Ingmar Schoen

Binding-Activated Localization Microscopy of DNA Structures

Many nucleic acid stains show a strong fluorescence enhancement upon binding to double-stranded DNA. Here we exploit this property to perform superresolution microscopy based on the localization of individual binding events. The dynamic labeling scheme and the optimization of fluorophore brightness yielded a resolution of ∼14 nm (fwhm) and a spatial sampling of 1/nm. We illustrate our approach with two different DNA-binding dyes and apply it to visualize the organization of the bacterial chromosome in fixed Escherichia coli cells. In general, the principle of binding-activated localization microscopy (BALM) can be extended to other dyes and targets such as protein structures.

Probing Cellular Traction Forces by Micropillar Arrays: Contribution of Substrate Warping to Pillar Deflection

Quantifying cellular forces relies on accurate calibrations of the sensor stiffness. Neglecting deformations of elastic substrates to which elastic pillars are anchored systematically overestimates the applied forces (up to 40%). A correction factor considering substrate warping is derived analytically and verified experimentally. The factor scales with the dimensionless pillar aspect ratio. This has significant implications when designing pillar arrays or comparing absolute forces measured on different pillar geometries during cell spreading, motility, or rigidity sensing.

Extracellular Stimulation of Mammalian Neurons Through Repetitive Activation of Na+ Channels by Weak Capacitive Currents on a Silicon Chip

Reliable extracellular stimulation of neuronal activity is the prerequisite for electrical interfacing of cultured networks and brain slices, as well as for neural implants. Safe stimulation must be achieved without damage to the cells. With respect to a future application of highly integrated semiconductor chips, we present an electrophysiological study of capacitive stimulation of mammalian cells in the geometry of adhesion on an insulated titanium dioxide/silicon electrode. We used HEK293 cells with overexpressed Na(V)1.4 channels and neurons from rat hippocampus. Weak biphasic stimuli of falling and rising voltage ramps were applied in the absence of Faradaic current and electroporation. We recorded the response of the intra- and extracellular voltage and evaluated the concomitant polarization of the attached and free cell membranes. Falling ramps efficiently depolarized the central area of the attached membrane. A transient sodium inward current was activated that gave rise to a weak depolarization of the cell on the order of 1 mV. The depolarization could be enhanced step by step by a train of biphasic stimuli until self-excitation of sodium channels set in. We applied the same protocol to cultured rat neurons and found that pulse trains of weak capacitive stimuli were able to elicit action potentials. Our results provide a basis for safe extracellular stimulation not only for cultured neurons on insulated semiconductor electrodes, but also more generally for metal electrodes in cell culture and brain tissue.

Hybridization kinetics is different inside cells

It is generally expected that the kinetics of reactions inside living cells differs from the situation in bulk solutions. Macromolecular crowding and specific binding interactions could change the diffusion properties and the availability of free molecules. Their impact on reaction kinetics in the relevant context of living cells is still elusive, mainly because the difficulty of capturing fast kinetics in vivo. This article shows spatially resolved measurements of DNA hybridization kinetics in single living cells. HeLa cells were transfected with a FRET-labeled dsDNA probe by lipofection. We characterized the hybridization reaction kinetics with a kinetic range of 10 μs to 1 s by a combination of laser-driven temperature oscillations and stroboscopic fluorescence imaging. The time constant of the hybridization depended on DNA concentration within individual cells and between cells. A quantitative analysis of the concentration dependence revealed several-fold accelerated kinetics as compared with free solution for a 16-bp probe and decelerated kinetics for a 12-bp probe. We did not find significant effects of crowding agents on the hybridization kinetics in vitro. Our results suggest that the reaction rates in vivo are specifically modulated by binding interactions for the two probes, possibly triggered by their different lengths. In general, the presented imaging modality of temperature oscillation optical lock-in microscopy allows to probe biomolecular interactions in different cell compartments in living cells for systems biology.

Molecular architecture of native fibronectin fibrils

Fibronectin fibrils within the extracellular matrix play central roles in physiological and pathological processes, yet many structural details about their hierarchical and molecular assembly remain unknown. Here we combine site-specific protein labelling with single-molecule localization by stepwise photobleaching or direct stochastic optical reconstruction microscopy (dSTORM), and determine the relative positions of various labelled sites within native matrix fibrils. Single end-labelled fibronectin molecules in fibrils display an average end-to-end distance of ∼133 nm. Sampling of site-specific antibody epitopes along the thinnest fibrils (protofibrils) shows periodic punctate label patterns with ∼95 nm repeats and alternating N- and C-terminal regions. These measurements suggest an antiparallel 30–40 nm overlap between N-termini, suggesting that the first five type I modules bind type III modules of the adjacent molecule. Thicker fibres show random bundling of protofibrils without a well-defined line-up. This super-resolution microscopy approach can be applied to other fibrillar protein assemblies of unknown structure.

Disentangling the multifactorial contributions of fibronectin, collagen and cyclic strain on MMP expression and extracellular matrix remodeling by fibroblasts

Early wound healing is associated with fibroblasts assembling a provisional fibronectin-rich extracellular matrix (ECM), which is subsequently remodeled and interlaced by type I collagen. This exposes fibroblasts to time-variant sets of matrices during different stages of wound healing. Our goal was thus to gain insight into the ECM-driven functional regulation of human foreskin fibroblasts (HFFs) being either anchored to a fibronectin (Fn) or to a collagen-decorated matrix, in the absence or presence of cyclic mechanical strain. While the cells reoriented in response to the onset of uniaxial cyclic strain, cells assembled exogenously added Fn with a preferential Fn-fiber alignment along their new orientation. Exposure of HFFs to exogenous Fn resulted in an increase in matrix metalloproteinase (MMP) expression levels, i.e. MMP-15 (RT-qPCR), and MMP-9 activity (zymography), while subsequent exposure to collagen slightly reduced MMP-15 expression and MMP-9 activity compared to Fn-exposure alone. Cyclic strain upregulated Fn fibrillogenesis and actin stress fiber formation, but had comparatively little effect on MMP activity. We thus propose that the appearance of collagen might start to steer HFFs towards homeostasis, as it decreased both MMP secretion and the tension of Fn matrix fibrils as assessed by Fluorescence Resonance Energy Transfer. These results suggest that HFFs might have a high ECM remodeling or repair capacity in contact with Fn alone (early event), which is reduced in the presence of Col1 (later event), thereby down-tuning HFF activity, a processes which would be required in a tissue repair process to finally reach tissue homeostasis.

Conformational distribution of surface-adsorbed fibronectin molecules explored by single molecule localization microscopy

Adsorbed proteins that promote cell adhesion mediate the response of cells to biomaterials and scaffolds. As proteins undergo conformational changes upon surface adsorption, their functional display may be significantly affected by surface chemistry or solution conditions during the adsorption process. A high-resolution localization microscopy technique is extended here to probe the conformation of individual fibronectin (Fn) molecules at the glass-water interface under physiological buffer conditions. To map distances, four available cysteines located on the modules FnIII7 and FnIII15 of dimeric Fn were site-specifically labeled with Cy3B, and their relative positions were determined by stepwise photobleaching with nanometer precision. The four labels on single Fn molecules did not show a uniform or linear arrangement. The distances between label positions were distributed asymmetrically around 33 nm with a tail towards higher distances. Exposure of Fn to denaturing solution conditions during adsorption increased the average distances up to 43 nm for 4 M guanidinium HCl, while changing the solution conditions after the adsorption had no effect, indicating that the observed intra-molecular distances are locked-in during the adsorption process. Also surface coatings of different hydrophobicity altered the conformational distribution, shifting label distances from a median of 24 nm on hydrophilic to 49 nm on hydrophobic surfaces. These results further highlight that the conformation of macromolecules at interfaces depends on the adsorption history. While illustrated here for surface adsorbed Fn, the power of localization-based microscopy extends the repertoire of techniques to characterize biomolecules at interfaces.

Activation of Na+ channels in cell membrane by capacitive stimulation with silicon chip

Sodium channels are the crucial electrical elements of neuronal excitation. As a step toward hybrid neuron-semiconductor devices, we studied the activation of recombinant NaV1.4 sodium channels in human embryonic kidney (HEK293) cells by stimulation from an electrolyte/oxide/silicon (EOS) capacitor. HfO2 was used as an insulator to attain a high capacitance. An effective activation was achieved by decaying voltage ramps at constant intracellular voltage at a depleted NaCl concentration in the bath to enhance the resistance of the cell-chip contact. We were also able to open sodium channels at a NaCl concentration close to physiological conditions. This experiment provides a basis for noninvasive capacitive stimulation of nerve cells with semiconductor chips.

Nanopore diameters tune strain in extruded fibronectin fibers

Fibronectin is present in the extracellular matrix and can be assembled into nanofibers in vivo by undergoing conformational changes. Here, we present a novel approach to prepare fibronectin nanofibers under physiological conditions using an extrusion approach through nanoporous aluminum oxide membranes. This one-step process can prepare nanofiber bundles up to a millimeter in length and with uniform fiber diameters in the nanometer range. Most importantly, by using different pore diameters and protein concentrations in the extrusion process, we could induce varying lasting structural changes in the fibers, which were monitored by Förster resonance energy transfer and should impose different physiological functions.

Robotically controlled microprey to resolve initial attack modes preceding phagocytosis

The behavior of phagocytes to capture intruders is tracked using remotely rotated and translated nanoparticles. Phagocytes, predatory cells of the immune system, continuously probe their cellular microenvironment on the hunt for invaders. This requires prey recognition followed by the formation of physical contacts sufficiently stable for pickup. Although immune cells must apply physical forces to pick up their microbial prey, little is known about their hunting behavior preceding phagocytosis because of a lack of appropriate technologies. To study phagocyte hunting behavior in which the adhesive bonds by which the prey holds on to surfaces must be broken, we exploited the use of microrobotic probes to mimic bacteria. We simulate different hunting scenarios by confronting single macrophages with prey-mimicking micromagnets using a 5–degree of freedom magnetic tweezers system (5D-MTS). The energy landscape that guided the translational and rotational movement of these microparticles was dynamically adjusted to explore how translational and rotational resistive forces regulate the modes of macrophage attacks. For translational resistive prey, distinct push-pull attacks were observed. For rod-shaped, nonresistive prey, which mimic free-floating pathogens, cells co-aligned their prey with their long axis to facilitate pickup. Increasing the rotational trap stiffness to mimic resistive or surface-bound prey disrupts this realignment process. At stiffness levels on the order of 105 piconewton nanometer radian−1, macrophages failed to realign their prey, inhibiting uptake. Our 5D-MTS was used as a proof-of-concept study to probe the translational and rotational attack modes of phagocytes with high spatial and temporal resolution, although the system can also be used for a variety of other mechanobiology studies at length scales ranging from single cells to organ-on-a-chip devices.