Quantifying pH in Malaria Using pHluorin and Flow Cytometry

Intracellular pH (pH_i) plays a critical role in the regulation of numerous biological functions where specific pH ranges are required for optimal operation within cells. Slight pH changes can impact the regulation of diverse molecular processes, including enzymatic activities, ion channels, and transporters, which all play a role in cell functions. Methods for quantifying pH_i continue to evolve and include various optical methods using fluorescent pH indicators. Here, we provide a protocol to measure pH_i in the cytosol of Plasmodium falciparum blood stage parasites by means of flow cytometry and using pHluorin2, a pH-sensitive fluorescent protein that has been introduced into the genome of the parasite.

Encoding capability prediction of acquisition schedules in CEST MR fingerprinting for pH quantification

PURPOSE

To identify a reliable metric for predicting the encoding capability of CEST MR fingerprinting acquisition schedules for pH quantification, which may facilitate CEST MR fingerprinting protocol optimization.

METHODS

Numerical simulations and Cr phantom MRI experiments were conducted at 3 Tesla under representative CEST MR fingerprinting sampling scenarios, including the pseudorandomization of imaging parameters (e.g., saturation power B₁ , saturation frequency offset, saturation time, and relaxation time), and variation of the maximum saturation power B_1max , B₁ number, and sampling pattern. The CEST effect at 2 ppm was measured using asymmetry analysis and matched to a predefined dictionary to determine the pH. The pH quantification error was assessed using RMSE. Three metrics, namely the Cramer-Rao bound, dot product, and Euclidean distance, were calculated for each sampling scenario, and their relationships with the pH RMSE were investigated to examine their effectiveness for predicting the encoding capability of sampling schedules for pH quantification.

RESULTS

Both simulation and phantom studies revealed that the Cramer-Rao bound metric consistently exhibited superior performance for predicting the pH quantification error. Although dot product exhibited good encoding capability prediction in most sampling scenarios, it failed in the scenario with varied B₁ numbers. In contrast, Euclidean distance exhibited the worst performance among the 3 metrics in all scenarios.

CONCLUSION

Superior over dot product and Euclidean distance, the Cramer-Rao bound metric may reliably predicting the encoding capability of CEST MR fingerprinting sampling strategies and may be useful for guiding CEST MRI protocol optimization.

A DNA-Based MRI Contrast Agent for Quantitative pH Measurement

Extracellular pH is important in clinical measurements due to its correlation to cell metabolism and disease progression. In MRI, T₁/T₂ ratiometric analysis and other methods have been previously applied to quantify pH using conventional pulse sequences. However, for nanoparticle-based approaches, heterogeneity in size and surface functionalization tends toward qualitative rather than quantitative results. To address this limitation, we developed a novel DNA-based MRI contrast agent, pH-DMRCA, which utilizes a highly programmable and reproducible nanostructure. The pH-DMRCA is a dendritic DNA scaffold that is functionalized with a pH-responsive MRI-sensitive construct, Gd(NP-DO3A), at the end of each DNA arm. We first evaluated the r₁ and r₂ response of our pH-DMRCA over a range of pH values (pH = 5-9) to establish a relaxometric model of pH. These MRI-based assessments of pH were validated in a separate set of samples using a pH electrode (n = 18) and resulted in a good linear correlation (R² = 0.99, slope = 0.98, intercept = 0). A Bland-Altman analysis of the results also showed reasonable agreement between the calculated pH and measured pH. Moreover, these pH comparisons were consistent across three different pH-DMRCA concentrations, demonstrating concentration-independence of the method. This MRI-based pH quantification methodology was further verified in human blood plasma. Given the versatility of the DNA-based nanostructures, the contrast agent has a potential to be applied to a wide variety of imaging applications where extracellular pH is important including cancer, stroke, cardiovascular disease, and other important diseases.

Vacuolar ATPase in phago(lyso)some biology

Many eukaryotic cells ingest extracellular particles in a process termed phagocytosis which entails the generation of a new intracellular compartment, the phagosome. Phagosomes change their composition over time and this maturation process culminates in their fusion with acidic, hydrolase-rich lysosomes. During the maturation process, degradation and, when applicable, killing of the cargo may ensue. Many of the events that are pathologically relevant depend on strong acidification of phagosomes by the 'vacuolar' ATPase (V-ATPase). This protein complex acidifies the lumen of some intracellular compartments at the expense of ATP hydrolysis. We discuss here the roles and importance of V-ATPase in intracellular trafficking, its distribution, inhibition and activities, its role in the defense against microorganisms and the counteractivities of pathogens.