INDIANA: An in-cell diffusion method to characterize the size, abundance and permeability of cells

Molecular Imaging with Aquaporin-Based Reporter Genes: Quantitative Considerations from Monte Carlo Diffusion Simulations

Aquaporins provide a unique approach for imaging genetic activity in deep tissues by increasing the rate of cellular water diffusion, which generates a magnetic resonance contrast. However, distinguishing aquaporin signals from the tissue background is challenging because water diffusion is influenced by structural factors, such as cell size and packing density. Here, we developed a Monte Carlo model to analyze how cell radius and intracellular volume fraction quantitatively affect aquaporin signals. We demonstrated that a differential imaging approach based on subtracting signals at two diffusion times can improve specificity by unambiguously isolating aquaporin signals from the tissue background. We further used Monte Carlo simulations to analyze the connection between diffusivity and the percentage of cells engineered to express aquaporin and established a mapping that accurately determined the volume fraction of aquaporin-expressing cells in mixed populations. The quantitative framework developed in this study will enable a broad range of applications in biomedical synthetic biology, requiring the use of aquaporins to noninvasively monitor the location and function of genetically engineered devices in live animals.

Molecular imaging with aquaporin-based reporter genes: quantitative considerations from Monte Carlo diffusion simulations

Aquaporins provide a new class of genetic tools for imaging molecular activity in deep tissues by increasing the rate of cellular water diffusion, which generates magnetic resonance contrast. However, distinguishing aquaporin contrast from the tissue background is challenging because water diffusion is also influenced by structural factors such as cell size and packing density. Here, we developed and experimentally validated a Monte Carlo model to analyze how cell radius and intracellular volume fraction quantitatively affect aquaporin signals. We demonstrated that a differential imaging approach based on time-dependent changes in diffusivity can improve specificity by unambiguously isolating aquaporin-driven contrast from the tissue background. Finally, we used Monte Carlo simulations to analyze the connection between diffusivity and the percentage of cells engineered to express aquaporin, and established a simple mapping that accurately determined the volume fraction of aquaporin-expressing cells in mixed populations. This study creates a framework for broad applications of aquaporins, particularly in biomedicine and in vivo synthetic biology, where quantitative methods to measure the location and performance of genetic devices in whole vertebrates are necessary.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Cell-permeable lanthanide-platinum(IV) anti-cancer prodrugs

Platinum compounds are a vital part of our anti-cancer arsenal, and determining the location and speciation of platinum compounds is crucial. We have synthesised a lanthanide complex bearing a salicylic group (Ln = Gd, Eu) which demonstrates excellent cellular accumulation and minimal cytotoxicity. Derivatisation enabled access to bimetallic lanthanide-platinum(ii) and lanthanide-platinum(iv) complexes. Luminescence from the europium-platinum(iv) system was quenched, and reduction to platinum(ii) with ascorbic acid resulted in a "switch-on" luminescence enhancement. We used diffusion-based 1H NMR spectroscopic methods to quantify cellular accumulation. The gadolinium-platinum(ii) and gadolinium-platinum(iv) complexes demonstrated appreciable cytotoxicity. A longer delay following incubation before cytotoxicity was observed for the gadolinium-platinum(iv) compared to the gadolinium-platinum(ii) complex. Functionalisation with octanoate ligands resulted in enhanced cellular accumulation and an even greater latency in cytotoxicity.

A single-shot measurement of time-dependent diffusion over sub-millisecond timescales using static field gradient NMR

Time-dependent diffusion behavior is probed over sub-millisecond timescales in a single shot using a nuclear magnetic resonance static gradient time-incremented echo train acquisition (SG-TIETA) framework. The method extends the Carr-Purcell-Meiboom-Gill cycle under a static field gradient by discretely incrementing the π-pulse spacings to simultaneously avoid off-resonance effects and probe a range of timescales (50-500 µs). Pulse spacings are optimized based on a derived ruleset. The remaining effects of pulse inaccuracy are examined and found to be consistent across pure liquids of different diffusivities: water, decane, and octanol-1. A pulse accuracy correction is developed. Instantaneous diffusivity, Dinst(t), curves (i.e., half of the time derivative of the mean-squared displacement in the gradient direction) are recovered from pulse accuracy-corrected SG-TIETA decays using a model-free log-linear least squares inversion method validated by Monte Carlo simulations. A signal-averaged 1-min experiment is described. A flat Dinst(t) is measured on pure dodecamethylcyclohexasiloxane, whereas decreasing Dinst(t) is measured on yeast suspensions, consistent with the expected short-time Dinst(t) behavior for confining microstructural barriers on the order of micrometers.

Constant gradient FEXSY: A time-efficient method for measuring exchange

Filter-Exchange NMR Spectroscopy (FEXSY) is a method for measurement of apparent transmembranal water exchange rates. The experiment is comprised of two co-linear sequential pulsed-field gradient (PFG) blocks, separated by a mixing period in which exchange takes place. The first block remains constant and serves as a diffusion-based filter that removes signal coming from fast-diffusing water. The mixing time and the gradient area (q-value) of the second block are varied on repeated iterations to produce a 2D data set that is analyzed using a bi-compartmental model which assumes that intra- and extra-cellular water are slow and fast diffusing, respectively. Here we suggest a variant of the FEXSY method in which measurements for different mixing times are taken at a constant gradient. This Constant Gradient FEXSY (CG-FEXSY) allows for the determination of the exchange rate by using a smaller 1D data set, so that the same information can be gathered during a considerably shorter scan time. Furthermore, in the limit of high diffusion weighting, such that the extra-cellular water signal is removed while the intra-cellular signal is retained, CG-FEXSY also allows for determination of the intra-cellular mean residence time (MRT). The theoretical results are validated on a living yeast cells sample and on a fixed porcine optic nerve, where the values obtained from the two methods are shown to be in agreement.