Intracellular Diffusion Research Articles

MODL-39. CHARACTERIZING NON-ENHANCING TUMOR USING MULTI-SHELL DIFFUSION MRI

Abstract Characterizing infiltration in the non-enhancing tumor (NET) is clinically crucial as infiltration leads to progression, and a reduction in survival times. As voxel-wise biopsy of these regions is infeasible, a non-invasive MRI-based identification of infiltration would be a significant contribution. Diffusion MRI (dMRI), with its ability to model different levels of water restriction, as is caused by infiltration and edema, is well positioned to model the NET. This is achieved via multicomparment modeling (MCM) of the dMRI where infiltration, vasogenic edema and healthy tissue (with complex fibers) form the different compartments. Current MCM approaches are either not designed for NET or rely on advanced MRI scans currently not feasible in the clinic. The simplest ball-tensor models, including Hoy 2014 using multi-shell data and FERNET 2020 for single-shell data, consists of a free water compartment that models vasogenic edema and a tensor modeling underlying tissue. These single-tensor methods cannot model complex WM fibers. Our proposed model consists of two steps. First, two bundles are fit: an isotropic bundle with two balls that model isotropic free diffusivity and restricted diffusivity, and a bundle containing stick and zeppelin, corresponding to intra-cellular and extra-cellular diffusion of axons, respectively. Next, a fiber orientation distribution (FOD) is estimated from the fitted parameters. We applied our modeling to multi-shell data from eight patients with glioblastoma, and one patient with a metastatic brain tumor. Our method produces maps corresponding to free water (CSF), restricted diffusion, intra-cellular, and extra-cellular volume fractions. Preliminary results show that restricted diffusivity map of NET comprises 46% of vasogenic metastatic edema compare to 15% of infiltrated GBM edema. In conclusion, we demonstrate that our proposed model shows promise to characterize the NET region of various brain tumors, and distinguishing tumor types. These compartments will provide invaluable radiomic features that no other modality can capture.

Pituitary Macroadenoma – Evaluation of Mean Metabolic Ratios and Mean and Normalized Apparent Diffusion Coefficient Values Using Magnetic Resonance Spectroscopy and Diffusion-weighted Imaging in a Central Indian Rural Hospital Setup

Background: MRS and disregard MRI spectroscopy offers the capability of using magnetic resonance imaning (MRI) to noninvasively study tissue biochemistry. MRS is noninvasive technique that is used to study metabolic variance in brain tumors. Furthermore, diffusion-weighted imaging depicts the degree of water molecules diffusing across the unit volume of the region of interest as a result of sophisticated and dedicated software packages. Differences in apparent diffusion coefficient (ADC) values are related to changes in cellularity, cell membrane permeability, intracellular and extracellular diffusion, and tissue structure. Diffusion-weighted MRI is a powerful tool in the characterization of brain neoplasms. The present study attempts to derive the mean metabolite ratios as well as mean values of ADC with normalization in the setting of pituitary macroadenoma. Aim: (1) To evaluate mean metabolic ratios in pituitary macroadenomas using magnetic resonance spectroscopy (MRS) in rural hospital setup in Central India, (2) To evaluate mean apparent diffusion coefficient value with normalization in pituitary macroadenoma using magnetic resonance spectroscopy in a rural hospital setup in Central India. Materials and Methods: A cross-sectional hospital-based observational study conducted over 2 years. All cases registered with Acharya Vinoba Bhave Rural Hospital Sawangi, Wardha, diagnosed as pituitary macroadenomas were included in the present study. All patients were examined on GE Brivo MRI machine with 1.5 Tesla magnetic field strength in the Department of Radiodiagnosis. Diagnostic acumen was augmented with radiological features of brain tumors with metabolic ratios derived from metabolic values and ADC values. Results: Out of 142 patients included, pituitary macroadenoma cases were 18 in number. Observed metabolite ratios were derived from metabolic values obtained on MRS for choline (Cho), creatinine (Cr), lipid lactate, myoinositol, and n-acetyl aspartate (NAA). Ratios were calculated for Cho: Cr, Cho: NAA, Cho: myoinositol and Cho: lipid lactate. The range for Cho: Cr, Cho: NAA, Cho: myoinositol, and Cho: lipid lactate was 1.04–4.73, 0.96–4.12, 1.21–3.12, and 0.72–1.812, respectively. The mean values for Cho: Cr, Cho: NAA, Cho: myoinositol, and Cho: lipid lactate were 1.8655, 1.6094, 1.5561, and 1.4567, respectively. The range of ADC values observed was from 0.821 × 10−3 mm2/s to 1.523 × 10−3 mm2/s. Normalized ADC values were calculated on basis of observed ADC values in the numerator and the average ADC value of gray matter in the denominator which is taken as 0.8 and was in the range of 1.02625 × 10−3 mm2/s to 1.90375 × 10−3 mm2/s. The mean ADC value was calculated as 1.22 × 10−3 mm2/s. The mean normalized ADC value was calculated as 1.52 × 10−3 mm2/s. Conclusion: The research gap analysis toward which research question was framed stands filled up by generated new knowledge in terms of “mean metabolic ratios” and “ADC” values with reference to pituitary macroadenomas in the present study.

White matter microstructure shows sex differences in late childhood: Evidence from 6797 children.

Sex differences in white matter microstructure have been robustly demonstrated in the adult brain using both conventional and advanced diffusion-weighted magnetic resonance imaging approaches. However, sex differences in white matter microstructure prior to adulthood remain poorly understood; previous developmental work focused on conventional microstructure metrics and yielded mixed results. Here, we rigorously characterized sex differences in white matter microstructure among over 6000 children from the Adolescent Brain Cognitive Development study who were between 9 and 10 years old. Microstructure was quantified using both the conventional model-diffusion tensor imaging (DTI)-and an advanced model, restriction spectrum imaging (RSI). DTI metrics included fractional anisotropy (FA) and mean, axial, and radial diffusivity (MD, AD, RD). RSI metrics included normalized isotropic, directional, and total intracellular diffusion (N0, ND, NT). We found significant and replicable sex differences in DTI or RSI microstructure metrics in every white matter region examined across the brain. Sex differences in FA were regionally specific. Across white matter regions, boys exhibited greater MD, AD, and RD than girls, on average. Girls displayed increased N0, ND, and NT compared to boys, on average, suggesting greater cell and neurite density in girls. Together, these robust and replicable findings provide an important foundation for understanding sex differences in health and disease.

Intraoperative lesion characterization after focused ultrasound thalamotomy.

Outcomes after focused ultrasound ablation (FUSA) for essential tremor remain heterogeneous, despite therapeutic promise. Clinical outcomes are directly related to the volume and location of the therapeutic lesions, consistent with CNS ablative therapies. Recent data demonstrate that postoperative diffusion MRI, specifically the quantification of intracellular diffusion by restricted diffusion imaging (RDI), can accurately characterize focused ultrasound lesions. However, it is unclear whether RDI can reliably detect focused ultrasound lesions intraoperatively (i.e., within a few minutes of lesioning) and whether the intraoperative lesions predict delayed clinical outcomes. An intraoperative imaging protocol was implemented that included RDI and T2-weighted imaging in addition to intraoperative MR thermography. Lesion characteristics were defined with each sequence and then compared. An imaging-outcomes analysis was performed to determine lesion characteristics associated with delayed clinical outcomes. Intraoperative RDI accurately identified the volume and location of focused ultrasound lesions. Intraoperative T2-weighted imaging underestimated the lesion volume but accurately identified the location. Intraoperative RDI revealed that lesions of the ventral border of the ventral intermediate nucleus were significantly associated with postoperative tremor improvement. In contrast, the lesions extending into the inferolateral white matter were associated with postoperative ataxia. These data support the acquisition of intraoperative RDI to characterize focused ultrasound lesions. Future research should test the histological correlates of intraoperative RDI and test whether it can be developed as feedback to optimize the current technique of FUSA.

Temporal and spatial summation of laser heat stimuli in cultured nociceptive neurons of the rat

We studied the efficacy of a near-infrared laser (1475 nm) to activate rat dorsal root ganglion (DRG) neurons with short punctate radiant heat pulses (55 µm diameter) and investigated temporal and spatial summation properties for the transduction process for noxious heat at a subcellular level. Strength-duration curves (10–80 ms range) indicated a minimum power of 30.2mW for the induction of laser-induced calcium transients and a chronaxia of 13.9 ms. However, threshold energy increased with increasing stimulus duration suggesting substantial radial cooling of the laser spot. Increasing stimulus duration demonstrated suprathreshold intensity coding of calcium transients with less than linear gains (Stevens exponents 0.29/35mW, 0.38/60mW, 0.46/70mW). The competitive TRPV1 antagonist capsazepine blocked responses to short near-threshold stimuli and significantly reduced responses to longer duration suprathreshold heat. Heating 1/3 of the soma of a neuron was sufficient to induce calcium transients significantly above baseline (p < 0.05), but maximum amplitude was only achieved by centering the laser over the entire neuron. Heat-induced calcium increase was highest in heated cell parts but rapidly reached unstimulated areas reminiscent of spreading depolarization and opening of voltage-gated calcium channels. Full intracellular equilibrium took about 3 s, consistent with a diffusion process. In summary, we investigated transduction mechanisms for noxious laser heat pulses in native sensory neurons at milliseconds temporal and subcellular spatial resolution and characterized strength duration properties, intensity coding, and spatial summation within single neurons. Thermal excitation of parts of a nociceptor spread via both membrane depolarization and intracellular calcium diffusion.

Rat Brain Global Ischemia-Induced Diffusion Changes Revisited: Biophysical Modeling of the Water and NAA MR "Diffusion Signal".

To assess changes in intracellular diffusion as a mechanism for the reduction in water ADC that accompanies brain injury. Using NAA as a marker of neuronal cytoplasmic diffusion, NAA diffusion was measured before and after global ischemia (immediately postmortem) in the female Sprague-Dawley rat. Diffusion-weighted PRESS spectra, with diffusion encoding in a single direction, were acquired from large voxels of rat brain gray matter in vivo and postischemia employing either pairs of pulsed half-sine-shaped gradients (in vivo and postischemia, bmax = 19 ms/μm2 ) or sinusoidal oscillating gradients (in vivo only) with frequencies of 99.2-250 Hz. A 2D randomly oriented cylinder (neurite) model gave estimates of longitudinal and transverse diffusivities (DL and DT , respectively). In this model, DL represents the "free" diffusivity of NAA, whereas DT reflects highly restricted diffusion. Using oscillating gradients, the frequency dependence of DT [DT (ω)] gave estimates of the cylinder (axon/dendrite) radius. A 10% decrease in DL,NAA followed global ischemia, dropping from 0.391 ± 0.012μm2 /ms to 0.350 ± 0.009μm2 /ms. Modeling DT,NAA (ω) provided an estimate of the neurite radius of 1.0± 0.6μm. Whereas the increase in apparent intraneuronal viscosity suggested by changes in DL,NAA may contribute to the overall reduction in water ADC associated with brain injury, it is not sufficient to be the sole explanation. Estimates of neurite radius based on DT (ω) were consistent with literature values.

Narrow capture problem: An encounter-based approach to partially reactive targets.

A general topic of current interest is the analysis of diffusion problems in singularly perturbed domains with small interior targets or traps (the narrow capture problem). One major application is to intracellular diffusion, where the targets typically represent some form of reactive biochemical substrate. Most studies of the narrow capture problem treat the target boundaries as totally absorbing (Dirichlet), that is, the chemical reaction occurs immediately on first encounter between particle and target surface. In this paper, we analyze the three-dimensional narrow capture problem in the more realistic case of partially reactive target boundaries. We begin by considering classical Robin boundary conditions. Matching inner and outer solutions of the single-particle probability density, we derive an asymptotic expansion of the Laplace transformed flux into each reactive surface in powers of ε, where ερ is a given target size. In turn, the fluxes determine the splitting probabilities for target absorption. We then extend our analysis to more general types of reactive targets by combining matched asymptotic analysis with an encounter-based formulation of diffusion-mediated surface reactions. That is, we derive an asymptotic expansion of the joint probability density for particle position and the so-called boundary local time, which characterizes the amount of time that a Brownian particle spends in the neighborhood of a point on a totally reflecting boundary. The effects of surface reactions are then incorporated via an appropriate stopping condition for the boundary local time. Robin boundary conditions are recovered in the special case of an exponential law for the stopping local times. Finally, we illustrate the theory by exploring how the leading-order contributions to the splitting probabilities depend on the choice of surface reactions. In particular, we show that there is an effective renormalization of the target radius of the form ρ→ρ-Ψ[over ̃](1/ρ), where Ψ[over ̃] is the Laplace transform of the stopping local time distribution.

Local accumulation time for diffusion in cells with gap junction coupling.

In this paper we analyze the relaxation to steady state of intracellular diffusion in a pair of cells with gap-junction coupling. Gap junctions are prevalent in most animal organs and tissues, providing a direct diffusion pathway for both electrical and chemical communication between cells. Most analytical models of gap junctions focus on the steady-state diffusive flux and the associated effective diffusivity. Here we investigate the relaxation to steady state in terms of the so-called local accumulation time. The latter is commonly used to estimate the time to form a protein concentration gradient during morphogenesis. The basic idea is to treat the fractional deviation from the steady-state concentration as a cumulative distribution for the local accumulation time. One of the useful features of the local accumulation time is that it takes into account the fact that different spatial regions can relax at different rates. We consider both static and dynamic gap junction models. The former treats the gap junction as a resistive channel with effective permeability μ, whereas the latter represents the gap junction as a stochastic gate that randomly switches between an open and closed state. The local accumulation time is calculated by solving the diffusion equationin Laplace space and then taking the small-s limit. We show that the accumulation time is a monotonically increasing function of spatial position, with a jump discontinuity at the gap junction. This discontinuity vanishes in the limit μ→∞ for a static junction and β→0 for a stochastically gated junction, where β is the rate at which the gate closes. Finally, our results are generalized to the case of a linear array of cells with nearest-neighbor gap junction coupling.

Accumulation time of diffusion in a two-dimensional singularly perturbed domain

A general problem of current interest is the analysis of diffusion problems in singularly perturbed domains, within which small subdomains are removed from the domain interior and boundary conditions imposed on the resulting holes. One major application is to intracellular diffusion, where the holes could represent organelles or biochemical substrates. In this paper, we use a combination of matched asymptotic analysis and Green’s function methods to calculate the so-called accumulation time for relaxation to steady state. The standard measure of the relaxation rate is in terms of the principal non-zero eigenvalue of the negative Laplacian. However, this global measure does not account for possible differences in the relaxation rate at different spatial locations, is independent of the initial conditions, and relies on the assumption that the eigenvalues have sufficiently large spectral gaps. As previously established for diffusion-based morphogen gradient formation, the accumulation time provides a better measure of the relaxation process.

Multi-Contrast Magnetic Resonance Imaging of Visual White Matter Pathways in Patients With Glaucoma.

PurposeGlaucoma is a disorder that involves visual field loss caused by retinal ganglion cell damage. Previous diffusion magnetic resonance imaging (dMRI) studies have demonstrated that retinal ganglion cell damage affects tissues in the optic tract (OT) and optic radiation (OR). However, because previous studies have used a simple diffusion tensor model to analyze dMRI data, the microstructural interpretation of white matter tissue changes remains uncertain. In this study, we used a multi-contrast MRI approach to further clarify the type of microstructural damage that occurs in patients with glaucoma.MethodsWe collected dMRI data from 17 patients with glaucoma and 30 controls using 3-tesla (3T) MRI. Using the dMRI data, we estimated three types of tissue property metrics: intracellular volume fraction (ICVF), orientation dispersion index (ODI), and isotropic volume fraction (IsoV). Quantitative T1 (qT1) data, which may be relatively specific to myelin, were collected from all subjects.ResultsIn the OT, all four metrics showed significant differences between the glaucoma and control groups. In the OR, only the ICVF showed significant between-group differences. ICVF was significantly correlated with qT1 in the OR of the glaucoma group, although qT1 did not show any abnormality at the group level.ConclusionsOur results suggest that, at the group level, tissue changes in OR caused by glaucoma might be explained by axonal damage, which is reflected in the intracellular diffusion signals, rather than myelin damage. The significant correlation between ICVF and qT1 suggests that myelin damage might also occur in a smaller number of severe cases.

Transient Anomalous Diffusion MRI in Excised Mouse Spinal Cord: Comparison Among Different Diffusion Metrics and Validation With Histology.

Neural tissue is a hierarchical multiscale system with intracellular and extracellular diffusion compartments at different length scales. The normal diffusion of bulk water in tissues is not able to detect the specific features of a complex system, providing nonlocal, diffusion measurement averaged on a 10-20 μm length scale. Being able to probe tissues with sub-micrometric diffusion length and quantify new local parameters, transient anomalous diffusion (tAD) would dramatically increase the diagnostic potential of diffusion MRI (DMRI) in detecting collective and sub-micro architectural changes of human tissues due to pathological damage. In DMRI, the use of tAD parameters quantified using specific DMRI acquisition protocols and their interpretation has often aroused skepticism. Although the derived formulas may accurately fit experimental diffusion-weighted data, the relationships between the postulated dynamical feature and the underlying geometrical structure remains elusive, or at most only suggestive. This work aimed to elucidate and validate the image contrast and information that can be obtained using the tAD model in white matter (WM) through a direct comparison between different diffusion metrics and histology. Towards this goal, we compared tAD metrics extracted from pure subdiffusion (α-imaging) and super-pseudodiffusion (γ-imaging) in excised mouse spinal cord WM, together with T2 and T2* relaxometry, conventional (normal diffusion-based) diffusion tensor imaging (DTI) and q-space imaging (QSI), with morphologic measures obtained by optical microscopy, to determine which structural and topological characteristics of myelinated axons influenced tAD contrast. Axon diameter (AxDiam), the standard deviation of diameters (SDax.diam), axonal density (AxDens) and effective local density (ELD) were extracted from optical images in several WM tracts. Among all the diffusion parameters obtained at 9.4 T, γ-metrics confirmed a strong dependence on magnetic in-homogeneities quantified by R2* = 1/T2* and showed the strongest associations with AxDiam and ELD. On the other hand, α-metrics showed strong associations with SDax.diam and was significantly related to AxDens, suggesting its ability to quantify local heterogeneity degree in neural tissue. These results elucidate the biophysical mechanism underpinning tAD parameters and show the clinical potential of tAD-imaging, considering that both physiologic and pathologic neurodegeneration translate into alterations of WM morphometry and topology.

The role of NM2 rearrangement during cytokinesis

The cellular distribution of non-muscle myosin 2 (NM2) is essential for plethora of cellular movements, such as axonal growth and cytokinesis. However, it is poorly understood how the role of NM2 in the dynamics of cytokinesis is related to its intracellular distribution and the ATPase inhibition. Like in stress fibers, NM2 has a crucial role in governing the normal progression of cytokinesis via cross-linking actin filaments in the cytokinetic ring. Recently, we showed that partial inhibition of the ATPase activity of NM2 results in increased diffusion rates of NM2 in load-bearing stress fibers while complete inhibition blocks their intracellular diffusion.

Machine learning aided analysis of intracellular diffusion using FCS time series data

Machine learning aided analysis of intracellular diffusion using FCS time series data

Association of Outdoor Ambient Fine Particulate Matter With Intracellular White Matter Microstructural Properties Among Children

Outdoor particulate matter 2.5 μm or less in diameter (PM2.5) is a ubiquitous environmental neurotoxicant that may affect the developing brain. Little is known about associations between PM2.5 and white matter connectivity. To assess associations between annual residential PM2.5 exposure and white matter microstructure health in a US sample of children 9 to 10 years of age and to examine whether associations are specific to certain white matter pathways or vary across neuroimaging diffusion markers reflective of intracellular and extracellular microstructural processes. This cross-sectional study, the Adolescent Brain and Cognitive Development (ABCD) Study, was composed of 21 study sites across the US and used baseline data collected from children 9 to 10 years of age from September 1, 2016, to October 15, 2018. Data analysis was performed from September 15, 2020, to June 30, 2021. Annual mean PM2.5 exposure estimated by ensemble-based models and assigned to the primary residential addresses at baseline. Diffusion-weighted imaging (DWI) and tractography were used to delineate white matter tracts. The biophysical modeling technique of restriction spectrum imaging (RSI) was implemented to examine total hindered diffusion and restricted isotropic and anisotropic intracellular diffusion in each tract. Hierarchical mixed-effects models with natural splines were used to analyze the associations between PM2.5 exposure and DWI. In a study population of 7602 children (mean [SD] age, 119.1 [7.42] months; 3955 [52.0%] female; 160 [ 21.%] Asian, 1025 [13.5%] Black, 1616 [21.3%] Hispanic, 4025 [52.9%] White, and 774 [10.2%] other [identified by parents as American Indian/Native American or Alaska Native; Native Hawaiian, Guamanian, Samoan, other Pacific Islander; Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, or other Asian; or other race]), associations were seen between annual ambient PM2.5 and hemispheric differences in white matter microstructure. Hemisphere-stratified models revealed significant associations between PM2.5 exposure and restricted isotropic intracellular diffusion in the left cingulum, in the left superior longitudinal fasciculus, and bilaterally in the fornix and uncinate fasciculus. In tracts with strong positive associations, a PM2.5 increase from 8 to 12 μg/m3 was associated with increases of 2.16% (95% CI, 0.49%-3.84%) in the left cingulum, 1.95% (95% CI, 0.43%-3.47%) in the left uncinate, and 1.68% (95% CI, 0.01%-3.34%) in the right uncinate. Widespread negative associations were observed between PM2.5 and mean diffusivity. The findings of this cross-sectional study suggest that annual mean PM2.5 exposure during childhood is associated with increased restricted isotropic diffusion and decreased mean diffusivity of specific white matter tracts, potentially reflecting differences in the composition of white matter microarchitecture.

Cell fate determination is influenced by Notch heterogeneity.

Notch signaling (NS) determines the fate of adjacent cells during metazoans development. This intercellular signaling mechanism regulates diverse development processes like cell differentiation, proliferation, survival and is considered responsible for maintaining cellular homeostasis. In this study, we elucidate the role of Notch heterogeneity (NH) in cell fate determination. We studied the role of NH at intercellular, intracellular and the coexistence of Notch variation simultaneously at the intracellular and intercellular level in direct cell-cell signaling on an irregular cell mosaic. In addition, the effect of intracellular Notch receptor diffusion on an irregular cell lattice is also taken into account during Delta-Notch lateral inhibition (LI) process. Through mathematical and computational models, we discovered that the classical checkerboard pattern formation can be reproduced with an accuracy of 70-81% by accounting for NH in a realistic epithelial layer of multicellular organisms.

Backstage of rising body temperature: Advances in research on intracellular heat diffusion

Backstage of rising body temperature: Advances in research on intracellular heat diffusion

Neuroimaging measures of iron and gliosis explain memory performance in aging.

Evidence from animal and histological studies has indicated that accumulation of iron in the brain results in reactive gliosis that contributes to cognitive deficits. The current study extends these findings to human cognitive aging and suggests that magnetic resonance imaging (MRI) techniques like quantitative relaxometry can be used to study iron and its effects in vivo. The effects of iron on microstructure and memory performance were examined using a combination of quantitative relaxometry and multicompartment diffusion imaging in 35 young (21.06 ± 2.18 years) and 28 older (72.58 ± 6.47 years) adults, who also completed a memory task. Replicating past work, results revealed age‐related increases in iron content (R2*) and diffusion, and decreases in memory performance. Independent of age group, iron content was significantly related to restricted (intracellular) diffusion in regions with low‐moderate iron (hippocampus, caudate) and to all diffusion metrics in regions with moderate‐high iron (putamen, globus pallidus). This pattern is consistent with different stages of iron‐related gliosis, ranging from astrogliosis that may influence intracellular diffusion to microglial proliferation and increased vascular permeability that may influence all sources of diffusion. Further, hippocampal restricted diffusion was significantly related to memory performance, with a third of this effect related to iron content; consistent with the hypothesis that higher iron‐related astrogliosis in the hippocampus is associated with poorer memory performance. These results demonstrate the sensitivity of MRI to iron‐related gliosis and extend our understanding of its impact on cognition by showing that this relationship also explains individual differences in memory performance.

Assessment of the effects of mimicking tissue microstructural properties on apparent diffusion coefficient and apparent exchange rate in diffusion MRI via a series of specially designed phantoms.

Diffusion MRI provides a valuable tool for imaging tissue microstructure. However, due to the lack of related experimental methods and specially designed phantoms, no experimental study has been conducted yet to quantitatively assess the effects of membrane permeability, intracellular volume fraction (IVF), and intracellular diffusivity on the apparent diffusion coefficient (ADC) obtained from diffusion weighted imaging (DWI), and the effects of membrane permeability on the apparent exchange rate (AXR) obtained from filter exchange imaging (FEXI). A series of phantoms with three adjustable parameters was designed to mimic tissue microstructural properties including membrane permeability, IVF, and intracellular diffusivity. Quantitative experiments were conducted to assess the effects of these properties on ADC and AXR. DWI scans were performed to obtain axial and radial ADC values. FEXI scans were performed to obtain AXR values. Axial ADC values range from 1.148 μm2 /ms to 2.157 μm2 /ms, and radial ADC values range from 0.904 μm2 /ms to 2.067 μm2 /ms. Radial ADC decreased with a decrease in fiber permeability. Decreased axial and radial ADC values with increased intra-fiber volume fraction, and increased polyvinylpyrrolidone (PVP) concentration of the intra-fiber space were observed. AXR values range from 2.1 s-1 to 4.9 s-1 . AXR increases with fiber permeability. The proposed phantoms can quantitatively evaluate the effects of mimicking tissue microstructural properties on ADC and AXR. This new phantom design provides a potential method for further understanding the biophysical mechanisms underlying the change in ADC and diffusion exchange.

SPHERIOUSLY? The challenges of estimating sphere radius non-invasively in the human brain from diffusion MRI

The Soma and Neurite Density Imaging (SANDI) three-compartment model was recently proposed to disentangle cylindrical and spherical geometries, attributed to neurite and soma compartments, respectively, in brain tissue. There are some recent advances in diffusion-weighted MRI signal encoding and analysis (including the use of multiple so-called ’b-tensor’ encodings and analysing the signal in the frequency-domain) that have not yet been applied in the context of SANDI. In this work, using: (i) ultra-strong gradients; (ii) a combination of linear, planar, and spherical b-tensor encodings; and (iii) analysing the signal in the frequency domain, three main challenges to robust estimation of sphere size were identified: First, the Rician noise floor in magnitude-reconstructed data biases estimates of sphere properties in a non-uniform fashion. It may cause overestimation or underestimation of the spherical compartment size and density. This can be partly ameliorated by accounting for the noise floor in the estimation routine. Second, even when using the strongest diffusion-encoding gradient strengths available for human MRI, there is an empirical lower bound on the spherical signal fraction and radius that can be detected and estimated robustly. For the experimental setup used here, the lower bound on the sphere signal fraction was approximately 10%. We employed two different ways of establishing the lower bound for spherical radius estimates in white matter. The first, examining power-law relationships between the DW-signal and diffusion weighting in empirical data, yielded a lower bound of 7μm, while the second, pure Monte Carlo simulations, yielded a lower limit of 3μm and in this low radii domain, there is little differentiation in signal attenuation. Third, if there is sensitivity to the transverse intra-cellular diffusivity in cylindrical structures, e.g., axons and cellular projections, then trying to disentangle two diffusion-time-dependencies using one experimental parameter (i.e., change in frequency-content of the encoding waveform) makes spherical radii estimates particularly challenging. We conclude that due to the aforementioned challenges spherical radii estimates may be biased when the corresponding sphere signal fraction is low, which must be considered.

Determining the domain-level reaction-diffusion properties of an actin-binding protein transgelin-2 within cells

Proteins in cells undergo repeated binding to other molecules, thereby reducing the apparent extent of their intracellular diffusion. While much effort has been made to analytically decouple these combined effects of pure diffusion and chemical binding, it is difficult with conventional approaches to attribute the measured quantities to the nature of specific domains of the proteins. Motivated by the common goal in cell signaling research aimed at identifying the domains responsible for particular intermolecular interactions, here we describe a framework for determining the local physicochemical properties of cellular proteins associated with immobile scaffolds. To validate this new approach, we apply it to transgelin-2, an actin-binding protein whose intracellular dynamics remains elusive. We develop a fluorescence recovery after photobleaching (FRAP)-based framework, in which comprehensive combinations of domain-deletion mutants are created, and the difference among them in FRAP response is analyzed. We demonstrate that transgelin-2 in actin stress fibers (SFs) interacts with F-actin via two separate domains, and the chemical properties are determined for the individual domains. Its pure diffusion properties independent of the association to F-actin is also obtained. Our approach will thus be useful, as presented here for transgelin-2, in addressing the signaling mechanism of cellular proteins associated with SFs.