The random walker's toolbox for analyzing single-particle tracking data.

Technological advances and a burst of new microscopy methods have boosted the use of quantitative tracking experiments, in Soft Matter and Biological Physics but also in the Life Sciences. However, in contrast to highly advanced measurement techniques and tracking tools, subsequent analyses of trajectories frequently do not exploit the data's full potential. Aiming especially at experimental laboratories and early-career scientists, we introduce, discuss, and apply in this Tutorial Review a large set of versatile measures that have proven to be useful for analyzing trajectories from single-particle tracking experiments, beyond a simple extraction of diffusion constants from mean squared displacements. To support a direct test and application of these measures, we supplement the text with a download package that comprises a low-threshold toolbox of ready-to-use routines and training data sets, hence relaxing the need to develop home-brewed solutions and/or to create suitable benchmark data.

Metal-Induced Energy Transfer (MIET) for Live-Cell Imaging with Fluorescent Proteins.

Metal-induced energy transfer (MIET) imaging is an easy-to-implement super-resolution modality that achieves nanometer resolution along the optical axis of a microscope. Although its capability in numerous biological and biophysical studies has been demonstrated, its implementation for live-cell imaging with fluorescent proteins is still lacking. Here, we present its applicability and capabilities for live-cell imaging with fluorescent proteins in diverse cell types (adult human stem cells, human osteo-sarcoma cells, and Dictyostelium discoideum cells), and with various fluorescent proteins (GFP, mScarlet, RFP, YPet). We show that MIET imaging achieves nanometer axial mapping of living cellular and subcellular components across multiple time scales, from a few milliseconds to hours, with negligible phototoxic effects.

FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking.

Cytoskeletal pattern formation and structural dynamics are key to a variety of biological functions and a detailed and quantitative analysis yields insight into finely tuned and well-balanced homeostasis and potential pathological alterations. High content life cell imaging of fluorescently labeled cytoskeletal elements under physiological conditions is nowadays state-of-the-art and can record time lapse data for detailed experimental studies. However, systematic quantification of structures and in particular the dynamics (i.e. frame-to-frame tracking) are essential. Here, an unbiased, quantitative, and robust analysis workflow that can be highly automatized is needed. For this purpose we upgraded and expanded our fiber detection algorithm FilamentSensor (FS) to the FilamentSensor 2.0 (FS2.0) toolbox, allowing for automatic detection and segmentation of fibrous structures and the extraction of relevant data (center of mass, length, width, orientation, curvature) in real-time as well as tracking of these objects over time and cell event monitoring.

Measuring Nuclear Mechanics with Atomic Force Microscopy.

Atomic force microscopy is an ideal tool to map topography and mechanical properties of materials on the micro- and nanoscale. Here, we describe its application to measure and analyze the mechanics, in particular the effective Young's elastic modulus E* of the mammalian nucleus in live cells. We present three approaches which enable the mechanics to be probed under varying conditions. This includes fully adhered cells, initially adhered cells which lack an established cytoskeleton, and purified nuclei to study their isolated response.

A Focal Adhesion Filament Cross-correlation Kit for fast, automated segmentation and correlation of focal adhesions and actin stress fibers in cells.

Focal adhesions (FAs) and associated actin stress fibers (SFs) form a complex mechanical system that mediates bidirectional interactions between cells and their environment. This linked network is essential for mechanosensing, force production and force transduction, thus directly governing cellular processes like polarization, migration and extracellular matrix remodeling. We introduce a tool for fast and robust coupled analysis of both FAs and SFs named the Focal Adhesion Filament Cross-correlation Kit (FAFCK). Our software can detect and record location, axes lengths, area, orientation, and aspect ratio of focal adhesion structures as well as the location, length, width and orientation of actin stress fibers. This enables users to automate analysis of the correlation of FAs and SFs and study the stress fiber system in a higher degree, pivotal to accurately evaluate transmission of mechanocellular forces between a cell and its surroundings. The FAFCK is particularly suited for unbiased and systematic quantitative analysis of FAs and SFs necessary for novel approaches of traction force microscopy that uses the additional data from the cellular side to calculate the stress distribution in the substrate. For validation and comparison with other tools, we provide datasets of cells of varying quality that are labelled by a human expert. Datasets and FAFCK are freely available as open source under the GNU General Public License.

High internal phase Pickering emulsions stabilized by dialdehyde amylopectin/chitosan complex nanoparticles.

High internal phase Pickering emulsions (HIPPEs) have attracted intensive interest for their great potential in foods, cosmetics, and biomedical applications. However, the relatively poor biodegradability and biocompatibility of inorganic and synthetic particulate emulsifiers greatly limit their practical applications. Here, a kind of biobased nanoparticles, namely dialdehyde amylopectin/chitosan complex nanoparticles (DAPCNPs), were fabricated by Schiff base reaction between dialdehyde amylopectin and chitosan with the assistance of ultrasonication treatment. The resultant DAPCNPs were employed to stabilize O/W HIPPEs with various oils, such as toluene, cyclohexane, styrene and edible rapeseed oil. Moreover, the resultant DAPCNPs-stabilized HIPPEs showed high stability under various environmental stresses (80 °C; 20 mM and 100 mM aqueous NaCl solutions). Furthermore, porous scaffolds were also fabricated by freeze-drying cyclohexane-in-water HIPPEs stabilized by DAPCNPs after the introduction of polyvinyl alcohol (PVA) into the continuous phase. These findings would give inspiration for designing polysaccharides-based nanoparticles to stabilize HIPPEs and improve their practical applications.

DNA damage alters nuclear mechanics through chromatin reorganization.

DNA double-strand breaks drive genomic instability. However, it remains unknown how these processes may affect the biomechanical properties of the nucleus and what role nuclear mechanics play in DNA damage and repair efficiency. Here, we have used Atomic Force Microscopy to investigate nuclear mechanical changes, arising from externally induced DNA damage. We found that nuclear stiffness is significantly reduced after cisplatin treatment, as a consequence of DNA damage signalling. This softening was linked to global chromatin decondensation, which improves molecular diffusion within the organelle. We propose that this can increase recruitment for repair factors. Interestingly, we also found that reduction of nuclear tension, through cytoskeletal relaxation, has a protective role to the cell and reduces accumulation of DNA damage. Overall, these changes protect against further genomic instability and promote DNA repair. We propose that these processes may underpin the development of drug resistance.

Metasurface-based total internal reflection microscopy.

Recent years have seen a tremendous progress in the development of dielectric metasurfaces for visible light applications. Such metasurfaces are ultra-thin optical devices that can manipulate optical wavefronts in an arbitrary manner. Here, we present a newly developed metasurface which allows for coupling light into a microscopy coverslip to achieve total internal reflection (TIR) excitation. TIR fluorescence microscopy (TIRFM) is an important bioimaging technique used specifically to image cellular membranes or surface-localized molecules with high contrast and low background. Its most commonly used modality is objective-type TIRFM where one couples a focused excitation laser beam at the edge of the back focal aperture of an oil-immersion objective with high numerical aperture (N.A.) to realize a high incident-angle plane wave excitation above the critical TIR angle in sample space. However, this requires bulky and expensive objectives with a limited field-of-view (FOV). The metasurface which we describe here represents a low cost and easy-to-use alternative for TIRFM. It consists of periodic 2D arrays of asymmetric structures fabricated in TiO2 on borosilicate glass. It couples up to 70% of the incident non-reflected light into the first diffraction order at an angle of 65° in glass, which is above the critical TIR angle for a glass-water interface. Only ∼7% of the light leaks into propagating modes traversing the glass surface, thus minimizing any spurious background fluorescence originating far outside the glass substrate. We describe in detail design and fabrication of the metasurface, and validate is applicability for TIRFM by imaging immunostained human mesenchymal stem cells over a FOV of 200 µm x 200 µm. We envision that these kinds of metasurfaces can become a valuable tool for low-cost and TIRFM, offering high contrast, low photodamage, and high surface selectivity in fluorescence excitation and detection.

Effect of Adhesion and Substrate Elasticity on Neutrophil Extracellular Trap Formation.

Neutrophils are the most abundant type of white blood cells. Upon stimulation, they are able to decondense and release their chromatin as neutrophil extracellular traps (NETs). This process (NETosis) is part of immune defense mechanisms but also plays an important role in many chronic and inflammatory diseases such as atherosclerosis, rheumatoid arthritis, diabetes, and cancer. For this reason, much effort has been invested into understanding biochemical signaling pathways in NETosis. However, the impact of the mechanical micro-environment and adhesion on NETosis is not well-understood. Here, we studied how adhesion and especially substrate elasticity affect NETosis. We employed polyacrylamide (PAA) gels with distinctly defined elasticities (Young's modulus E) within the physiologically relevant range from 1 to 128 kPa and coated the gels with integrin ligands (collagen I, fibrinogen). Neutrophils were cultured on these substrates and stimulated with potent inducers of NETosis: phorbol 12-myristate 13-acetate (PMA) and lipopolysaccharide (LPS). Interestingly, PMA-induced NETosis was neither affected by substrate elasticity nor by different integrin ligands. In contrast, for LPS stimulation, NETosis rates increased with increasing substrate elasticity (E > 20 kPa). LPS-induced NETosis increased with increasing cell contact area, while PMA-induced NETosis did not require adhesion at all. Furthermore, inhibition of phosphatidylinositide 3 kinase (PI3K), which is involved in adhesion signaling, completely abolished LPS-induced NETosis but only slightly decreased PMA-induced NETosis. In summary, we show that LPS-induced NETosis depends on adhesion and substrate elasticity while PMA-induced NETosis is completely independent of adhesion.

Thermoresponsive Water Transportation in Dually Electrostatically Crosslinked Nanocomposite Hydrogels.

Controlling water transportation within hydrogels makes hydrogels attractive for diverse applications, but it is still a very challenging task. Herein, a novel type of dually electrostatically crosslinked nanocomposite hydrogel showing thermoresponsive water absorption, distribution, and dehydration processes are developed. The nanocomposite hydrogels are stabilized via electrostatic interactions between negatively charged poly(acrylic acid) and positively charged layered double hydroxide (LDH) nanosheets as well as poly(3-acrylamidopropyltrimethylammonium chloride). Both LDH nanosheets as crosslinkers and the surrounding temperatures played pivotal roles in tuning the water transportation within these nanocomposite hydrogels. By changing the surrounding temperature from 60 to 4 °C, these hydrogels showed widely adjustable swelling times between 2 and 45 days, while the dehydration process lasted between 7 and 27 days. A swift temperature decrease, for example, from 60 to 25 °C, generated supersaturation within these nanocomposite hydrogels, which further retarded the water transportation and distribution in hydrogel networks. Benefiting from modified water transportation and rapidly alternating water uptake capability during temperature change, pre-loaded compounds can be used to track and visualize these processes within nanocomposite hydrogels. At the same time, the discharge of water and loaded compounds from the interior of hydrogels demonstrates a thermoresponsive sustained release process.

Liquid-Behaviors-Assisted Fabrication of Multidimensional Birefringent Materials from Dynamic Hybrid Hydrogels.

Liquid-solid transition is a widely used strategy to shape polymeric materials and encode their microstructures. However, it is still challenging to fully exploit liquid behaviors of material precursors. In particular, the dynamic and static liquid behaviors naturally conflict with each other, which makes it difficult to integrate their advantages in the same materials. Here, by utilizing a shear-thinning phenomenon in the dynamic hybrid hydrogels, we achieve a hydrodynamic alignment of cellulose nanocrystals (CNC) and preserve it in the relaxed hydrogel networks due to the much faster relaxation of polymer networks (within 500 s) than CNC after the unloading of external force. During the following drying process, the surface tension of hydrogels further enhances the orientation index of CNC up to 0.872 in confined geometry, and these anisotropic microstructures demonstrate highly tunable birefringence (up to 0.004 14). Due to the presence of the boundaries of dynamic hydrogels, diverse xerogels including fibers, films, and even complex three-dimensional structures with variable anisotropic microstructures can be fabricated without any external molds.

Lipid Emulsion-Based OCT Angiography for Ex Vivo Imaging of the Aqueous Outflow Tract.

Purpose: Contrast agents applicable for optical coherence tomography (OCT) imaging are rare. The intrascleral aqueous drainage system would be a potential application for a contrast agent, because the aqueous veins are of small diameter and located deep inside the highly scattering sclera. We tested lipid emulsions (LEs) as candidate OCT contrast agents in vitro and ex vivo, including milk and the anesthetic substance Propofol. Methods: Commercial OCT and OCT angiography (OCTA) devices were used. Maximum reflectivity and signal transmission of LE were determined in tube phantoms. Absorption spectra and light scattering was analyzed. The anterior chamber of enucleated porcine eyes was perfused with LEs, and OCTA imaging of the LEs drained via the aqueous outflow tract was performed. Results: All LEs showed a significantly higher reflectivity than water (P < 0.001). Higher milk lipid content was positively correlated with maximum reflectivity and negatively with signal transmission. Propofol exhibited the best overall performance. Due to a high degree of signal fluctuation, OCTA could be applied for detection of LE. Compared with blood, the OCTA signal of Propofol was significantly stronger (P = 0.001). As a proof of concept, time-resolved aqueous angiography of porcine eyes was performed. The three-dimensional (3D) structure and dynamics of the aqueous outflow were significantly different from humans. Conclusions: LEs induced a strong signal in OCT and OCTA. LE-based OCTA allowed the ability to obtain time-resolved 3D datasets of aqueous outflow. Possible interactions of LE with inner eye's structures need to be further investigated before in vivo application.

Agonistic and antagonistic roles of fibroblasts and cardiomyocytes on viscoelastic stiffening of engineered human myocardium.

Cardiomyocyte and stroma cell cross-talk is essential for the formation of collagen-based engineered heart muscle, including engineered human myocardium (EHM). Fibroblasts are a main component of the myocardial stroma. We hypothesize that fibroblasts, by compacting the surrounding collagen network, support the self-organization of cardiomyocytes into a functional syncytium. With a focus on early self-organization processes in EHM, we studied the molecular and biophysical adaptations mediated by defined populations of fibroblasts and embryonic stem cell-derived cardiomyocytes in a collagen type I hydrogel. After a short phase of cell-independent collagen gelation (30 min), tissue compaction was progressively mediated by fibroblasts. Fibroblast-mediated tissue stiffening was attenuated in the presence of cardiomyocytes allowing for the assembly of stably contracting, force-generating EHM within 4 weeks. Comparative RNA-sequencing data corroborated that fibroblasts are particularly sensitive to the tissue compaction process, resulting in the fast activation of transcription profiles, supporting heart muscle development and extracellular matrix synthesis. Large amplitude oscillatory shear (LAOS) measurements revealed nonlinear strain stiffening at physiological strain amplitudes (>2%), which was reduced in the presence of cells. The nonlinear stress-strain response could be characterized by a mathematical model. Collectively, our study defines the interplay between fibroblasts and cardiomyocytes during human heart muscle self-organization in vitro and underscores the relevance of fibroblasts in the biological engineering of a cardiomyogenesis-supporting viscoelastic stroma. We anticipate that the established mathematical model will facilitate future attempts to optimize EHM for in vitro (disease modelling) and in vivo applications (heart repair).

Myotubularin related protein-2 and its phospholipid substrate PIP2 control Piezo2-mediated mechanotransduction in peripheral sensory neurons.

Piezo2 ion channels are critical determinants of the sense of light touch in vertebrates. Yet, their regulation is only incompletely understood. We recently identified myotubularin related protein-2 (Mtmr2), a phosphoinositide (PI) phosphatase, in the native Piezo2 interactome of murine dorsal root ganglia (DRG). Here, we demonstrate that Mtmr2 attenuates Piezo2-mediated rapidly adapting mechanically activated (RA-MA) currents. Interestingly, heterologous Piezo1 and other known MA current subtypes in DRG appeared largely unaffected by Mtmr2. Experiments with catalytically inactive Mtmr2, pharmacological blockers of PI(3,5)P2 synthesis, and osmotic stress suggest that Mtmr2-dependent Piezo2 inhibition involves depletion of PI(3,5)P2. Further, we identified a PI(3,5)P2 binding region in Piezo2, but not Piezo1, that confers sensitivity to Mtmr2 as indicated by functional analysis of a domain-swapped Piezo2 mutant. Altogether, our results propose local PI(3,5)P2 modulation via Mtmr2 in the vicinity of Piezo2 as a novel mechanism to dynamically control Piezo2-dependent mechanotransduction in peripheral sensory neurons.

Topology determines force distributions in one-dimensional random spring networks.

Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber-reinforced materials are also common in technology. An important characteristic of such materials is their resistance to failure under load. Rupture occurs when fibers break under excessive force and when that failure propagates. Therefore, it is crucial to understand force distributions. Force distributions within such networks are typically highly inhomogeneous and are not well understood. Here we construct a simple one-dimensional model system with periodic boundary conditions by randomly placing linear springs on a circle. We consider ensembles of such networks that consist of N nodes and have an average degree of connectivity z but vary in topology. Using a graph-theoretical approach that accounts for the full topology of each network in the ensemble, we show that, surprisingly, the force distributions can be fully characterized in terms of the parameters (N,z). Despite the universal properties of such (N,z) ensembles, our analysis further reveals that a classical mean-field approach fails to capture force distributions correctly. We demonstrate that network topology is a crucial determinant of force distributions in elastic spring networks.

Topology Counts: Force Distributions in Circular Spring Networks.

Filamentous polymer networks govern the mechanical properties of many biological materials. Force distributions within these networks are typically highly inhomogeneous, and, although the importance of force distributions for structural properties is well recognized, they are far from being understood quantitatively. Using a combination of probabilistic and graph-theoretical techniques, we derive force distributions in a model system consisting of ensembles of random linear spring networks on a circle. We show that characteristic quantities, such as the mean and variance of the force supported by individual springs, can be derived explicitly in terms of only two parameters: (i) average connectivity and (ii) number of nodes. Our analysis shows that a classical mean-field approach fails to capture these characteristic quantities correctly. In contrast, we demonstrate that network topology is a crucial determinant of force distributions in an elastic spring network. Our results for 1D linear spring networks readily generalize to arbitrary dimensions.

Dual-color metal-induced and Förster resonance energy transfer for cell nanoscopy.

We report a novel method, dual-color axial nanometric localization by metal--induced energy transfer, and combine it with Förster resonance energy transfer (FRET) for resolving structural details in cells on the molecular level. We demonstrate the capability of this method on cytoskeletal elements and adhesions in human mesenchymal stem cells. Our approach is based on fluorescence-lifetime-imaging microscopy and allows for precise determination of the three-dimensional architecture of stress fibers anchoring at focal adhesions, thus yielding crucial information to understand cell-matrix mechanics. In addition to resolving nanometric structural details along the z-axis, we use FRET to gain precise information on the distance between actin and vinculin at focal adhesions.

Rhombic organization of microvilli domains found in a cell model of the human intestine.

Symmetry is rarely found on cellular surfaces. An exception is the brush border of microvilli, which are essential for the proper function of transport epithelia. In a healthy intestine, they appear densely packed as a 2D-hexagonal lattice. For in vitro testing of intestinal transport the cell line Caco-2 has been established. As reported by electron microscopy, their microvilli arrange primarily in clusters developing secondly into a 2D-hexagonal lattice. Here, atomic force microscopy (AFM) was employed under aqueous buffer conditions on Caco-2 cells, which were cultivated on permeable filter membranes for optimum differentiation. For analysis, the exact position of each microvillus was detected by computer vision; subsequent Fourier transformation yielded the type of 2D-lattice. It was confirmed, that Caco-2 cells can build a hexagonal lattice of microvilli and form clusters. Moreover, a second type of arrangement was discovered, namely a rhombic lattice, which appeared at sub-maximal densities of microvilli with (29 ± 4) microvilli / µm2. Altogether, the findings indicate the existence of a yet undescribed pattern in cellular organization.

The 2018 correlative microscopy techniques roadmap.

Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.

Coordinated increase of nuclear tension and lamin-A with matrix stiffness outcompetes lamin-B receptor that favors soft tissue phenotypes.

Matrix stiffness that is sensed by a cell or measured by a purely physical probe reflects the intrinsic elasticity of the matrix and also how thick or thin the matrix is. Here, mesenchymal stem cells (MSCs) and their nuclei spread in response to thickness-corrected matrix microelasticity, with increases in nuclear tension and nuclear stiffness resulting from increases in myosin-II and lamin-A,C. Linearity between the widely varying projected area of a cell and its nucleus across many matrices, timescales, and myosin-II activity levels indicates a constant ratio of nucleus-to-cell volume, despite MSCs' lineage plasticity. Nuclear envelope fluctuations are suppressed on the stiffest matrices, and fluctuation spectra reveal a high nuclear tension that matches trends from traction force microscopy and from increased lamin-A,C. Transcriptomes of many diverse tissues and MSCs further show that lamin-A,C's increase with tissue or matrix stiffness anti-correlates with lamin-B receptor (LBR), which contributes to lipid/sterol biosynthesis. Adipogenesis (a soft lineage) indeed increases LBR:lamin-A,C protein stoichiometry in MSCs versus osteogenesis (stiff). The two factors compete for lamin-B in response to matrix elasticity, knockdown, myosin-II inhibition, and even constricted migration that disrupts and segregates lamins in situ. Matrix stiffness-driven contractility thus tenses the nucleus to favor lamin-A,C accumulation and suppress soft tissue phenotypes.