We present a real-time fitter for 3D single-molecule localization microscopy using experimental point spread functions (PSFs) that achieves optimal 3D resolution on any microscope and is compatible with any PSF engineering approach. This allowed us to image cellular structures with a 3D resolution unprecedented for astigmatic PSFs. The fitter compensates for most optical aberrations and makes accurate 3D superresolution microscopy broadly accessible, even on standard microscopes without dedicated 3D optics.

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.Keywords traction force; mechanotransduction; cell motility; rigidity sensing Generation of mechanical forces is central for regulating the attachment of cells to a substrate, for cell spreading and migration (for reviews see 1 -6). In turn, cells sensitively respond to physical parameters of their environment, e.g. geometry or rigidity 7 -17 and even malignancy is promoted by crosslinking of extracellular matrix fibers which increases the stiffness of the matrix 18 . Via micron-sized cell adhesion sites, cells can locally apply up to several nN of force 19,20 . The force is generated via the cytoskeletal motor protein myosin II which pulls on actin filaments 21,22 that are coupled via adaptor proteins to transmembrane integrins which anchor cells to the outside world 23,24 . Proteins that are part of the force-bearing physical connection linking the cytoskeleton to the outside can act as mechano-chemical signal converters 6,16,[25][26][27] . To elucidate the detailed underpinning mechanisms that control mechanotransduction processes, accurate knowledge of the forces that cells apply via adhesions to substrates is required.Over the last ten years, a variety of experimental methods has been employed to quantify cellular forces 28 , 29 , such diverse as atomic force microscopy (AFM) 30 , 31, optical traps 32 , 33, flat elastic substrates (traction force microscopy) 19, 34 -37, or elastic substrates with arrays of micro or nanoscopic pillars (see Fig. 1 A) 14,[38][39][40][41][42][43][44][45][46] . They are based on measuring force-induced deformations of the sensor and converting them into actual force values via its elastic properties. For small deformations, the force F is assumed to be proportional to the deformation δ (Hooke's law). Accurate force calculations require a proper calibration of the sensor's stiffness (spring constant k) and need to be corrected for possible crosstalk between adjacent measurement sites. In this paper we theoretically and experimentally address these important issues in the context of elastic pillar substrates.Pillar arrays for cellular studies are typically made of poly(dimethylsiloxane) (PDMS) and characterized by pillar dimensions and spacing (Fig. 1 B). The spring stiffness of a pillar is determined by the combination of the material's Young's modulus E and the absolute dimensions (height L, diameter D) and typically lies in the range 1 to 200 nN/µm. In most experimental studies, only bending of a botto...

Many nucleic acid stains show a strong fluorescence enhancement upon binding to doublestranded 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.

According to the Chinese yin-yang concept, seemingly opposing forces give rise and respond to each other. Opposing forces, whether passive or active, are also at work when cells adhere to a substrate or extracellular matrix, sense environmental properties, and finally respond to them. In this review, we describe molecular elements inside and outside of the cell that establish labile physical connections, and how forces regulate their interplay, namely formation, reinforcement, breakage, and reconfiguration of these elements. What a cell locally feels thus depends not only on the displacement of materials, but also on the stability of molecular interactions, on the conversion of mechanical forces to biochemical signals by stretching proteins into structural intermediates (mechano-chemical signal conversion), and on the micro- and nanoscopic features of the extracellular material. Current methodologies for quantifying forces in the cellular context at different length scales are also critically assessed.

It is generally expected that the kinetics of reactions inside livingDNA ͉ in vivo ͉ molecular crowding ͉ temperature oscillation ͉ optical lock-in microscopy

Extracellular excitation of neurons is applied in studies of cultured networks and brain tissue, as well as in neuroprosthetics. We elucidate its mechanism in an electrophysiological approach by comparing voltage-clamp and current-clamp recordings of individual neurons on an insulated planar electrode. Noninvasive stimulation of neurons from pedal ganglia of Lymnaea stagnalis is achieved by defined voltage ramps applied to an electrolyte/HfO2/silicon capacitor. Effects on the smaller attached cell membrane and the larger free membrane are distinguished in a two-domain-stimulation model. Under current-clamp, we study the polarization that is induced for closed ion channels. Under voltage-clamp, we determine the capacitive gating of ion channels in the attached membrane by falling voltage ramps and for comparison also the gating of all channels by conventional variation of the intracellular voltage. Neuronal excitation is elicited under current-clamp by two mechanisms: Rising voltage ramps depolarize the free membrane such that an action potential is triggered. Falling voltage ramps depolarize the attached membrane such that local ion currents are activated that depolarize the free membrane and trigger an action potential. The electrophysiological analysis of extracellular stimulation in the simple model system is a basis for its systematic optimization in neuronal networks and brain tissue.

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.

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.