorable electrochemical properties. Using such sensors, it is possible to study physiological mechanisms at the cellular, tissue, and organ levels and determine the state of health and diseases. In this review, we highlight recent advances in the application of electrochemical sensors for measuring neurotransmitters, oxygen, ascorbate, drugs, pH values, and other analytes in vivo. The evolution of electrochemical sensors is discussed, with a particular focus on the development of significant fabrication schemes. Finally, we highlight the extensive applications of electrochemical sensors in medicine and biological science.

Rapid Determination of the Acidity, Alkalinity and Carboxyl Content of Aqueous Samples by 1H NMR with Minimal Sample Quantity

The titratable acidity, alkalinity, and carboxylate content are fundamental properties required for the understanding of aqueous chemical systems. Here, we present a set of new methods that allow these properties to be determined directly by ¹H NMR without the labor, cost, and sample quantity associated with running separate potentiometric or conductometric titrations. Our methods require only the measurement of the pH-sensitive ¹H chemical shifts of indicator molecules and do not require the tedious titration of reagents into a sample. To determine the titratable acidity, an excess of 2-methylimidazole (2MI) is added to a sample and the quantity of protons absorbed by 2MI is determined from its ¹H chemical shifts. The titratable alkalinity of a sample can be similarly determined using acetic acid. To determine the concentration of deprotonated carboxylates, a sample is acidified with HCl, and the quantity of H⁺ absorbed is determined from the ¹H chemical shift of methylphosphonic acid. We validate our methods by demonstrating the measurement of the acidity of fruit-flavored drinks, the alkalinity of tap water, and the carboxylate content of nanocellulose dispersions.

Carbon dots with pH-responsive fluorescence: a review on synthesis and cell biological applications

This review summarizes state of the art synthesis and applications of carbon dots (CDs) with pH-responsive fluorescence. Following an introduction, the first section covers methods for the preparation of pH-responsive CDs, with subsections on general methods for preparing CDs (by hydrothermal, solvothermal, electrochemical, microwave, laser ablation, pyrolysis or chemical oxidation polymerization methods), and on precursors for synthesis. This is followed by a section on the mechanisms of pH-responsivity (by creating new functional groups, change of energy levels, protonation and deprotonation, aggregation, or by introduction shells). Several Tables are presented that give an overview of the wealth of methods and materials. A final section covers applications of carbon dots (CDs) with pH-responsive fluorescence for sensing, drug delivery, and imaging. The conclusion summarizes the current status, addresses challenges, and gives an outlook on potential future trends. Graphical abstract The synthesis and biological applications of carbon dots(CDs) with pH-responsive fluorescence are summarized. Precursors and methods for preparation of pH-responsive CDs, mechanisms of pH-responsivity, and biological applications of CDs with pH-responsive fluorescence for sensing, drug delivery, and imaging are discussed.

pH detection in biological samples by 1D and 2D 1H-31P NMR

The chemical shifts of several important endogenous phosphorus compounds under different pH conditions were explored, including adenosine-5'-triphosphate, adenosine-5'-diphosphate, adenosine-5'-monophosphate, phosphorylcholine and phosphorylethanolamine. Their ³¹P NMR and ¹H NMR chemical shifts were all pH-sensitive in the similar pH range. Two dimensional (2D) ¹H-³¹P NMR spectra were found helpful to identify these endogenous phosphorus markers in biological samples from rather complicated NMR spectra. Herein, for the first time, a pH sensor based on 2D ¹H-³¹P NMR was established and applied to biological samples analysis with pH values determined in good agreement with those by potentiometric method. Apart from being simple, green, rapid and less sample-consuming, information concerning both the endogenous phosphorus markers and pH status could be attained in a single NMR run, which demonstrated the great potential of this method in rare sample analysis and even disease diagnosis.

Metabolic plasticity in CLL: adaptation to the hypoxic niche

Metabolic transformation in cancer is increasingly well understood. However, little is known about the metabolic responses of cancer cells that permit their survival in different microenvironments. We have used a nuclear magnetic resonance based approach to monitor metabolism in living primary chronic lymphoid leukemia (CLL) cells and to interrogate their real-time metabolic responses to hypoxia. Our studies demonstrate considerable metabolic plasticity in CLL cells. Despite being in oxygenated blood, circulating CLL cells are primed for hypoxia as measured by constitutively low level hypoxia-inducible factor (HIF-1α) activity and modest lactate production from glycolysis. Upon entry to hypoxia we observed rapid upregulation of metabolic rates. CLL cells that had adapted to hypoxia returned to the 'primed' state when re-oxygenated and again showed the same adaptive response upon secondary exposure to hypoxia. We also observed HIF-1α independent differential utilization of pyruvate in oxygenated and hypoxic conditions. When oxygenated, CLL cells released pyruvate, but in hypoxia imported pyruvate to protect against hypoxia-associated oxidative stress. Finally, we identified a marked association of slower resting glucose and glutamine consumption, and lower alanine and lactate production with Binet A0 stage samples indicating that CLL may be divided into tumors with higher and lower metabolic states that reflect disease stage.

A low cytotoxic and ratiometric fluorescent nanosensor based on carbon-dots for intracellular pH sensing and mapping

Intracellular pH plays a critical role in the function of cells, and its regulation is essential for most cellular processes. In this study, we demonstrate a fluorescence resonance energy transfer (FRET)-based ratiometric pH nanosensor with carbon-dot (CD) as the carrier. The sensor was prepared by covalently linking a pH-sensitive fluorescent dye (fluorescein isothiocyanate, FITC) onto carbon-dot. As the FRET donor, the carbon-dot exhibits bright fluorescence emission as well as λex-dependent photoluminescence emission, and a suitable excitation wavelength for the donor (CD) can be chosen to match the energy acceptor (fluorescein moiety). The fluorescein moieties on a CD undergo structural and spectral conversion as the pH changes, affording the nanoplatform a FRET-based pH sensor. The CD-based system exhibits a significant change in fluorescence intensity ratio between pH 4 and 8 with a pKa value of 5.69. It also displays excellent water dispersibility, good spectral reversibility, satisfactory cell permeability and low cytotoxicity. Following the living cell uptake, this nanoplatform with dual-chromatic emissions can facilitate real-time visualization of the pH evolution involved in the endocytic pathway of the nanosensor. This reversible and low cytotoxic fluorescent nanoplatform may be highly valuable in a variety of biological studies, such as endocytic trafficking, endosome/lysosome maturation, and pH regulation in subcellular organelles.

Citron and lemon under the lens of HR-MAS NMR spectroscopy

High Resolution Magic Angle Spinning (HR-MAS) is an NMR technique that can be applied to semi-solid samples. Flavedo, albedo, pulp, seeds, and oil gland content of lemon and citron were studied through HR-MAS NMR spectroscopy, which was used directly on intact tissue specimens without any physicochemical manipulation. HR-MAS NMR proved to be a very suitable technique for detecting terpenes, sugars, organic acids, aminoacids and osmolites. It is valuable in observing changes in sugars, principal organic acids (mainly citric and malic) and ethanol contents of pulp specimens and this strongly point to its use to follow fruit ripening, or commercial assessment of fruit maturity. HR-MAS NMR was also used to derive the molar percentage of fatty acid components of lipids in seeds, which can change depending on the Citrus species and varieties. Finally, this technique was employed to elucidate the metabolic profile of mold flavedo.

Effect of a peat humic acid on morphogenesis in leaf explants of Pyrus communis and Cydonia oblonga . Metabolomic analysis at an early stage of regeneration

Plant regeneration is a critical step in most in vitro breeding techniques. This paper studies the effects of a low-molecular-weight humic acid (HA) on morphogenesis from pear and quince leaf explants. Variable HA amounts [0 (control), 1, 5, 10, and 20 mg C L(-1)] were added to the regeneration media. A dose-response effect was observed in pear for root and shoot production; it was improved at HA 1 mg C L(-1) and considerably reduced at the highest amounts. HA was, instead, ineffective in quince. The (1)H HR-MAS NMR analyses of calli in the induction phase showed more evident metabolite (asparagine, alanine, and γ-aminobutyric acid) signals in quince than in pear. The assignment of overlapped signals in both genotypes was supported by the 2D NMR analyses. Spectroscopic characterization suggested also an enhancement of asparagine contents in morphogenic calli of pear with respect to the control and higher HA amount treatments.

The kinetics of thiol-mediated decomposition of S-nitrosothiols

The reaction of sulfhydryl (SH)-containing molecules (thiols) with S-nitrosothiols (RSNO) has been shown to be of biological importance. Biologically or therapeutically relevant thiols generally have a pKa value ranging from 8 to 10 for the SH group. In addition, some of these thiols contain a carboxyl group and are acidic, which should be considered in studying the reaction between RSNO and thiols. In the present study, the kinetics of thiol-mediated decomposition of RSNO was investigated in a commonly used phosphate buffer, phosphate buffered saline (PBS; containing 6.9 mM phosphates; buffer capacity = 3.8 mM/pH). The thiols studied can be divided into 2 groups, depending on their pH perturbation capacity. The kinetics was studied using a wide range of thiol concentrations (ie, from 0.1 to 10 mM). A high-performance liquid chromatography (HPLC) method was used to determine RSNO concentrations. The results showed that the acidic thiols, including glutathione, captopril, N-acetylcysteine, and tiopronin, stimulated RSNO decomposition at low millimolar concentrations up to 2 mM. The stimulatory effect, however, became attenuated at concentrations higher than 2 mM in PBS. Increasing the concentration of acidic thiols caused a decrease in solution pH, which was attributable to the inhibitory effect at high thiol concentrations. The effect of thiols on the pH of reaction solution, and the resulting bell-shaped rate profiles, can be predicted by a quantitative analysis, from which a comparison of the intrinsic reactivity toward RSNO, among 8 thiols, was possible. The intrinsic reactivity in general followed the Brønsted relation.

Microscopic images of intraspheroidal pH by 1H magnetic resonance chemical shift imaging of pH sensitive indicators

OBJECTIVE

We investigate microscopic pH heterogeneity within tumor spheroids using a novel 1H NMR methodology that provides high resolution measurements of intraspheroidal pH.

MATERIAL AND METHODS

High resolution microscopic images of intraspheroidal pH were obtained by 1H NMR using chemical shift selective excitation of the H2 resonance of imidazole added to the incubation medium. Imidazole accumulated in the intraspheroidal space in a pH dependent manner. Maps of intraspheroidal pH could be obtained by transforming pixel by pixel (32 x 32 micro) the regional variation of imidazole H2 intensity into a relative pH scale.

RESULTS

Our analysis revealed drastic intraspheroidal pH alterations depending on the size of the spheroid, ca. 0.6 pH units more acidic in the necrotic core than in the periphery, for spheroids of 600 mum diameter. The presence of concentric regions having similar intraspheroidal pH was consistently observed. The thickness of these regions decreased from pH 7.2 to pH 6.8 and increased below the latter pH value.

CONCLUSION

Our observations are compatible with the general model of spheroid growth where the more external layers of cells are in active growth and depict more alkaline pH values while the inner layers remain quiescent or evolve to a necrotic core, depicting more acidic pH values.

Detection of intracellular lactate with localized diffusion {1H-13C}-spectroscopy in rat glioma in vivo

The aim of this study was to compare the diffusion characteristic of lactate and alanine in a brain tumor model to that of normal brain metabolites known to be mainly intracellular such as N-acetylaspartate or creatine. The diffusion of (13)C-labeled metabolites was measured in vivo with localized NMR spectroscopy at 9.4 T (400 MHz) using a previously described localization and editing pulse sequence known as ACED-STEAM ('adiabatic carbon editing and decoupling'). (13)C-labeled glucose was administered and the apparent diffusion coefficients of the glycolytic products, {(1)H-(13)C}-lactate and {(1)H-(13)C}-alanine, were determined in rat intracerebral 9L glioma. To obtain insights into {(1)H-(13)C}-lactate compartmentation (intra- versus extracellular), the pulse sequence used very large diffusion weighting (50 ms/microm(2)). Multi-exponential diffusion attenuation of the lactate metabolite signals was observed. The persistence of a lactate signal at very large diffusion weighting provided direct experimental evidence of significant intracellular lactate concentration. To investigate the spatial distribution of lactate and other metabolites, (1)H spectroscopic images were also acquired. Lactate and choline-containing compounds were consistently elevated in tumor tissue, but not in necrotic regions and surrounding normal-appearing brain. Overall, these findings suggest that lactate is mainly associated with tumor tissue and that within the time-frame of these experiments at least some of the glycolytic product ([(13)C] lactate) originates from an intracellular compartment.

In vivo magnetic resonance spectroscopy in cancer

Magnetic resonance spectroscopy (MRS) has been used for more than two decades to interrogate metabolite distributions in living cells and tissues. Techniques have been developed that allow multiple spectra to be obtained simultaneously with individual volume elements as small as 1 uL of tissue (i.e., 1 x 1 x 1 mm(3)). The most common modern applications of in vivo MRS use endogenous signals from (1)H, (31)P, or (23)Na. Important contributions have also been made using exogenous compounds containing (19)F, (13)C, or (17)O. MRS has been used to investigate cardiac and skeletal muscle energetics, neurobiology, and cancer. This review focuses on the latter applications, with specific reference to the measurement of tissue choline, which has proven to be a tumor biomarker that is significantly affected by anticancer therapies.