Polymerized LB films imaged with a combined atomic force microscope-fluorescence microscope

The first results obtained with a new stand-alone atomic force microscope (AFM) integrated with a standard Zeiss optical fluorescence microscope are presented. The optical microscope allows location and selection of objects to be imaged with the high-resolution AFM. Furthermore, the combined microscope enables a direct comparison between features observed in the fluorescence microscope and those observed in the images obtained with the AFM, in air or under liquid. The cracks in polymerized Langmuir-Blodgett films of lO,l2-pentacosadiynoic acid as observed in the fluorescence microscope run parallel to one of the lattice directions of the crystal as revealed by molecular resolution images obtained with the AFM. The orientation of these cracks also coincides with the polarization direction of the fluorescent light, indicating that the cracks run along the polymer backbone. Ripple-like corrugations on a submicrometer scale have been observed, which may be due to mechanical stress created during the polymerization process

Tip-sample interactions in atomic force microscopy: I. Modulating adhesion between silicon nitride and glass

An adhesive interaction between a silicon nitride AFM tip and glass substrate in water is described. This adhesion is in the range 5-40 nN, of which a large component is likely to be due to hydrogen bonding between the silanol groups on both surfaces. The interaction can be modulated by a variety of buffers commonly used in biochemical and biological research, including sodium phosphate, tris(hydroxymethyl)aminomethane, glycine, and N-2-hydroxyethyl-piperazine N'-2-ethanesulfonic acid. Using these buffers it appears that there are effects of ion concentration, ion type and pH on the measured adhesion. Of the conditions examined, phosphate was most effective at reducing adhesion and could be used at concentrations as low as 10 mM at neutral pH. The results demonstrate that the chemical interactions between tip and sample can be modulated, and provide a basis for designing conditions for imaging and manipulating biological molecules and structures

Membrane-membrane and membrane-substrate adhesion during dissection of gap junctions with the atomic-force microscope

The gap junction is a specialized region of the plasma membrane that consists of an array of cell-to-cell ion channels. These channels form where the membranes from two cells come together, and the gap junction is therefore composed of two lipid bilayers. The atomic force microscope (AFM) can be used to dissect the gap junction, removing one membrane and exposing the extracellular domains of the second. The force required to dissect the membrane, near 10^(-8) N vertical force for gap junctions adsorbed to mica, provides a measure of the strength of the interaction between the two membranes. Since a single membrane is left in contact with the mica, this interaction must be stronger than the membrane-membrane interaction. Non-junctional membrane attached to the gap junctions is easily removed with the AFM tip while the gap junction membrane remains attached to the mica, providing evidence that the interaction with the mica is mainly mediated by protein-mica interactions. Consistent with this hypothesis is the observation that material trapped under the membrane sometimes results in pieces of membrane above the material being pulled out during dissection. These results lay the foundation for examining the molecular details of the basis for membrane- membrane and membrane-substrate adhesion

Membrane-membrane and membrane-substrate adhesion during dissection of gap junctions with the atomic-force microscope

The gap junction is a specialized region of the plasma membrane that consists of an array of cell-to-cell ion channels. These channels form where the membranes from two cells come together, and the gap junction is therefore composed of two lipid bilayers. The atomic force microscope (AFM) can be used to dissect the gap junction, removing one membrane and exposing the extracellular domains of the second. The force required to dissect the membrane, near 10^(-8) N vertical force for gap junctions adsorbed to mica, provides a measure of the strength of the interaction between the two membranes. Since a single membrane is left in contact with the mica, this interaction must be stronger than the membrane-membrane interaction. Non-junctional membrane attached to the gap junctions is easily removed with the AFM tip while the gap junction membrane remains attached to the mica, providing evidence that the interaction with the mica is mainly mediated by protein-mica interactions. Consistent with this hypothesis is the observation that material trapped under the membrane sometimes results in pieces of membrane above the material being pulled out during dissection. These results lay the foundation for examining the molecular details of the basis for membrane- membrane and membrane-substrate adhesion

Scalable Bayesian Functional Connectivity Inference for Multi-Electrode Array Recordings

Multi-electrode arrays (MEAs) can record extracellular action potentials (also known as 'spikes') from hundreds or thousands of neurons simultaneously. Inference of a functional network from a spike train is a fundamental and formidable computational task in neuroscience. With the advancement of MEA technology, it has become increasingly crucial to develop statistical tools for analyzing multiple neuronal activity as a network. In this paper, we propose a scalable Bayesian framework for inference of functional networks from MEA data. Our framework makes use of the hierarchical structure of networks of neurons. We split the large scale recordings into smaller local networks for network inference, which not only eases the computational burden from Bayesian sampling but also provides useful insights on regional connections in organoids and brains. We speed up the expensive Bayesian sampling process by using parallel computing. Experiments on both synthetic datasets and large-scale real-world MEA recordings show the effectiveness and efficiency of the scalable Bayesian framework. Inference of networks from controlled experiments exposing neural cultures to cadmium presents distinguishable results and further confirms the utility of our framework.Comment: in BIOKDD 202

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution

Real-time microdamage and strain detection during micromechanical testing of single trabeculae

For the assessment of local deformations, we recently combined mechanical testing of trabecular bone with high-speed photography. In a previous study on cuboids of human vertebral trabecular bone we found strained trabeculae to whiten, and scanning electron microscopy showed excessive microdamage in whitened zones. In the presented study we tested single trabeculae from bovine femur and tibia in a three-point-bending geometry. Whitening was detected in the form of an ellipsoid zone on the tension side on tested trabeculae. Upon crack formation the whitening fades and a whitened zone following the propagating crack tip can be seen In addition to whitening/microdamage assessment we use ink marks applied to the samples and a modified digital image correlation to obtain the local strains involved in whitening and formation. In the presented loading case the tensile strain along the long axis of the trabecula qualitatively correlates best with the whitening zones seen. Whitening and thus microdamage initiates around a local tensile strain of 3%, whereas crack initiation occurs at strains around 13%. Our results allow for the first time to correlate microdamage and local strains directly, which is direly needed for the development of realistic damage models used in finite element analyses