Mesoscopic Resolution Research Articles

Closed-loop fMRI at the mesoscopic scale of columns and layers: Can we do it and why would we want to?

Technological advances in fMRI including ultra-high magnetic fields (≥ 7 T) and acquisition methods that increase spatial specificity have paved the way for studies of the human cortex at the scale of layers and columns. This mesoscopic scale promises an improved mechanistic understanding of human cortical function so far only accessible to invasive animal neurophysiology. In recent years, an increasing number of studies have applied such methods to better understand the cortical function in perception and cognition. This future perspective article asks whether closed-loop fMRI studies could equally benefit from these methods to achieve layer and columnar specificity. We outline potential applications and discuss the conceptual and concrete challenges, including data acquisition and volitional control of mesoscopic brain activity. We anticipate an important role of fMRI with mesoscopic resolution for closed-loop fMRI and neurofeedback, yielding new insights into brain function and potentially clinical applications.This article is part of the theme issue 'Neurofeedback: new territories and neurocognitive mechanisms of endogenous neuromodulation'.

Scanning WAXS microscopy of regenerated cellulose fibers at mesoscopic resolution.

In this work, regenerated cellulose textile fibers, Ioncell-F, dry-wet spun with different draw ratios, have been investigated by scanning wide-angle X-ray scattering (WAXS) using a mesoscopic X-ray beam. The fibers were found to be homogeneous on the 500 nm length scale. Analysis of the azimuthal angular dependence of a crystalline Bragg spot intensity revealed a radial dependence of the degree of orientation of crystallites that was found to increase with the distance from the center of the fiber. We attribute this to radial velocity gradients during the extrusion of the spin dope and the early stage of drawing. On the other hand, the fiber crystallinity was found to be essentially homogeneous over the fiber cross section.

Light-Sheet Microscopic Imaging of Whole-Mouse Vascular Network with Fluorescent Microsphere Perfusion.

Visualizing the whole vascular network system is crucial for understanding the pathogenesis of specific diseases and devising targeted therapeutic interventions. Although the combination of light sheet microscopy and tissue-clearing methods has emerged as a promising approach for investigating the blood vascular network, leveraging the spatial resolution down to the capillary level and the ability to image centimeter-scale samples remains difficult. Especially, as the resolution improves, the issue of photobleaching outside the field of view poses a challenge to image the whole vascular network of adult mice at capillary resolution. Here, we devise a fluorescent microsphere vascular perfusion method to enable labeling of the whole vascular network in adult mice, which overcomes the photobleaching limit during the imaging of large samples. Moreover, by combining the utilization of a large-scale light-sheet microscope and tissue clearing protocols for whole-mouse samples, we achieve the capillary-level imaging resolution (3.2 × 3.2 × 6.5 μm) of the whole vascular network with dimensions of 45 × 15 × 82 mm in adult mice. This method thus holds great potential to deliver mesoscopic resolution images of various tissue organs for whole-animal imaging.

Layer-specific microstructural patterns of anterior hippocampus in Alzheimer's disease with ex vivo diffusion MRI at 14.1T.

High-resolution ex vivo diffusion MRI (dMRI) can provide exquisite mesoscopic details and microstructural information of the human brain. Microstructural pattern of the anterior part of human hippocampus, however, has not been well elucidated with ex vivo dMRI, either in normal or disease conditions. The present study collected high-resolution (0.1 mm isotropic) dMRI of post-mortem anterior hippocampal tissues from four Alzheimer's diseases (AD), three primary age-related tauopathy (PART), and three healthy control (HC) brains on a 14.1T spectrometer. We evaluated how AD affected dMRI-based microstructural features in different layers and subfields of anterior hippocampus. In the HC samples, we found higher anisotropy, lower diffusivity, and more streamlines in the layers within cornu ammonis (CA) than those within dentate gyrus (DG). Comparisons between disease groups showed that (1) anisotropy measurements in the CA layers of AD, especially stratum lacunosum (SL) and stratum radiatum (SR), had higher regional variability than the other two groups; (2) streamline density in the DG layers showed a gradually increased variance from HC to PART to AD; (3) AD also showed the higher variability in terms of inter-layer connectivity than HC or PART. Moreover, voxelwise correlation analysis between the coregistered dMRI and histopathology images revealed significant correlations between dMRI measurements and the contents of amyloid beta (Aβ)/tau protein in specific layers of AD samples. These findings may reflect layer-specific microstructural characteristics in different hippocampal subfields at the mesoscopic resolution, which were associated with protein deposition in the anterior hippocampus of AD patients.

Selective plane illumination microscopy (SPIM) with time-domain fluorescence lifetime imaging microscopy (FLIM) for volumetric measurement of cleared mouse brain samples.

We have developed an imaging technique which combines selective plane illumination microscopy with time-domain fluorescence lifetime imaging microscopy (SPIM-FLIM) for three-dimensional volumetric imaging of cleared mouse brains with micro- to mesoscopic resolution. The main features of the microscope include a wavelength-adjustable pulsed laser source (Ti:sapphire) (near-infrared) laser, a BiBO frequency-doubling photonic crystal, a liquid chamber, an electrically focus-tunable lens, a cuvette based sample holder, and an air (dry) objective lens. The performance of the system was evaluated with a lifetime reference dye and micro-bead phantom measurements. Intensity and lifetime maps of three-dimensional human embryonic kidney (HEK) cell culture samples and cleared mouse brain samples expressing green fluorescent protein (GFP) (donor only) and green and red fluorescent protein [positive Förster (fluorescence) resonance energy transfer] were acquired. The results show that the SPIM-FLIM system can be used for sample sizes ranging from single cells to whole mouse organs and can serve as a powerful tool for medical and biological research.

Multiscale Modeling of the HKUST-1/Poly(vinyl alcohol) Interface: From an Atomistic to a Coarse Graining Approach

We present a computational multiscale study of a metal–organic framework (MOF)/polymer composite combining micro- and mesoscopic resolution, by coupling atomistic and coarse grained (CG) force field-based molecular dynamics simulations. As a proof of concept, we describe the copper paddlewheel-based HKUST-1 MOF/poly(vinyl alcohol) composite. Our newly developed CG model reproduces the salient features of the interface in excellent agreement with the atomistic model and allows the investigation of substantially larger systems. The polymer penetrates into the open pores of the MOF as a result of the interactions between its OH groups and the O and Cu atoms in the pores, suggesting an excellent MOF/polymer compatibility. Polymer structure is affected by the MOF surface up to a distance of ∼2.4 times its radius of gyration. This study paves the way toward understanding important interfacial phenomena such as aggregation and phase separation in these mixed matrix systems.

Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations.

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

Diffuse-interface modeling of solute trapping in rapid solidification: Predictions of the hyperbolic phase-field model and parabolic model with finite interface dissipation

Two recently developed phase-field models, a hyperbolic model and a parabolic model with finite interface dissipation, are employed to study the solute trapping in a Si-0.25 at.% As alloy during rapid solidification. The hyperbolic model is applied at the nanometer scale of the interface width δ. The parabolic model is derived by a coarse-graining procedure and is intended to operate with mesoscopic resolution of the interface η. The coarse-graining numerical parameters, namely interface width η and the interface permeability P, are adjusted in the parabolic model to fit the segregation coefficient calculated by the microscopic model on the nanoscale. Based on the optimal sets of η and P selected at small interface velocity, a linear relation between their logarithm values is obtained. This logarithmic relation provides a theoretical basis for choosing the appropriate values of η and P in the numerical phase-field simulation in three spatial dimensions.

Automated classification of breast pathology using local measures of broadband reflectance

We demonstrate that morphological features pertinent to a tissue's pathology may be ascertained from localized measures of broadband reflectance, with a mesoscopic resolution (100-μm lateral spot size) that permits scanning of an entire margin for residual disease. The technical aspects and optimization of a k-nearest neighbor classifier for automated diagnosis of pathologies are presented, and its efficacy is validated in 29 breast tissue specimens. When discriminating between benign and malignant pathologies, a sensitivity and specificity of 91 and 77% was achieved. Furthermore, detailed subtissue-type analysis was performed to consider how diverse pathologies influence scattering response and overall classification efficacy. The increased sensitivity of this technique may render it useful to guide the surgeon or pathologist where to sample pathology for microscopic assessment.

Different analysis solutions for different spatial resolutions? Moving towards a mesoscopic mapping of functional architecture in the human brain

This comment challenges the dichtotomy that Kriegeskorte and Bandettini (this issue) propose to exist between “activation-based” and “information-based” approaches to fMRI analyses and argues that multi-variate analyses are just a special case within the overall repertoire of methods for analyzing paradigm-related BOLD signal variations. Moreover, this comment argues that using multi-variate approaches comes at a price, trading-off spatial resolution for sensitivity, and thus partially cancels potential benefits from high-field fMRI. Paradoxically, this comment thus concludes that pattern analyses provide a powerful complement to existing methods but not the complement that will actually permit to map functional architecture at mesoscopic resolution, i.e., one of the most interesting applications of high-field fMRI.

Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution

We report molecular dynamics (MD) simulations of three protein-water systems (ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1), from which we compute the dielectric properties of the solutions. Since two of the proteins studied have a net charge, we develop the necessary theory to account for the presence of charged species in a form suitable for computer simulations. In order to ensure convergence of the time correlation functions needed for the analysis, the minimum length of the MD simulations was 20 ns. The system sizes (box length, number of waters) were chosen so that the resulting protein concentrations are comparable to experimental conditions. A dielectric component analysis was carried out to analyze the contributions from protein and water to the frequency-dependent dielectric susceptibility chi(omega) of the solutions. Additionally, an even finer decomposition into protein, two solvation shells, and the remaining water (bulk water) was carried out. The results of these dielectric decompositions were used to study protein solvation at mesoscopic resolution, i.e., in terms of protein, first and second solvation layers, and bulk water. This study, therefore, complements the structural and dynamical analyses at molecular resolution that are presented in the companion paper. The dielectric component contributions from the second shell and bulk water are very similar in all three systems. We find that the proteins influence the dielectric properties of water even beyond the second solvation shell, in agreement with what was observed for the mean residence times of water molecules in protein solutions. By contrast, the protein contributions, as well as the contributions of the first solvation shell, are system specific. Most importantly, the protein and the first water shell around ubiquitin and apo-calbindin are anticorrelated, whereas the first water shell around the SH2 domain is positively correlated.

Crystallization of Transmembrane Proteins in cubo: Mechanisms of Crystal Growth and Defect Formation

Crystallization of membrane proteins is a major stumbling block en route to elucidating their structure and understanding their function. The novel concept of membrane protein crystallization from lipidic cubic phases, "in cubo", has yielded well-ordered crystals and high-resolution structures of several membrane proteins, yet progress has been slow due to the lack of understanding of the molecular mechanisms of protein transport, crystal nucleation, growth, and defect formation in cubo. Here, we examine at molecular and mesoscopic resolution with atomic force microscopy the morphology of in cubo grown bacteriorhodopsin crystals in inert buffers and during etching by detergent. The results reveal that crystal nucleation occurs following local rearrangement of the highly curved lipidic cubic phase into a lamellar structure, which is akin to that of the native membrane. Crystals grow within the bulk cubic phase surrounded by such lamellar structures, whereby transport towards a growing crystalline layer is constrained to within an individual lamella. This mechanism leads to lack of dislocations, generation of new crystalline layers at numerous locations, and to voids and block boundaries. The characteristic macroscopic lengthscale of these defects suggests that the crystals grow by attachment of single molecules to the nuclei. These insights into the mechanisms of nucleation, growth and transport in cubo provide guidance en route to a rational design of membrane protein crystallization, and promise to further advance the field.

Stereochemical effects in supramolecular self-assembly at surfaces: 1-D versus 2-D enantiomorphic ordering for PVBA and PEBA on Ag(111).

We present investigations on noncovalent bonding and supramolecular self-assembly of two related molecular building blocks at a noble metal surface: 4-[trans-2-(pyrid-4-yl-vinyl)]benzoic acid (PVBA) and 4-[(pyrid-4-yl-ethynyl)]benzoic acid (PEBA). These rigid, rodlike molecules comprising the same complementary moieties for hydrogen bond formation are comparable in shape and size. For PVBA, the ethenylene moiety accounts for two-dimensional (2-D) chirality upon confinement to a surface; PEBA is linear and thus 2-D achiral. Molecular films were deposited on a Ag(111) surface by organic molecular beam epitaxy and characterized by scanning tunneling microscopy. At low temperatures (around 150 K), both species form irregular networks of flat lying molecules linked via their endgroups in a diffusion-limited aggregation process. In the absence of kinetic limitations (adsorption or annealing at room temperature), hydrogen-bonded supramolecular assemblies form which are markedly different. With PVBA, enantiomorphic twin chains in two mirror-symmetric species running along a high-symmetry direction of the substrate lattice form by diastereoselective self-assembly of one enantiomer. The chirality signature is strictly correlated between neighboring twin chains. Enantiopure one-dimensional (1-D) supramolecular nanogratings with tunable periodicity evolve at intermediate coverages, reflecting chiral resolution in micrometer domains. In contrast, PEBA assembles in 2-D hydrogen-bonded islands, which are enantiomorphic because of the orientation of the supramolecular arrangements along low-symmetry directions of the substrate. Thus, for PVBA, chiral molecules form 1-D enantiomorphic supramolecular structures because of mesoscopic resolution of a 2-D chiral species, whereas with PEBA, the packing of an achiral species causes 2-D enantiomorphic arrangements. Model simulations of supramolecular ordering provide a deeper understanding of the stability of these systems.