Agent-based computational modeling of wounded epithelial cell monolayers

Computational modeling of biological systems, or in silico biology, is an emerging tool for understanding structure and order in biological tissues. Computational models of the behavior of epithelial cells in monolayer cell culture have been developed and used to predict the healing characteristics of scratch wounds made to urothelial cell cultures maintained in low- and physiological [Ca/sup 2+/] environments. Both computational models and in vitro experiments demonstrated that in low exogenous [Ca/sup 2+/], the closure of 500-/spl mu/m scratch wounds was achieved primarily by cell migration into the denuded area. The wound healing rate in low (0.09 mM) [Ca/sup 2+/] was approximately twice as rapid as in physiological (2 mM) [Ca/sup 2+/]. Computational modeling predicted that in cell cultures that are actively proliferating, no increase in the fraction of cells in the S-phase would be expected, and this conclusion was supported experimentally in vitro by bromodeoxyuridine incorporation assay. We have demonstrated that a simple rule-based model of cell behavior, incorporating rules relating to contact inhibition of proliferation and migration, is sufficient to qualitatively predict the calcium-dependent pattern of wound closure observed in vitro. Differences between the in vitro and in silico models suggest a role for wound-induced signaling events in urothelial cell cultures.     

Electrical impedance simulation and characterization of cell growth using the Fricke model

For label-free and real-time monitoring of biological cells, electrical impedance sensing of the cells attached to the microelectrode has been used. In this article, the electrical impedance analysis of the cell growth using the Fricke model that consisted of the extracellular resistance parallel to the series combination of an intracellular resistance and the membrane-related capacitance was investigated. To relate the morphological changes in the cells that accompanied the cell growth in the Fricke model parameters, the impedance spectra of a cell model were simulated at different cell sizes and cell-cell gaps using the finite element method. The simulated results showed that the increase in the cell size results in an increment of the extracellular resistance and that the decrease in the cell-cell gap leads to an increment of the extracellular resistance and a decrement of the capacitance. Based on the theoretical relationship between the model parameters and the considered cellular behavior, it was shown that the measured impedance spectra of the cells were mostly governed by the change in the cell-cell gap at the beginning of the culture time, and then by the cell size or the density of the cells that covered the electrode surface with a limited area.     

Guiding Cell Network Assembly using Shape-Morphing Hydrogels

Forces and relative movement between cells and extracellular matrix (ECM) are crucial to the self-organization of tissues during development. However, the spatial range over which these dynamics can be controlled in engineering approaches is limited, impeding progress toward the construction of large, structurally mature tissues. Herein, shape-morphing materials called “kinomorphs” that rationally control the shape and size of multicellular networks are described. Kinomorphs are sheets of ECM that change their shape, size, and density depending on patterns of cell contractility within them. It is shown that these changes can manipulate structure-forming behaviors of epithelial cells in many spatial locations at once. Kinomorphs are built using a new photolithographic technology to pattern single cells into ECM sheets that are >10× larger than previously described. These patterns are designed to partially mimic the branch geometry of the embryonic kidney epithelial network. Origami-inspired simulations are then used to predict changes in kinomorph shapes. Last, kinomorph dynamics are shown to provide a centimeter-scale program that sets specific spatial locations in which ≈50 µm-diameter epithelial tubules form by cell coalescence and structural maturation. The kinomorphs may significantly advance organ-scale tissue construction by extending the spatial range of cell self-organization in emerging model systems such as organoids.     

The effects of proteoglycan surface patterning on neuronal pathfinding

Protein micropatterning techniques are increasingly applied in cell choice assays to investigate fundamental biological phenomena that contribute to the host response to implanted biomaterials, and to explore the effects of protein stability and biological activity on cell behavior for in vitro cell studies. In the area of neuronal regeneration the protein micropatterning and cell choice assays are used to improve our understanding of the mechanisms directing nervous system during development and regenerative failure in the central nervous system (CNS) wound healing environment. In these cell assays, protein micropatterns need to be characterized for protein stability, bioactivity, and spatial distribution and then correlated with observed mammalian cell behavior using appropriate model system for CNS development and repair. This review provides the background on protein micropatterning for cell choice assays and describes some novel patterns that were developed to interrogate neuronal adaptation to inhibitory signals encountered in CNS injuries.     

From radiation-induced chromosome damage to cell death: modelling basic mechanisms and applications to boron neutron capture therapy

Cell death is a crucial endpoint in radiation-induced biological damage: on one side, cell death is a reference endpoint to characterise the action of radiation in biological targets; on the other side, any cancer therapy aims to kill tumour cells. Starting from Lea's target theory, many models have been proposed to interpret radiation-induced cell killing; after briefly discussing some of these models, in this paper, a mechanistic approach based on an experimentally observed link between chromosome aberrations and cell death was presented. More specifically, a model and a Monte Carlo code originally developed for chromosome aberrations were extended to simulate radiation-induced cell death applying an experimentally observed one-to-one relationship between the average number of 'lethal aberrations' (dicentrics, rings and deletions) per cell and -ln S, S being the fraction of surviving cells. Although such observation was related to X rays, in the present work, the approach was also applied to protons and alpha particles. A good agreement between simulation outcomes and literature data provided a model validation for different radiation types. The same approach was then successfully applied to simulate the survival of cells enriched with boron and irradiated with thermal neutrons at the Triga Mark II reactor in Pavia, to mimic a typical treatment for boron neutron capture therapy.     

Cells exploit a phase transition to mechanically remodel the fibrous extracellular matrix

Through mechanical forces, biological cells remodel the surrounding collagen network, generating striking deformation patterns. Tethers—tracts of high densification and fibre alignment—form between cells, thinner bands emanate from cell clusters. While tethers facilitate cell migration and communication, how they form is unclear. Combining modelling, simulation and experiment, we show that tether formation is a densification phase transition of the extracellular matrix, caused by buckling instability of network fibres under cell-induced compression, featuring unexpected similarities with martensitic microstructures. Multiscale averaging yields a two-phase, bistable continuum energy landscape for fibrous collagen, with a densified/aligned second phase. Simulations predict strain discontinuities between the undensified and densified phase, which localizes within tethers as experimentally observed. In our experiments, active particles induce similar localized patterns as cells. This shows how cells exploit an instability to mechanically remodel the extracellular matrix simply by contracting, thereby facilitating mechanosensing, invasion and metastasis.     

Réseaux et genèse de la forme: perspectives épistémologiques

Our paper focuses on Stuart Kauffman’s theory from 1993 to 2004. Kauffman is looking for an explanation of the genesis of living beings by genetic networks. From interactions to cell types, Kauffman’s viewpoint is concerned with differentiation and self-organization as network’s properties. His approach of morphogenetic processes is interesting but it is insufficient. According to Sole, Fernandez and Kauffman [2003], networks would give an explanation of the diversity in patterns and cell types. Some other authors [as Perkins et al., 2004] consider that it is necessary to explore interactions, not with logical methods only, but non-linear systems too. Network’s structure is related to biological diversity. It supposes genes’ power’s mediators within the cells and between them.     

Dynamics of the cell and its extracellular matrix--a simple mathematical approach

The extracellular matrix (ECM) is produced by the cells and secreted into the surrounding medium, and consists of a complex mixture of structural and functional proteins. It has been recently observed that the ECM can influence the behavior of cell growth in vitro quite remarkably. A simple mathematical model has been constructed based on negative feedback control mechanisms to represent the dynamics of ECM deposition and cellular differentiation. The model analysis shows a strong relationship between the numerical solution and the experimental observations in cell-polymer constructs for the design of engineered cartilage. The current paper may be a useful guide for those who want to explore the studies on cell-matrix interactions.     

Controlled two-photon photodegradation of PEG hydrogels to study and manipulate subcellular interactions on soft materials

Cell adhesion and detachment to and from the extracellular matrix (ECM) are critical regulators of cell function and fate due to the exchange of mechanical signals between the cell and its microenvironment. To study this cell mechanobiology, researchers have developed several innovative methods to investigate cell adhesion in vitro; however, most of these culture platforms are unnaturally stiff or static. To better capture the soft, dynamic nature of the ECM, we present a PEG-based hydrogel in which the context and geometry of the extracellular space can be precisely controlled in situ via two-photon induced erosion. Here, we characterize the two-photon erosion process, demonstrate its efficacy in the presence of cells, and subsequently exploit it to induce subcellular detachment from soft hydrogels. A working space was established for a range of laser powers required to induce complete erosion of the gel, and these data are plotted with model predictions. From this working space, two-photon irradiation parameters were selected for complete erosion in the presence of cells. Micron-scale features were eroded on and within a gel to demonstrate the resolution of patterning with these irradiation conditions. Lastly, two-photon irradiation was used to erode the material at the cell-gel interface to remove cell adhesion sites selectively, and cell retraction was monitored to quantify the mesenchymal stem cell (MSC) response to subcellular detachment from soft materials.     

Patterning multiple cell types in co-cultures: A review

With progress in materials, microelectronics, biological science, and some imagination we are in the position to manipulate and precisely control the local cellular environment to probe cell biology at the micron level. This precise control is important as cells interact strongly with their local environment including the extracellular matrix and neighboring cells. While various papers have reviewed the many techniques to pattern single-cell types, very few have focused on techniques to pattern multiple cell types in co-culture systems. Therefore, this review will explore various methods used to create patterned local cellular environments and the applications these techniques have found in probing cell–cell interactions. Emphasis will be placed on the creation of patterns incorporating multiple cell types in culture to study the interactions between different cell types in well controlled and biologically relevant environments. Such designs can be considered one of the greatest challenges bioengineers face to date.     

Decoupling the Direct and Indirect Biological Effects of ZnO Nanoparticles Using a Communicative Dual Cell‐Type Tissue Construct

While matter at the nanoscale can be manipulated, the knowledge of the interactions between these nanoproducts and the biological systems remained relatively laggard. Current nanobiology study is rooted on in vitro study using conventional 2D cell culture model. A typical study employs monolayer cell culture that simplifies the real context of which to measure any nanomaterial effect; unfortunately, this simplification also demonstrated the limitations of 2D cell culture in predicting the actual biological response of some tissues. In fact, some of the characteristics of tissue such as spatial arrangement of cells and cell–cell interaction, which are simplified in 2D cell culture model, play important roles in how cells respond to a stimulus. To more accurately recapitulate the features and microenvironment of tissue for nanotoxicity assessments, an improved organotypic‐like in vitro multicell culture system to mimic the kidney endoepithelial bilayer is introduced. Results showed that important nano‐related parameters such as the diffusion, direct and indirect toxic effects of ZnO nanoparticles can be studied by combining this endoepithelial bilayer tissue model and traditional monolayer culture setting.     

Effect of a synthetic link N peptide nanofiber scaffold on the matrix deposition of aggrecan and type II collagen in rabbit notochordal cells

Self-assembling peptide nanofiber scaffolds have been studied extensively as biological materials for 3-dimensional cell culture and repairing tissue defects in animals. However, few studies have applied peptide nanofiber scaffolds in the tissue engineering of intervertebral discs (IVDs). In this study, a novel functionalized peptide scaffold was specifically designed for IVD tissue engineering, and notochordal cells (NCs) as an alternative cell source for IVD degeneration were selected to investigate the bioactive scaffold material. The novel RADA16-Link N self-assembling peptide scaffold material was designed by direct coupling to a bioactive motif link N. The link N nanofiber scaffold (LN-NS) material was obtained by mixing pure RADA16-I and RADA16-Link N (1:1) designer peptide solutions. Although live/dead cell assays showed that LN-NS and RADA16-I scaffold materials were both biocompatible with NCs, the LN-NS material significantly promoted NC adhesion compared with that of the pure RADA16-I SAP scaffold material. The depositions of aggrecan and type II collagen, which are significant markers for IVD cells, were remarkably increased. Furthermore, the results indicated that the link N motif, the matrix analog of the nucleus pulposus, significantly promoted the accumulation of other extracellular matrices in vitro. We conclude that the novel LN-NS material is a promising biological scaffold material, and may have a broad range of applications in IVD tissue engineering.     

Use of auricular chondrocytes for lining artificial surfaces: a mathematical model

Auricular elastic cartilage is a potential source for lining of luminal surfaces of implantable vascular devices, such as stents and left ventricular assist devices with the purpose to improve their biocompatibility. Auricular chondrocytes are easily accessible, harvested, and isolated, and they have been shown to provide a strong adherent cell lining for left ventricular assist devices. Additionally, Dr. Rosenstrauch have shown that it is possible to genetically engineer auricular chondrocytes to produce antithrombogenic factors. Thus, implantable vascular devices, such as coronary stents covered with genetically engineered auricular chondrocytes might lower restenosis rates and provide a long-lasting biocompatible prosthesis. In this paper, to optimize the process of lining of artificial surfaces with auricular cartilage, we devise a mathematical model that describes the rate of cell division and growth of extracellular matrix as a function of the initial cell count, proximity to other cells, and the type of artificial surface. Our mathematical model was experimentally tested using two different cell cultures (auricular chondrocytes and dermal fibroblasts) seeded on different artificial surfaces (tc-treated polystyrene and aluminum foil). Excellent agreement between the model and experiment was obtained. This mathematical model can be used to, for example, determine the optimum number of initially seaded cells that would provide fastest coverage of a given artificial surface.     

Fe3O4纳米粒子与细胞的相互作用研究

研究10 nm粒径的表面未修饰Fe3O4纳米粒子在体外对人正常肝细胞HL-7702及人肝癌细胞SMMC-7721的生长影响.通过倒置显微镜、透射电镜(TEM)观察加入Fe3O4纳米粒子后肝癌细胞和正常肝细胞的形态变化及磁性纳米粒子在细胞内分布状态.用CCK-8测定加入磁性纳米粒子培养后细胞增殖能力的变化.倒置显微镜、透...     

3D Scaffolds to Study Basic Cell Biology

Mimicking the properties of the extracellular matrix is crucial for developing in vitro models of the physiological microenvironment of living cells. Among other techniques, 3D direct laser writing (DLW) has emerged as a promising technology for realizing tailored 3D scaffolds for cell biology studies. Here, results based on DLW addressing basic biological issues, e.g., cell‐force measurements and selective 3D cell spreading on functionalized structures are reviewed. Continuous future progress in DLW materials engineering and innovative approaches for scaffold fabrication will enable further applications of DLW in applied biomedical research and tissue engineering.     

Experimental and computational validation of Hele-Shaw stagnation flow with varying shear stress

An in vitro flow model system with continuous variation of fluid shear stress can be used to test cell responses to a range of shear stresses. In this investigation, we validated such a flow system computationally for steady and unsteady flow conditions and experimentally for steady flow conditions. The unsteady flow validation is important for studying cells such as endothelial cells that experience unsteady flow conditions in their native environment. The system is capable of exposing cells in different regions of the chamber to steady or unsteady shear stress conditions with average values ranging linearly from 0 to 30 dyn/cm $^{2}$ . These tests and analyses demonstrate that the variable-width parallel plate flow system can be used to test the influence of a range of steady and unsteady fluid shear stress levels on cell activities.     

Adaptive coevolutionary networks: a review.

Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel studies from different fields, ranging from genomics to game theory. Here we review these recent developments and show that they can be viewed from a unique angle. We demonstrate that all these studies are characterized by common themes, most prominently: complex dynamics and robust topological self-organization based on simple local rules.     

Osteoblast-like cellular response to dynamic changes in the ionic extracellular environment produced by calcium-deficient hydroxyapatite

Solution-mediated reactions due to ionic substitutions are increasingly explored as a strategy to improve the biological performance of calcium phosphate-based materials. Yet, cellular response to well-defined dynamic changes of the ionic extracellular environment has so far not been carefully studied in a biomaterials context. In this work, we present kinetic data on how osteoblast-like SAOS-2 cellular activity and calcium-deficient hydroxyapatite (CDHA) influenced extracellular pH as well as extracellular concentrations of calcium and phosphate in standard in vitro conditions. Since cells were grown on membranes permeable to ions and proteins, they could share the same aqueous environment with CDHA, but still be physically separated from the material. In such culture conditions, it was observed that gradual material-induced adsorption of calcium and phosphate from the medium had only minor influence on cellular proliferation and alkaline phosphatase activity, but that competition for calcium and phosphate between cells and the biomaterial delayed and reduced significantly the cellular capacity to deposit calcium in the extracellular matrix. The presented work thus gives insights into how and to what extent solution-mediated reactions can influence cellular response, and this will be necessary to take into account when interpreting CDHA performance both in vitro and in vivo.