Surface deformation tracking and modelling of soft materials

Biomechanics and Modeling in Mechanobiology - Many computer vision algorithms have been presented to track surface deformations, but few have provided a direct comparison of measurements with other...     

Comparison of models for flow induced deformation of soft biological tissue

The behaviour of a deformable porous medium during the flow of fluid under a pressure difference is examined for both infinitesimal and finite deformations. Models for both cases are solved for the problem of steady one-dimensional compression and compared with experimental data from Parker et al. (J. appl. Mech. 54, 794-800, 1987) for a polyurethane sponge. The purpose of this study is to identify a simple model which agrees qualitatively with these published results. To relate the stress relations for biological tissues to the data for polymer sponges (Parker et al., 1987) a translation of 1.1 kPa was introduced. This allows for some structural differences between the two media. It was found that the infinitesimal models were adequate up to 20% strain, but significant divergence occurred for higher strains. A finite deformation model with the permeability depending exponentially on the strain gave the most consistent results and required the fitting of only two parameters.     

Nonlinear machine learning in simulations of soft and biological materials

Abstract

Interpretable parameterisations of free energy landscapes for soft and biological materials calculated from molecular simulation require the availability of ‘good’ collective variables (CVs) capable of discriminating the metastable states of the system and the barriers between them. If these CVs are coincident with the slow collective modes governing the long-time dynamical evolution, then they also furnish good coordinates in which to perform enhanced sampling to surmount high free energy barriers and efficiently explore and recover the landscape. Non-linear manifold learning techniques provide a means to systematically extract such CVs from molecular simulation trajectories by identifying and extracting low-dimensional manifolds lying latent within the high-dimensional coordinate space. We survey recent advances in data-driven CV discovery and enhanced sampling using non-linear manifold learning, describe the mathematical and theoretical underpinnings of these techniques, and present illustrative examples to molecular folding and colloidal self-assembly. We close with our outlook and perspective on future advances in this rapidly evolving field.     

Mechanical anisotropy of adherent cells probed by a three-dimensional magnetic twisting device

We describe a three-dimensional magnetic twisting device that is useful in characterizing the mechanical properties of cells. With the use of three pairs of orthogonally aligned coils, oscillatory mechanical torque was applied to magnetic beads about any chosen axis. Frequencies up to 1 kHz could be attained. Cell deformation was measured in response to torque applied via an RGD-coated, surface-bound magnetic bead. In both unpatterned and micropatterned elongated cells on extracellular matrix, the mechanical stiffness transverse to the long axis of the cell was less than half that parallel to the long axis. Elongated cells on poly-L-lysine lost stress fibers and exhibited little mechanical anisotropy; disrupting the actin cytoskeleton or decreasing cytoskeletal tension substantially decreased the anisotropy. These results suggest that mechanical anisotropy originates from intrinsic cytoskeletal tension within the stress fibers. Deformation patterns of the cytoskeleton and the nucleolus were sensitive to loading direction, suggesting anisotropic mechanical signaling. This technology may be useful for elucidating the structural basis of mechanotransduction. cytoskeleton; prestress; stress fibers; mechanotransduction; mechanical deformation     

A thermodynamically consistent constitutive equation for the elastic force-length relation of soft biological materials

Starting from the laws of thermodynamics of reversible processes, a temperature-dependent constitutive equation is derived for the elastic force-length relation of soft biological tissues. These tissues are composed of a network of fibres (mainly collagen). The equation is based on a model which uses a simplified two-dimensional representation of the alpha-helix of collagen.     

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the calgary biofilm device

Microbes frequently live within multicellular, solid surface-attached assemblages termed biofilms. These microbial communities have architectural features that contribute to population heterogeneity and consequently to emergent cell functions. Therefore, three-dimensional (3D) features of biofilm structure are important for understanding the physiology and ecology of these microbial systems. This paper details several protocols for scanning electron microscopy and confocal laser scanning microscopy (CLSM) of biofilms grown on polystyrene pegs in the Calgary Biofilm Device (CBD). Furthermore, a procedure is described for image processing of CLSM data stacks using amira™, a virtual reality tool, to create surface and/or volume rendered 3D visualizations of biofilm microorganisms. The combination of microscopy with microbial cultivation in the CBD — an apparatus that was designed for highthroughput susceptibility testing — allows for structure-function analysis of biofilms under multivariate growth and exposure conditions.     

Versatile and inexpensive Hall-Effect force sensor for mechanical characterization of soft biological materials

Mismatch of hierarchical structure and mechanical properties between tissue-engineered implants and native tissue may result in signal cues that negatively impact repair and remodeling. With bottom-up tissue engineering approaches, designing tissue components with proper microscale mechanical properties is crucial to achieve necessary macroscale properties in the final implant. However, characterizing microscale mechanical properties is challenging, and current methods do not provide the versatility and sensitivity required to measure these fragile, soft biological materials. Here, we developed a novel, highly sensitive Hall-Effect based force sensor that is capable of measuring mechanical properties of biological materials over wide force ranges (μN to N), allowing its use at all steps in layer-by-layer fabrication of engineered tissues. The force sensor design can be easily customized to measure specific force ranges, while remaining easy to fabricate using inexpensive, commercial materials. Although we used the force sensor to characterize mechanics of single-layer cell sheets and silk fibers, the design can be easily adapted for different applications spanning larger force ranges (>N). This platform is thus a novel, versatile, and practical tool for mechanically characterizing biological and biomimetic materials.     

Autometallographic enhancement of the Golgi-Cox staining enables high resolution visualization of dendrites and spines

We present a method for autometallographic (AMG) enhancement of the Golgi-Cox staining enabling high resolution visualization of dendrites and spines. The method is cheaper and more flexible than conventional enhancement procedures performed with commercial photographic developers. The staining procedure is thoroughly described and we demonstrate with qualitative and quantitative data, how histological tissue sectioning, Golgi-Cox immersion time and different AMG enhancement length may influence the staining of dendrites and spines in the rat hippocampus. The described method will be of value for future behavioural-anatomical studies, examining changes in dendrite branching and spine density caused by brain diseases and their subsequent treatment.     

Reconstruction of elastic properties of soft biological tissues from data about it's deformation under dynamic load

The present work continues theoretical investigations on developing new noninvasive methods for diagnostics of tissue pathologies. These methods are based on tissue elasticity reconstruction using the measured internal displacements occurring due to the deformation of the object under study. Dynamic loading of the object is considered. The robustness of the proposed elasticity reconstruction procedure is demonstrated using numerical modeling of the displacement fields inside the nonhomogeneous object.     

JColorGrid: software for the visualization of biological measurements

Background  

Two-dimensional data colourings are an effective medium by which to represent three-dimensional data in two dimensions. Such "color-grid" representations have found increasing use in the biological sciences (e.g. microarray 'heat maps' and bioactivity data) as they are particularly suited to complex data sets and offer an alternative to the graphical representations included in traditional statistical software packages. The effectiveness of color-grids lies in their graphical design, which introduces a standard for customizable data representation. Currently, software applications capable of generating limited color-grid representations can be found only in advanced statistical packages or custom programs (e.g. micro-array analysis tools), often associated with steep learning curves and requiring expert knowledge.     

Data-dependent visualization of biological networks in the web-browser with NDExEdit

Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. The most prominent software in the field for the visualization of biological networks is Cytoscape, a desktop modeling environment also including many features for analysis.A further challenge when working with networks is their distribution. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. A well-established solution is provided by the NDEx platform where users can upload a network, share it with selected colleagues or make it publicly available.NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. With our tool, plain networks can be enhanced easily for further usage in presentations and publications. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. The web tool is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools, Cytoscape and NDEx. Therefore the modified network can be directly exported to the NDEx platform or saved as a compatible CX file, additionally to standard image formats like PNG and JPEG.     

Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain

Visualizing entire neuronal networks for analysis in the intact brain has been impossible up to now. Techniques like computer tomography or magnetic resonance imaging (MRI) do not yield cellular resolution, and mechanical slicing procedures are insufficient to achieve high-resolution reconstructions in three dimensions. Here we present an approach that allows imaging of whole fixed mouse brains. We modified 'ultramicroscopy' by combining it with a special procedure to clear tissue. We show that this new technique allows optical sectioning of fixed mouse brains with cellular resolution and can be used to detect single GFP-labeled neurons in excised mouse hippocampi. We obtained three-dimensional (3D) images of dendritic trees and spines of populations of CA1 neurons in isolated hippocampi. Also in fruit flies and in mouse embryos, we were able to visualize details of the anatomy by imaging autofluorescence. Our method is ideally suited for high-throughput phenotype screening of transgenic mice and thus will benefit the investigation of disease models.     

Apical cell protrusions cause vertical deformation of the soft cancer nucleus

Breast cancer nuclei have highly irregular shapes, which are diagnostic and prognostic markers of breast cancer progression. The mechanisms by which irregular cancer nuclear shapes develop are not well understood. Here we report the existence of vertical, apical cell protrusions in cultured MDA-MB-231 breast cancer cells. Once formed, these protrusions persist over time scales of hours and are associated with vertically upward nuclear deformations. They are absent in normal mammary epithelial cells (MCF-10A cells). Microtubule disruption enriched these protrusions preferentially in MDA-MB-231 cells compared with MCF-10A cells, whereas inhibition of nonmuscle myosin II (NMMII) abolished this enrichment. Dynamic confocal imaging of the vertical cell and nuclear shape revealed that the apical cell protrusions form first, and in response, the nucleus deforms and/or subsequently gets vertically extruded into the apical protrusion. Overexpression of lamin A/C in MDA-MB-231 cells reduced nuclear deformation in apical protrusions. These data highlight the role of mechanical stresses generated by moving boundaries, as well as abnormal nuclear mechanics in the development of abnormal nuclear shapes in breast cancer cells.     

Affine versus non-affine deformation in soft biological tissues, measured by the reorientation and stretching of collagen fibres through the thickness of compressed porcine skin

Skin is a complex three-dimensional structure of cells, collagen fibres and other proteins. However most mechanical analyses treat skin as a two-dimensional membrane, neglecting the through thickness structure. In this paper we investigate through thickness reorientation of collagen fibres. The mode of deformation of skin is also considered. For modelling purposes deformation is usually assumed to be affine. This assumption was tested by constructing a simple geometrical, affine deformation model to predict the through thickness reorientation of collagen fibres, from their initial through thickness angle and the measured deformations of skin samples during compression. The measured reorientation of collagen fibres was found to be very variable, however the average reorientations were consistent with the predictions of the model, with the inclusion of a systematic error. The variation in the reorientation of individual fibres can be explained by the variations in the structure at a micrometre scale. The systematic deviation of reorientations from the model predictions can be explained by a non-affine relationship between the collagen fibres and ground substance at a micrometre scale. However, non-affine deformations at a micrometre scale caused by irregularities of structure are likely to average out at a millimetre scale, because at this level material is evenly distributed.     

Enhanced visualization of soft tissues in the study of aborted fetuses through the use of xeroradiography

As part of the diagnostic workup following an episode of fetal loss, it is generally recommended that fetal tissue be submitted for chromosome analysis and that the fetus be photographed and radiographed. Our recent clinical experience has suggested that, in those fetuses where size is compatible, xeroradiography may be superior to standard radiography. Xeroradiography utilizes principles similar to those in film radiology, with low-energy photon beams and relatively long exposure times. The physical characteristics of the beam and imaging system provide optimal soft tissue visualization. We have found this technique to be of use in studying a broad variety of abortuses with abnormalities. Examples of fetal abnormalities in which we have used this technique include acardia, neural tube defects, nuchal cystic hygroma, and arthrogryposis. In fetuses weighing 500-1,000 gm, the exposure settings are 25 MA, 1 second, 40 KVP. For larger fetuses the KVP should be increased by 1 or 2. This technique has not been useful for a complete body view of large fetuses due to the size limitations of the xeroradiographic cassette itself.     

A structural criterion for the biological compatibility of materials

The principles of searching and selection of the polymeric materials compatible with biological tissues are offered, based on structural features of the hydration shells of biopolymers.