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Sample records for 3d dynamic cell

  1. Dynamic 3D cell culture via a chemoselective photoactuated ligand.

    PubMed

    Westcott, Nathan P; Luo, Wei; Goldstein, Jeffrey; Yousaf, Muhammad N

    2014-09-01

    A new strategy to create a dynamic scaffold for three-dimensional (3D) cell experiments based on a photo-activated cell adhesive peptide ligand is described. After polymerization, the inert matrix becomes cell adhesive by chemoselective modification through the conjugation of oxyamine-terminated ligands. Furthermore, spatial and temporal control of cell culture within the 3D matrix was achieved by the use of a biospecific photoprotected peptide and visualized by confocal microscopy.

  2. 3D Protein Dynamics in the Cell Nucleus.

    PubMed

    Singh, Anand P; Galland, Rémi; Finch-Edmondson, Megan L; Grenci, Gianluca; Sibarita, Jean-Baptiste; Studer, Vincent; Viasnoff, Virgile; Saunders, Timothy E

    2017-01-10

    The three-dimensional (3D) architecture of the cell nucleus plays an important role in protein dynamics and in regulating gene expression. However, protein dynamics within the 3D nucleus are poorly understood. Here, we present, to our knowledge, a novel combination of 1) single-objective based light-sheet microscopy, 2) photoconvertible proteins, and 3) fluorescence correlation microscopy, to quantitatively measure 3D protein dynamics in the nucleus. We are able to acquire >3400 autocorrelation functions at multiple spatial positions within a nucleus, without significant photobleaching, allowing us to make reliable estimates of diffusion dynamics. Using this tool, we demonstrate spatial heterogeneity in Polymerase II dynamics in live U2OS cells. Further, we provide detailed measurements of human-Yes-associated protein diffusion dynamics in a human gastric cancer epithelial cell line.

  3. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions.

    PubMed

    Doyle, Andrew D; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M

    2015-11-09

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils.

  4. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

    NASA Astrophysics Data System (ADS)

    Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

    2015-11-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils.

  5. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

    PubMed Central

    Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

    2015-01-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils. PMID:26548801

  6. Segmentation of Whole Cells and Cell Nuclei From 3-D Optical Microscope Images Using Dynamic Programming

    PubMed Central

    McCullough, Dean P.; Gudla, Prabhakar R.; Harris, Bradley S.; Collins, Jason A.; Meaburn, Karen J.; Nakaya, Masa-Aki; Yamaguchi, Terry P.; Misteli, Tom; Lockett, Stephen J.

    2009-01-01

    Communications between cells in large part drive tissue development and function, as well as disease-related processes such as tumorigenesis. Understanding the mechanistic bases of these processes necessitates quantifying specific molecules in adjacent cells or cell nuclei of intact tissue. However, a major restriction on such analyses is the lack of an efficient method that correctly segments each object (cell or nucleus) from 3-D images of an intact tissue specimen. We report a highly reliable and accurate semi-automatic algorithmic method for segmenting fluorescence-labeled cells or nuclei from 3-D tissue images. Segmentation begins with semi-automatic, 2-D object delineation in a user-selected plane, using dynamic programming (DP) to locate the border with an accumulated intensity per unit length greater that any other possible border around the same object. Then the two surfaces of the object in planes above and below the selected plane are found using an algorithm that combines DP and combinatorial searching. Following segmentation, any perceived errors can be interactively corrected. Segmentation accuracy is not significantly affected by intermittent labeling of object surfaces, diffuse surfaces, or spurious signals away from surfaces. The unique strength of the segmentation method was demonstrated on a variety of biological tissue samples where all cells, including irregularly shaped cells, were accurately segmented based on visual inspection. PMID:18450544

  7. Segmentation of whole cells and cell nuclei from 3-D optical microscope images using dynamic programming.

    PubMed

    McCullough, D P; Gudla, P R; Harris, B S; Collins, J A; Meaburn, K J; Nakaya, M A; Yamaguchi, T P; Misteli, T; Lockett, S J

    2008-05-01

    Communications between cells in large part drive tissue development and function, as well as disease-related processes such as tumorigenesis. Understanding the mechanistic bases of these processes necessitates quantifying specific molecules in adjacent cells or cell nuclei of intact tissue. However, a major restriction on such analyses is the lack of an efficient method that correctly segments each object (cell or nucleus) from 3-D images of an intact tissue specimen. We report a highly reliable and accurate semi-automatic algorithmic method for segmenting fluorescence-labeled cells or nuclei from 3-D tissue images. Segmentation begins with semi-automatic, 2-D object delineation in a user-selected plane, using dynamic programming (DP) to locate the border with an accumulated intensity per unit length greater that any other possible border around the same object. Then the two surfaces of the object in planes above and below the selected plane are found using an algorithm that combines DP and combinatorial searching. Following segmentation, any perceived errors can be interactively corrected. Segmentation accuracy is not significantly affected by intermittent labeling of object surfaces, diffuse surfaces, or spurious signals away from surfaces. The unique strength of the segmentation method was demonstrated on a variety of biological tissue samples where all cells, including irregularly shaped cells, were accurately segmented based on visual inspection.

  8. Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

    PubMed Central

    Härmä, Ville; Schukov, Hannu-Pekka; Happonen, Antti; Ahonen, Ilmari; Virtanen, Johannes; Siitari, Harri; Åkerfelt, Malin; Lötjönen, Jyrki; Nees, Matthias

    2014-01-01

    Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports

  9. Brownian nanoimaging of interface dynamics and ligand-receptor binding at cell surfaces in 3-D.

    PubMed

    Kuznetsov, Igor R; Evans, Evan A

    2013-04-01

    We describe a method for nanoimaging interfacial dynamics and ligand-receptor binding at surfaces of live cells in 3-D. The imaging probe is a 1-μm diameter glass bead confined by a soft laser trap to create a "cloud" of fluctuating states. Using a facile on-line method of video image analysis, the probe displacements are reported at ~10 ms intervals with bare precisions (±SD) of 4-6 nm along the optical axis (elevation) and 2 nm in the transverse directions. We demonstrate how the Brownian distributions are analyzed to characterize the free energy potential of each small probe in 3-D taking into account the blur effect of its motions during CCD image capture. Then, using the approach to image interactions of a labeled probe with lamellae of leukocytic cells spreading on cover-glass substrates, we show that deformations of the soft distribution in probe elevations provide both a sensitive long-range sensor for defining the steric topography of a cell lamella and a fast telemetry for reporting rare events of probe binding with its surface receptors. Invoking established principles of Brownian physics and statistical thermodynamics, we describe an off-line method of super resolution that improves precision of probe separations from a non-reactive steric boundary to ~1 nm.

  10. Migration dynamics of breast cancer cells in a tunable 3D interstitial flow chamber.

    PubMed

    Haessler, Ulrike; Teo, Jeremy C M; Foretay, Didier; Renaud, Philippe; Swartz, Melody A

    2012-04-01

    The migration of cells such as leukocytes, tumor cells, and fibroblasts through 3D matrices is critical for regulating homeostasis and immunity and for driving pathogenesis. Interstitial flow through the extracellular matrix, which can substantially increase during inflammation and in the tumor microenvironment, can influence cell migration in multiple ways. Leukocytes and tumor cells are heterogeneous in their migration responses to flow, yet most 3D migration studies use endpoint measurements representing average characteristics. Here we present a robust new microfluidic device for 3D culture with live imaging under well-controlled flow conditions, along with a comparison of analytical methods for describing the migration behavior of heterogeneous cell populations. We then use the model to provide new insight on how interstitial flow affects MDA-MB-231 breast cancer cell invasion, phenomena that are not seen from averaged or endpoint measurements. Specifically, we find that interstitial flow increases the percentage of cells that become migratory, and increases migrational speed in about 20% of the cells. It also increases the migrational persistence of a subpopulation (5-10% of cells) in the positive or negative flow direction. Cells that migrated upstream moved faster but with less directedness, whereas cells that migrated in the direction of flow moved at slower speeds but with higher directedness. These findings demonstrate how fluid flow in the tumor microenvironment can enhance tumor cell invasion by directing a subpopulation of tumor cells in the flow direction; i.e., towards the draining lymphatic vessels, a major route of metastasis.

  11. Measuring dynamic cell-material interactions and remodeling during 3D human mesenchymal stem cell migration in hydrogels.

    PubMed

    Schultz, Kelly M; Kyburz, Kyle A; Anseth, Kristi S

    2015-07-21

    Biomaterials that mimic aspects of the extracellular matrix by presenting a 3D microenvironment that cells can locally degrade and remodel are finding increased applications as wound-healing matrices, tissue engineering scaffolds, and even substrates for stem cell expansion. In vivo, cells do not simply reside in a static microenvironment, but instead, they dynamically reengineer their surroundings. For example, cells secrete proteases that degrade extracellular components, attach to the matrix through adhesive sites, and can exert traction forces on the local matrix, causing its spatial reorganization. Although biomaterials scaffolds provide initially well-defined microenvironments for 3D culture of cells, less is known about the changes that occur over time, especially local matrix remodeling that can play an integral role in directing cell behavior. Here, we use microrheology as a quantitative tool to characterize dynamic cellular remodeling of peptide-functionalized poly(ethylene glycol) (PEG) hydrogels that degrade in response to cell-secreted matrix metalloproteinases (MMPs). This technique allows measurement of spatial changes in material properties during migration of encapsulated cells and has a sensitivity that identifies regions where cells simply adhere to the matrix, as well as the extent of local cell remodeling of the material through MMP-mediated degradation. Collectively, these microrheological measurements provide insight into microscopic, cellular manipulation of the pericellular region that gives rise to macroscopic tracks created in scaffolds by migrating cells. This quantitative and predictable information should benefit the design of improved biomaterial scaffolds for medically relevant applications.

  12. Dynamic Assessment of Fibroblast Mechanical Activity during Rac-induced Cell Spreading in 3-D Culture

    PubMed Central

    Petroll, W. Matthew; Ma, Lisha; Kim, Areum; Ly, Linda; Vishwanath, Mridula

    2009-01-01

    The goal of this study was to determine the morphological and sub-cellular mechanical effects of Rac activation on fibroblasts within 3-D collagen matrices. Corneal fibroblasts were plated at low density inside 100 μm thick fibrillar collagen matrices and cultured for 1 to 2 days in serum-free media. Time-lapse imaging was then performed using Nomarski DIC. After an acclimation period, perfusion was switched to media containing PDGF. In some experiments, Y-27632 or blebbistatin were used to inhibit Rho-kinase (ROCK) or myosin II, respectively. PDGF activated Rac and induced cell spreading, which resulted in an increase in cell length, cell area, and the number of pseudopodial processes. Tractional forces were generated by extending pseudopodia, as indicated by centripetal displacement and realignment of collagen fibrils. Interestingly, the pattern of pseudopodial extension and local collagen fibril realignment was highly dependent upon the initial orientation of fibrils at the leading edge. Following ROCK or myosin II inhibition, significant ECM relaxation was observed, but small displacements of collagen fibrils continued to be detected at the tips of pseudopodia. Taken together, the data suggests that during Rac-induced cell spreading within 3-D matrices, there is a shift in the distribution of forces from the center to the periphery of corneal fibroblasts. ROCK mediates the generation of large myosin II-based tractional forces during cell spreading within 3-D collagen matrices, however residual forces can be generated at the tips of extending pseudopodia that are both ROCK and myosin II-independent. PMID:18452153

  13. Quantifying Transient 3D Dynamical Phenomena of Single mRNA Particles in Live Yeast Cell Measurements

    PubMed Central

    Calderon, Christopher P.; Thompson, Michael A.; Casolari, Jason M.; Paffenroth, Randy C.; Moerner, W. E.

    2013-01-01

    Single-particle tracking (SPT) has been extensively used to obtain information about diffusion and directed motion in a wide range of biological applications. Recently, new methods have appeared for obtaining precise (10s of nm) spatial information in three dimensions (3D) with high temporal resolution (measurements obtained every 4ms), which promise to more accurately sense the true dynamical behavior in the natural 3D cellular environment. Despite the quantitative 3D tracking information, the range of mathematical methods for extracting information about the underlying system has been limited mostly to mean-squared displacement analysis and other techniques not accounting for complex 3D kinetic interactions. There is a great need for new analysis tools aiming to more fully extract the biological information content from in vivo SPT measurements. High-resolution SPT experimental data has enormous potential to objectively scrutinize various proposed mechanistic schemes arising from theoretical biophysics and cell biology. At the same time, methods for rigorously checking the statistical consistency of both model assumptions and estimated parameters against observed experimental data (i.e. goodness-of-fit tests) have not received great attention. We demonstrate methods enabling (1) estimation of the parameters of 3D stochastic differential equation (SDE) models of the underlying dynamics given only one trajectory; and (2) construction of hypothesis tests checking the consistency of the fitted model with the observed trajectory so that extracted parameters are not over-interpreted (the tools are applicable to linear or nonlinear SDEs calibrated from non-stationary time series data). The approach is demonstrated on high-resolution 3D trajectories of single ARG3 mRNA particles in yeast cells in order to show the power of the methods in detecting signatures of transient directed transport. The methods presented are generally relevant to a wide variety of 2D and 3D SPT

  14. Measurement of dynamic cell-induced 3D displacement fields in vitro for traction force optical coherence microscopy.

    PubMed

    Mulligan, Jeffrey A; Bordeleau, François; Reinhart-King, Cynthia A; Adie, Steven G

    2017-02-01

    Traction force microscopy (TFM) is a method used to study the forces exerted by cells as they sense and interact with their environment. Cell forces play a role in processes that take place over a wide range of spatiotemporal scales, and so it is desirable that TFM makes use of imaging modalities that can effectively capture the dynamics associated with these processes. To date, confocal microscopy has been the imaging modality of choice to perform TFM in 3D settings, although multiple factors limit its spatiotemporal coverage. We propose traction force optical coherence microscopy (TF-OCM) as a novel technique that may offer enhanced spatial coverage and temporal sampling compared to current methods used for volumetric TFM studies. Reconstructed volumetric OCM data sets were used to compute time-lapse extracellular matrix deformations resulting from cell forces in 3D culture. These matrix deformations revealed clear differences that can be attributed to the dynamic forces exerted by normal versus contractility-inhibited NIH-3T3 fibroblasts embedded within 3D Matrigel matrices. Our results are the first step toward the realization of 3D TF-OCM, and they highlight the potential use of OCM as a platform for advancing cell mechanics research.

  15. Measurement of dynamic cell-induced 3D displacement fields in vitro for traction force optical coherence microscopy

    PubMed Central

    Mulligan, Jeffrey A.; Bordeleau, François; Reinhart-King, Cynthia A.; Adie, Steven G.

    2017-01-01

    Traction force microscopy (TFM) is a method used to study the forces exerted by cells as they sense and interact with their environment. Cell forces play a role in processes that take place over a wide range of spatiotemporal scales, and so it is desirable that TFM makes use of imaging modalities that can effectively capture the dynamics associated with these processes. To date, confocal microscopy has been the imaging modality of choice to perform TFM in 3D settings, although multiple factors limit its spatiotemporal coverage. We propose traction force optical coherence microscopy (TF-OCM) as a novel technique that may offer enhanced spatial coverage and temporal sampling compared to current methods used for volumetric TFM studies. Reconstructed volumetric OCM data sets were used to compute time-lapse extracellular matrix deformations resulting from cell forces in 3D culture. These matrix deformations revealed clear differences that can be attributed to the dynamic forces exerted by normal versus contractility-inhibited NIH-3T3 fibroblasts embedded within 3D Matrigel matrices. Our results are the first step toward the realization of 3D TF-OCM, and they highlight the potential use of OCM as a platform for advancing cell mechanics research. PMID:28271010

  16. Stroma Regulates Increased Epithelial Lateral Cell Adhesion in 3D Culture: A Role for Actin/Cadherin Dynamics

    PubMed Central

    Chambers, Karen F.; Pearson, Joanna F.; Aziz, Naveed; O'Toole, Peter; Garrod, David; Lang, Shona H.

    2011-01-01

    Background Cell shape and tissue architecture are controlled by changes to junctional proteins and the cytoskeleton. How tissues control the dynamics of adhesion and cytoskeletal tension is unclear. We have studied epithelial tissue architecture using 3D culture models and found that adult primary prostate epithelial cells grow into hollow acinus-like spheroids. Importantly, when co-cultured with stroma the epithelia show increased lateral cell adhesions. To investigate this mechanism further we aimed to: identify a cell line model to allow repeatable and robust experiments; determine whether or not epithelial adhesion molecules were affected by stromal culture; and determine which stromal signalling molecules may influence cell adhesion in 3D epithelial cell cultures. Methodology/Principal Findings The prostate cell line, BPH-1, showed increased lateral cell adhesion in response to stroma, when grown as 3D spheroids. Electron microscopy showed that 9.4% of lateral membranes were within 20 nm of each other and that this increased to 54% in the presence of stroma, after 7 days in culture. Stromal signalling did not influence E-cadherin or desmosome RNA or protein expression, but increased E-cadherin/actin co-localisation on the basolateral membranes, and decreased paracellular permeability. Microarray analysis identified several growth factors and pathways that were differentially expressed in stroma in response to 3D epithelial culture. The upregulated growth factors TGFβ2, CXCL12 and FGF10 were selected for further analysis because of previous associations with morphology. Small molecule inhibition of TGFβ2 signalling but not of CXCL12 and FGF10 signalling led to a decrease in actin and E-cadherin co-localisation and increased paracellular permeability. Conclusions/Significance In 3D culture models, paracrine stromal signals increase epithelial cell adhesion via adhesion/cytoskeleton interactions and TGFβ2-dependent mechanisms may play a key role. These

  17. µ-Particle tracking velocimetry and computational fluid dynamics study of cell seeding within a 3D porous scaffold.

    PubMed

    Marin, A Campos; Grossi, T; Bianchi, E; Dubini, G; Lacroix, D

    2017-08-03

    Cell seeding of 3D scaffolds is a critical step in tissue engineering since the final tissue properties are related to the initial cell distribution and density within the scaffold unit. Perfusion systems can transport cells to the scaffold however; the fact that cells flow inside the scaffold pores does not guarantee cell deposition onto the scaffold substrate and cell attachment. The aim of this study was to investigate how fluid flow conditions modulate cell motion and deposition during perfusion. For such a purpose, a multiphase-based computational fluid dynamics (CFD) model was developed in conjunction with particle tracking velocimetry experiments (PTV) which for the first time were applied to observe cell seeding inside a 3D scaffold. CFD and PTV results showed the strong effect of gravity for lower flow rates leading to cell sedimentation and poor transport of cells to the scaffold. Higher flow rates help overcome the effect of gravity so more cells travelling inside the scaffold were found. Nonetheless, fluid flow drags cells along the fluid streamlines without intercepting the scaffold substrate. As a consequence, if cells do not deposit into the scaffold substrate, cell adhesion cannot occur. Therefore, cell-scaffold interception should be promoted and the present computational model which predicts the effect of gravity and fluid drag on cells trajectories could serve to optimise bioreactors and enhance cell seeding efficiency. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. A Novel Flow-Perfusion Bioreactor Supports 3D Dynamic Cell Culture

    PubMed Central

    Sailon, Alexander M.; Allori, Alexander C.; Davidson, Edward H.; Reformat, Derek D.; Allen, Robert J.; Warren, Stephen M.

    2009-01-01

    Background. Bone engineering requires thicker three-dimensional constructs than the maximum thickness supported by standard cell-culture techniques (2 mm). A flow-perfusion bioreactor was developed to provide chemotransportation to thick (6 mm) scaffolds. Methods. Polyurethane scaffolds, seeded with murine preosteoblasts, were loaded into a novel bioreactor. Control scaffolds remained in static culture. Samples were harvested at days 2, 4, 6, and 8 and analyzed for cellular distribution, viability, metabolic activity, and density at the periphery and core. Results. By day 8, static scaffolds had a periphery cell density of 67% ± 5.0%, while in the core it was 0.3% ± 0.3%. Flow-perfused scaffolds demonstrated peripheral cell density of 94% ± 8.3% and core density of 76% ± 3.1% at day 8. Conclusions. Flow perfusion provides chemotransportation to thick scaffolds. This system may permit high throughput study of 3D tissues in vitro and enable prefabrication of biological constructs large enough to solve clinical problems. PMID:20037739

  19. Quantifying Modes of 3D Cell Migration.

    PubMed

    Driscoll, Meghan K; Danuser, Gaudenz

    2015-12-01

    Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to the analyses performed today on cells crawling on flat substrates.

  20. Quantifying modes of 3D cell migration

    PubMed Central

    Driscoll, Meghan K.; Danuser, Gaudenz

    2015-01-01

    Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to the analyses performed today on cells crawling on flat substrates. PMID:26603943

  1. [3D emulation of epicardium dynamic mapping].

    PubMed

    Lu, Jun; Yang, Cui-Wei; Fang, Zu-Xiang

    2005-03-01

    In order to realize epicardium dynamic mapping of the whole atria, 3-D graphics are drawn with OpenGL. Some source codes are introduced in the paper to explain how to produce, read, and manipulate 3-D model data.

  2. Static & Dynamic Response of 3D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

    NIKE3D is a large deformations 3D finite element code used to obtain the resulting displacements and stresses from multi-body static and dynamic structural thermo-mechanics problems with sliding interfaces. Many nonlinear and temperature dependent constitutive models are available.

  3. 3D culture for cardiac cells.

    PubMed

    Zuppinger, Christian

    2016-07-01

    This review discusses historical milestones, recent developments and challenges in the area of 3D culture models with cardiovascular cell types. Expectations in this area have been raised in recent years, but more relevant in vitro research, more accurate drug testing results, reliable disease models and insights leading to bioartificial organs are expected from the transition to 3D cell culture. However, the construction of organ-like cardiac 3D models currently remains a difficult challenge. The heart consists of highly differentiated cells in an intricate arrangement.Furthermore, electrical “wiring”, a vascular system and multiple cell types act in concert to respond to the rapidly changing demands of the body. Although cardiovascular 3D culture models have been predominantly developed for regenerative medicine in the past, their use in drug screening and for disease models has become more popular recently. Many sophisticated 3D culture models are currently being developed in this dynamic area of life science. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.

  4. Dynamics of amino acid metabolism of primary human liver cells in 3D bioreactors

    PubMed Central

    Zeilinger, K.; Sickinger, S.; Schmidt-Heck, W.; Buentemeyer, H.; Iding, K.; Lehmann, J.; Pfaff, M.; Pless, G.; Gerlach, J.C.

    2006-01-01

    The kinetics of 18 amino acids, ammonia (NH3) and urea (UREA) in 18 liver cell bioreactor runs were analyzed and simulated by a two-compartment model consisting of a system of 42 differential equations. The model parameters, most of them representing enzymatic activities, were identified and their values discussed with respect to the different liver cell bioreactor performance levels. The nitrogen balance based model was used as a tool to quantify the variability of runs and to describe different kinetic patterns of the amino acid metabolism, in particular with respect to glutamate (GLU) and aspartate (ASP). PMID:16550345

  5. High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures

    PubMed Central

    Chen, Yu-Chih; Lou, Xia; Zhang, Zhixiong; Ingram, Patrick; Yoon, Euisik

    2015-01-01

    Photodynamic therapy (PDT), wherein light sensitive non-toxic agents are locally and selectively activated using light, has emerged as an appealing alternative to traditional cancer chemotherapy. Yet to date, PDT efficacy has been mostly characterized using 2D cultures. Compared to 2D cultures, 3D sphere culture generates unique spatial distributions of nutrients and oxygen for the cells that better mimics the in-vivo conditions. Using a novel polyHEMA (non-adherent polymer) fabrication process, we developed a microfluidic sphere formation platform that can (1) generate 1,024 uniform (size variation <10%) cancer spheres within a 2 cm by 2 cm core area, (2) culture spheres for more than 2 weeks, and (3) allow the retrieval of spheres. Using the presented platform, we have successfully characterized the different responses in 2D and 3D cell culture to PDT. Furthermore, we investigated the treatment resistance effect in cancer cells induced by tumor associated fibroblasts (CAF). Although the CAFs can enhance the resistance to traditional chemotherapy agents, no significant difference in PDT was observed. The preliminary results suggest that the PDT can be an attractive alternative cancer therapy, which is less affected by the therapeutic resistance induced by cancer associated cells. PMID:26153550

  6. High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chih; Lou, Xia; Zhang, Zhixiong; Ingram, Patrick; Yoon, Euisik

    2015-07-01

    Photodynamic therapy (PDT), wherein light sensitive non-toxic agents are locally and selectively activated using light, has emerged as an appealing alternative to traditional cancer chemotherapy. Yet to date, PDT efficacy has been mostly characterized using 2D cultures. Compared to 2D cultures, 3D sphere culture generates unique spatial distributions of nutrients and oxygen for the cells that better mimics the in-vivo conditions. Using a novel polyHEMA (non-adherent polymer) fabrication process, we developed a microfluidic sphere formation platform that can (1) generate 1,024 uniform (size variation <10%) cancer spheres within a 2 cm by 2 cm core area, (2) culture spheres for more than 2 weeks, and (3) allow the retrieval of spheres. Using the presented platform, we have successfully characterized the different responses in 2D and 3D cell culture to PDT. Furthermore, we investigated the treatment resistance effect in cancer cells induced by tumor associated fibroblasts (CAF). Although the CAFs can enhance the resistance to traditional chemotherapy agents, no significant difference in PDT was observed. The preliminary results suggest that the PDT can be an attractive alternative cancer therapy, which is less affected by the therapeutic resistance induced by cancer associated cells.

  7. Novel method to dynamically load cells in 3D-hydrogels culture for blast injury studies

    NASA Astrophysics Data System (ADS)

    Sory, David R.; Areias, Anabela C.; Overby, Darryl R.; Proud, William G.

    2017-01-01

    For at least a century explosive devices have been one of the most important causes of injuries in military conflicts as well as in terrorist attacks. Although significant experimental and modelling efforts have been focussed on blast injuries at the organ or tissue level, few studies have investigated the mechanisms of blast injuries at the cellular level. This paper introduces an in vitro method compatible with living cells to examine the effects of high stress and short-duration pulses relevant to blast loadings and blunt trauma. The experimental phase involves high strain-rate axial compression of cylindrical specimens within an hermetically sealed chamber made of biocompatible polymer. Numerical simulations were performed in order to verify the experimental loading conditions and to characterize the loading path within the sample. A proof of concept is presented so as to establish a new window to address fundamental questions regarding blast injury at the cellular level.

  8. Nonrigid Registration of 2-D and 3-D Dynamic Cell Nuclei Images for Improved Classification of Subcellular Particle Motion

    PubMed Central

    Kim, Il-Han; Chen, Yi-Chun M.; Spector, David L.; Eils, Roland; Rohr, Karl

    2012-01-01

    The observed motion of subcellular particles in fluorescence microscopy image sequences of live cells is generally a superposition of the motion and deformation of the cell and the motion of the particles. Decoupling the two types of movements to enable accurate classification of the particle motion requires the application of registration algorithms. We have developed an intensity-based approach for nonrigid registration of multi-channel microscopy image sequences of cell nuclei. First, based on 3-D synthetic images we demonstrate that cell nucleus deformations change the observed motion types of particles and that our approach allows to recover the original motion. Second, we have successfully applied our approach to register 2-D and 3-D real microscopy image sequences. A quantitative experimental comparison with previous approaches for nonrigid registration of cell microscopy has also been performed. PMID:20840894

  9. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    SciTech Connect

    Steven R Prescott; Curtis Smith

    2011-07-01

    provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  10. Nonlinear dynamics of 3D massive gravity

    NASA Astrophysics Data System (ADS)

    de Rham, Claudia; Gabadadze, Gregory; Pirtskhalava, David; Tolley, Andrew J.; Yavin, Itay

    2011-06-01

    We explore the nonlinear classical dynamics of the three-dimensional theory of "New Massive Gravity" proposed by Bergshoeff, Hohm and Townsend. We find that the theory passes remarkably highly nontrivial consistency checks at the nonlinear level. In particular, we show that: (1) In the decoupling limit of the theory, the interactions of the helicity-0 mode are described by a single cubic term — the so-called cubic Galileon — previously found in the context of the DGP model and in certain 4D massive gravities. (2) The conformal mode of the metric coincides with the helicity-0 mode in the decoupling limit. Away from this limit the nonlinear dynamics of the former is described by a certain generalization of Galileon interactions, which like the Galileons themselves have a well-posed Cauchy problem. (3) We give a non-perturbative argument based on the presence of additional symmetries that the full theory does not lead to any extra degrees of freedom, suggesting that a 3D analog of the 4D Boulware-Deser ghost is not present in this theory. Last but not least, we generalize "New Massive Gravity" and construct a class of 3D cubic order massive models that retain the above properties.

  11. Dynamics of 3D isolated thermal filaments

    NASA Astrophysics Data System (ADS)

    Walkden, N. R.; Easy, L.; Militello, F.; Omotani, J. T.

    2016-11-01

    Simulations have been carried out to establish how electron thermal physics, introduced in the form of a dynamic electron temperature, affects isolated filament motion and dynamics in 3D. It is found that thermal effects impact filament motion in two major ways when the pressure perturbation within the filament is supported primarily through a temperature increase as opposed to density: they lead to a strong increase in filament propagation in the bi-normal direction and a significant decrease in net radial propagation. Both effects arise from the temperature dependence of the sheath current which leads to a non-uniform floating potential, with the latter effect supplemented by faster pressure loss. The reduction in radial velocity can only occur when the filament cross-section loses angular symmetry. The behaviour is observed across different filament sizes and suggests that filaments with much larger temperature perturbations than density perturbations are more strongly confined to the near SOL region.

  12. 3D Hall MHD Reconnection Dynamics

    NASA Astrophysics Data System (ADS)

    Huba, J. D.; Rudakov, L.

    2002-05-01

    A 3D Hall MHD simulation code (VooDoo) has recently been developed at the Naval Research Laboratory. We present preliminary results of a fully 3D magnetic reconnection study using this code. The initial configuration of the plasma system is as follows. The ambient, reversed magnetic field is in the x-direction and is proportional to B0 tanh(y/Ly) where Ly is the scale length of the current sheet. Perturbation fields δ Bx and δ By are introduced to initiate the reconnection process. This initial configuration is similar to that used in the 2D GEM reconnection study. However, the perturbation fields are localized in the z-direction. We consider two cases: no guide field (Bz = 0) and a weak guide field (Bz = 0.1B0). We find that the reconnection process is not stationary in the z-direction but propagates in the B x ∇ n direction consistent with Hall drift physics. Hence, an asymmetric disruption of the current sheet ensues. The flow structure of the plasma in the vicinity of the X-point is complex. We find that the `neutral line' (i.e, along the z-direction) is not an ignorable coordinate and is not periodic in Hall MHD reconnection dynamics; two assumptions that are often made in reconnection studies. \\ Research supported by NASA and ONR

  13. 3D Cell Culture in Alginate Hydrogels

    PubMed Central

    Andersen, Therese; Auk-Emblem, Pia; Dornish, Michael

    2015-01-01

    This review compiles information regarding the use of alginate, and in particular alginate hydrogels, in culturing cells in 3D. Knowledge of alginate chemical structure and functionality are shown to be important parameters in design of alginate-based matrices for cell culture. Gel elasticity as well as hydrogel stability can be impacted by the type of alginate used, its concentration, the choice of gelation technique (ionic or covalent), and divalent cation chosen as the gel inducing ion. The use of peptide-coupled alginate can control cell–matrix interactions. Gelation of alginate with concomitant immobilization of cells can take various forms. Droplets or beads have been utilized since the 1980s for immobilizing cells. Newer matrices such as macroporous scaffolds are now entering the 3D cell culture product market. Finally, delayed gelling, injectable, alginate systems show utility in the translation of in vitro cell culture to in vivo tissue engineering applications. Alginate has a history and a future in 3D cell culture. Historically, cells were encapsulated in alginate droplets cross-linked with calcium for the development of artificial organs. Now, several commercial products based on alginate are being used as 3D cell culture systems that also demonstrate the possibility of replacing or regenerating tissue. PMID:27600217

  14. Nanoimaging of Focal Adhesion Dynamics in 3D

    PubMed Central

    Chiu, Chi-Li; Aguilar, Jose S.; Tsai, Connie Y.; Wu, GuiKai; Gratton, Enrico; Digman, Michelle A.

    2014-01-01

    Organization and dynamics of focal adhesion proteins have been well characterized in cells grown on two-dimensional (2D) cell culture surfaces. However, much less is known about the dynamic association of these proteins in the 3D microenvironment. Limited imaging technologies capable of measuring protein interactions in real time and space for cells grown in 3D is a major impediment in understanding how proteins function under different environmental cues. In this study, we applied the nano-scale precise imaging by rapid beam oscillation (nSPIRO) technique and combined the scaning-fluorescence correlation spectroscopy (sFCS) and the number and molecular brightness (N&B) methods to investigate paxillin and actin dynamics at focal adhesions in 3D. Both MDA-MB-231 cells and U2OS cells produce elongated protrusions with high intensity regions of paxillin in cell grown in 3D collagen matrices. Using sFCS we found higher percentage of slow diffusing proteins at these focal spots, suggesting assembling/disassembling processes. In addition, the N&B analysis shows paxillin aggregated predominantly at these focal contacts which are next to collagen fibers. At those sites, actin showed slower apparent diffusion rate, which indicated that actin is either polymerizing or binding to the scaffolds in these locals. Our findings demonstrate that by multiplexing these techniques we have the ability to spatially and temporally quantify focal adhesion assembly and disassembly in 3D space and allow the understanding tumor cell invasion in a more complex relevant environment. PMID:24959851

  15. From Dynamic Live Cell Imaging to 3D Ultrastructure: Novel Integrated Methods for High Pressure Freezing and Correlative Light-Electron Microscopy

    PubMed Central

    Spiegelhalter, Coralie; Tosch, Valérie; Hentsch, Didier; Koch, Marc; Kessler, Pascal; Schwab, Yannick; Laporte, Jocelyn

    2010-01-01

    Background In cell biology, the study of proteins and organelles requires the combination of different imaging approaches, from live recordings with light microscopy (LM) to electron microscopy (EM). Methodology To correlate dynamic events in adherent cells with both ultrastructural and 3D information, we developed a method for cultured cells that combines confocal time-lapse images of GFP-tagged proteins with electron microscopy. With laser micro-patterned culture substrate, we created coordinates that were conserved at every step of the sample preparation and visualization processes. Specifically designed for cryo-fixation, this method allowed a fast freezing of dynamic events within seconds and their ultrastructural characterization. We provide examples of the dynamic oligomerization of GFP-tagged myotubularin (MTM1) phosphoinositides phosphatase induced by osmotic stress, and of the ultrastructure of membrane tubules dependent on amphiphysin 2 (BIN1) expression. Conclusion Accessible and versatile, we show that this approach is efficient to routinely correlate functional and dynamic LM with high resolution morphology by EM, with immuno-EM labeling, with 3D reconstruction using serial immuno-EM or tomography, and with scanning-EM. PMID:20140253

  16. A 3D Hybrid Model for Tissue Growth: The Interplay between Cell Population and Mass Transport Dynamics

    PubMed Central

    Cheng, Gang; Markenscoff, Pauline; Zygourakis, Kyriacos

    2009-01-01

    Abstract To provide theoretical guidance for the design and in vitro cultivation of bioartificial tissues, we have developed a multiscale computational model that can describe the complex interplay between cell population and mass transport dynamics that governs the growth of tissues in three-dimensional scaffolds. The model has three components: a transient partial differential equation for the simultaneous diffusion and consumption of a limiting nutrient; a cellular automaton describing cell migration, proliferation, and collision; and equations that quantify how the varying nutrient concentration modulates cell division and migration. The hybrid discrete-continuous model was parallelized and solved on a distributed-memory multicomputer to study how transport limitations affect tissue regeneration rates under conditions encountered in typical bioreactors. Simulation results show that the severity of transport limitations can be estimated by the magnitude of two dimensionless groups: the Thiele modulus and the Biot number. Key parameters including the initial seeding mode, cell migration speed, and the hydrodynamic conditions in the bioreactor are shown to affect not only the overall rate, but also the pattern of tissue growth. This study lays the groundwork for more comprehensive models that can handle mixed cell cultures, multiple nutrients and growth factors, and other cellular processes, such as cell death. PMID:19619455

  17. High-dose radiotherapy in inoperable nonsmall cell lung cancer: Comparison of volumetric modulated arc therapy, dynamic IMRT and 3D conformal radiotherapy

    SciTech Connect

    Bree, Ingrid de; Hinsberg, Marieelle G.E. van; Veelen, Lieneke R. van

    2012-01-01

    Conformal 3D radiotherapy (3D-CRT) combined with chemotherapy for inoperable non-small cell lung cancer (NSCLC) to the preferable high dose is often not achievable because of dose-limiting organs. This reduces the probability of regional tumor control. Therefore, the surplus value of using intensity-modulated radiation therapy (IMRT) techniques, specifically volumetric modulated arc therapy (RapidArc [RA]) and dynamic IMRT (d-IMRT) has been investigated. RA and d-IMRT plans were compared with 3D-CRT treatment plans for 20 patients eligible for concurrent high-dose chemoradiotherapy, in whom a dose of 60 Gy was not achievable. Comparison of dose delivery in the target volume and organs at risk was carried out by evaluating 3D dose distributions and dose-volume histograms. Quality of the dose distribution was assessed using the inhomogeneity and conformity index. For most patients, a higher dose to the target volume can be delivered using RA or d-IMRT; in 15% of the patients a dose {>=}60 Gy was possible. Both IMRT techniques result in a better conformity of the dose (p < 0.001). There are no significant differences in homogeneity of dose in the target volume. IMRT techniques for NSCLC patients allow higher dose to the target volume, thus improving regional tumor control.

  18. Comparison of the transcriptomic profile of hepatic human induced pluripotent stem like cells cultured in plates and in a 3D microscale dynamic environment.

    PubMed

    Leclerc, Eric; Kimura, Keiichi; Shinohara, Marie; Danoy, Mathieu; Le Gall, Morgane; Kido, Taketomo; Miyajima, Atsushi; Fujii, Teruo; Sakai, Yasuyuki

    2017-01-01

    We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells. However, the overall tissue still presented characteristic of immature and foetal patterns. Nevertheless, the biochip culture provided a specific micro-environment in which a complex multicellular differentiation toward liver could be oriented.

  19. NIKE3D96. Static & Dynamic Response of 3D Solids

    SciTech Connect

    Maker, B.; Hallquist, J.O.; Ferencz, R.M.

    1991-02-01

    NIKE3D is a large deformations 3D finite element code used to obtain the resulting displacements and stresses from multi-body static and dynamic structural thermo-mechanics problems with sliding interfaces. Many nonlinear and temperature dependent constitutive models are available.

  20. Integrating focal adhesion dynamics, cytoskeleton remodeling, and actin motor activity for predicting cell migration on 3D curved surfaces of the extracellular matrix.

    PubMed

    Kim, Min-Cheol; Kim, Choong; Wood, Levi; Neal, Devin; Kamm, Roger D; Asada, H Harry

    2012-11-01

    An integrative cell migration model incorporating focal adhesion (FA) dynamics, cytoskeleton and nucleus remodeling and actin motor activity is developed for predicting cell migration behaviors on 3-dimensional curved surfaces, such as cylindrical lumens in the 3-D extracellular matrix (ECM). The work is motivated by 3-D microfluidic migration experiments suggesting that the migration speed and direction may vary depending on the cross sectional shape of the lumen along which the cell migrates. In this paper, the mechanical structure of the cell is modeled as double elastic membranes of cell and nucleus. The two elastic membranes are connected by stress fibers, which are extended from focal adhesions on the cell surface to the nuclear membrane. The cell deforms and gains traction as transmembrane integrins distributed over the outer cell membrane bind to ligands on the ECM, form focal adhesions, and activate stress fibers. Probabilities at which integrin ligand-receptor bonds are formed as well as ruptures are affected by the surface geometry, resulting in diverse migration behaviors that depend on the curvature of the surface. Monte Carlo simulations of the integrative model reveal that (a) the cell migration speed is dependent on the cross sectional area of the lumen with a maximum speed at a particular diameter or width, (b) as the lumen diameter increases, the cell tends to spread and migrate around the circumference of the lumen, while it moves in the longitudinal direction as the lumen diameter narrows, (c) once the cell moves in one direction, it tends to stay migrating in the same direction despite the stochastic nature of migration. The relationship between the cell migration speed and the lumen width agrees with microfluidic experimental data for cancer cell migration.

  1. Real-time monitoring of 3D cell culture using a 3D capacitance biosensor.

    PubMed

    Lee, Sun-Mi; Han, Nalae; Lee, Rimi; Choi, In-Hong; Park, Yong-Beom; Shin, Jeon-Soo; Yoo, Kyung-Hwa

    2016-03-15

    Three-dimensional (3D) cell cultures have recently received attention because they represent a more physiologically relevant environment compared to conventional two-dimensional (2D) cell cultures. However, 2D-based imaging techniques or cell sensors are insufficient for real-time monitoring of cellular behavior in 3D cell culture. Here, we report investigations conducted with a 3D capacitance cell sensor consisting of vertically aligned pairs of electrodes. When GFP-expressing human breast cancer cells (GFP-MCF-7) encapsulated in alginate hydrogel were cultured in a 3D cell culture system, cellular activities, such as cell proliferation and apoptosis at different heights, could be monitored non-invasively and in real-time by measuring the change in capacitance with the 3D capacitance sensor. Moreover, we were able to monitor cell migration of human mesenchymal stem cells (hMSCs) with our 3D capacitance sensor.

  2. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

    Laser scanning confocal microscopy was used to study the dynamics of 3D assemblies spontaneously formed in microtubule (MT) solutions. Microtubule solutions prepared by mixing and incubating tubulin in the presence of GTP and Oregon Green conjugated taxol in PM buffer were placed in long, sub-millimeter thin glass cells by the capillary action. Within 24 hours, starting with a uniform distribution, microtubules were found to be gradually separated into a few large ``buckled'' bundles along the long direction, and in the middle plane, of the sample cell. A well-defined wavelength of the buckling sinusoids was around 510 μm. The cross section of these round bundles was approximately 40 μm in diameter and the lengths were several centimeters. Detailed analysis of the 3-D image within the bundles revealed that each bundle seemed to consist of loosely packed MTs. It appeared that MTs were phase separated resulting from attractive interactions between charged MT fibers. The ``buckling'' behavior could be the result of geometrical constraints of the repulsive cell walls and the repulsive interaction between bundles. Detailed 3-D observations of the dynamic evolution of MT assembly could provide insight to the mechanisms of cellular MT organization and phase separation of charged colloidal rods.

  3. A microfluidic device for 2D to 3D and 3D to 3D cell navigation

    NASA Astrophysics Data System (ADS)

    Shamloo, Amir; Amirifar, Leyla

    2016-01-01

    Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be obtained by diffusion. The device was designed by a numerical simulation so that the uniformity of the concentration gradients throughout the cell culture chamber was obtained. Adult neural cells were cultured within this device and they showed different branching and axonal navigation phenotypes within varying nerve growth factor (NGF) concentration profiles. Neural stem cells were also cultured within varying collagen matrix densities while exposed to NGF concentrations and they experienced 3D to 3D collective migration. By generating vascular endothelial growth factor concentration gradients, adult human dermal microvascular endothelial cells also migrated in a 2D to 3D manner and formed a stable lumen within a specific collagen matrix density. It was observed that a minimum absolute concentration and concentration gradient were required to stimulate migration of all types of the cells. This device has the advantage of changing multiple parameters simultaneously and is expected to have wide applicability in cell studies.

  4. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    NASA Astrophysics Data System (ADS)

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

    2011-09-01

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

  5. Novel method to dynamically load cells in 3D-gel culture for primary blast injury studies

    NASA Astrophysics Data System (ADS)

    Sory, David; Cepa-Areias, Anabela; Overby, Darryl; Proud, William; Institute of Shock Physics, Department of Bioengineering; Royal British Legion CentreBlast I Collaboration

    2015-06-01

    For at least a century explosive devices have been reported as one of the most important causes of injuries on battlefield in military conflicts as well as in terrorist attacks. Although significant experimental and modelling efforts have been focussed on blast injury at the organ or tissue level, few studies have investigated the mechanism of blast injury at the cellular level. This paper introduces an in vitro method compatible with living cells to examine the effects of high stress and short-duration pulses similar to those observed in blast waves. The experimental phase involved high strain rate axial compression of biological cylindrical specimens within a hermetically sealed sample holder made of a biocompatible polymer. Numerical simulations were performed in order to characterize the loading path within the sample and assess the loading conditions. A proof of concept is presented so as to establish a new window to address fundamental questions regarding primary blast injury at the cellular level. The Institute of Shock Physics acknowledges the support of AWE, Aldermaston, UK and Imperial College London. The Centre for Blast Injury Studies acknowledges the support of the Royal British Legion and Imperial College London.

  6. 3-D Particle Tracking in a Two-Photon Microscope: Application to the Study of Molecular Dynamics in Cells

    PubMed Central

    Levi, Valeria; Ruan, QiaoQiao; Gratton, Enrico

    2005-01-01

    We developed a method for tracking particles in three dimensions designed for a two-photon microscope, which holds great promise to study cellular processes because of low photodamage, efficient background rejection, and improved depth discrimination. During a standard cycle of the tracking routine (32 ms), the laser beam traces four circular orbits surrounding the particle in two z planes above and below the particle. The radius of the orbits is half of the x,y-width of the point spread function, and the distance between the z planes is the z-width of the point spread function. The z-position is adjusted by moving the objective with a piezoelectric-nanopositioner. The particle position is calculated on the fly from the intensity profile obtained during the cycle, and these coordinates are used to set the scanning center for the next cycle. Applying this method, we were able to follow the motion of 500-nm diameter fluorescent polystyrene microspheres moved by a nanometric stage in either steps of 20–100 nm or sine waves of 0.1–10 μm amplitude with 20 nm precision. We also measured the diffusion coefficient of fluorospheres in glycerol solutions and recovered the values expected according to the Stokes-Einstein relationship for viscosities higher than 3.7 cP. The feasibility of this method for live cell measurements is demonstrated studying the phagocytosis of protein-coated fluorospheres by fibroblasts. PMID:15653748

  7. DYNAMIC 3D QSAR TECHNIQUES: APPLICATIONS IN TOXICOLOGY

    EPA Science Inventory

    Two dynamic techniques recently developed to account for conformational flexibility of chemicals in 3D QSARs are presented. In addition to the impact of conformational flexibility of chemicals in 3D QSAR models, the applicability of various molecular descriptors is discussed. The...

  8. DYNAMIC 3D QSAR TECHNIQUES: APPLICATIONS IN TOXICOLOGY

    EPA Science Inventory

    Two dynamic techniques recently developed to account for conformational flexibility of chemicals in 3D QSARs are presented. In addition to the impact of conformational flexibility of chemicals in 3D QSAR models, the applicability of various molecular descriptors is discussed. The...

  9. 3D joint dynamics analysis of healthy children's gait.

    PubMed

    Samson, William; Desroches, Guillaume; Cheze, Laurence; Dumas, Raphaël

    2009-11-13

    The 3D joint moments and 2D joint powers have been largely explored in the literature of healthy children's gait, in particular to compare them with pathologic subjects' gait. However, no study reported on 3D joint power in children which could be due to the difficulties in interpreting the results. Recently, the analysis of the 3D angle between the joint moment and the joint angular velocity vectors has been proposed in order to help 3D joint power interpretation. Our hypothesis is that this 3D angle may help in characterizing the level of gait maturation. The present study explores 3D joint moments, 3D joint power and the proposed 3D angle for both children's and adults' gaits to highlight differences in the strategies used. The results seem to confirm that children have an alternative strategy of mainly ankle stabilization and hip propulsion compared to the adults' strategy of mainly ankle resistance and propulsion and hip stabilization. In the future, the same 3D angle analysis should be applied to different age groups for better describing the evolution of the 3D joint dynamic strategies during the growth.

  10. Conservative boundary conditions for 3D gas dynamics problems

    NASA Technical Reports Server (NTRS)

    Gerasimov, B. P.; Karagichev, A. B.; Semushin, S. A.

    1986-01-01

    A method is described for 3D-gas dynamics computer simulation in regions of complicated shape by means of nonadjusted rectangular grids providing unified treatment of various problems. Some test problem computation results are given.

  11. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    SciTech Connect

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably

  12. Tissuelike 3D Assemblies of Human Broncho-Epithelial Cells

    NASA Technical Reports Server (NTRS)

    Goodwin, Thomas J.

    2010-01-01

    Three-dimensional (3D) tissuelike assemblies (TLAs) of human broncho-epithelial (HBE) cells have been developed for use in in vitro research on infection of humans by respiratory viruses. The 2D monolayer HBE cell cultures heretofore used in such research lack the complex cell structures and interactions characteristic of in vivo tissues and, consequently, do not adequately emulate the infection dynamics of in-vivo microbial adhesion and invasion. In contrast, the 3D HBE TLAs are characterized by more-realistic reproductions of the geometrical and functional complexity, differentiation of cells, cell-to-cell interactions, and cell-to-matrix interactions characteristic of human respiratory epithelia. Hence, the 3D HBE TLAs are expected to make it possible to perform at least some of the research in vitro under more-realistic conditions, without need to infect human subjects. The TLAs are grown on collagen-coated cyclodextran microbeads under controlled conditions in a nutrient liquid in the simulated microgravitational environment of a bioreactor of the rotating- wall-vessel type. Primary human mesenchymal bronchial-tracheal cells are used as a foundation matrix, while adult human bronchial epithelial immortalized cells are used as the overlying component. The beads become coated with cells, and cells on adjacent beads coalesce into 3D masses. The resulting TLAs have been found to share significant characteristics with in vivo human respiratory epithelia including polarization, tight junctions, desmosomes, and microvilli. The differentiation of the cells in these TLAs into tissues functionally similar to in vivo tissues is confirmed by the presence of compounds, including villin, keratins, and specific lung epithelium marker compounds, and by the production of tissue mucin. In a series of initial infection tests, TLA cultures were inoculated with human respiratory syncytial viruses and parainfluenza type 3 viruses. Infection was confirmed by photomicrographs that

  13. Dynamic 3-D visualization of vocal tract shaping during speech.

    PubMed

    Zhu, Yinghua; Kim, Yoon-Chul; Proctor, Michael I; Narayanan, Shrikanth S; Nayak, Krishna S

    2013-05-01

    Noninvasive imaging is widely used in speech research as a means to investigate the shaping and dynamics of the vocal tract during speech production. 3-D dynamic MRI would be a major advance, as it would provide 3-D dynamic visualization of the entire vocal tract. We present a novel method for the creation of 3-D dynamic movies of vocal tract shaping based on the acquisition of 2-D dynamic data from parallel slices and temporal alignment of the image sequences using audio information. Multiple sagittal 2-D real-time movies with synchronized audio recordings are acquired for English vowel-consonant-vowel stimuli /ala/, /a.ιa/, /asa/, and /a∫a/. Audio data are aligned using mel-frequency cepstral coefficients (MFCC) extracted from windowed intervals of the speech signal. Sagittal image sequences acquired from all slices are then aligned using dynamic time warping (DTW). The aligned image sequences enable dynamic 3-D visualization by creating synthesized movies of the moving airway in the coronal planes, visualizing desired tissue surfaces and tube-shaped vocal tract airway after manual segmentation of targeted articulators and smoothing. The resulting volumes allow for dynamic 3-D visualization of salient aspects of lingual articulation, including the formation of tongue grooves and sublingual cavities, with a temporal resolution of 78 ms.

  14. Dynamic dimension: system for simultaneous 3D and monoscopic viewing

    NASA Astrophysics Data System (ADS)

    Redert, Andre

    2004-05-01

    We propose the 'Dynamic Dimension' system that enables simultaneous viewing of 3D and monoscopic content on glasses-based stereo displays (e.g. CRT, Plasma, LCD). A viewer can choose to wear glasses and see content in 3D, or he may decide not to wear glasses, and see high-quality monoscopic content. The Dynamic Dimension system is based on simple image processing such as addition and subtraction. The input images can be captured by a triple camera setup or be rendered from so-called RGBD video, an ad-hoc standard for 3D video. From several subjective tests, we conclude that Dynamic Dimension produces a very much present and appealing 3D effect, while the monoscopic image quality remains high and totally unaffected.

  15. Single molecule microscopy in 3D cell cultures and tissues.

    PubMed

    Lauer, Florian M; Kaemmerer, Elke; Meckel, Tobias

    2014-12-15

    From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Protrusive waves guide 3D cell migration along nanofibers.

    PubMed

    Guetta-Terrier, Charlotte; Monzo, Pascale; Zhu, Jie; Long, Hongyan; Venkatraman, Lakshmi; Zhou, Yue; Wang, PeiPei; Chew, Sing Yian; Mogilner, Alexander; Ladoux, Benoit; Gauthier, Nils C

    2015-11-09

    In vivo, cells migrate on complex three-dimensional (3D) fibrous matrices, which has made investigation of the key molecular and physical mechanisms that drive cell migration difficult. Using reductionist approaches based on 3D electrospun fibers, we report for various cell types that single-cell migration along fibronectin-coated nanofibers is associated with lateral actin-based waves. These cyclical waves have a fin-like shape and propagate up to several hundred micrometers from the cell body, extending the leading edge and promoting highly persistent directional movement. Cells generate these waves through balanced activation of the Rac1/N-WASP/Arp2/3 and Rho/formins pathways. The waves originate from one major adhesion site at leading end of the cell body, which is linked through actomyosin contractility to another site at the back of the cell, allowing force generation, matrix deformation and cell translocation. By combining experimental and modeling data, we demonstrate that cell migration in a fibrous environment requires the formation and propagation of dynamic, actin based fin-like protrusions.

  17. Protrusive waves guide 3D cell migration along nanofibers

    PubMed Central

    Guetta-Terrier, Charlotte; Monzo, Pascale; Zhu, Jie; Long, Hongyan; Venkatraman, Lakshmi; Zhou, Yue; Wang, PeiPei; Chew, Sing Yian; Mogilner, Alexander

    2015-01-01

    In vivo, cells migrate on complex three-dimensional (3D) fibrous matrices, which has made investigation of the key molecular and physical mechanisms that drive cell migration difficult. Using reductionist approaches based on 3D electrospun fibers, we report for various cell types that single-cell migration along fibronectin-coated nanofibers is associated with lateral actin-based waves. These cyclical waves have a fin-like shape and propagate up to several hundred micrometers from the cell body, extending the leading edge and promoting highly persistent directional movement. Cells generate these waves through balanced activation of the Rac1/N-WASP/Arp2/3 and Rho/formins pathways. The waves originate from one major adhesion site at leading end of the cell body, which is linked through actomyosin contractility to another site at the back of the cell, allowing force generation, matrix deformation and cell translocation. By combining experimental and modeling data, we demonstrate that cell migration in a fibrous environment requires the formation and propagation of dynamic, actin based fin-like protrusions. PMID:26553933

  18. An Evaluative Review of Simulated Dynamic Smart 3d Objects

    NASA Astrophysics Data System (ADS)

    Romeijn, H.; Sheth, F.; Pettit, C. J.

    2012-07-01

    Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.

  19. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis.

    PubMed

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC(+)/5mC(-), 5hmC(+)/5mC(+), and 5hmC(-)/5mC(+) cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC(+)/5mC(+) cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in remodeling. We

  20. Stem cell reprogramming: A 3D boost

    NASA Astrophysics Data System (ADS)

    Abilez, Oscar J.; Wu, Joseph C.

    2016-03-01

    Biophysical factors in an optimized three-dimensional microenvironment enhance the reprogramming efficiency of human somatic cells into pluripotent stem cells when compared to traditional cell-culture substrates.

  1. Multizone Paper Platform for 3D Cell Cultures

    PubMed Central

    Derda, Ratmir; Hong, Estrella; Mwangi, Martin; Mammoto, Akiko; Ingber, Donald E.; Whitesides, George M.

    2011-01-01

    In vitro 3D culture is an important model for tissues in vivo. Cells in different locations of 3D tissues are physiologically different, because they are exposed to different concentrations of oxygen, nutrients, and signaling molecules, and to other environmental factors (temperature, mechanical stress, etc). The majority of high-throughput assays based on 3D cultures, however, can only detect the average behavior of cells in the whole 3D construct. Isolation of cells from specific regions of 3D cultures is possible, but relies on low-throughput techniques such as tissue sectioning and micromanipulation. Based on a procedure reported previously (“cells-in-gels-in-paper” or CiGiP), this paper describes a simple method for culture of arrays of thin planar sections of tissues, either alone or stacked to create more complex 3D tissue structures. This procedure starts with sheets of paper patterned with hydrophobic regions that form 96 hydrophilic zones. Serial spotting of cells suspended in extracellular matrix (ECM) gel onto the patterned paper creates an array of 200 micron-thick slabs of ECM gel (supported mechanically by cellulose fibers) containing cells. Stacking the sheets with zones aligned on top of one another assembles 96 3D multilayer constructs. De-stacking the layers of the 3D culture, by peeling apart the sheets of paper, “sections” all 96 cultures at once. It is, thus, simple to isolate 200-micron-thick cell-containing slabs from each 3D culture in the 96-zone array. Because the 3D cultures are assembled from multiple layers, the number of cells plated initially in each layer determines the spatial distribution of cells in the stacked 3D cultures. This capability made it possible to compare the growth of 3D tumor models of different spatial composition, and to examine the migration of cells in these structures. PMID:21573103

  2. Multitasking the code ARC3D. [for computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Barton, John T.; Hsiung, Christopher C.

    1986-01-01

    The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.

  3. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

    The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

  4. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

    The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

  5. Towards Single Cell Traction Microscopy within 3D Collagen Matrices

    PubMed Central

    Hall, Matthew S.; Long, Rong; Feng, Xinzeng; Huang, YuLing; Hui, Chung-Yuen; Wu, Mingming

    2013-01-01

    Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion, and migration. Cells require the three dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, current understanding of cell-ECM and cell-cell mechanical interactions is largely derived from 2D cell traction force microscopy, in which cells are cultured on a flat substrate. 3D cell traction microscopy is emerging for mapping traction fields of single animal cells embedded in either synthetic or natively derived fibrous gels. We discuss here the development of 3D cell traction microscopy, its current limitations, and perspectives on the future of this technology. Emphasis is placed on strategies for applying 3D cell traction microscopy to individual tumor cells migration within collagen gels. PMID:23806281

  6. Toward single cell traction microscopy within 3D collagen matrices.

    PubMed

    Hall, Matthew S; Long, Rong; Feng, Xinzeng; Huang, Yuling; Hui, Chung-Yuen; Wu, Mingming

    2013-10-01

    Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion, and migration. Cells require the three-dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, current understanding of cell-ECM and cell-cell mechanical interactions is largely derived from 2D cell traction force microscopy, in which cells are cultured on a flat substrate. 3D cell traction microscopy is emerging for mapping traction fields of single animal cells embedded in either synthetic or natively derived fibrous gels. We discuss here the development of 3D cell traction microscopy, its current limitations, and perspectives on the future of this technology. Emphasis is placed on strategies for applying 3D cell traction microscopy to individual tumor cell migration within collagen gels. © 2013 Elsevier Inc. All rights reserved.

  7. Controlled architectural and chemotactic studies of 3D cell migration.

    PubMed

    Tayalia, Prakriti; Mazur, Eric; Mooney, David J

    2011-04-01

    Chemotaxis plays a critical role in tissue development and wound repair, and is widely studied using ex vivo model systems in applications such as immunotherapy. However, typical chemotactic models employ 2D systems that are less physiologically relevant or use end-point assays, that reveal little about the stepwise dynamics of the migration process. To overcome these limitations, we developed a new model system using microfabrication techniques, sustained drug delivery approaches, and theoretical modeling of chemotactic agent diffusion. This model system allows us to study the effects of 3D architecture and chemotactic agent gradient on immune cell migration in real time. We find that dendritic cell migration is characterized by a strong interplay between matrix architecture and chemotactic gradients, and migration is also influenced dramatically by the cell activation state. Our results indicate that Lipopolysaccharide-activated dendritic cells studied in a traditional transwell system actually exhibit anomalous migration behavior. Such a 3D ex vivo system lends itself for analyzing cell migratory behavior in response to single or multiple competitive cues and could prove useful in vaccine development.

  8. The Vibrational Dynamics of 3D HOCl Above Dissociation

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Der; Reichl, Linda; Jung, Christof

    2015-03-01

    We have analyzed the vibrational dynamics of HOCl above dissociation using a 3D energy surface which governs the vibrational dynamics of HOCl above dissociation. The dynamics is dominated by an invariant manifold which is transversally unstable for small spacing between Cl and HO complex, and stable for large spacing. Above dissociation, the InM separates two mirror image periodic orbits, embedded in a large chaotic sea, that can hold a large number of quantum states. These periodic orbits have the capability of forming significant quasibound states of the molecule above dissociation. Welch Foundation.

  9. 3D motion analysis of keratin filaments in living cells

    NASA Astrophysics Data System (ADS)

    Herberich, Gerlind; Windoffer, Reinhard; Leube, Rudolf; Aach, Til

    2010-03-01

    We present a novel and efficient approach for 3D motion estimation of keratin intermediate filaments in vitro. Keratin filaments are elastic cables forming a complex scaffolding within epithelial cells. To understand the mechanisms of filament formation and network organisation under physiological and pathological conditions, quantitative measurements of dynamic network alterations are essential. Therefore we acquired time-lapse series of 3D images using a confocal laser scanning microscope. Based on these image series, we show that a dense vector field can be computed such that the displacements from one frame to the next can be determined. Our method is based on a two-step registration process: First, a rigid pre-registration is applied in order to compensate for possible global cell movement. This step enables the subsequent nonrigid registration to capture only the sought local deformations of the filaments. As the transformation model of the deformable registration algorithm is based on Free Form Deformations, it is well suited for modeling filament network dynamics. The optimization is performed using efficient linear programming techniques such that the huge amount of image data of a time series can be efficiently processed. The evaluation of our results illustrates the potential of our approach.

  10. "Constructing" the Cell Cycle in 3D

    ERIC Educational Resources Information Center

    Koc, Isil; Turan, Merve

    2012-01-01

    The cycle of duplication and division, known as the "cell cycle," is the essential mechanism by which all living organisms reproduce. This activity allows students to develop an understanding of the main events that occur during the typical eukaryotic cell cycle mostly in the process of mitotic phase that divides the duplicated genetic material…

  11. "Constructing" the Cell Cycle in 3D

    ERIC Educational Resources Information Center

    Koc, Isil; Turan, Merve

    2012-01-01

    The cycle of duplication and division, known as the "cell cycle," is the essential mechanism by which all living organisms reproduce. This activity allows students to develop an understanding of the main events that occur during the typical eukaryotic cell cycle mostly in the process of mitotic phase that divides the duplicated genetic material…

  12. Collective Motion of Mammalian Cell Cohorts in 3D

    PubMed Central

    Sharma, Yasha; Vargas, Diego A.; Pegoraro, Adrian F.; Lepzelter, David; Weitz, David A.; Zaman, Muhammad H

    2016-01-01

    Collective cell migration is ubiquitous in biology, from development to cancer; it occurs in complex systems comprised of heterogeneous cell types, signals and matrices, and requires large scale regulation in space and time. Understanding how cells achieve organized collective motility is crucial to addressing cellular and tissue function and disease progression. While current two-dimensional model systems recapitulate the dynamic properties of collective cell migration, quantitative three-dimensional equivalent model systems have proved elusive. To establish such a model system, we study cell collectives by tracking individuals within cell cohorts embedded in three dimensional collagen scaffolding. We develop a custom algorithm to quantify the temporal and spatial heterogeneity of motion in cell cohorts during motility events. In the absence of external driving agents, we show that these cohorts rotate in short bursts, <2 hours, and translate for up to 6 hours. We observe, track, and analyze three dimensional motion of cell cohorts composed of 3–31 cells, and pave a path toward understanding cell collectives in 3D as a complex emergent system. PMID:26549557

  13. Myosin IIA dependent retrograde flow drives 3D cell migration.

    PubMed

    Shih, Wenting; Yamada, Soichiro

    2010-04-21

    Epithelial cell migration is an essential part of embryogenesis and tissue regeneration, yet their migration is least understood. Using our three-dimensional (3D) motility analysis, migrating epithelial cells formed an atypical polarized cell shape with the nucleus leading the cell front and a contractile cell rear. Migrating epithelial cells exerted traction forces to deform both the anterior and posterior extracellular matrix toward the cell body. The cell leading edge exhibited a myosin II-dependent retrograde flow with the magnitude and direction consistent with surrounding network deformation. Interestingly, on a two-dimensional substrate, myosin IIA-deficient cells migrated faster than wild-type cells, but in a 3D gel, these myosin IIA-deficient cells were unpolarized and immobile. In contrast, the migration rates of myosin IIB-deficient cells were similar to wild-type cells. Therefore, myosin IIA, not myosin IIB, is required for 3D epithelial cell migration.

  14. Cyto-3D-print to attach mitotic cells.

    PubMed

    Castroagudin, Michelle R; Zhai, Yujia; Li, Zhi; Marnell, Michael G; Glavy, Joseph S

    2016-08-01

    The Cyto-3D-print is an adapter that adds cytospin capability to a standard centrifuge. Like standard cytospinning, Cyto-3D-print increases the surface attachment of mitotic cells while giving a higher degree of adaptability to other slide chambers than available commercial devices. The use of Cyto-3D-print is cost effective, safe, and applicable to many slide designs. It is durable enough for repeated use and made of biodegradable materials for environment-friendly disposal.

  15. Modeling cell migration in 3D: Status and challenges.

    PubMed

    Rangarajan, Rajagopal; Zaman, Muhammad H

    2008-01-01

    Cell migration is a multi-scale process that integrates signaling, mechanics and biochemical reaction kinetics. Various mathematical models accurately predict cell migration on 2D surfaces, but are unable to capture the complexities of 3D migration. Additionally, quantitative 3D cell migration models have been few and far between. In this review we look and characterize various mathematical models available in literature to predict cell migration in 3D matrices and analyze their strengths and possible changes to these models that could improve their predictive capabilities.

  16. Toward single cell traction microscopy within 3D collagen matrices

    SciTech Connect

    Hall, Matthew S.; Long, Rong; Feng, Xinzeng; Huang, YuLing; Hui, Chung-Yuen; Wu, Mingming

    2013-10-01

    Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion, and migration. Cells require the three-dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, current understanding of cell–ECM and cell–cell mechanical interactions is largely derived from 2D cell traction force microscopy, in which cells are cultured on a flat substrate. 3D cell traction microscopy is emerging for mapping traction fields of single animal cells embedded in either synthetic or natively derived fibrous gels. We discuss here the development of 3D cell traction microscopy, its current limitations, and perspectives on the future of this technology. Emphasis is placed on strategies for applying 3D cell traction microscopy to individual tumor cell migration within collagen gels. - Highlights: • Review of the current state of the art in 3D cell traction force microscopy. • Bulk and micro-characterization of remodelable fibrous collagen gels. • Strategies for performing 3D cell traction microscopy within collagen gels.

  17. 3D tomography of cells in micro-channels

    NASA Astrophysics Data System (ADS)

    Quint, S.; Christ, A. F.; Guckenberger, A.; Himbert, S.; Kaestner, L.; Gekle, S.; Wagner, C.

    2017-09-01

    We combine confocal imaging, microfluidics, and image analysis to record 3D-images of cells in flow. This enables us to recover the full 3D representation of several hundred living cells per minute. Whereas 3D confocal imaging has thus far been limited to steady specimens, we overcome this restriction and present a method to access the 3D shape of moving objects. The key of our principle is a tilted arrangement of the micro-channel with respect to the focal plane of the microscope. This forces cells to traverse the focal plane in an inclined manner. As a consequence, individual layers of passing cells are recorded, which can then be assembled to obtain the volumetric representation. The full 3D information allows for a detailed comparison with theoretical and numerical predictions unfeasible with, e.g., 2D imaging. Our technique is exemplified by studying flowing red blood cells in a micro-channel reflecting the conditions prevailing in the microvasculature. We observe two very different types of shapes: "croissants" and "slippers." Additionally, we perform 3D numerical simulations of our experiment to confirm the observations. Since 3D confocal imaging of cells in flow has not yet been realized, we see high potential in the field of flow cytometry where cell classification thus far mostly relies on 1D scattering and fluorescence signals.

  18. The ER in 3D: a multifunctional dynamic membrane network.

    PubMed

    Friedman, Jonathan R; Voeltz, Gia K

    2011-12-01

    The endoplasmic reticulum (ER) is a large, singular, membrane-bound organelle that has an elaborate 3D structure with a diversity of structural domains. It contains regions that are flat and cisternal, ones that are highly curved and tubular, and others adapted to form contacts with nearly every other organelle and with the plasma membrane. The 3D structure of the ER is determined by both integral ER membrane proteins and by interactions with the cytoskeleton. In this review, we describe some of the factors that are known to regulate ER structure and discuss how this structural organization and the dynamic nature of the ER membrane network allow it to perform its many different functions. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. 3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics

    PubMed Central

    Sison, Miguel; Chakrabortty, Sabyasachi; Extermann, Jérôme; Nahas, Amir; James Marchand, Paul; Lopez, Antonio; Weil, Tanja; Lasser, Theo

    2017-01-01

    We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds without significant cell damage. By combining temporal autocorrelation analysis with a classical diffusion model, we quantify mitochondrial dynamics and cast these results into 3D maps showing the heterogeneity of diffusion parameters across the whole cell volume. PMID:28230188

  20. 3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics

    NASA Astrophysics Data System (ADS)

    Sison, Miguel; Chakrabortty, Sabyasachi; Extermann, Jérôme; Nahas, Amir; James Marchand, Paul; Lopez, Antonio; Weil, Tanja; Lasser, Theo

    2017-02-01

    We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds without significant cell damage. By combining temporal autocorrelation analysis with a classical diffusion model, we quantify mitochondrial dynamics and cast these results into 3D maps showing the heterogeneity of diffusion parameters across the whole cell volume.

  1. Peptide hydrogelation and cell encapsulation for 3D culture of MCF-7 breast cancer cells.

    PubMed

    Huang, Hongzhou; Ding, Ying; Sun, Xiuzhi S; Nguyen, Thu A

    2013-01-01

    Three-dimensional (3D) cell culture plays an invaluable role in tumor biology by providing in vivo like microenviroment and responses to therapeutic agents. Among many established 3D scaffolds, hydrogels demonstrate a distinct property as matrics for 3D cell culture. Most of the existing pre-gel solutions are limited under physiological conditions such as undesirable pH or temperature. Here, we report a peptide hydrogel that shows superior physiological properties as an in vitro matrix for 3D cell culture. The 3D matrix can be accomplished by mixing a self-assembling peptide directly with a cell culture medium without any pH or temperature adjustment. Results of dynamic rheological studies showed that this hydrogel can be delivered multiple times via pipetting without permanently destroying the hydrogel architecture, indicating the deformability and remodeling ability of the hydrogel. Human epithelial cancer cells, MCF-7, are encapsulated homogeneously in the hydrogel matrix during hydrogelation. Compared with two-dimensional (2D) monolayer culture, cells residing in the hydrogel matrix grow as tumor-like clusters in 3D formation. Relevant parameters related to cell morphology, survival, proliferation, and apoptosis were analyzed using MCF-7 cells in 3D hydrogels. Interestingly, treatment of cisplatin, an anti-cancer drug, can cause a significant decrease of cell viability of MCF-7 clusters in hydrogels. The responses to cisplatin were dose- and time-dependent, indicating the potential usage of hydrogels for drug testing. Results of confocal microscopy and Western blotting showed that cells isolated from hydrogels are suitable for downstream proteomic analysis. The results provided evidence that this peptide hydrogel is a promising 3D cell culture material for drug testing.

  2. Untangling Slab Dynamics Using 3-D Numerical and Analytical Models

    NASA Astrophysics Data System (ADS)

    Holt, A. F.; Royden, L.; Becker, T. W.

    2016-12-01

    Increasingly sophisticated numerical models have enabled us to make significant strides in identifying the key controls on how subducting slabs deform. For example, 3-D models have demonstrated that subducting plate width, and the related strength of toroidal flow around the plate edge, exerts a strong control on both the curvature and the rate of migration of the trench. However, the results of numerical subduction models can be difficult to interpret, and many first order dynamics issues remain at least partially unresolved. Such issues include the dominant controls on trench migration, the interdependence of asthenospheric pressure and slab dynamics, and how nearby slabs influence each other's dynamics. We augment 3-D, dynamically evolving finite element models with simple, analytical force-balance models to distill the physics associated with subduction into more manageable parts. We demonstrate that for single, isolated subducting slabs much of the complexity of our fully numerical models can be encapsulated by simple analytical expressions. Rates of subduction and slab dip correlate strongly with the asthenospheric pressure difference across the subducting slab. For double subduction, an additional slab gives rise to more complex mantle pressure and flow fields, and significantly extends the range of plate kinematics (e.g., convergence rate, trench migration rate) beyond those present in single slab models. Despite these additional complexities, we show that much of the dynamics of such multi-slab systems can be understood using the physics illuminated by our single slab study, and that a force-balance method can be used to relate intra-plate stress to viscous pressure in the asthenosphere and coupling forces at plate boundaries. This method has promise for rapid modeling of large systems of subduction zones on a global scale.

  3. 3D printing of biomimetic microstructures for cancer cell migration

    PubMed Central

    Huang, Tina Qing; Qu, Xin; Liu, Justin; Chen, Shaochen

    2013-01-01

    To understand the physical behavior and migration of cancer cells, a 3D in vitro micro-chip in hydrogel was created using 3D projection printing. The micro-chip has a honeycomb branched structure, aiming to mimic 3D vascular morphology to test, monitor, and analyze differences in the behavior of cancer cells (i.e. HeLa) vs. non-cancerous cell lines (i.e. 10T1/2). The 3D Projection Printing system can fabricate complex structures in seconds from user-created designs. The fabricated microstructures have three different channel widths of 25, 45, and 120 microns wide to reflect a range of blood vessel diameters. HeLa and 10T1/2 cells seeded within the micro-chip were then analyzed for morphology and cell migration speed. 10T1/2 cells exhibited greater changes in morphology due to channel size width than HeLa cells; however, channel width had a limited effect on 10T1/2 cell migration while HeLa cancer cell migration increased as channel width decreased. This physiologically relevant 3D cancer tissue model has the potential to be a powerful tool for future drug discoveries and cancer migration studies PMID:24150602

  4. Single Cell Traction Microscopy within 3D Collagen Matrices

    NASA Astrophysics Data System (ADS)

    Wu, Mingming

    2014-03-01

    Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion and migration. Cells require the three dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, our current understanding of cell-ECM and cell-cell mechanical interactions is largely derived from 2D traction force microscopy, in which cells are cultured on a flat substrate. It is now clear that what we learn about cellular behavior on a 2D substrate does not always apply to cells embedded within a 3D biomatrix. 3D traction microscopy is emerging for mapping traction fields of single cells embedded in 3D gel, but current methods cannot account for the fibrous and nonlinear properties of collagen gel. In this talk, I will present a forward computation algorithm that we have developed for 3D cell traction measurements within collagen gels. The application of this technology to understanding cancer migration and invasion will be discussed. This work is supported by the National Center for Research Resources (5R21RR025801-03, NIH) and the National Institute of General Medical Sciences (8 R21 GM103388-03,NIH), and the Cornell Center on the Microenvironment & Metastasis.

  5. 3D printing of biomimetic microstructures for cancer cell migration.

    PubMed

    Huang, Tina Qing; Qu, Xin; Liu, Justin; Chen, Shaochen

    2014-02-01

    To understand the physical behavior and migration of cancer cells, a 3D in vitro micro-chip in hydrogel was created using 3D projection printing. The micro-chip has a honeycomb branched structure, aiming to mimic 3D vascular morphology to test, monitor, and analyze differences in the behavior of cancer cells (i.e. HeLa) vs. non-cancerous cell lines (i.e. 10 T1/2). The 3D Projection Printing system can fabricate complex structures in seconds from user-created designs. The fabricated microstructures have three different channel widths of 25, 45, and 120 microns wide to reflect a range of blood vessel diameters. HeLa and 10 T1/2 cells seeded within the micro-chip were then analyzed for morphology and cell migration speed. 10 T1/2 cells exhibited greater changes in morphology due to channel size width than HeLa cells; however, channel width had a limited effect on 10 T1/2 cell migration while HeLa cancer cell migration increased as channel width decreased. This physiologically relevant 3D cancer tissue model has the potential to be a powerful tool for future drug discoveries and cancer migration studies.

  6. Dynamical Systems Analysis of Fully 3D Ocean Features

    NASA Astrophysics Data System (ADS)

    Pratt, L. J.

    2011-12-01

    Dynamical systems analysis of transport and stirring processes has been developed most thoroughly for 2D flow fields. The calculation of manifolds, turnstile lobes, transport barriers, etc. based on observations of the ocean is most often conducted near the sea surface, whereas analyses at depth, usually carried out with model output, is normally confined to constant-z surfaces. At the meoscale and larger, ocean flows are quasi 2D, but smaller scale (submesoscale) motions, including mixed layer phenomena with significant vertical velocity, may be predominantly 3D. The zoology of hyperbolic trajectories becomes richer in such cases and their attendant manifolds are much more difficult to calculate. I will describe some of the basic geometrical features and corresponding Lagrangian Coherent Features expected to arise in upper ocean fronts, eddies, and Langmuir circulations. Traditional GFD models such as the rotating can flow may capture the important generic features. The dynamical systems approach is most helpful when these features are coherent and persistent and the implications and difficulties for this requirement in fully 3D flows will also be discussed.

  7. 3D Dynamic Crack Rupture by a Finite Volume Method

    NASA Astrophysics Data System (ADS)

    Ben Jemaa, M.; Glinsky-Olivier, N.; Cruz-Atienza, V. M.; Virieux, J.

    2007-12-01

    Dynamic rupture of a 3D spontaneous crack of arbitrary shape has been investigated using a Finite Volume (FV) approach. The full domain is decomposed in tetrahedra while the surface on which the rupture is supposed to take place is discretized with triangles which are faces of tetrahedra. Because of this meshing strategy, any shape of the rupture surface could be designed and is performed once before simulations start. First of all, the elastodynamic equations are described into a pseudo-conservative form for easy application of the FV discretisation. Explicit boundary conditions are given using criteria based on the conservation of discrete energy through the crack surface. Using a stress-threshold criterion, these conditions specify fluxes through those triangles which have suffered rupture. On these broken surfaces, stress follows A linear slip-weakening law although other friction laws can be implemented as well. Numerical solutions on a planar fault are achieved for the problem version 3 of the SCEC community dynamic-rupture benchmark exercise (Harris and Archuleta, 2004) and compared with those provided by a Finite Difference (FD) technique (Day et al, 2005). Another benchmark problem is also tackled involving a nonplanar curved fault (Cruz-Atienza et al, 2007). Solutions for this difficult exercise are compared with those computed with a Boundary Integral (BI) method (Aochi et al, 2000). In both benchmarck problems, comparisons show that rupture fronts are well modelled with a slight delay in time especially along the antiplane direction related to the low-order interpolation of the FV approach which requires further mesh refinement or/and an higher-order interpolation strategy as for Galerkin Discontinuous approach. Slip-rate and shear stress amplitudes are well modelled as well as stopping phases and stress overshoots. We expect this method, which is well adapted to multi-preocessor parallel computing to be competitive with others for solving large scale

  8. Dynamic Heterogeneity of DNA Methylation and Hydroxymethylation in Embryonic Stem Cell Populations Captured by Single-Cell 3D High-Content Analysis

    PubMed Central

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    2015-01-01

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a ten-day differentiation course in vitro: by means of confocal and super-resolution imaging together with high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU per day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17:0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, DNA global methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC+/5mC−, 5hmC+/5mC+, and 5hmC−/5mC+ cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC+/5mC+ cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in remodeling. We

  9. Dynamic deformable models for 3D MRI heart segmentation

    NASA Astrophysics Data System (ADS)

    Zhukov, Leonid; Bao, Zhaosheng; Gusikov, Igor; Wood, John; Breen, David E.

    2002-05-01

    Automated or semiautomated segmentation of medical images decreases interstudy variation, observer bias, and postprocessing time as well as providing clincally-relevant quantitative data. In this paper we present a new dynamic deformable modeling approach to 3D segmentation. It utilizes recently developed dynamic remeshing techniques and curvature estimation methods to produce high-quality meshes. The approach has been implemented in an interactive environment that allows a user to specify an initial model and identify key features in the data. These features act as hard constraints that the model must not pass through as it deforms. We have employed the method to perform semi-automatic segmentation of heart structures from cine MRI data.

  10. 3D Dynamic Earthquake Fracture Simulation (Test Case)

    NASA Astrophysics Data System (ADS)

    Korkusuz Öztürk, Yasemin; Meral Özel, Nurcan; Ando, Ryosuke

    2016-04-01

    A 3D dynamic earthquake fracture simulation is being developed for the fault structures which are non-planar to understand heterogeneous stress states in the Marmara Sea. Locating in a seismic gap, a large earthquake is expected in the center of the Sea of Marmara. Concerning the fact that more than 14 million inhabitants of İstanbul, located very closely to the Marmara Sea, the importance of the analysis of the Central Marmara Sea is extremely high. A few 3D dynamic earthquake fracture studies have been already done in the Sea of Marmara for pure right lateral strike-slip stress regimes (Oglesby and Mai, 2012; Aochi and Ulrich, 2015). In this study, a 3D dynamic earthquake fracture model with heterogeneous stress patches from the TPV5, a SCEC code validation case, is adapted. In this test model, the fault and the ground surfaces are gridded by a scalene triangulation technique using GMSH program. For a grid size changing between 0.616 km and 1.050 km the number of elements for the fault surface is 1984 and for the ground surface is 1216. When these results are compared with Kaneko's results for TPV5 from SPECFEM3D, reliable findings could be observed for the first 6.5 seconds (stations on the fault) although a stability problem is encountered after this time threshold. To solve this problem grid sizes are made smaller, so the number of elements increase 7986 for the fault surface and 4867 for the ground surface. On the other hand, computational problems arise in that case, since the computation time is directly proportional to the number of total elements and the required memory also increases with the square of that. Therefore, it is expected that this method can be adapted for less coarse grid cases, regarding the main difficulty coming from the necessity of an effective supercomputer and run time limitations. The main objective of this research is to obtain 3D dynamic earthquake rupture scenarios, concerning not only planar and non-planar faults but also

  11. Cell proliferation and migration in silk fibroin 3D scaffolds.

    PubMed

    Mandal, Biman B; Kundu, Subhas C

    2009-05-01

    Pore architecture in 3D polymeric scaffolds is known to play a critical role in tissue engineering as it provides the vital framework for the seeded cells to organize into a functioning tissue. In this report, we investigated the effects of different freezing temperature regimes on silk fibroin protein 3D scaffold pore microstructure. The fabricated scaffolds using freeze-dry technique were used as a 3D model to monitor cell proliferation and migration. Pores of 200-250microm diameter were formed by slow cooling at temperatures of -20 and -80 degrees C but were found to be limited in porosity and pore interconnectivity as observed through scanning electron microscopic images. In contrast, highly interconnected pores with 96% porosity were observed when silk solutions were rapidly frozen at -196 degrees C. A detailed study was conducted to assess the affect of pore size, porosity and interconnectivity on human dermal fibroblast cell proliferation and migration on these 3D scaffolds using confocal microscopy. The cells were observed to migrate within the scaffold interconnectivities and were found to reach scaffold periphery within 28 days of culture. Confocal images further confirmed normal cell attachment and alignment of actin filaments within the porous scaffold matrix with well-developed nuclei. This study indicates rapid freeze-drying technique as an alternative method to fabricate highly interconnected porous scaffolds for developing functional 3D silk fibroin matrices for potential tissue engineering, biomedical and biotechnological applications.

  12. Contributions of 3D Cell Cultures for Cancer Research.

    PubMed

    Ravi, Maddaly; Ramesh, Aarthi; Pattabhi, Aishwarya

    2017-10-01

    Cancer cell lines have contributed immensely in understanding the complex physiology of cancers. They are excellent material for studies as they offer homogenous samples without individual variations and can be utilised with ease and flexibility. Also, the number of assays and end-points one can study is almost limitless; with the advantage of improvising, modifying or altering several variables and methods. Literally, a new dimension to cancer research has been achieved by the advent of 3Dimensional (3D) cell culture techniques. This approach increased many folds the ways in which cancer cell lines can be utilised for understanding complex cancer biology. 3D cell culture techniques are now the preferred way of using cancer cell lines to bridge the gap between the 'absolute in vitro' and 'true in vivo'. The aspects of cancer biology that 3D cell culture systems have contributed include morphology, microenvironment, gene and protein expression, invasion/migration/metastasis, angiogenesis, tumour metabolism and drug discovery, testing chemotherapeutic agents, adaptive responses and cancer stem cells. We present here, a comprehensive review on the applications of 3D cell culture systems for these aspects of cancers. J. Cell. Physiol. 232: 2679-2697, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  13. 3D dynamic holographic display by modulating complex amplitude experimentally.

    PubMed

    Li, Xin; Liu, Juan; Jia, Jia; Pan, Yijie; Wang, Yongtian

    2013-09-09

    Complex amplitude modulation method is presented theoretically and performed experimentally for three-dimensional (3D) dynamic holographic display with reduced speckle using a single phase-only spatial light modulator. The determination of essential factors is discussed based on the basic principle and theory. The numerical simulations and optical experiments are performed, where the static and animated objects without refinement on the surfaces and without random initial phases are reconstructed successfully. The results indicate that this method can reduce the speckle in reconstructed images effectively; furthermore, it will not cause the internal structure in the reconstructed pixels. Since the complex amplitude modulation is based on the principle of phase-only hologram, it does not need the stringent alignment of pixels. This method can be used for high resolution imaging or measurement in various optical areas.

  14. Modeling tree crown dynamics with 3D partial differential equations

    PubMed Central

    Beyer, Robert; Letort, Véronique; Cournède, Paul-Henry

    2014-01-01

    We characterize a tree's spatial foliage distribution by the local leaf area density. Considering this spatially continuous variable allows to describe the spatiotemporal evolution of the tree crown by means of 3D partial differential equations. These offer a framework to rigorously take locally and adaptively acting effects into account, notably the growth toward light. Biomass production through photosynthesis and the allocation to foliage and wood are readily included in this model framework. The system of equations stands out due to its inherent dynamic property of self-organization and spontaneous adaptation, generating complex behavior from even only a few parameters. The density-based approach yields spatially structured tree crowns without relying on detailed geometry. We present the methodological fundamentals of such a modeling approach and discuss further prospects and applications. PMID:25101095

  15. A skinning prediction scheme for dynamic 3D mesh compression

    NASA Astrophysics Data System (ADS)

    Mamou, Khaled; Zaharia, Titus; Prêteux, Françoise

    2006-08-01

    This paper presents a new prediction-based compression technique for dynamic 3D meshes with constant connectivity and time-varying geometry. The core of the proposed algorithm is a skinning model used for motion compensation. The mesh is first partitioned within vertex clusters that can be described by a single affine motion model. The proposed segmentation technique automatically determines the number of clusters and relays on a decimation strategy privileging the simplification of vertices exhibiting the same affine motion over the whole animation sequence. The residual prediction errors are finally compressed using a temporal-DCT representation. The performances of our encoder are objectively evaluated on a data set of eight animation sequences with various sizes, geometries and topologies, and exhibiting both rigid and elastic motions. The experimental evaluation shows that the proposed compression scheme outperforms state of the art techniques such as MPEG-4/AFX, Dynapack, RT, GV, MCGV, TDCT, PCA and RT compression schemes.

  16. Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

    SciTech Connect

    Han, Ju; Chang, Hang; Giricz, Orsi; Lee, Genee; Baehner, Frederick; Gray, Joe; Bissell, Mina; Kenny, Paraic; Parvin, Bahram

    2010-02-01

    Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPAR? has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPAR? has been validated through two supporting biological assays.

  17. Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

    PubMed Central

    Han, Ju; Chang, Hang; Giricz, Orsi; Lee, Genee Y.; Baehner, Frederick L.; Gray, Joe W.; Bissell, Mina J.; Kenny, Paraic A.; Parvin, Bahram

    2010-01-01

    Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPARγ has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPARγ has been validated through two supporting biological assays. PMID:20195492

  18. 3D map of the human corneal endothelial cell

    PubMed Central

    He, Zhiguo; Forest, Fabien; Gain, Philippe; Rageade, Damien; Bernard, Aurélien; Acquart, Sophie; Peoc’h, Michel; Defoe, Dennis M.; Thuret, Gilles

    2016-01-01

    Corneal endothelial cells (CECs) are terminally differentiated cells, specialized in regulating corneal hydration and transparency. They are highly polarized flat cells that separate the cornea from the aqueous humor. Their apical surface, in contact with aqueous humor is hexagonal, whereas their basal surface is irregular. We characterized the structure of human CECs in 3D using confocal microscopy of immunostained whole corneas in which cells and their interrelationships remain intact. Hexagonality of the apical surface was maintained by the interaction between tight junctions and a submembraneous network of actomyosin, braced like a drum. Lateral membranes, which support enzymatic pumps, presented complex expansions resembling interdigitated foot processes at the basal surface. Using computer-aided design and drafting software, we obtained a first simplified 3D model of CECs. By comparing their expression with those in epithelial, stromal and trabecular corneal cells, we selected 9 structural or functional proteins for which 3D patterns were specific to CECs. This first 3D map aids our understanding of the morphologic and functional specificity of CECs and could be used as a reference for characterizing future cell therapy products destined to treat endothelial dysfunctions. PMID:27381832

  19. Preservation of the 3D Phenotype Upon Dispersal of Cultured Cell Spheroids Into Monolayer Cultures.

    PubMed

    Koshkin, Vasilij; Ailles, Laurie E; Liu, Geoffrey; Krylov, Sergey N

    2017-01-01

    In functional cytometric studies, cultured cells are exposed to effectors (e.g., drugs), and the heterogeneity of cell responses are studied using cytometry techniques (e.g., image cytometry). Such studies are difficult to perform on 3D cell cultures. A solution is to disperse 3D clusters and transfer the cells to the 2D state before applying effectors and using cytometry. This approach requires that the lifetime of the 3D phenotype be longer than the duration of the experiment. Here we studied the dynamics of phenotype transformation from 3D to 2D and searched for means of slowing this transformation down in dispersed spheroids of MCF7 cells. We found three functional biomarkers of the 3D phenotype in MCF7 cell spheroids that are absent in the 2D cell culture: (i) the presence of a subpopulation with an elevated drug-expelling capacity; (ii) the presence of a subpopulation with an elevated cytoprotective capacity; and (iii) the accumulation of cells in the G1 phase of the cell cycle. Monitoring these biomarkers in cells transferred from the 3D state to the 2D state revealed their gradual extinction. We found that the combined application of an elevated cell density and thiol-containing medium supplements increased the lifetime of the 3D phenotype by several fold to as long as 96 h. Our results suggest that extending the lifetime of the 3D phenotype in the cells transferred from the 3D state to the 2D state can facilitate detailed functional cytometric studies, such as measurements of population heterogeneity of cytotoxicity, chemosensitivity, and radiosensitivity. J. Cell. Biochem. 118: 154-162, 2017. © 2016 Wiley Periodicals, Inc.

  20. Computer acquisition of 3D images utilizing dynamic speckles

    NASA Astrophysics Data System (ADS)

    Kamshilin, Alexei A.; Semenov, Dmitry V.; Nippolainen, Ervin; Raita, Erik

    2006-05-01

    We present novel technique for fast non-contact and continuous profile measurements of rough surfaces by use of dynamic speckles. The dynamic speckle pattern is generated when the laser beam scans the surface under study. The most impressive feature of the proposed technique is its ability to work at extremely high scanning speed of hundreds meters per second. The technique is based on the continuous frequency measurements of the light-power modulation after spatial filtering of the scattered light. The complete optical-electronic system was designed and fabricated for fast measurement of the speckles velocity, its recalculation into the distance, and further data acquisition into computer. The measured surface profile is displayed in a PC monitor in real time. The response time of the measuring system is below 1 μs. Important parameters of the system such as accuracy, range of measurements, and spatial resolution are analyzed. Limits of the spatial filtering technique used for continuous tracking of the speckle-pattern velocity are shown. Possible ways of further improvement of the measurements accuracy are demonstrated. Owing to its extremely fast operation, the proposed technique could be applied for online control of the 3D-shape of complex objects (e.g., electronic circuits) during their assembling.

  1. Building 3D data sets of flux tube dynamics

    NASA Astrophysics Data System (ADS)

    Loseth, B.; Intrator, T. P.; Sears, J.

    2010-11-01

    Magnetic Reconnection occurs when oppositely directed magnetic fields are advected towards each other as plasma flow. The magnetic fields diffuse through a small region where the frozen flux condition of ideal magnetohydrodynamics (MHD) breaks down and the field lines lose their identity and reconnect to other fields. The reconnection process is important in the confinement of fusion plasmas as well as long-standing solar-physics issues in solar flares, geomagnetic storms, and black hole accretion discs. The Reconnection Scaling Experiment (RSX) uses plasma guns to create one, two, or more parallel flux ropes in a cylindrical chamber with an axial magnetic guide field. The plasma channels twist helically and merge or bounce depending on the attractive force due to the parallel currents and the repulsive force associated with axial and azimuthal magnetic field line bending. The dynamics of merging and bouncing may lead to a new understanding of the statistical mechanics of magnetic fields and provide a means of visualizing three-dimensional MHD turbulence. An update of the RSX vessel including an adjustable magnetic probe array is currently under way and will allow for the building of 3D data sets of these dynamics.

  2. Flexible 3D pharmacophores as descriptors of dynamic biological space.

    PubMed

    Nettles, James H; Jenkins, Jeremy L; Williams, Chris; Clark, Alex M; Bender, Andreas; Deng, Zhan; Davies, John W; Glick, Meir

    2007-10-01

    Development of a pharmacophore hypothesis related to small-molecule activity is pivotal to chemical optimization of a series, since it defines features beneficial or detrimental to activity. Although crystal structures may provide detailed 3D interaction information for one molecule with its receptor, docking a different ligand to that model often leads to unreliable results due to protein flexibility. Graham Richards' lab was one of the first groups to utilize "fuzzy" pattern recognition algorithms taken from the field of image processing to solve problems in protein modeling. Thus, descriptor "fuzziness" was partly able to emulate conformational flexibility of the target while simultaneously enhancing the speed of the search. In this work, we extend these developments to a ligand-based method for describing and aligning molecules in flexible chemical space termed FEature POint PharmacophoreS (FEPOPS), which allows exploration of dynamic biological space. We develop a novel, combinatorial algorithm for molecular comparisons and evaluate it using the WOMBAT dataset. The new approach shows superior retrospective virtual screening performance than earlier shape-based or charge-based algorithms. Additionally, we use target prediction to evaluate how FEPOPS alignments match the molecules biological activity by identifying the atoms and features that make the key contributions to overall chemical similarity. Overall, we find that FEPOPS are sufficiently fuzzy and flexible to find not only new ligand scaffolds, but also challenging molecules that occupy different conformational states of dynamic biological space as from induced fits.

  3. Analysis and dynamic 3D visualization of cerebral blood flow combining 3D and 4D MR image sequences

    NASA Astrophysics Data System (ADS)

    Forkert, Nils Daniel; Säring, Dennis; Fiehler, Jens; Illies, Till; Möller, Dietmar; Handels, Heinz

    2009-02-01

    In this paper we present a method for the dynamic visualization of cerebral blood flow. Spatio-temporal 4D magnetic resonance angiography (MRA) image datasets and 3D MRA datasets with high spatial resolution were acquired for the analysis of arteriovenous malformations (AVMs). One of the main tasks is the combination of the information of the 3D and 4D MRA image sequences. Initially, in the 3D MRA dataset the vessel system is segmented and a 3D surface model is generated. Then, temporal intensity curves are analyzed voxelwise in the 4D MRA image sequences. A curve fitting of the temporal intensity curves to a patient individual reference curve is used to extract the bolus arrival times in the 4D MRA sequences. After non-linear registration of both MRA datasets the extracted hemodynamic information is transferred to the surface model where the time points of inflow can be visualized color coded dynamically over time. The dynamic visualizations computed using the curve fitting method for the estimation of the bolus arrival times were rated superior compared to those computed using conventional approaches for bolus arrival time estimation. In summary the procedure suggested allows a dynamic visualization of the individual hemodynamic situation and better understanding during the visual evaluation of cerebral vascular diseases.

  4. 3D morphometry of red blood cells by digital holography.

    PubMed

    Memmolo, Pasquale; Miccio, Lisa; Merola, Francesco; Gennari, Oriella; Netti, Paolo Antonio; Ferraro, Pietro

    2014-12-01

    Three dimensional (3D) morphometric analysis of flowing and not-adherent cells is an important aspect for diagnostic purposes. However, diagnostics tools need to be quantitative, label-free and, as much as possible, accurate. Recently, a simple holographic approach, based on shape from silhouette algorithm, has been demonstrated for accurate calculation of cells biovolume and displaying their 3D shapes. Such approach has been adopted in combination with holographic optical tweezers and successfully applied to cells with convex shape. Nevertheless, unfortunately, the method fails in case of specimen with concave surfaces. Here, we propose an effective approach to achieve correct 3D shape measurement that can be extended in case of cells having concave surfaces, thus overcoming the limit of the previous technique. We prove the new procedure for healthy red blood cells (RBCs) (i.e., discocytes) having a concave surface in their central region. Comparative analysis of experimental results with a theoretical 3D geometrical model of RBC is discussed in order to evaluate accuracy of the proposed approach. Finally, we show that the method can be also useful to classify, in terms of morphology, different varieties of RBCs.

  5. Influence of scaffold design on 3D printed cell constructs.

    PubMed

    Souness, Auryn; Zamboni, Fernanda; Walker, Gavin M; Collins, Maurice N

    2017-02-14

    Additive manufacturing is currently receiving significant attention in the field of tissue engineering and biomaterial science. The development of precise, affordable 3D printing technologies has provided a new platform for novel research to be undertaken in 3D scaffold design and fabrication. In the past, a number of 3D scaffold designs have been fabricated to investigate the potential of a 3D printed scaffold as a construct which could support cellular life. These studies have shown promising results; however, few studies have utilized a low-cost desktop 3D printing technology as a potential rapid manufacturing route for different scaffold designs. Here six scaffold designs were manufactured using a Fused deposition modeling, a "bottom-up" solid freeform fabrication approach, to determine optimal scaffold architecture for three-dimensional cell growth. The scaffolds, produced from PLA, are coated using pullulan and hyaluronic acid to assess the coating influence on cell proliferation and metabolic rate. Scaffolds are characterized both pre- and postprocessing using water uptake analysis, mechanical testing, and morphological evaluation to study the inter-relationships between the printing process, scaffold design, and scaffold properties. It was found that there were key differences between each scaffold design in terms of porosity, diffusivity, swellability, and compressive strength. An optimal design was chosen based on these physical measurements which were then weighted in accordance to design importance based on literature and utilizing a design matrix technique. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2017.

  6. A support-operator method for 3-D rupture dynamics

    NASA Astrophysics Data System (ADS)

    Ely, Geoffrey P.; Day, Steven M.; Minster, Jean-Bernard

    2009-06-01

    We present a numerical method to simulate spontaneous shear crack propagation within a heterogeneous, 3-D, viscoelastic medium. Wave motions are computed on a logically rectangular hexahedral mesh, using the generalized finite-difference method of Support Operators (SOM). This approach enables modelling of non-planar surfaces and non-planar fault ruptures. Our implementation, the Support Operator Rupture Dynamics (SORD) code, is highly scalable, enabling large-scale, multiprocessors calculations. The fault surface is modelled by coupled double nodes, where rupture occurs as dictated by the local stress conditions and a frictional failure law. The method successfully performs test problems developed for the Southern California Earthquake Center (SCEC)/U.S. Geological Survey (USGS) dynamic earthquake rupture code validation exercise, showing good agreement with semi-analytical boundary integral method results. We undertake further dynamic rupture tests to quantify numerical errors introduced by shear deformations to the hexahedral mesh. We generate a family of meshes distorted by simple shearing, in the along-strike direction, up to a maximum of 73°. For SCEC/USGS validation problem number 3, grid-induced errors increase with mesh shear angle, with the logarithm of error approximately proportional to angle over the range tested. At 73°, rms misfits are about 10 per cent for peak slip rate, and 0.5 per cent for both rupture time and total slip, indicating that the method (which, up to now, we have applied mainly to near-vertical strike-slip faulting) is also capable of handling geometries appropriate to low-angle surface-rupturing thrust earthquakes. Additionally, we demonstrate non-planar rupture effects, by modifying the test geometry to include, respectively, cylindrical curvature and sharp kinks.

  7. 3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells

    PubMed Central

    Luo, Tong; Chen, Huan; Kassab, Ghassan S.

    2016-01-01

    Aims The 3D geometry of individual vascular smooth muscle cells (VSMCs), which are essential for understanding the mechanical function of blood vessels, are currently not available. This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation. Methods and Results A total of 112 VSMCs from six porcine coronary arteries were used in the analysis. A 3D semi-automatic segmentation method was developed to reconstruct individual VSMCs from cell clumps as well as to extract the 3D geometry of VSMCs. A new edge blocking model was introduced to recognize cell boundary while an edge growing was developed for optimal interpolation and edge verification. The proposed methods were designed based on Region of Interest (ROI) selected by user and interactive responses of limited key edges. Enhanced cell boundary features were used to construct the cell’s initial boundary for further edge growing. A unified framework of morphological parameters (dimensions and orientations) was proposed for the 3D volume data. Virtual phantom was designed to validate the tilt angle measurements, while other parameters extracted from 3D segmentations were compared with manual measurements to assess the accuracy of the algorithm. The length, width and thickness of VSMCs were 62.9±14.9μm, 4.6±0.6μm and 6.2±1.8μm (mean±SD). In longitudinal-circumferential plane of blood vessel, VSMCs align off the circumferential direction with two mean angles of -19.4±9.3° and 10.9±4.7°, while an out-of-plane angle (i.e., radial tilt angle) was found to be 8±7.6° with median as 5.7°. Conclusions A 3D segmentation algorithm was developed to reconstruct individual VSMCs of blood vessel walls based on optical image stacks. The results were validated by a virtual phantom and manual measurement. The obtained 3D geometries can be utilized in mathematical models and leads a better understanding of vascular mechanical properties and function. PMID:26882342

  8. Bioimpedance monitoring of 3D cell culturing--complementary electrode configurations for enhanced spatial sensitivity.

    PubMed

    Canali, Chiara; Heiskanen, Arto; Muhammad, Haseena Bashir; Høyum, Per; Pettersen, Fred-Johan; Hemmingsen, Mette; Wolff, Anders; Dufva, Martin; Martinsen, Ørjan Grøttem; Emnéus, Jenny

    2015-01-15

    A bioimpedance platform is presented as a promising tool for non-invasive real-time monitoring of the entire process of three-dimensional (3D) cell culturing in a hydrogel scaffold. In this study, the dynamics involved in the whole process of 3D cell culturing, starting from polymerisation of a bare 3D gelatin scaffold, to human mesenchymal stem cell (MSC) encapsulation and proliferation, was monitored over time. The platform consists of a large rectangular culture chamber with four embedded vertical gold plate electrodes that were exploited in two- and three terminal (2T and 3T) measurement configurations. By switching between the different combinations of electrode couples, it was possible to generate a multiplexing-like approach, which allowed for collecting spatially distributed information within the 3D space. Computational finite element (FE) analysis and electrochemical impedance spectroscopic (EIS) characterisation were used to determine the configurations' sensitivity field localisation. The 2T setup gives insight into the interfacial phenomena at both electrode surfaces and covers the central part of the 3D cell culture volume, while the four 3T modes provide focus on the dynamics at the corners of the 3D culture chamber. By combining a number of electrode configurations, complementary spatially distributed information on a large 3D cell culture can be obtained with maximised sensitivity in the entire 3D space. The experimental results show that cell proliferation can be monitored within the tested biomimetic environment, paving the way to further developments in bioimpedance tracking of 3D cell cultures and tissue engineering.

  9. A new 3D dynamical biomechanical tongue model

    NASA Astrophysics Data System (ADS)

    Gerard, Jean-Michel; Perrier, Pascal; Payan, Yohan; Wilhelms-Tricarico, Reiner

    2004-05-01

    A new dynamical biomechanical tongue model is being developed to study speech motor control. In spite of its computational complexity, a 3D representation was chosen in order to account for various contacts between tongue and external structures such as teeth, palate, and vocal tract walls. A fair representation of tongue muscle anatomy is provided, by designing the finite element mesh from the visible human data set (female subject). Model geometry was then matched to a human speaker, so that simulations can be quantitatively compared to experimental MRI data. A set of 11 muscles is modeled, whose role in speech gestures is well established. Each muscle is defined by a set of elements whose elastic properties change with muscle activation. Muscles forces are applied to the tongue model via macrofibers defined within the mesh by muscle specific sets of nodes. These forces are currently specified as step functions. Boundary conditions are set using zero-displacement nodes simulating attachments of tongue on bony structures. The nonlinear mechanical properties of tongue soft tissues are modeled using a hyperelastic material. Three-dimensional tongue deformations generated by each muscle, using FEM software ANSYS for computation, will be presented. Implications for speech motor control will be proposed.

  10. A new 3D dynamical biomechanical tongue model

    NASA Astrophysics Data System (ADS)

    Gerard, Jean-Michel; Perrier, Pascal; Payan, Yohan; Wilhelms-Tricarico, Reiner

    2001-05-01

    A new dynamical biomechanical tongue model is being developed to study speech motor control. In spite of its computational complexity, a 3D representation was chosen in order to account for various contacts between tongue and external structures such as teeth, palate, and vocal tract walls. A fair representation of tongue muscle anatomy is provided, by designing the finite element mesh from the visible human data set (female subject). Model geometry was then matched to a human speaker, so that simulations can be quantitatively compared to experimental MRI data. A set of 11 muscles is modeled, whose role in speech gestures is well established. Each muscle is defined by a set of elements whose elastic properties change with muscle activation. Muscles forces are applied to the tongue model via macrofibers defined within the mesh by muscle specific sets of nodes. These forces are currently specified as step functions. Boundary conditions are set using zero-displacement nodes simulating attachments of tongue on bony structures. The nonlinear mechanical properties of tongue soft tissues are modeled using a hyperelastic material. Three-dimensional tongue deformations generated by each muscle, using FEM software ANSYS for computation, will be presented. Implications for speech motor control will be proposed.

  11. Vortex dynamics in 3D shock-bubble interaction

    NASA Astrophysics Data System (ADS)

    Hejazialhosseini, Babak; Rossinelli, Diego; Koumoutsakos, Petros

    2013-11-01

    The dynamics of shock-bubble interaction involve an interplay of vortex stretching, dilation, and baroclinic vorticity generation. Here, we quantify the interplay of these contributions through high resolution 3D simulations for several Mach and Atwood numbers. We present a volume rendering of density and vorticity magnitude fields of shock-bubble interaction at M = 3 and air/helium density ratio η = 7.25 to elucidate the evolution of the flow structures. We distinguish the vorticity growth rates due to baroclinicity, stretching, and dilatation at low and high Mach numbers as well as the late time evolution of the circulation. The results demonstrate that a number of analytical models need to be revised in order to predict the late time circulation of shock-bubble interactions at high Mach numbers. To this effect, we propose a simple model for the dependence of the circulation to Mach number and ambient to bubble density ratio for air/helium shock-bubble interactions.

  12. Microfluidic titer plate for stratified 3D cell culture.

    PubMed

    Trietsch, Sebastiaan J; Israëls, Guido D; Joore, Jos; Hankemeier, Thomas; Vulto, Paul

    2013-09-21

    Human tissues and organs are inherently heterogeneous. Their functionality is determined by the interplay between different cell types, their secondary architecture, vascular system and gradients of signaling molecules and metabolites. Here we propose a stratified 3D cell culture platform, in which adjacent lanes of gels and liquids are patterned by phaseguides to capture this tissue heterogeneity. We demonstrate 3D cell culture of HepG2 hepatocytes under continuous perfusion, a rifampicin toxicity assay and co-culture with fibroblasts. 4T1 breast cancer cells are used to demonstrate invasion and aggregation models. The platform is incorporated in a microtiter plate format that renders it fully compatible with automation and high-content screening equipment. The extended functionality, ease of handling and full compatibility to standard equipment is an important step towards adoption of Organ-on-a-Chip technology for screening in an industrial setting.

  13. Fabricating gradient hydrogel scaffolds for 3D cell culture.

    PubMed

    Chatterjee, Kaushik; Young, Marian F; Simon, Carl G

    2011-05-01

    Optimizing cell-material interactions is critical for maximizing regeneration in tissue engineering. Combinatorial and high-throughput (CHT) methods can be used to systematically screen tissue scaffolds to identify optimal biomaterial properties. Previous CHT platforms in tissue engineering have involved a two-dimensional (2D) cell culture format where cells were cultured on material surfaces. However, these platforms are inadequate to predict cellular response in a three-dimensional (3D) tissue scaffold. We have developed a simple CHT platform to screen cell-material interactions in 3D culture format that can be applied to screen hydrogel scaffolds. Herein we provide detailed instructions on a method to prepare gradients in elastic modulus of photopolymerizable hydrogels.

  14. A microfabricated platform with hydrogel arrays for 3D mechanical stimulation of cells.

    PubMed

    Liu, Haijiao; Usprech, Jenna; Sun, Yu; Simmons, Craig A

    2016-04-01

    Cellular microenvironments present cells with multiple stimuli, including not only soluble biochemical and insoluble matrix cues but also mechanical factors. Biomaterial array platforms have been used to combinatorially and efficiently probe and define two-dimensional (2D) and 3D microenvironmental cues to guide cell functions for tissue engineering applications. However, there are few examples of array platforms that include dynamic mechanical forces, particularly to enable stretching of 3D cell-seeded biomaterials, which is relevant to engineering connective and cardiovascular tissues. Here we present a deformable membrane platform that enables 3D dynamic mechanical stretch of arrayed biomaterial constructs. Cell-seeded polyethylene glycol norbornene (PEG-NB) hydrogels were bound to miniaturized deformable membranes via a thiol-ene reaction with off-stoichiometry thiol-ene based polydimethylsiloxane (OSTE-PDMS) as the membrane material. Bonding to OSTE-PDMS enabled the 3D hydrogel microconstructs to be cyclically deformed and stretched by the membrane. As a first demonstration, human mesenchymal stromal cells (MSCs) embedded in PEG-NB were stretched for several days. They were found to be viable, spread in the 3D hydrogels, and exhibited a contractile myofibroblast phenotype when exposed to dynamic 3D mechanical deformation. This platform, which is readily scalable to larger arrays, enables systematic interrogation of the relationships between combinations of 3D mechanobiological cues and cellular responses, and thus has the potential to identify strategies to predictably control the construction of functional engineered tissues. Current high-throughput biomaterial screening approaches fail to consider the effects of dynamic mechanical stimulation, despite its importance in a wide variety of regenerative medicine applications. To meet this need, we developed a deformable membrane platform that enables 3D dynamic stretch of arrayed biomaterial constructs. Our

  15. 3D calcite heterostructures for dynamic and deformable mineralized matrices

    DOE PAGES

    Yi, Jaeseok; Wang, Yucai; Jiang, Yuanwen; ...

    2017-09-11

    Scales are rooted in soft tissues, and are regenerated by specialized cells. The realization of dynamic synthetic analogues with inorganic materials has been a significant challenge, because the abiological regeneration sites that could yield deterministic growth behavior are hard to form. Here we overcome this fundamental hurdle by constructing a mutable and deformable array of three-dimensional calcite heterostructures that are partially locked in silicone. Individual calcite crystals exhibit asymmetrical dumbbell shapes and are prepared by a parallel tectonic approach under ambient conditions. Furthermore, the silicone matrix immobilizes the epitaxial nucleation sites through self-templated cavities, which enables symmetry breaking in reactionmore » dynamics and scalable manipulation of the mineral ensembles. With this platform, we devise several mineral-enabled dynamic surfaces and interfaces. For example, we show that the induced growth of minerals yields localized inorganic adhesion for biological tissue and reversible focal encapsulation for sensitive components in flexible electronics.« less

  16. 3D visualization of membrane failures in fuel cells

    NASA Astrophysics Data System (ADS)

    Singh, Yadvinder; Orfino, Francesco P.; Dutta, Monica; Kjeang, Erik

    2017-03-01

    Durability issues in fuel cells, due to chemical and mechanical degradation, are potential impediments in their commercialization. Hydrogen leak development across degraded fuel cell membranes is deemed a lifetime-limiting failure mode and potential safety issue that requires thorough characterization for devising effective mitigation strategies. The scope and depth of failure analysis has, however, been limited by the 2D nature of conventional imaging. In the present work, X-ray computed tomography is introduced as a novel, non-destructive technique for 3D failure analysis. Its capability to acquire true 3D images of membrane damage is demonstrated for the very first time. This approach has enabled unique and in-depth analysis resulting in novel findings regarding the membrane degradation mechanism; these are: significant, exclusive membrane fracture development independent of catalyst layers, localized thinning at crack sites, and demonstration of the critical impact of cracks on fuel cell durability. Evidence of crack initiation within the membrane is demonstrated, and a possible new failure mode different from typical mechanical crack development is identified. X-ray computed tomography is hereby established as a breakthrough approach for comprehensive 3D characterization and reliable failure analysis of fuel cell membranes, and could readily be extended to electrolyzers and flow batteries having similar structure.

  17. 3D calcite heterostructures for dynamic and deformable mineralized matrices.

    PubMed

    Yi, Jaeseok; Wang, Yucai; Jiang, Yuanwen; Jung, Il Woong; Liu, Wenjun; De Andrade, Vincent; Xu, Ruqing; Parameswaran, Ramya; Peters, Ivo R; Divan, Ralu; Xiao, Xianghui; Sun, Tao; Lee, Youjin; Park, Won Il; Tian, Bozhi

    2017-09-11

    Scales are rooted in soft tissues, and are regenerated by specialized cells. The realization of dynamic synthetic analogues with inorganic materials has been a significant challenge, because the abiological regeneration sites that could yield deterministic growth behavior are hard to form. Here we overcome this fundamental hurdle by constructing a mutable and deformable array of three-dimensional calcite heterostructures that are partially locked in silicone. Individual calcite crystals exhibit asymmetrical dumbbell shapes and are prepared by a parallel tectonic approach under ambient conditions. The silicone matrix immobilizes the epitaxial nucleation sites through self-templated cavities, which enables symmetry breaking in reaction dynamics and scalable manipulation of the mineral ensembles. With this platform, we devise several mineral-enabled dynamic surfaces and interfaces. For example, we show that the induced growth of minerals yields localized inorganic adhesion for biological tissue and reversible focal encapsulation for sensitive components in flexible electronics.Minerals are rarely explored as building blocks for dynamic inorganic materials. Here, the authors derive inspiration from fish scales to create mutable surfaces based on arrays of calcite crystals, in which one end of each crystal is immobilized in and regenerated from silicone, and the other functional end is left exposed.

  18. Role of dynamin in elongated cell migration in a 3D matrix.

    PubMed

    Lees, Justin G; Gorgani, Nick N; Ammit, Alaina J; McCluskey, Adam; Robinson, Phillip J; O'Neill, Geraldine M

    2015-03-01

    The use of 3-dimensional (3D) collagen gels has yielded new insights into the migratory behaviour of cancer cells. While the large GTPase dynamin has emerged as an important regulator of cancer cell migration and invasion under 2D conditions, its role in 3D migration is unclear. We have used a potent dynamin modulator, a bis-tyrphostin derivative, Ryngo® 1-23, to investigate the role of dynamin in 3D migration in 3 different cell lines. The compound specifically inhibits persistent, elongated 3D migration in U87MG and SMA-560 cells. Treated U87MG cells adopt a rounded morphology that is not due to apoptosis, loss of matrix metalloprotease activity or inhibition of clathrin-mediated endocytosis. Given that Ryngo 1-23 is known to regulate dynamin oligomerisation and actin dynamics at the leading edge, we analysed actin filament distribution. Ryngo 1-23 induced a switch in actin filament organization in 3D cultures resulting in the generation of multiple short actin-rich microspikes. Correlated with the change in actin filament distribution, cells displayed reduced collagen gel contraction. Since acto-myosin force transmission to the extra-cellular matrix underpins persistent, elongated migration, our results suggest that Ryngo 1-23 modulates this process in 3D migration via dynamin-mediated regulation of acto-myosin force transmission to the extra-cellular matrix.

  19. Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments

    PubMed Central

    Welf, Erik S.; Driscoll, Meghan K.; Dean, Kevin M.; Schäfer, Claudia; Chu, Jun; Davidson, Michael W.; Lin, Michael Z.; Danuser, Gaudenz; Fiolka, Reto

    2016-01-01

    The microenvironment determines cell behavior, but the underlying molecular mechanisms are poorly understood because quantitative studies of cell signaling and behavior have been challenging due to insufficient spatial and/or temporal resolution and limitations on microenvironmental control. Here we introduce microenvironmental selective plane illumination microscopy (meSPIM) for imaging and quantification of intracellular signaling and submicrometer cellular structures as well as large-scale cell morphological and environmental features. We demonstrate the utility of this approach by showing that the mechanical properties of the microenvironment regulate the transition of melanoma cells from actin-driven protrusion to blebbing, and we present tools to quantify how cells manipulate individual collagen fibers. We leverage the nearly isotropic resolution of meSPIM to quantify the local concentration of actin and phosphatidylinositol 3-kinase signaling on the surfaces of cells deep within 3D collagen matrices and track the many small membrane protrusions that appear in these more physiologically relevant environments. PMID:26906741

  20. 3D cancer cell migration in a confined matrix

    NASA Astrophysics Data System (ADS)

    Alobaidi, Amani; Sun, Bo

    Cancer cell migration is widely studied in 2D motion, which does not mimic the invasion processes in vivo. More recently, 3D cell migration studies have been performed. The ability of cancer cells to migrate within the extracellular matrix depends on the physical and biochemical features of the extracellular matrix. We present a model of cell motility in confined matrix geometry. The aim of the study is to study cancer migration in collagen matrix, as a soft tissue, to investigate their motility within the confined and surrounding collagen environment. Different collagen concentrations have been used to show the ability of these cancer cells to move through such a complex structure by measuring Cancer cell migration velocity as well as the displacement. Graduate student physics department.

  1. Pluripotency in 3D: Genome organization in pluripotent cells

    PubMed Central

    Denholtz, Matthew; Plath, Kathrin

    2012-01-01

    Cells face the challenge of storing two meters of DNA in the three-dimensional (3D) space of the nucleus that spans only a few microns. The nuclear organization that is required to overcome this challenge must allow for the accessibility of the gene regulatory machinery to the DNA and, in the case of embryonic stem cells (ESCs), for the transcriptional and epigenetic changes that accompany differentiation. Recent technological advances have allowed for the mapping of genome organization at an unprecedented resolution and scale. These breakthroughs have lead to a deluge of new data, and a sophisticated understanding of the relationship between gene regulation and 3D genome organization is beginning to form. In this review we summarize some of the recent findings illuminating the 3D structure of the eukaryotic genome, as well as the relationship between genome topology and function from the level of whole chromosomes to enhancer-promoter loops with a focus on features affecting genome organization in ESCs and changes in nuclear organization during differentiation. PMID:23199754

  2. Vinculin Regulates Directionality and Cell Polarity in 2D, 3D Matrix and 3D Microtrack Migration.

    PubMed

    Rahman, Aniqua; Carey, Shawn P; Kraning-Rush, Casey M; Goldblatt, Zachary E; Bordeleau, Francois; Lampi, Marsha C; Lin, Deanna Y; García, Andrés J; Reinhart-King, Cynthia A

    2016-03-09

    During metastasis, cells can use proteolytic activity to form tube-like "microtracks" within the extracellular matrix (ECM). Using these microtracks, cells can migrate unimpeded through the stroma. To investigate the molecular mechanisms of microtrack migration, we developed an in vitro 3D micromolded collagen platform. When in microtracks, cells tend to migrate unidirectionally. Since focal adhesions are the primary mechanism by which cells interact with the ECM, we examined the roles of several focal adhesion molecules in driving unidirectional motion. Vinculin knockdown results in the repeated reversal of migration direction compared with control cells. Tracking the position of the Golgi centroid relative to the position of the nucleus centroid reveals that vinculin knockdown disrupts cell polarity in microtracks. Vinculin also directs migration on 2D substrates and in 3D uniform collagen matrices, indicated by reduced speed, shorter net displacement and decreased directionality in vinculin-deficient cells. In addition, vinculin is necessary for Focal Adhesion Kinase (FAK) activation in 3D as vinculin knockdown results in reduced FAK activation in both 3D uniform collagen matrices and microtracks, but not on 2D substrates, and accordingly, FAK inhibition halts cell migration in 3D microtracks. Together, these data indicate that vinculin plays a key role in polarization during migration.

  3. Quasi-3D cytoskeletal dynamics of osteocytes under fluid flow.

    PubMed

    Baik, Andrew D; Lu, X Lucas; Qiu, Jun; Huo, Bo; Hillman, Elizabeth M C; Dong, Cheng; Guo, X Edward

    2010-11-03

    Osteocytes respond to dynamic fluid shear loading by activating various biochemical pathways, mediating a dynamic process of bone formation and resorption. Whole-cell deformation and regional deformation of the cytoskeleton may be able to directly regulate this process. Attempts to image cellular deformation by conventional microscopy techniques have been hindered by low temporal or spatial resolution. In this study, we developed a quasi-three-dimensional microscopy technique that enabled us to simultaneously visualize an osteocyte's traditional bottom-view profile and a side-view profile at high temporal resolution. Quantitative analysis of the plasma membrane and either the intracellular actin or microtubule (MT) cytoskeletal networks provided characterization of their deformations over time. Although no volumetric dilatation of the whole cell was observed under flow, both the actin and MT networks experienced primarily tensile strains in all measured strain components. Regional heterogeneity in the strain field of normal strains was observed in the actin networks, especially in the leading edge to flow, but not in the MT networks. In contrast, side-view shear strains exhibited similar subcellular distribution patterns in both networks. Disruption of MT networks caused actin normal strains to decrease, whereas actin disruption had little effect on the MT network strains, highlighting the networks' mechanical interactions in osteocytes. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Quasi-3D Cytoskeletal Dynamics of Osteocytes under Fluid Flow

    PubMed Central

    Baik, Andrew D.; Lu, X. Lucas; Qiu, Jun; Huo, Bo; Hillman, Elizabeth M.C.; Dong, Cheng; Guo, X. Edward

    2010-01-01

    Osteocytes respond to dynamic fluid shear loading by activating various biochemical pathways, mediating a dynamic process of bone formation and resorption. Whole-cell deformation and regional deformation of the cytoskeleton may be able to directly regulate this process. Attempts to image cellular deformation by conventional microscopy techniques have been hindered by low temporal or spatial resolution. In this study, we developed a quasi-three-dimensional microscopy technique that enabled us to simultaneously visualize an osteocyte's traditional bottom-view profile and a side-view profile at high temporal resolution. Quantitative analysis of the plasma membrane and either the intracellular actin or microtubule (MT) cytoskeletal networks provided characterization of their deformations over time. Although no volumetric dilatation of the whole cell was observed under flow, both the actin and MT networks experienced primarily tensile strains in all measured strain components. Regional heterogeneity in the strain field of normal strains was observed in the actin networks, especially in the leading edge to flow, but not in the MT networks. In contrast, side-view shear strains exhibited similar subcellular distribution patterns in both networks. Disruption of MT networks caused actin normal strains to decrease, whereas actin disruption had little effect on the MT network strains, highlighting the networks' mechanical interactions in osteocytes. PMID:21044578

  5. Microfluidic 3D cell culture: potential application for tissue-based bioassays

    PubMed Central

    Li, XiuJun (James); Valadez, Alejandra V.; Zuo, Peng; Nie, Zhihong

    2014-01-01

    Current fundamental investigations of human biology and the development of therapeutic drugs, commonly rely on two-dimensional (2D) monolayer cell culture systems. However, 2D cell culture systems do not accurately recapitulate the structure, function, physiology of living tissues, as well as highly complex and dynamic three-dimensional (3D) environments in vivo. The microfluidic technology can provide micro-scale complex structures and well-controlled parameters to mimic the in vivo environment of cells. The combination of microfluidic technology with 3D cell culture offers great potential for in vivo-like tissue-based applications, such as the emerging organ-on-a-chip system. This article will review recent advances in microfluidic technology for 3D cell culture and their biological applications. PMID:22793034

  6. 3D Surface Topology Guides Stem Cell Adhesion and Differentiation

    PubMed Central

    Viswanathan, Priyalakshmi; Ondeck, Matthew G.; Chirasatitsin, Somyot; Nghamkham, Kamolchanok; Reilly, Gwendolen C.; Engler, Adam J.; Battaglia, Giuseppe

    2015-01-01

    Polymerized high internal phase emulsion (polyHIPE) foams are extremely versatile materials for investigating cell-substrate interactions in vitro. Foam morphologies can be controlled by polymerization conditions to result in either open or closed pore structures with different levels of connectivity, consequently enabling the comparison between 2D and 3D matrices using the same substrate with identical surface chemistry conditions. Additionally, here we achieve the control of pore surface topology (i.e. how different ligands are clustered together) using amphiphilic block copolymers as emulsion stabilisers. We demonstrate that adhesion of human mesenchymal progenitor (hES-MP) cells cultured on polyHIPE foams is dependent on foam surface topology and chemistry but is independent of porosity and interconnectivity. We also demonstrate that the interconnectivity, architecture and surface topology of the foams has an effect on the osteogenic differentiation potential of hES-MP cells. Together these data demonstrate that the adhesive heterogeneity of a 3D scaffold could regulate not only mesenchymal stem cell attachment but also cell behavior in the absence of soluble growth factors. PMID:25818420

  7. Gamified Assessment Supported by a Dynamic 3D Collaborative Game

    ERIC Educational Resources Information Center

    Mavridis, Apostolos; Tsiatsos, Thrasyvoulos; Chatzakis, Michalis; Kitsikoudis, Konstantinos; Lazarou, Efthymios

    2015-01-01

    This study examined whether a 3D collaborative gave can be used as a midterm examination method and investigated the impact of this game on students' attitude towards collaboration. A total of 89 students and one coordinating professor participated in this study. The intervention lasted five weeks and took place in a computer science department.…

  8. Gamified Assessment Supported by a Dynamic 3D Collaborative Game

    ERIC Educational Resources Information Center

    Mavridis, Apostolos; Tsiatsos, Thrasyvoulos; Chatzakis, Michalis; Kitsikoudis, Konstantinos; Lazarou, Efthymios

    2015-01-01

    This study examined whether a 3D collaborative gave can be used as a midterm examination method and investigated the impact of this game on students' attitude towards collaboration. A total of 89 students and one coordinating professor participated in this study. The intervention lasted five weeks and took place in a computer science department.…

  9. A novel mechanotactic 3D modeling of cell morphology

    NASA Astrophysics Data System (ADS)

    Jamaleddin Mousavi, Seyed; Hamdy Doweidar, Mohamed

    2014-08-01

    Cell morphology plays a critical role in many biological processes, such as cell migration, tissue development, wound healing and tumor growth. Recent investigations demonstrate that, among other stimuli, cells adapt their shapes according to their substrate stiffness. Until now, the development of this process has not been clear. Therefore, in this work, a new three-dimensional (3D) computational model for cell morphology has been developed. This model is based on a previous cell migration model presented by the same authors. The new model considers that during cell-substrate interaction, cell shape is governed by internal cell deformation, which leads to an accurate prediction of the cell shape according to the mechanical characteristic of its surrounding micro-environment. To study this phenomenon, the model has been applied to different numerical cases. The obtained results, which are qualitatively consistent with well-known related experimental works, indicate that cell morphology not only depends on substrate stiffness but also on the substrate boundary conditions. A cell located within an unconstrained soft substrate (several kPa) with uniform stiffness is unable to adhere to its substrate or to send out pseudopodia. When the substrate stiffness increases to tens of kPa (intermediate and rigid substrates), the cell can adequately adhere to its substrate. Subsequently, as the traction forces exerted by the cell increase, the cell elongates and its shape changes. Within very stiff (hard) substrates, the cell cannot penetrate into its substrate or send out pseudopodia. On the other hand, a cell is found to be more elongated within substrates with a constrained surface. However, this elongation decreases when the cell approaches it. It can be concluded that the higher the net traction force, the greater the cell elongation, the larger the cell membrane area, and the less random the cell alignment.

  10. General mechanism and dynamics of the solar wind interaction with lunar magnetic anomalies from 3-D particle-in-cell simulations

    NASA Astrophysics Data System (ADS)

    Deca, Jan; Divin, Andrey; Lembège, Bertrand; Horányi, Mihály; Markidis, Stefano; Lapenta, Giovanni

    2015-08-01

    We present a general model of the solar wind interaction with a dipolar lunar crustal magnetic anomaly (LMA) using three-dimensional full-kinetic and electromagnetic simulations. We confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the lunar surface, forming a so-called "minimagnetosphere," as suggested by spacecraft observations and theory. We show that the LMA configuration is driven by electron motion because its scale size is small with respect to the gyroradius of the solar wind ions. We identify a population of back-streaming ions, the deflection of magnetized electrons via the E × B drift motion, and the subsequent formation of a halo region of elevated density around the dipole source. Finally, it is shown that the presence and efficiency of the processes are heavily impacted by the upstream plasma conditions and, on their turn, influence the overall structure and evolution of the LMA system. Understanding the detailed physics of the solar wind interaction with LMAs, including magnetic shielding, particle dynamics and surface charging is vital to evaluate its implications for lunar exploration.

  11. 3D-printed external light trap for solar cells.

    PubMed

    van Dijk, Lourens; Paetzold, Ulrich W; Blab, Gerhard A; Schropp, Ruud E I; di Vece, Marcel

    2016-05-01

    We present a universally applicable 3D-printed external light trap for enhanced absorption in solar cells. The macroscopic external light trap is placed at the sun-facing surface of the solar cell and retro-reflects the light that would otherwise escape. The light trap consists of a reflective parabolic concentrator placed on top of a reflective cage. Upon placement of the light trap, an improvement of 15% of both the photocurrent and the power conversion efficiency in a thin-film nanocrystalline silicon (nc-Si:H) solar cell is measured. The trapped light traverses the solar cell several times within the reflective cage thereby increasing the total absorption in the cell. Consequently, the trap reduces optical losses and enhances the absorption over the entire spectrum. The components of the light trap are 3D printed and made of smoothened, silver-coated thermoplastic. In contrast to conventional light trapping methods, external light trapping leaves the material quality and the electrical properties of the solar cell unaffected. To explain the theoretical operation of the external light trap, we introduce a model that predicts the absorption enhancement in the solar cell by the external light trap. The corresponding calculated path length enhancement shows good agreement with the empirically derived value from the opto-electrical data of the solar cell. Moreover, we analyze the influence of the angle of incidence on the parasitic absorptance to obtain full understanding of the trap performance. © 2015 The Authors. Progress in Photovoltaics: Research and Applications published by John Wiley & Sons, Ltd.

  12. Face recognition based on matching of local features on 3D dynamic range sequences

    NASA Astrophysics Data System (ADS)

    Echeagaray-Patrón, B. A.; Kober, Vitaly

    2016-09-01

    3D face recognition has attracted attention in the last decade due to improvement of technology of 3D image acquisition and its wide range of applications such as access control, surveillance, human-computer interaction and biometric identification systems. Most research on 3D face recognition has focused on analysis of 3D still data. In this work, a new method for face recognition using dynamic 3D range sequences is proposed. Experimental results are presented and discussed using 3D sequences in the presence of pose variation. The performance of the proposed method is compared with that of conventional face recognition algorithms based on descriptors.

  13. DREAM3D simulations of inner-belt dynamics

    SciTech Connect

    Cunningham, Gregory Scott

    2015-05-26

    A 1973 paper by Lyons and Thorne explains the two-belt structure for electrons in the inner magnetosphere as a balance between inward radial diffusion and loss to the atmosphere, where the loss to the atmosphere is enabled by pitch-angle scattering from Coulomb and wave-particle interactions. In the 1973 paper, equilibrium solutions to a decoupled set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium two-belt structure. Each 1D radial diffusion equation incorporated an L-and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This decoupling of the problem is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering. However, for some values of μ and L the lifetime associated with pitch-angle scattering is comparable to the timescale associated with radial diffusion, suggesting that the true equilibrium solutions might reflect `coupled modes' involving pitch-angle scattering and radial diffusion and thus requiring a 3D diffusion model. In the work we show here, we have computed the equilibrium solutions using our 3D diffusion model, DREAM3D, that allows for such coupling. We find that the 3D equilibrium solutions are quite similar to the solutions shown in the 1973 paper when we use the same physical models for radial diffusion and pitch-angle scattering from hiss. However, we show that the equilibrium solutions are quite sensitive to various aspects of the physics model employed in the 1973 paper that can be improved, suggesting that additional work needs to be done to understand the two-belt structure.

  14. Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming.

    PubMed

    Krijger, Peter Hugo Lodewijk; Di Stefano, Bruno; de Wit, Elzo; Limone, Francesco; van Oevelen, Chris; de Laat, Wouter; Graf, Thomas

    2016-05-05

    Forced expression of reprogramming factors can convert somatic cells into induced pluripotent stem cells (iPSCs). Here we studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale topologically associated domain (TAD) repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic-cell-specific genome structures while establishing an embryonic stem-cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable recognition of their cell of origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin-dependent gene expression patterns. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

    PubMed Central

    Krijger, Peter Hugo Lodewijk; Di Stefano, Bruno; de Wit, Elzo; Limone, Francesco; van Oevelen, Chris; de Laat, Wouter; Graf, Thomas

    2016-01-01

    Summary Forced expression of reprogramming factors can convert somatic cells into induced pluripotent stem cells (iPSCs). Here we studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale topologically associated domain (TAD) repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic-cell-specific genome structures while establishing an embryonic stem-cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable recognition of their cell of origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin-dependent gene expression patterns. PMID:26971819

  16. Surface modified alginate microcapsules for 3D cell culture

    NASA Astrophysics Data System (ADS)

    Chen, Yi-Wen; Kuo, Chiung Wen; Chueh, Di-Yen; Chen, Peilin

    2016-06-01

    Culture as three dimensional cell aggregates or spheroids can offer an ideal platform for tissue engineering applications and for pharmaceutical screening. Such 3D culture models, however, may suffer from the problems such as immune response and ineffective and cumbersome culture. This paper describes a simple method for producing microcapsules with alginate cores and a thin shell of poly(L-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG) to encapsulate mouse induced pluripotent stem (miPS) cells, generating a non-fouling surface as an effective immunoisolation barrier. We demonstrated the trapping of the alginate microcapsules in a microwell array for the continuous observation and culture of a large number of encapsulated miPS cells in parallel. miPS cells cultured in the microcapsules survived well and proliferated to form a single cell aggregate. Droplet formation of monodisperse microcapsules with controlled size combined with flow cytometry provided an efficient way to quantitatively analyze the growth of encapsulated cells in a high-throughput manner. The simple and cost-effective coating technique employed to produce the core-shell microcapsules could be used in the emerging field of cell therapy. The microwell array would provide a convenient, user friendly and high-throughput platform for long-term cell culture and monitoring.

  17. Microfabricated polymeric vessel mimetics for 3-D cancer cell culture

    PubMed Central

    Jaeger, Ashley A.; Das, Chandan K.; Morgan, Nicole Y.; Pursley, Randall H.; McQueen, Philip G.; Hall, Matthew D.; Pohida, Thomas J.; Gottesman, Michael M.

    2013-01-01

    Modeling tumor growth in vitro is essential for cost-effective testing of hypotheses in preclinical cancer research. 3-D cell culture offers an improvement over monolayer culture for studying cellular processes in cancer biology because of the preservation of cell-cell and cell-ECM interactions. Oxygen transport poses a major barrier to mimicking in vivo environments and is not replicated in conventional cell culture systems. We hypothesized that we can better mimic the tumor microenvironment using a bioreactor system for controlling gas exchange in cancer cell cultures with silicone hydrogel synthetic vessels. Soft-lithography techniques were used to fabricate oxygen-permeable silicone hydrogel membranes containing arrays of micropillars. These membranes were inserted into a bioreactor and surrounded by basement membrane extract (BME) within which fluorescent ovarian cancer (OVCAR8) cells were cultured. Cell clusters oxygenated by synthetic vessels showed a ∼100um drop-off to anoxia, consistent with in vivo studies of tumor nodules fed by the microvasculature. We showed oxygen tension gradients inside the clusters oxygenated by synthetic vessels had a ∼100 µm drop-off to anoxia, which is consistent with in vivo studies. Oxygen transport in the bioreactor system was characterized by experimental testing with a dissolved oxygen probe and finite element modeling of convective flow. Our study demonstrates differing growth patterns associated with controlling gas distributions to better mimic in vivo conditions. PMID:23911071

  18. Phenomenological modelling and simulation of cell clusters in 3D cultures.

    PubMed

    González-Valverde, I; Semino, C; García-Aznar, J M

    2016-10-01

    Cell clustering and aggregation are fundamental processes in the development of several tissues and the progression of many diseases. The formation of these aggregates also has a direct impact on the oxygen concentration in their surroundings due to cellular respiration and poor oxygen diffusion through clusters. In this work, we propose a mathematical model that is capable of simulating cell cluster formation in 3D cultures through combining a particle-based and a finite element approach to recreate complex experimental conditions. Cells are modelled considering cell proliferation, cell death and cell-cell mechanical interactions. Additionally, the oxygen concentration profile is calculated through finite element analysis using a reaction-diffusion model that considers cell oxygen consumption and diffusion through the extracellular matrix and the cell clusters. In our model, the local oxygen concentration in the medium determines both cell proliferation and cell death. Numerical predictions are also compared with experimental data from the literature. The simulation results indicate that our model can predict cell clustering, cluster growth and oxygen distribution in 3D cultures. We conclude that the initial cell distribution, cell death and cell proliferation dynamics determine the size and density of clusters. Moreover, these phenomena are directly affected by the oxygen transport in the 3D culture. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Multi-Scale Modeling of Tissues Using CompuCell3D

    PubMed Central

    Swat, Maciej H.; Thomas, Gilberto L.; Belmonte, Julio M.; Shirinifard, Abbas; Hmeljak, Dimitrij; Glazier, James A.

    2013-01-01

    The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. This tutorial introduces the lattice-based Glazier–Graner–Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi-cellular behaviors in the context of tissue formation and subsequent dynamics. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D. PMID:22482955

  20. 3D numerical simulations of vesicle and inextensible capsule dynamics

    NASA Astrophysics Data System (ADS)

    Farutin, Alexander; Biben, Thierry; Misbah, Chaouqi

    2014-10-01

    Vesicles are locally-inextensible fluid membranes, capsules are endowed with in-plane shear elasticity mimicking the cytoskeleton of red blood cells (RBCs), but are extensible, while RBCs are inextensible. We use boundary integral (BI) methods based on the Green function techniques to model and solve numerically their dynamics. We regularize the single layer integral by subtraction of exact identities for the terms involving the normal and the tangential components of the force. The stability and precision of BI calculation is enhanced by taking advantage of additional quadrature nodes located in vertices of an auxiliary mesh, constructed by a standard refinement procedure from the main mesh. We extend the partition of unity technique to boundary integral calculation on triangular meshes. The proposed algorithm offers the same treatment of near-singular integration regardless whether the source and the target points belong to the same surface or not. Bending forces are calculated by using expressions derived from differential geometry. Membrane incompressibility is handled by using two penalization parameters per suspended entity: one for deviation of the global area from prescribed value and another for the sum of squares of local strains defined on each vertex. Extensible or inextensible capsules, a model of RBC, are studied by storing the position in the reference configuration for each vertex. The elastic force is then calculated by direct variation of the elastic energy. Various nonequilibrium physical examples on vesicles and capsules will be presented and the convergence and precision tests highlighted. Overall, a good convergence is observed with numerical error inversely proportional to the number of vertices used for surface discretization, the highest order of convergence allowed by piece-wise linear interpolation of the surface.

  1. Quasi-horizontal circulation cells in 3D seawater intrusion

    USGS Publications Warehouse

    Abarca, E.; Carrera, J.; Sanchez-Vila, X.; Voss, C.I.

    2007-01-01

    The seawater intrusion process is characterized by the difference in freshwater and seawater density that causes freshwater to float on seawater. Many confined aquifers have a large horizontal extension with respect to thickness. In these cases, while buoyancy acts in the vertical direction, flow is confined between the upper and bottom boundaries and the effect of gravity is controlled by variations of aquifer elevation. Therefore, the effective gravity is controlled by the slope and the shape of the aquifer boundaries. Variability in the topography of the aquifer boundaries is one case where 3D analysis is necessary. In this work, density-dependent flow processes caused by 3D aquifer geometry are studied numerically and specifically, considering a lateral slope of the aquifer boundaries. Sub-horizontal circulation cells are formed in the saltwater entering the aquifer. The penetration of the saltwater can be quantified by a dimensionless buoyancy number that measures the lateral slope of the aquifer relative to freshwater flux. The penetration of the seawater intrusion wedge is controlled more by this slope than by the aquifer thickness and dispersivity. Thus, the slope must be taken into account in order to accurately evaluate seawater intrusion. ?? 2007 Elsevier B.V. All rights reserved.

  2. DREAM3D simulations of inner-belt dynamics

    NASA Astrophysics Data System (ADS)

    Cunningham, G.

    2015-12-01

    A 1973 paper by Lyons and Thorne explains the two-belt structure for electrons in the inner magnetosphere as a balance between inward radial diffusion and loss to the atmosphere due to pitch-angle scattering from Coulomb and VLF wave-particle interactions. In this paper, equilibrium solutions to a set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium structure. Each diffusion equation incorporated an L- and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This model is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering, and that there is no acceleration caused by the VLF wave-particle interactions. We have revisited this model using our DREAM3D 3D diffusion code, which allows the user to explicitly model the diffusion in pitch-angle and momentum rather than using a lifetime. We find that a) replacing the lifetimes with an explicit model of pitch-angle diffusion, thus allowing for coupling between radial and pitch-angle diffusion, affects the equilibrium structure, and b) over the long time scales needed to reach equilibrium, significant acceleration due to VLF wave particle interactions takes place due to the 'cross-terms' in pitch-angle and momentum and the sharp gradient in the equilibrium pitch-angle distributions. We also find that the equilibrium solutions are quite sensitive to various aspects of the physics model employed in the 1973 paper that can be improved, suggesting that additional work needs to be done to fully understand the equilibirum nature of the trapped electron radiation belts.

  3. Scaffolds for tissue engineering and 3D cell culture.

    PubMed

    Carletti, Eleonora; Motta, Antonella; Migliaresi, Claudio

    2011-01-01

    In tissue engineering applications or even in 3D cell cultures, the biological cross talk between cells and the scaffold is controlled by the material properties and scaffold characteristics. In order to induce cell adhesion, proliferation, and activation, materials used for the fabrication of scaffolds must possess requirements such as intrinsic biocompatibility and proper chemistry to induce molecular biorecognition from cells. Materials, scaffold mechanical properties and degradation kinetics should be adapted to the specific tissue engineering application to guarantee the required mechanical functions and to accomplish the rate of the new-tissue formation. For scaffolds, pore distribution, exposed surface area, and porosity play a major role, whose amount and distribution influence the penetration and the rate of penetration of cells within the scaffold volume, the architecture of the produced extracellular matrix, and for tissue engineering applications, the final effectiveness of the regenerative process. Depending on the fabrication process, scaffolds with different architecture can be obtained, with random or tailored pore distribution. In the recent years, rapid prototyping computer-controlled techniques have been applied to the fabrication of scaffolds with ordered geometry. This chapter reviews the principal polymeric materials that are used for the fabrication of scaffolds and the scaffold fabrication processes, with examples of properties and selected applications.

  4. The vibrational dynamics of 3D HOCl above dissociation

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Der; Reichl, L. E.; Jung, Christof

    2015-03-01

    We explore the classical vibrational dynamics of the HOCl molecule for energies above the dissociation energy of the molecule. Above dissociation, we find that the classical dynamics is dominated by an invariant manifold which appears to stabilize two periodic orbits at energies significantly above the dissociation energy. These stable periodic orbits can hold a large number of quantum states and likely can support a significant quasibound state of the molecule, well above the dissociation energy. The classical dynamics and the lifetime of quantum states on the invariant manifold are determined.

  5. The vibrational dynamics of 3D HOCl above dissociation

    SciTech Connect

    Lin, Yi-Der; Reichl, L. E.; Jung, Christof

    2015-03-28

    We explore the classical vibrational dynamics of the HOCl molecule for energies above the dissociation energy of the molecule. Above dissociation, we find that the classical dynamics is dominated by an invariant manifold which appears to stabilize two periodic orbits at energies significantly above the dissociation energy. These stable periodic orbits can hold a large number of quantum states and likely can support a significant quasibound state of the molecule, well above the dissociation energy. The classical dynamics and the lifetime of quantum states on the invariant manifold are determined.

  6. Enhanced 3D fluorescence live cell imaging on nanoplasmonic substrate

    NASA Astrophysics Data System (ADS)

    Ranjan Gartia, Manas; Hsiao, Austin; Sivaguru, Mayandi; Chen, Yi; Logan Liu, G.

    2011-09-01

    We have created a randomly distributed nanocone substrate on silicon coated with silver for surface-plasmon-enhanced fluorescence detection and 3D cell imaging. Optical characterization of the nanocone substrate showed it can support several plasmonic modes (in the 300-800 nm wavelength range) that can be coupled to a fluorophore on the surface of the substrate, which gives rise to the enhanced fluorescence. Spectral analysis suggests that a nanocone substrate can create more excitons and shorter lifetime in the model fluorophore Rhodamine 6G (R6G) due to plasmon resonance energy transfer from the nanocone substrate to the nearby fluorophore. We observed three-dimensional fluorescence enhancement on our substrate shown from the confocal fluorescence imaging of chinese hamster ovary (CHO) cells grown on the substrate. The fluorescence intensity from the fluorophores bound on the cell membrane was amplified more than 100-fold as compared to that on a glass substrate. We believe that strong scattering within the nanostructured area coupled with random scattering inside the cell resulted in the observed three-dimensional enhancement in fluorescence with higher photostability on the substrate surface.

  7. 3D Clumped Cell Segmentation Using Curvature Based Seeded Watershed.

    PubMed

    Atta-Fosu, Thomas; Guo, Weihong; Jeter, Dana; Mizutani, Claudia M; Stopczynski, Nathan; Sousa-Neves, Rui

    2016-12-01

    Image segmentation is an important process that separates objects from the background and also from each other. Applied to cells, the results can be used for cell counting which is very important in medical diagnosis and treatment, and biological research that is often used by scientists and medical practitioners. Segmenting 3D confocal microscopy images containing cells of different shapes and sizes is still challenging as the nuclei are closely packed. The watershed transform provides an efficient tool in segmenting such nuclei provided a reasonable set of markers can be found in the image. In the presence of low-contrast variation or excessive noise in the given image, the watershed transform leads to over-segmentation (a single object is overly split into multiple objects). The traditional watershed uses the local minima of the input image and will characteristically find multiple minima in one object unless they are specified (marker-controlled watershed). An alternative to using the local minima is by a supervised technique called seeded watershed, which supplies single seeds to replace the minima for the objects. Consequently, the accuracy of a seeded watershed algorithm relies on the accuracy of the predefined seeds. In this paper, we present a segmentation approach based on the geometric morphological properties of the 'landscape' using curvatures. The curvatures are computed as the eigenvalues of the Shape matrix, producing accurate seeds that also inherit the original shape of their respective cells. We compare with some popular approaches and show the advantage of the proposed method.

  8. Next-generation regenerative medicine: organogenesis from stem cells in 3D culture.

    PubMed

    Sasai, Yoshiki

    2013-05-02

    The behavior of stem cells, when they work collectively, can be much more sophisticated than one might expect from their individual programming. This Perspective covers recent discoveries about the dynamic patterning and structural self-formation of complex organ buds in 3D stem cell culture, including the generation of various neuroectodermal and endodermal tissues. For some tissues, epithelial-mesenchymal interactions can also be manipulated in coculture to guide organogenesis. This new area of stem cell research-the spatiotemporal control of dynamic cellular interactions-will open a new avenue for next-generation regenerative medicine.

  9. First 3-D simulations of meteor plasma dynamics and turbulence

    NASA Astrophysics Data System (ADS)

    Oppenheim, Meers M.; Dimant, Yakov S.

    2015-02-01

    Millions of small but detectable meteors hit the Earth's atmosphere every second, creating trails of hot plasma that turbulently diffuse into the background atmosphere. For over 60 years, radars have detected meteor plasmas and used these signals to infer characteristics of the meteoroid population and upper atmosphere, but, despite the importance of meteor radar measurements, the complex processes by which these plasmas evolve have never been thoroughly explained or modeled. In this paper, we present the first fully 3-D simulations of meteor evolution, showing meteor plasmas developing instabilities, becoming turbulent, and inhomogeneously diffusing into the background ionosphere. These instabilities explain the characteristics and strength of many radar observations, in particular the high-resolution nonspecular echoes made by large radars. The simulations reveal how meteors create strong electric fields that dig out deep plasma channels along the Earth's magnetic fields. They also allow researchers to explore the impacts of the intense winds and wind shears, commonly found at these altitudes, on meteor plasma evolution. This study will allow the development of more sophisticated models of meteor radar signals, enabling the extraction of detailed information about the properties of meteoroid particles and the atmosphere.

  10. On human pluripotent stem cell control: The rise of 3D bioengineering and mechanobiology

    PubMed Central

    Shao, Yue; Sang, Jianming; Fu, Jianping

    2015-01-01

    Human pluripotent stem cells (hPSCs) provide promising resources for regenerating tissues and organs and modeling development and diseases in vitro. To fulfill their promise, the fate, function, and organization of hPSCs need to be precisely regulated in a three-dimensional (3D) environment to mimic cellular structures and functions of native tissues and organs. In the past decade, innovations in 3D culture systems with functional biomaterials have enabled efficient and versatile control of hPSC fate at the cellular level. However, we are just at the beginning of bringing hPSC-based regeneration and development and disease modeling to the tissue and organ levels. In this review, we summarize existing bioengineered culture platforms for controlling hPSC fate and function by regulating inductive mechanical and biochemical cues coexisting in the synthetic cell microenvironment. We highlight recent excitements in developing 3D hPSC-based in vitro tissue and organ models with in vivo-like cellular structures, interactions, and functions. We further discuss an emerging multifaceted mechanotransductive signaling network – with transcriptional coactivators YAP and TAZ at the center stage – that regulate fates and behaviors of mammalian cells, including hPSCs. Future development of 3D biomaterial systems should incorporate dynamically modulated mechanical and chemical properties targeting specific intracellular signaling events leading to desirable hPSC fate patterning and functional tissue formation in 3D. PMID:25818411

  11. Common-path biodynamic imaging for dynamic fluctuation spectroscopy of 3D living tissue

    NASA Astrophysics Data System (ADS)

    Li, Zhe; Turek, John; Nolte, David D.

    2017-03-01

    Biodynamic imaging is a novel 3D optical imaging technology based on short-coherence digital holography that measures intracellular motions of cells inside their natural microenvironments. Here both common-path and Mach-Zehnder designs are presented. Biological tissues such as tumor spheroids and ex vivo biopsies are used as targets, and backscattered light is collected as signal. Drugs are applied to samples, and their effects are evaluated by identifying biomarkers that capture intracellular dynamics from the reconstructed holograms. Through digital holography and coherence gating, information from different depths of the samples can be extracted, enabling the deep-tissue measurement of the responses to drugs.

  12. 3D vesicle dynamics simulations with a linearly triangulated surface

    NASA Astrophysics Data System (ADS)

    Boedec, G.; Leonetti, M.; Jaeger, M.

    2011-02-01

    Simulations of biomembranes have gained an increasing interest in the past years. Specificities of these membranes propose new challenges for the numerics. In particular, vesicle dynamics are governed by bending forces as well as a surface incompressibility constraint. A method to compute the bending force density resultant onto piecewise linearly triangulated surface meshes is described. This method is coupled with a boundary element method solver for inner and outer fluids, to compute vesicle dynamics under external flows. The surface incompressibility constraint is satisfied by the construction of a projection operator.

  13. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji

    2016-03-01

    Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer simulations and data analyses, including molecular dynamics (MD) simulations. In this study, we develop hybrid (MPI+OpenMP) parallelization schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD simulations. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to simulate one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.

  14. 3D structural and functional characterization of the transition from Hodgkin to Reed-Sternberg cells.

    PubMed

    Knecht, Hans; Brüderlein, Silke; Mai, Sabine; Möller, Peter; Sawan, Bassem

    2010-09-20

    Recent research using an innovative 3D quantitative FISH approach of nuclear remodelling associated with the transition from mononuclear Hodgkin to diagnostic multinuclear Reed-Sternberg cells revealed profound changes in the 3D nuclear organization of telomeres. Analogous 3D telomere dynamics were identified in Hodgkin's lymphoma derived cell-lines and diagnostic patient biopsies. These changes were observed in both, EBV positive and EBV-negative Hodgkin's lymphoma and independent of the age of the patients at presentation. Compared to mononuclear Hodgkin cells, multinuclear Reed-Sternberg cells are characterized by a highly significant increase of telomere aggregates, often composed of very short telomeres, telomere shortening and loss. RS-cells with telomere free "ghost" nuclei are regularly observed. The telomere protecting shelterin complex appears to be disrupted and deregulation of DNA-repair mechanisms is observed. Our findings are consistent with the hypothesis that distinct 3D telomere changes and shelterin disruption represent a common pathogenetic denominator in the generation of Reed-Sternberg cells. Copyright © 2010 Elsevier GmbH. All rights reserved.

  15. Noninvasive Imaging of 3D Dynamics in Thickly Fluorescent Specimens Beyond the Diffraction Limit

    PubMed Central

    Gao, Liang; Shao, Lin; Higgins, Christopher D.; Poulton, John S.; Peifer, Mark; Davidson, Michael W.; Wu, Xufeng; Goldstein, Bob; Betzig, Eric

    2013-01-01

    SUMMARY Optical imaging of the dynamics of living specimens involves tradeoffs between spatial resolution, temporal resolution, and phototoxicity, made more difficult in three-dimensions. Here, however, we report that rapid 3D dynamics can be studied beyond the diffraction limit in thick or densely fluorescent living specimens over many time points by combining ultra-thin planar illumination produced by scanned Bessel beams with superresolution structured illumination microscopy. We demonstrate in vivo karyotyping of chromosomes during mitosis and identify different dynamics for the actin cytoskeleton at the dorsal and ventral surfaces of fibroblasts. Compared to spinning disk confocal microscopy, we demonstrate substantially reduced photodamage when imaging rapid morphological changes in D. discoideum cells, as well as improved contrast and resolution at depth within developing C. elegans embryos. Bessel beam structured plane illumination thus promises new insights into complex biological phenomena that require 4D subcellular spatiotemporal detail in either a single or multicellular context. PMID:23217717

  16. Dynamics of 3D view invariance in monkey inferotemporal cortex

    PubMed Central

    Ratan Murty, N. Apurva

    2015-01-01

    Rotations in depth are challenging for object vision because features can appear, disappear, be stretched or compressed. Yet we easily recognize objects across views. Are the underlying representations view invariant or dependent? This question has been intensely debated in human vision, but the neuronal representations remain poorly understood. Here, we show that for naturalistic objects, neurons in the monkey inferotemporal (IT) cortex undergo a dynamic transition in time, whereby they are initially sensitive to viewpoint and later encode view-invariant object identity. This transition depended on two aspects of object structure: it was strongest when objects foreshortened strongly across views and were similar to each other. View invariance in IT neurons was present even when objects were reduced to silhouettes, suggesting that it can arise through similarity between external contours of objects across views. Our results elucidate the viewpoint debate by showing that view invariance arises dynamically in IT neurons out of a representation that is initially view dependent. PMID:25609108

  17. Introducing a New 3D Dynamical Model for Barred Galaxies

    NASA Astrophysics Data System (ADS)

    Jung, Christof; Zotos, Euaggelos E.

    2015-11-01

    The regular or chaotic dynamics of an analytical realistic three dimensional model composed of a spherically symmetric central nucleus, a bar and a flat disk is investigated. For describing the properties of the bar, we introduce a new simple dynamical model and we explore the influence on the character of orbits of all the involved parameters of it, such as the mass and the scale length of the bar, the major semi-axis and the angular velocity of the bar, as well as the energy. Regions of phase space with ordered and chaotic motion are identified in dependence on these parameters and for breaking the rotational symmetry. First, we study in detail the dynamics in the invariant plane z = pz = 0 using the Poincaré map as a basic tool and then study the full three-dimensional case using the Smaller Alignment index method as principal tool for distinguishing between order and chaos. We also present strong evidence obtained through the numerical simulations that our new bar model can realistically describe the formation and the evolution of the observed twin spiral structure in barred galaxies.

  18. 3D Clumped Cell Segmentation Using Curvature Based Seeded Watershed

    PubMed Central

    Atta-Fosu, Thomas; Guo, Weihong; Jeter, Dana; Mizutani, Claudia M.; Stopczynski, Nathan; Sousa-Neves, Rui

    2017-01-01

    Image segmentation is an important process that separates objects from the background and also from each other. Applied to cells, the results can be used for cell counting which is very important in medical diagnosis and treatment, and biological research that is often used by scientists and medical practitioners. Segmenting 3D confocal microscopy images containing cells of different shapes and sizes is still challenging as the nuclei are closely packed. The watershed transform provides an efficient tool in segmenting such nuclei provided a reasonable set of markers can be found in the image. In the presence of low-contrast variation or excessive noise in the given image, the watershed transform leads to over-segmentation (a single object is overly split into multiple objects). The traditional watershed uses the local minima of the input image and will characteristically find multiple minima in one object unless they are specified (marker-controlled watershed). An alternative to using the local minima is by a supervised technique called seeded watershed, which supplies single seeds to replace the minima for the objects. Consequently, the accuracy of a seeded watershed algorithm relies on the accuracy of the predefined seeds. In this paper, we present a segmentation approach based on the geometric morphological properties of the ‘landscape’ using curvatures. The curvatures are computed as the eigenvalues of the Shape matrix, producing accurate seeds that also inherit the original shape of their respective cells. We compare with some popular approaches and show the advantage of the proposed method. PMID:28280723

  19. Dynamics of 3D view invariance in monkey inferotemporal cortex.

    PubMed

    Ratan Murty, N Apurva; Arun, Sripati P

    2015-04-01

    Rotations in depth are challenging for object vision because features can appear, disappear, be stretched or compressed. Yet we easily recognize objects across views. Are the underlying representations view invariant or dependent? This question has been intensely debated in human vision, but the neuronal representations remain poorly understood. Here, we show that for naturalistic objects, neurons in the monkey inferotemporal (IT) cortex undergo a dynamic transition in time, whereby they are initially sensitive to viewpoint and later encode view-invariant object identity. This transition depended on two aspects of object structure: it was strongest when objects foreshortened strongly across views and were similar to each other. View invariance in IT neurons was present even when objects were reduced to silhouettes, suggesting that it can arise through similarity between external contours of objects across views. Our results elucidate the viewpoint debate by showing that view invariance arises dynamically in IT neurons out of a representation that is initially view dependent. Copyright © 2015 the American Physiological Society.

  20. Dynamic Concrete Beam Deformation Measuremnet with 3d Range Cameras

    NASA Astrophysics Data System (ADS)

    Qi, X.; Lichti, D.

    2012-07-01

    Concrete beams are used to construct bridges and other structures. Due to the traffic overloading or the decaying state of structures, deformation of bridges or other structures occurs frequently. Therefore, the requirement to measure concrete beam deformation, as integral components of structures, is well recognized. Many imaging techniques such as digital cameras, laser scanners and range cameras have been proven to be accurate and cost-effective methods for large-area measurement of deformation under static loading conditions. However, for obtaining useful information about the behaviour of the beams or monitoring real-time bridge deformation, the ability to measurement deformation under dynamic loading conditions is also necessary. This paper presents a relatively low-cost and high accuracy imaging technique to measure the deformation of concrete beams in response to dynamic loading with range cameras. However, due to the range camera measurement principle, target movement could lead to motion artefacts that degrade range measurement accuracy. The results of simulated and real-data investigation into the motion artefacts show that the lower sampling frequency leads to the more significant motion artefact. The results from real data experiments have indicated that periodic deformation can be recovered with sub-millimetre accuracy when the 3 Hz and 4 mm amplitude target motion is sampled at a rate of least 20 Hz and with 31 MHz range camera modulation frequency. When the modulation frequency is 29 MHz, the best sampling frequency is 20 Hz to keep the error under sub-millimetre.

  1. 3D arrays for high throughput assay of cell migration and electrotaxis.

    PubMed

    Zhao, Sanjun; Gao, Runchi; Devreotes, Peter N; Mogilner, Alex; Zhao, Min

    2013-09-01

    Cell behaviour in 3D environments can be significantly different from those in 2D cultures. With many different 3D matrices being developed and many experimental modalities used to modulate cell behaviour in 3D, it is necessary to develop high throughput techniques to study behaviour in 3D. We report on a 3D array on slide and have adapted this to our electrotaxis chamber, thereby offering a novel approach to quantify cellular responses to electric fields (EFs) in 3D conditions, in different matrices, with different strains of cells, under various field strengths. These developments used Dictyostelium cells to illustrate possible applications and limitations.

  2. 3D Probed Lipid Dynamics in Small Unilamellar Vesicles.

    PubMed

    Chao, Meng-Hsuan; Lin, Yen-Ting; Dhenadhayalan, Namasivayam; Lee, Hsin-Lung; Lee, Hsin-Yen; Lin, King-Chuen

    2017-04-01

    Single-molecule fluorescence correlation spectroscopy overcomes the resolution barrier of optical microscopy (10≈-20 nm) and is utilized to look into lipid dynamics in small unilamellar vesicles (SUVs; diameter < 100 nm). The fluorescence trajectories of lipid-like tracer 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine (DiD) in the membrane bilayers are acquired at a single-molecule level. The autocorrelation analysis yields the kinetic information on lipid organization, oxygen transport, and lateral diffusion in SUVs' membrane. First, the isomerization feasibility may be restricted by the addition of cholesterols, which form structure conjugation with DiD chromophore. Second, the oxygen transport is prevented from the ultrasmall cluster and cholesterol-rich regions, whereas it can pass through the membrane region with liquid-disordered phase (Ld ) and defects. Third, by analyzing 2D spectra correlating the lipid diffusion coefficient and triplet-state lifetime, the heterogeneity in lipid bilayer can be precisely visualized such as lipid domain with different phases, the defects of lipid packing, and DiD-induced "bouquet" ultrasmall clusters. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. The self-organization of grid cells in 3D

    PubMed Central

    Stella, Federico; Treves, Alessandro

    2015-01-01

    Do we expect periodic grid cells to emerge in bats, or perhaps dolphins, exploring a three-dimensional environment? How long will it take? Our self-organizing model, based on ring-rate adaptation, points at a complex answer. The mathematical analysis leads to asymptotic states resembling face centered cubic (FCC) and hexagonal close packed (HCP) crystal structures, which are calculated to be very close to each other in terms of cost function. The simulation of the full model, however, shows that the approach to such asymptotic states involves several sub-processes over distinct time scales. The smoothing of the initially irregular multiple fields of individual units and their arrangement into hexagonal grids over certain best planes are observed to occur relatively quickly, even in large 3D volumes. The correct mutual orientation of the planes, though, and the coordinated arrangement of different units, take a longer time, with the network showing no sign of convergence towards either a pure FCC or HCP ordering. DOI: http://dx.doi.org/10.7554/eLife.05913.001 PMID:25821989

  4. The self-organization of grid cells in 3D.

    PubMed

    Stella, Federico; Treves, Alessandro

    2015-03-30

    Do we expect periodic grid cells to emerge in bats, or perhaps dolphins, exploring a three-dimensional environment? How long will it take? Our self-organizing model, based on ring-rate adaptation, points at a complex answer. The mathematical analysis leads to asymptotic states resembling face centered cubic (FCC) and hexagonal close packed (HCP) crystal structures, which are calculated to be very close to each other in terms of cost function. The simulation of the full model, however, shows that the approach to such asymptotic states involves several sub-processes over distinct time scales. The smoothing of the initially irregular multiple fields of individual units and their arrangement into hexagonal grids over certain best planes are observed to occur relatively quickly, even in large 3D volumes. The correct mutual orientation of the planes, though, and the coordinated arrangement of different units, take a longer time, with the network showing no sign of convergence towards either a pure FCC or HCP ordering.

  5. Nucleus and nucleus-cytoskeleton connections in 3D cell migration.

    PubMed

    Liu, Lingling; Luo, Qing; Sun, Jinghui; Song, Guanbin

    2016-10-15

    Cell migration plays an important role in many physiological and pathological settings, ranging from embryonic development to cancer metastasis. Currently, accumulating data suggest that cells migrating in three-dimensional (3D) environments show well-defined differences compared to their well-established two-dimensional (2D) counterparts. During 3D migration, the cell body and nucleus must deform to allow cellular passage through the available spaces, and the deformability of the relatively rigid nucleus may constitute a limiting step. Here, we highlight the key evidence regarding the role of the nuclear mechanics in 3D migration, including the molecular components that govern the stiffness of the nucleus and review how the nuclear dynamics are connected to and controlled by cytoskeleton-based migration machinery. Intriguingly, nuclear movement must be coordinated with the cytoskeletal dynamics at the leading and trailing edges, which in turn impact the cytoplasmic dynamics that affect the migration efficiency. Thus, we suggest that alterations in the nuclear structure may facilitate cellular reorganizations that are necessary for efficient migration.

  6. Three-dimensional (3D) hydrodynamic focusing for continuous sampling and analysis of adherent cells.

    PubMed

    Xu, Chunxiu; Wang, Min; Yin, Xuefeng

    2011-10-07

    A simple three-dimensional (3D) hydrodynamic focusing microfluidic device integrated with continuous sampling, rapid dynamic lysis, capillary electrophoretic (CE) separation and detection of intracellular content is presented. One of the major difficulties in microfluidic cell analysis for adherent cells is that the cells are prone to attaching to the channel surface. To solve this problem, a cross microfluidic chip with three sheath-flow channels located on both sides of and below the sampling channel was developed. With the three sheath flows around the sample solution-containing cells, the formed soft fluid wall prevents the cells from adhering to the channel surface. Labeled cells were 3D hydrodynamically focused by the sheath-flow streams and smoothly introduced into the cross-section one by one. The introduction of sheath-flow streams not only ensured single-cell sampling but avoided blockage of the sampling channel by adherent cells as well. The maximum rate for introduction of individual cells into the separation channel was about 151 cells min(-1). With electric field applied on the separation channel, the aligned cells were driven into the separation channel and rapidly lysed within 400 ms at the entry of the channel by sodium dodecylsulfate (SDS) added in the sheath-flow solution. The microfluidic system was evaluated by analysis of reduced glutathione (GSH) and reactive oxygen species (ROS) in single HepG2 cells. The average analysis throughput of ROS and GSH in single cells was 16-18 cells min(-1).

  7. 3D niche microarrays for systems-level analyses of cell fate.

    PubMed

    Ranga, A; Gobaa, S; Okawa, Y; Mosiewicz, K; Negro, A; Lutolf, M P

    2014-07-14

    The behaviour of mammalian cells in a tissue is governed by the three-dimensional (3D) microenvironment and involves a dynamic interplay between biochemical and mechanical signals provided by the extracellular matrix (ECM), cell-cell interactions and soluble factors. The complexity of the microenvironment and the context-dependent cell responses that arise from these interactions have posed a major challenge to understanding the underlying regulatory mechanisms. Here we develop an experimental paradigm to dissect the role of various interacting factors by simultaneously synthesizing more than 1,000 unique microenvironments with robotic nanolitre liquid-dispensing technology and by probing their effects on cell fate. Using this novel 3D microarray platform, we assess the combined effects of matrix elasticity, proteolytic degradability and three distinct classes of signalling proteins on mouse embryonic stem cells, unveiling a comprehensive map of interactions involved in regulating self-renewal. This approach is broadly applicable to gain a systems-level understanding of multifactorial 3D cell-matrix interactions.

  8. 3D non-Planar Finite Difference Dynamic Rupture: Application to the Landers Earthquake

    NASA Astrophysics Data System (ADS)

    Cruz-Atienza, V. M.; Virieux, J.; Aochi, H.; Peyrat, S.

    2004-12-01

    Many aspects of seismic complexity have been explained in the last thirty years thanks to the development of numerical approaches allowing seismologists to simulate the dynamic rupture of earthquakes. Heterogeneities in both the initial stress field and the surrounding medium are extremely important elements. The constitutive law describing the physics of the breakdown process which relates the fault friction to fault kinematics is also determinant. However, given the increasing amount of high quality seismological data, more sophisticated approaches are needed to explain observations so that others important physical factors, such as the real fault geometry, could be integrated into simulations. Bearing in mind these new high quality observations along with the current computational power, a great interest has arisen in the last five years to develop 3D numerical codes to simulate earthquakes with real fault geometries. Recently, Cruz-Atienza and Virieux (2004) have introduced a 2D finite difference (FD) approach for modeling the dynamic rupture of non-planar faults. In this work we analyze the 3D extension of such an approach. On that account, the new 3D code may consider arbitrary heterogeneous media, composite friction laws and non-planar fault geometries. The numerical criteria for rupture boundary conditions to model rupture processes accurately were determined experimentally finding consistency with those determined for the 2D case: the source is discretized by a set of numerical cells. Given a spatial grid step for wave propagation, the number of grid nodes contained in each cell should be adapted accordingly. The smaller the spatial step the greater the number of nodes. We have performed dynamic rupture simulations for different curved 3D faults and compared results with those given by a BIE method (Aochi et al., 2000). Consistency between solutions yielded by different numerical approaches is essential since it is the only way to have confidence in these

  9. Controlling Shear Stress in 3D Bioprinting is a Key Factor to Balance Printing Resolution and Stem Cell Integrity.

    PubMed

    Blaeser, Andreas; Duarte Campos, Daniela Filipa; Puster, Uta; Richtering, Walter; Stevens, Molly M; Fischer, Horst

    2016-02-04

    A microvalve-based bioprinting system for the manufacturing of high-resolution, multimaterial 3D-structures is reported. Applying a straightforward fluid-dynamics model, the shear stress at the nozzle site can precisely be controlled. Using this system, a broad study on how cell viability and proliferation potential are affected by different levels of shear stress is conducted. Complex, multimaterial 3D structures are printed with high resolution. This work pioneers the investigation of shear stress-induced cell damage in 3D bioprinting and might help to comprehend and improve the outcome of cell-printing studies in the future.

  10. Uncovering cancer cell behavioral phenotype in 3-D in vitro metastatic landscapes

    NASA Astrophysics Data System (ADS)

    Liu, Liyu; Sun, Bo; Duclos, Guillaume; Kam, Yoonseok; Gatenby, Robert; Stone, Howard; Austin, Robert

    2012-02-01

    One well-known fact is that cancer cell genetics determines cell metastatic potentials. However, from a physics point of view, genetics as cell properties cannot directly act on metastasis. An agent is needed to unscramble the genetics first before generating dynamics for metastasis. Exactly this agent is cell behavioral phenotype, which is rarely studied due to the difficulties of real-time cell tracking in in vivo tissue. Here we have successfully constructed a micro in vitro environment with collagen based Extracellular Matrix (ECM) structures for cell 3-D metastasis. With stable nutrition (glucose) gradient inside, breast cancer cell MDA-MB-231 is able to invade inside the collagen from the nutrition poor site towards the nutrition rich site. Continuous confocal microscopy captures images of the cells every 12 hours and tracks their positions in 3-D space. The micro fluorescent beads pre-mixed inside the ECM demonstrate that invasive cells have altered the structures through mechanics. With the observation and the analysis of cell collective behaviors, we argue that game theory may exist between the pioneering cells and their followers in the metastatic cell group. The cell collaboration may explain the high efficiency of metastasis.

  11. Characterizations of individual mouse red blood cells parasitized by Babesia microti using 3-D holographic microscopy.

    PubMed

    Park, HyunJoo; Hong, Sung-Hee; Kim, Kyoohyun; Cho, Shin-Hyeong; Lee, Won-Ja; Kim, Youngchan; Lee, Sang-Eun; Park, YongKeun

    2015-06-03

    Babesia microti causes "emergency" human babesiosis. However, little is known about the alterations in B. microti invaded red blood cells (Bm-RBCs) at the individual cell level. Through quantitative phase imaging techniques based on laser interferometry, we present the simultaneous measurements of structural, chemical, and mechanical modifications in individual mouse Bm-RBCs. 3-D refractive index maps of individual RBCs and in situ parasite vacuoles are imaged, from which total contents and concentration of dry mass are also precisely quantified. In addition, we examine the dynamic membrane fluctuation of Bm-RBCs, which provide information on cell membrane deformability.

  12. Characterizations of individual mouse red blood cells parasitized by Babesia microti using 3-D holographic microscopy

    PubMed Central

    Park, HyunJoo; Hong, Sung-Hee; Kim, Kyoohyun; Cho, Shin-Hyeong; Lee, Won-Ja; Kim, Youngchan; Lee, Sang-Eun; Park, YongKeun

    2015-01-01

    Babesia microti causes “emergency” human babesiosis. However, little is known about the alterations in B. microti invaded red blood cells (Bm-RBCs) at the individual cell level. Through quantitative phase imaging techniques based on laser interferometry, we present the simultaneous measurements of structural, chemical, and mechanical modifications in individual mouse Bm-RBCs. 3-D refractive index maps of individual RBCs and in situ parasite vacuoles are imaged, from which total contents and concentration of dry mass are also precisely quantified. In addition, we examine the dynamic membrane fluctuation of Bm-RBCs, which provide information on cell membrane deformability. PMID:26039793

  13. Comparative mechanisms of cancer cell migration through 3D matrix and physiological microtracks.

    PubMed

    Carey, Shawn P; Rahman, Aniqua; Kraning-Rush, Casey M; Romero, Bethsabe; Somasegar, Sahana; Torre, Olivia M; Williams, Rebecca M; Reinhart-King, Cynthia A

    2015-03-15

    Tumor cell invasion through the stromal extracellular matrix (ECM) is a key feature of cancer metastasis, and understanding the cellular mechanisms of invasive migration is critical to the development of effective diagnostic and therapeutic strategies. Since cancer cell migration is highly adaptable to physiochemical properties of the ECM, it is critical to define these migration mechanisms in a context-specific manner. Although extensive work has characterized cancer cell migration in two- and three-dimensional (3D) matrix environments, the migration program employed by cells to move through native and cell-derived microtracks within the stromal ECM remains unclear. We previously reported the development of an in vitro model of patterned type I collagen microtracks that enable matrix metalloproteinase-independent microtrack migration. Here we show that collagen microtracks closely resemble channel-like gaps in native mammary stroma ECM and examine the extracellular and intracellular mechanisms underlying microtrack migration. Cell-matrix mechanocoupling, while critical for migration through 3D matrix, is not necessary for microtrack migration. Instead, cytoskeletal dynamics, including actin polymerization, cortical tension, and microtubule turnover, enable persistent, polarized migration through physiological microtracks. These results indicate that tumor cells employ context-specific mechanisms to migrate and suggest that selective targeting of cytoskeletal dynamics, but not adhesion, proteolysis, or cell traction forces, may effectively inhibit cancer cell migration through preformed matrix microtracks within the tumor stroma.

  14. 3D video-based deformation measurement of the pelvis bone under dynamic cyclic loading.

    PubMed

    Göpfert, Beat; Krol, Zdzislaw; Freslier, Marie; Krieg, Andreas H

    2011-07-17

    Dynamic three-dimensional (3D) deformation of the pelvic bones is a crucial factor in the successful design and longevity of complex orthopaedic oncological implants. The current solutions are often not very promising for the patient; thus it would be interesting to measure the dynamic 3D-deformation of the whole pelvic bone in order to get a more realistic dataset for a better implant design. Therefore we hypothesis if it would be possible to combine a material testing machine with a 3D video motion capturing system, used in clinical gait analysis, to measure the sub millimetre deformation of a whole pelvis specimen. A pelvis specimen was placed in a standing position on a material testing machine. Passive reflective markers, traceable by the 3D video motion capturing system, were fixed to the bony surface of the pelvis specimen. While applying a dynamic sinusoidal load the 3D-movement of the markers was recorded by the cameras and afterwards the 3D-deformation of the pelvis specimen was computed. The accuracy of the 3D-movement of the markers was verified with 3D-displacement curve with a step function using a manual driven 3D micro-motion-stage. The resulting accuracy of the measurement system depended on the number of cameras tracking a marker. The noise level for a marker seen by two cameras was during the stationary phase of the calibration procedure ± 0.036 mm, and ± 0.022 mm if tracked by 6 cameras. The detectable 3D-movement performed by the 3D-micro-motion-stage was smaller than the noise level of the 3D-video motion capturing system. Therefore the limiting factor of the setup was the noise level, which resulted in a measurement accuracy for the dynamic test setup of ± 0.036 mm. This 3D test setup opens new possibilities in dynamic testing of wide range materials, like anatomical specimens, biomaterials, and its combinations. The resulting 3D-deformation dataset can be used for a better estimation of material characteristics of the underlying

  15. Synthesis and display of dynamic holographic 3D scenes with real-world objects.

    PubMed

    Paturzo, Melania; Memmolo, Pasquale; Finizio, Andrea; Näsänen, Risto; Naughton, Thomas J; Ferraro, Pietro

    2010-04-26

    A 3D scene is synthesized combining multiple optically recorded digital holograms of different objects. The novel idea consists of compositing moving 3D objects in a dynamic 3D scene using a process that is analogous to stop-motion video. However in this case the movie has the exciting attribute that it can be displayed and observed in 3D. We show that 3D dynamic scenes can be projected as an alternative to complicated and heavy computations needed to generate realistic-looking computer generated holograms. The key tool for creating the dynamic action is based on a new concept that consists of a spatial, adaptive transformation of digital holograms of real-world objects allowing full control in the manipulation of the object's position and size in a 3D volume with very high depth-of-focus. A pilot experiment to evaluate how viewers perceive depth in a conventional single-view display of the dynamic 3D scene has been performed.

  16. Visualization and 3D reconstruction of flame cells of Taenia solium (cestoda).

    PubMed

    Valverde-Islas, Laura E; Arrangoiz, Esteban; Vega, Elio; Robert, Lilia; Villanueva, Rafael; Reynoso-Ducoing, Olivia; Willms, Kaethe; Zepeda-Rodríguez, Armando; Fortoul, Teresa I; Ambrosio, Javier R

    2011-03-11

    Flame cells are the terminal cells of protonephridial systems, which are part of the excretory systems of invertebrates. Although the knowledge of their biological role is incomplete, there is a consensus that these cells perform excretion/secretion activities. It has been suggested that the flame cells participate in the maintenance of the osmotic environment that the cestodes require to live inside their hosts. In live Platyhelminthes, by light microscopy, the cells appear beating their flames rapidly and, at the ultrastructural, the cells have a large body enclosing a tuft of cilia. Few studies have been performed to define the localization of the cytoskeletal proteins of these cells, and it is unclear how these proteins are involved in cell function. Parasites of two different developmental stages of T. solium were used: cysticerci recovered from naturally infected pigs and intestinal adults obtained from immunosuppressed and experimentally infected golden hamsters. Hamsters were fed viable cysticerci to recover adult parasites after one month of infection. In the present studies focusing on flame cells of cysticerci tissues was performed. Using several methods such as video, confocal and electron microscopy, in addition to computational analysis for reconstruction and modeling, we have provided a 3D visual rendition of the cytoskeletal architecture of Taenia solium flame cells. We consider that visual representations of cells open a new way for understanding the role of these cells in the excretory systems of Platyhelminths. After reconstruction, the observation of high resolution 3D images allowed for virtual observation of the interior composition of cells. A combination of microscopic images, computational reconstructions and 3D modeling of cells appears to be useful for inferring the cellular dynamics of the flame cell cytoskeleton.

  17. Visualization and 3D Reconstruction of Flame Cells of Taenia solium (Cestoda)

    PubMed Central

    Valverde-Islas, Laura E.; Arrangoiz, Esteban; Vega, Elio; Robert, Lilia; Villanueva, Rafael; Reynoso-Ducoing, Olivia; Willms, Kaethe; Zepeda-Rodríguez, Armando; Fortoul, Teresa I.; Ambrosio, Javier R.

    2011-01-01

    Background Flame cells are the terminal cells of protonephridial systems, which are part of the excretory systems of invertebrates. Although the knowledge of their biological role is incomplete, there is a consensus that these cells perform excretion/secretion activities. It has been suggested that the flame cells participate in the maintenance of the osmotic environment that the cestodes require to live inside their hosts. In live Platyhelminthes, by light microscopy, the cells appear beating their flames rapidly and, at the ultrastructural, the cells have a large body enclosing a tuft of cilia. Few studies have been performed to define the localization of the cytoskeletal proteins of these cells, and it is unclear how these proteins are involved in cell function. Methodology/Principal Findings Parasites of two different developmental stages of T. solium were used: cysticerci recovered from naturally infected pigs and intestinal adults obtained from immunosuppressed and experimentally infected golden hamsters. Hamsters were fed viable cysticerci to recover adult parasites after one month of infection. In the present studies focusing on flame cells of cysticerci tissues was performed. Using several methods such as video, confocal and electron microscopy, in addition to computational analysis for reconstruction and modeling, we have provided a 3D visual rendition of the cytoskeletal architecture of Taenia solium flame cells. Conclusions/Significance We consider that visual representations of cells open a new way for understanding the role of these cells in the excretory systems of Platyhelminths. After reconstruction, the observation of high resolution 3D images allowed for virtual observation of the interior composition of cells. A combination of microscopic images, computational reconstructions and 3D modeling of cells appears to be useful for inferring the cellular dynamics of the flame cell cytoskeleton. PMID:21412407

  18. Anticancer Drug Camptothecin Test in 3D Hydrogel Networks with HeLa cells

    PubMed Central

    Liang, Jun; Susan Sun, Xiuzhi; Yang, Zhilong; Cao, Shuai

    2017-01-01

    Development of a biomimetic 3D culture system for drug screening is necessary to fully understand the in vivo environment. Previously, a self-assembling peptide hydrogel has been reported; the hydrogel exhibited physiological properties superior to a 3D cell culture matrix. In this work, further research using H9e hydrogel with HeLa cells was carried out considering H9e hydrogel’s interaction with camptothecin, a hydrophobic drug. According to AFM images, a PGworks solution triggered H9e hydrogel fiber aggregation and forms a 3D matrix suitable for cell culture. Dynamic rheological studies showed that camptothecin was encapsulated within the hydrogel network concurrently with peptide self-assembly without permanently destroying the hydrogel’s architecture and remodeling ability. Fluorescence measurement indicated negligible interaction between the fluorophore part of camptothecin and the hydrogel, especially at concentration 0.25 and 0.5 wt%. Using a dialysis method, we found that H9e hydrogel could not significantly inhibit the diffusion of camptothecin encapsulated inside the hydrogel matrix. In the cell culture experiment, HeLa cells were simultaneously embedded in the H9e hydrogel with the initialization of hydrogelation. Most importantly, cell viability data after camptothecin treatment showed responses that were drug-dose dependent but unaffected by the H9e hydrogel concentration, indicating that the hydrogel did not inhibit the drug. PMID:28145436

  19. 3D correlative light and electron microscopy of cultured cells using serial blockface scanning electron microscopy

    PubMed Central

    Lerner, Thomas R.; Burden, Jemima J.; Nkwe, David O.; Pelchen-Matthews, Annegret; Domart, Marie-Charlotte; Durgan, Joanne; Weston, Anne; Jones, Martin L.; Peddie, Christopher J.; Carzaniga, Raffaella; Florey, Oliver; Marsh, Mark; Gutierrez, Maximiliano G.

    2017-01-01

    ABSTRACT The processes of life take place in multiple dimensions, but imaging these processes in even three dimensions is challenging. Here, we describe a workflow for 3D correlative light and electron microscopy (CLEM) of cell monolayers using fluorescence microscopy to identify and follow biological events, combined with serial blockface scanning electron microscopy to analyse the underlying ultrastructure. The workflow encompasses all steps from cell culture to sample processing, imaging strategy, and 3D image processing and analysis. We demonstrate successful application of the workflow to three studies, each aiming to better understand complex and dynamic biological processes, including bacterial and viral infections of cultured cells and formation of entotic cell-in-cell structures commonly observed in tumours. Our workflow revealed new insight into the replicative niche of Mycobacterium tuberculosis in primary human lymphatic endothelial cells, HIV-1 in human monocyte-derived macrophages, and the composition of the entotic vacuole. The broad application of this 3D CLEM technique will make it a useful addition to the correlative imaging toolbox for biomedical research. PMID:27445312

  20. 3D correlative light and electron microscopy of cultured cells using serial blockface scanning electron microscopy.

    PubMed

    Russell, Matthew R G; Lerner, Thomas R; Burden, Jemima J; Nkwe, David O; Pelchen-Matthews, Annegret; Domart, Marie-Charlotte; Durgan, Joanne; Weston, Anne; Jones, Martin L; Peddie, Christopher J; Carzaniga, Raffaella; Florey, Oliver; Marsh, Mark; Gutierrez, Maximiliano G; Collinson, Lucy M

    2017-01-01

    The processes of life take place in multiple dimensions, but imaging these processes in even three dimensions is challenging. Here, we describe a workflow for 3D correlative light and electron microscopy (CLEM) of cell monolayers using fluorescence microscopy to identify and follow biological events, combined with serial blockface scanning electron microscopy to analyse the underlying ultrastructure. The workflow encompasses all steps from cell culture to sample processing, imaging strategy, and 3D image processing and analysis. We demonstrate successful application of the workflow to three studies, each aiming to better understand complex and dynamic biological processes, including bacterial and viral infections of cultured cells and formation of entotic cell-in-cell structures commonly observed in tumours. Our workflow revealed new insight into the replicative niche of Mycobacterium tuberculosis in primary human lymphatic endothelial cells, HIV-1 in human monocyte-derived macrophages, and the composition of the entotic vacuole. The broad application of this 3D CLEM technique will make it a useful addition to the correlative imaging toolbox for biomedical research. © 2017. Published by The Company of Biologists Ltd.

  1. Precise stacking of decellularized extracellular matrix based 3D cell-laden constructs by a 3D cell printing system equipped with heating modules.

    PubMed

    Ahn, Geunseon; Min, Kyung-Hyun; Kim, Changhwan; Lee, Jeong-Seok; Kang, Donggu; Won, Joo-Yun; Cho, Dong-Woo; Kim, Jun-Young; Jin, Songwan; Yun, Won-Soo; Shim, Jin-Hyung

    2017-08-17

    Three-dimensional (3D) cell printing systems allow the controlled and precise deposition of multiple cells in 3D constructs. Hydrogel materials have been used extensively as printable bioinks owing to their ability to safely encapsulate living cells. However, hydrogel-based bioinks have drawbacks for cell printing, e.g. inappropriate crosslinking and liquid-like rheological properties, which hinder precise 3D shaping. Therefore, in this study, we investigated the influence of various factors (e.g. bioink concentration, viscosity, and extent of crosslinking) on cell printing and established a new 3D cell printing system equipped with heating modules for the precise stacking of decellularized extracellular matrix (dECM)-based 3D cell-laden constructs. Because the pH-adjusted bioink isolated from native tissue is safely gelled at 37 °C, our heating system facilitated the precise stacking of dECM bioinks by enabling simultaneous gelation during printing. We observed greater printability compared with that of a non-heating system. These results were confirmed by mechanical testing and 3D construct stacking analyses. We also confirmed that our heating system did not elicit negative effects, such as cell death, in the printed cells. Conclusively, these results hold promise for the application of 3D bioprinting to tissue engineering and drug development.

  2. A Cost-Effective Method to Assemble Biomimetic 3D Cell Culture Platforms

    PubMed Central

    Khalil, Sabreen; El-Badri, Nagwa; El-Mokhtaar, Mohamed; Al-Mofty, Saif; Farghaly, Mohamed; Ayman, Radwa; Habib, Dina; Mousa, Noha

    2016-01-01

    Developing effective stem cell based therapies requires the design of complex in vitro culture systems for more accurate representation of the stem cell niche. Attempts to improve conventional cell culture platforms include the use of biomaterial coated culture plates, sphere culture, microfluidic systems and bioreactors. Most of these platforms are not cost-effective, require industrial technical expertise to fabricate, and remain too simplistic compared to the physiological cell niche. The human amniotic membrane (hAM) has been used successfully in clinical grafting applications due to its unique biological composition and regenerative properties. In this study, we present a combinatorial platform that integrates the hAM with biomolecular, topographic and mechanical cues in one versatile model. Methods We utilized the hAM to provide the biological and the three dimensional (3D) topographic components of the prototype. The 3D nano-roughness of the hAM was characterized using surface electron microscopy and surface image analysis (ImageJ and SurfaceJ). We developed additional macro-scale and micro-scale versions of the platform which provided additional shear stress factors to simulate the fluid dynamics of the in vivo extracellular fluids. Results Three models of varying complexities of the prototype were assembled. A well-defined 3D surface modulation of the hAM in comparable to commercial 3D biomaterial culture substrates was achieved without complex fabrication and with significantly lower cost. Performance of the prototype was demonstrated through culture of primary human umbilical cord mononuclear blood cells (MNCs), human bone marrow mesenchymal stem cell line (hBMSC), and human breast cancer tissue. Conclusion This study presents methods of assembling an integrated, flexible and low cost biomimetic cell culture platform for diverse cell culture applications. PMID:27935982

  3. Ultrahigh-definition dynamic 3D holographic display by active control of volume speckle fields

    NASA Astrophysics Data System (ADS)

    Yu, Hyeonseung; Lee, Kyeoreh; Park, Jongchan; Park, Yongkeun

    2017-01-01

    Holographic displays generate realistic 3D images that can be viewed without the need for any visual aids. They operate by generating carefully tailored light fields that replicate how humans see an actual environment. However, the realization of high-performance, dynamic 3D holographic displays has been hindered by the capabilities of present wavefront modulator technology. In particular, spatial light modulators have a small diffraction angle range and limited pixel number limiting the viewing angle and image size of a holographic 3D display. Here, we present an alternative method to generate dynamic 3D images by controlling volume speckle fields significantly enhancing image definition. We use this approach to demonstrate a dynamic display of micrometre-sized optical foci in a volume of 8 mm × 8 mm × 20 mm.

  4. Laser irradiated fluorescent perfluorocarbon microparticles in 2-D and 3-D breast cancer cell models

    NASA Astrophysics Data System (ADS)

    Niu, Chengcheng; Wang, Long; Wang, Zhigang; Xu, Yan; Hu, Yihe; Peng, Qinghai

    2017-03-01

    Perfluorocarbon (PFC) droplets were studied as new generation ultrasound contrast agents via acoustic or optical droplet vaporization (ADV or ODV). Little is known about the ODV irradiated vaporization mechanisms of PFC-microparticle complexs and the stability of the new bubbles produced. In this study, fluorescent perfluorohexane (PFH) poly(lactic-co-glycolic acid) (PLGA) particles were used as a model to study the process of particle vaporization and bubble stability following excitation in two-dimensional (2-D) and three-dimensional (3-D) cell models. We observed localization of the fluorescent agent on the microparticle coating material initially and after vaporization under fluorescence microscopy. Furthermore, the stability and growth dynamics of the newly created bubbles were observed for 11 min following vaporization. The particles were co-cultured with 2-D cells to form 3-D spheroids and could be vaporized even when encapsulated within the spheroids via laser irradiation, which provides an effective basis for further work.

  5. Engineering Cellular Microenvironments with Photo- and Enzymatically Responsive Hydrogels: Toward Biomimetic 3D Cell Culture Models.

    PubMed

    Tam, Roger Y; Smith, Laura J; Shoichet, Molly S

    2017-03-27

    Conventional cell culture techniques using 2D polystyrene or glass have provided great insight into key biochemical mechanisms responsible for cellular events such as cell proliferation, differentiation, and cell-cell interactions. However, the physical and chemical properties of 2D culture in vitro are dramatically different than those found in the native cellular microenvironment in vivo. Cells grown on 2D substrates differ significantly from those grown in vivo, and this explains, in part, why many promising drug candidates discovered through in vitro drug screening assays fail when they are translated to in vivo animal or human models. To overcome this obstacle, 3D cell culture using biomimetic hydrogels has emerged as an alternative strategy to recapitulate native cell growth in vitro. Hydrogels, which are water-swollen polymers, can be synthetic or naturally derived. Many methods have been developed to control the physical and chemical properties of the hydrogels to match those found in specific tissues. Compared to 2D culture, cells cultured in 3D gels with the appropriate physicochemical cues can behave more like they naturally do in vivo. While conventional hydrogels involve modifications to the bulk material to mimic the static aspects of the cellular microenvironment, recent progress has focused on using more dynamic hydrogels, the chemical and physical properties of which can be altered with external stimuli to better mimic the dynamics of the native cellular microenvironment found in vivo. In this Account, we describe our progress in designing stimuli-responsive, optically transparent hydrogels that can be used as biomimetic extracellular matrices (ECMs) to study cell differentiation and migration in the context of modeling the nervous system and cancer. Specifically, we developed photosensitive agarose and hyaluronic acid hydrogels that are activated by single or two-photon irradiation for biomolecule immobilization at specific volumes within the 3D

  6. Development and Characterization of a Parallelizable Perfusion Bioreactor for 3D Cell Culture

    PubMed Central

    Egger, Dominik; Fischer, Monica; Clementi, Andreas; Ribitsch, Volker; Hansmann, Jan; Kasper, Cornelia

    2017-01-01

    The three dimensional (3D) cultivation of stem cells in dynamic bioreactor systems is essential in the context of regenerative medicine. Still, there is a lack of bioreactor systems that allow the cultivation of multiple independent samples under different conditions while ensuring comprehensive control over the mechanical environment. Therefore, we developed a miniaturized, parallelizable perfusion bioreactor system with two different bioreactor chambers. Pressure sensors were also implemented to determine the permeability of biomaterials which allows us to approximate the shear stress conditions. To characterize the flow velocity and shear stress profile of a porous scaffold in both bioreactor chambers, a computational fluid dynamics analysis was performed. Furthermore, the mixing behavior was characterized by acquisition of the residence time distributions. Finally, the effects of the different flow and shear stress profiles of the bioreactor chambers on osteogenic differentiation of human mesenchymal stem cells were evaluated in a proof of concept study. In conclusion, the data from computational fluid dynamics and shear stress calculations were found to be predictable for relative comparison of the bioreactor geometries, but not for final determination of the optimal flow rate. However, we suggest that the system is beneficial for parallel dynamic cultivation of multiple samples for 3D cell culture processes.

  7. Concentric gel system to study the biophysical role of matrix microenvironment on 3D cell migration.

    PubMed

    Kurniawan, Nicholas Agung; Chaudhuri, Parthiv Kant; Lim, Chwee Teck

    2015-04-03

    The ability of cells to migrate is crucial in a wide variety of cell functions throughout life from embryonic development and wound healing to tumor and cancer metastasis. Despite intense research efforts, the basic biochemical and biophysical principles of cell migration are still not fully understood, especially in the physiologically relevant three-dimensional (3D) microenvironments. Here, we describe an in vitro assay designed to allow quantitative examination of 3D cell migration behaviors. The method exploits the cell's mechanosensing ability and propensity to migrate into previously unoccupied extracellular matrix (ECM). We use the invasion of highly invasive breast cancer cells, MDA-MB-231, in collagen gels as a model system. The spread of cell population and the migration dynamics of individual cells over weeks of culture can be monitored using live-cell imaging and analyzed to extract spatiotemporally-resolved data. Furthermore, the method is easily adaptable for diverse extracellular matrices, thus offering a simple yet powerful way to investigate the role of biophysical factors in the microenvironment on cell migration.

  8. Effects of extracellular fiber architecture on cell membrane shear stress in a 3D fibrous matrix.

    PubMed

    Pedersen, John A; Boschetti, Federica; Swartz, Melody A

    2007-01-01

    Interstitial fluid flow has been shown to affect the organization and behavior of cells in 3D environments in vivo and in vitro, yet the forces driving such responses are not clear. Due to the complex architecture of the extracellular matrix (ECM) and the difficulty of measuring fluid flow near cells embedded in it, the levels of shear stress experienced by cells in this environment are typically estimated using bulk-averaged matrix parameters such as hydraulic permeability. While this is useful for estimating average stresses, it cannot yield insight into how local matrix fiber architecture-which is cell-controlled in the immediate pericellular environment-affects the local stresses imposed on the cell surface. To address this, we used computational fluid dynamics to study flow through an idealized mesh constructed of a cubic lattice of fibers simulating a typical in vitro collagen gel. We found that, in such high porosity matrices, the fibers strongly affect the flow fields near the cell, with peak shear stresses up to five times higher than those predicted by the Brinkman equation. We also found that minor remodeling of the fibers near the cell surface had major effects on the shear stress profile on the cell. These findings demonstrate the importance of fiber architecture to the fluid forces on a cell embedded in a 3D matrix, and also show how small modifications in the local ECM can lead to large changes in the mechanical environment of the cell.

  9. On the dynamics of jellyfish locomotion via 3D particle tracking velocimetry

    NASA Astrophysics Data System (ADS)

    Piper, Matthew; Kim, Jin-Tae; Chamorro, Leonardo P.

    2016-11-01

    The dynamics of jellyfish (Aurelia aurita) locomotion is experimentally studied via 3D particle tracking velocimetry. 3D locations of the bell tip are tracked over 1.5 cycles to describe the jellyfish path. Multiple positions of the jellyfish bell margin are initially tracked in 2D from four independent planes and individually projected in 3D based on the jellyfish path and geometrical properties of the setup. A cubic spline interpolation and the exponentially weighted moving average are used to estimate derived quantities, including velocity and acceleration of the jellyfish locomotion. We will discuss distinctive features of the jellyfish 3D motion at various swimming phases, and will provide insight on the 3D contraction and relaxation in terms of the locomotion, the steadiness of the bell margin eccentricity, and local Reynolds number based on the instantaneous mean diameter of the bell.

  10. Application of FLASH-3D dynamic contrast-enhanced imaging for diagnosis of endometrial carcinoma.

    PubMed

    Du, Lixin; Li, Xiaohu; Qiu, Xixiong; Liu, Xiaolei; Wang, Yuli; Yu, Yongqiang

    2016-10-01

    To investigate the application and value of fast low-angle shot three-dimensional (FLASH-3D) dynamic contrast-enhanced MRI for the pre-operative staging of endometrial carcinoma. This prospective study enrolled 48 patients with complete clinical data and pathologically confirmed endometrial carcinoma from July 2012 to March 2014. After routine MRI examination, subjects underwent FLASH-3D dynamic contrast-enhanced examination. The dynamically enhanced features of the uterine wall and tumours were analyzed. FLASH-3D pre-operative staging and findings in relation to myometrial invasion were compared with post-operative pathological results in a double-blind manner. There were 48 cases of pathologically proven endometrial carcinoma, including 34 patients with Stage I (Stage Ia 22 cases and Stage Ib 12 cases), 9 with Stage II, 3 with Stage III and 2 with Stage IV. The staging accuracy for endometrial carcinoma was 81% (39/48) using FLASH-3D dynamic contrast-enhanced sequences. The sensitivity, specificity and accuracy for the determination of deep myometrial invasion were 84%, 90% and 88%, respectively. There was no significant difference compared with the results of post-operative pathology (p > 0.05). FLASH-3D dynamic contrast-enhanced imaging may be valuable for the early diagnosis and pre-operative staging of endometrial carcinoma. Its high accuracy for assessing deep myometrial invasion makes FLASH-3D imaging an important tool for selecting the optimal therapeutic protocol and for prognosis estimation. FLASH-3D can significantly improve the accurate assessment of the depth of tumour invasion into the myometrium and may thus help to guide clinical surgical choices and post-operative evaluation. FLASH-3D is thus a promising technique for the routine examination of female pelvic tumours.

  11. Dynamic visual image modeling for 3D synthetic scenes in agricultural engineering

    NASA Astrophysics Data System (ADS)

    Gao, Li; Yan, Juntao; Li, Xiaobo; Ji, Yatai; Li, Xin

    The dynamic visual image modeling for 3D synthetic scenes by using dynamic multichannel binocular visual image based on the mobile self-organizing network. Technologies of 3D modeling synthetic scenes have been widely used in kinds of industries. The main purpose of this paper is to use multiple networks of dynamic visual monitors and sensors to observe an unattended area, to use the advantages of mobile network in rural areas for improving existing mobile network information service further and providing personalized information services. The goal of displaying is to provide perfect representation of synthetic scenes. Using low-power dynamic visual monitors and temperature/humidity sensor or GPS installed in the node equipment, monitoring data will be sent at scheduled time. Then through the mobile self-organizing network, 3D model is rebuilt by synthesizing the returned images. On this basis, we formalize a novel algorithm for multichannel binocular visual 3D images based on fast 3D modeling. Taking advantage of these low prices mobile, mobile self-organizing networks can get a large number of video from where is not suitable for human observation or unable to reach, and accurately synthetic 3D scene. This application will play a great role in promoting its application in agriculture.

  12. Ultrasound array photoacoustic microscopy for dynamic in vivo 3D imaging

    NASA Astrophysics Data System (ADS)

    Song, Liang; Maslov, Konstantin; Shung, K. Kirk; Wang, Lihong V.

    2010-02-01

    Using realtime ultrasound array photoacoustic microscopy (UA-PAM), we demonstrated the feasibility of noninvasive in vivo imaging of human pulsatile dynamics, as well as 3-D dynamic imaging of sentinel lymph nodes (SLNs) in a murine model. The system, capable of realtime B-scan imaging at 50 Hz and high-speed 3-D imaging, was validated by imaging the subcutaneous microvasculature in rats and humans. After the validation, a human superficial palmar was imaged, and its pulsatile dynamics monitored, with 20-ms B-scan imaging temporal resolution. In addition, noninvasive photoacoustic sentinel lymph node (SLN) mapping with high spatial resolution has the potential to reduce the false negative rate and eliminate the use of radioactive tracers. Upon intra-dermal injection of Evans blue, the system maps SLNs accurately in mice and rats. Furthermore, the ~6 s 3-D imaging temporal resolution offers the capability to quantitatively and noninvasively monitor the dye dynamics in SLNs in vivo through sequential 3-D imaging. The demonstrated capability suggests that high-speed 3-D photoacoustic imaging should facilitate the understanding of the dynamics of various dyes in SLNs, and potentially help identify SLNs with high accuracy. With the results shown in this study, we believe that UA-PAM can potentially enable many new possibilities for studying functional and physiological dynamics in both preclinical and clinical imaging settings.

  13. Potential and limitations of microscopy and Raman spectroscopy for live-cell analysis of 3D cell cultures.

    PubMed

    Charwat, Verena; Schütze, Karin; Holnthoner, Wolfgang; Lavrentieva, Antonina; Gangnus, Rainer; Hofbauer, Pablo; Hoffmann, Claudia; Angres, Brigitte; Kasper, Cornelia

    2015-07-10

    Today highly complex 3D cell culture formats that closely mimic the in vivo situation are increasingly available. Despite their wide use, the development of analytical methods and tools that can work within the depth of 3D-tissue constructs lags behind. In order to get the most information from a 3D cell sample, adequate and reliable assays are required. However, the majority of tools and methods used today have been originally designed for 2D cell cultures and translation to a 3D environment is in general not trivial. Ideally, an analytical method should be non-invasive and allow for repeated observation of living cells in order to detect dynamic changes in individual cells within the 3D cell culture. Although well-established laser confocal microscopy can be used for these purposes, this technique has serious limitations including penetration depth and availability. Focusing on two relevant analytical methods for live-cell monitoring, we discuss the current challenges of analyzing living 3D samples: microscopy, which is the most widely used technology to observe and examine cell cultures, has been successfully adapted for 3D samples by recording of so-called "z-stacks". However the required equipment is generally very expensive and therefore access is often limited. Consequently alternative and less advanced approaches are often applied that cannot capture the full structural complexity of a 3D sample. Similarly, image analysis tools for quantification of microscopic images range from highly specialized and costly to simplified and inexpensive. Depending on the actual sample composition and scientific question the best approach needs to be assessed individually. Another more recently introduced technology for non-invasive cell analysis is Raman micro-spectroscopy. It enables label-free identification of cellular metabolic changes with high sensitivity and has already been successful applied to 2D and 3D cell cultures. However, its future significance for cell

  14. Focal adhesion kinase activity is required for actomyosin contractility-based invasion of cells into dense 3D matrices

    PubMed Central

    Mierke, Claudia T.; Fischer, Tony; Puder, Stefanie; Kunschmann, Tom; Soetje, Birga; Ziegler, Wolfgang H.

    2017-01-01

    The focal adhesion kinase (FAK) regulates the dynamics of integrin-based cell adhesions important for motility. FAK’s activity regulation is involved in stress-sensing and focal-adhesion turnover. The effect of FAK on 3D migration and cellular mechanics is unclear. We analyzed FAK knock-out mouse embryonic fibroblasts and cells expressing a kinase-dead FAK mutant, R454-FAK, in comparison to FAK wild-type cells. FAK knock-out and FAKR454/R454 cells invade dense 3D matrices less efficiently. These results are supported by FAK knock-down in wild-type fibroblasts and MDA-MB-231 human breast cancer cells showing reduced invasiveness. Pharmacological interventions indicate that in 3D matrices, cells deficient in FAK or kinase-activity behave similarly to wild-type cells treated with inhibitors of Src-activity or actomyosin-contractility. Using magnetic tweezers experiments, FAKR454/R454 cells are shown to be softer and exhibit impaired adhesion to fibronectin and collagen, which is consistent with their reduced 3D invasiveness. In line with this, FAKR454/R454 cells cannot contract the matrix in contrast to FAK wild-type cells. Finally, our findings demonstrate that active FAK facilitates 3D matrix invasion through increased cellular stiffness and transmission of actomyosin-dependent contractile force in dense 3D extracellular matrices. PMID:28202937

  15. Observation of Dynamic Structure Using Ultrasound 3D Imaging System with Encoded Wave Front

    NASA Astrophysics Data System (ADS)

    Ishigami, Satoshi; Yanagida, Hirotaka; Tamura, Yasutaka; Ishihara, Chiaki; Okada, Nagaya

    2003-05-01

    Dynamic ultrasound three-dimensional (3D) imaging using coded transmission is described. A sequence of 3D images of moving objects is reconstructed for each transmission of pulses modulated by Walsh functions. Then, the dynamic structure of the objects is extracted from the image sequence. In this paper, we discuss the relationship of the system performance to the parameters of the transmitting code such as duration time, repetition period, and total transmission length. A Doppler shift estimation and motion compensated image reconstruction method is described. The computer simulation for the motion compensation image reconstruction was carried out. Ultrasound 3D stroboscopic photography was demonstrated by a preliminary experiment utilizing the evaluation system in a 3D medical diagnostic scanner which has 32 transmitters and 32 receivers.

  16. Concentric Gel System to Study the Biophysical Role of Matrix Microenvironment on 3D Cell Migration

    PubMed Central

    Kurniawan, Nicholas Agung; Chaudhuri, Parthiv Kant; Lim, Chwee Teck

    2015-01-01

    The ability of cells to migrate is crucial in a wide variety of cell functions throughout life from embryonic development and wound healing to tumor and cancer metastasis. Despite intense research efforts, the basic biochemical and biophysical principles of cell migration are still not fully understood, especially in the physiologically relevant three-dimensional (3D) microenvironments. Here, we describe an in vitro assay designed to allow quantitative examination of 3D cell migration behaviors. The method exploits the cell’s mechanosensing ability and propensity to migrate into previously unoccupied extracellular matrix (ECM). We use the invasion of highly invasive breast cancer cells, MDA-MB-231, in collagen gels as a model system. The spread of cell population and the migration dynamics of individual cells over weeks of culture can be monitored using live-cell imaging and analyzed to extract spatiotemporally-resolved data. Furthermore, the method is easily adaptable for diverse extracellular matrices, thus offering a simple yet powerful way to investigate the role of biophysical factors in the microenvironment on cell migration. PMID:25867104

  17. Observing molecular dynamics with time-resolved 3D momentum imaging

    NASA Astrophysics Data System (ADS)

    Sturm, F. P.; Wright, T.; Bocharova, I.; Ray, D.; Shivaram, N.; Cryan, J.; Belkacem, A.; Weber, T.; Dörner, R.

    2014-05-01

    Photo-excitation and ionization trigger rich dynamics in molecular systems which play a key role in many important processes in nature such as vision, photosynthesis or photoprotection. Observing those reactions in real-time without significantly disturbing the molecules by a strong electric field has been a great challenge. Recent experiments using Time-of-Flight and Velocity Map Imaging techniques have revealed important information on the dynamics of small molecular systems upon photo-excitation. We have developed an apparatus for time-resolved momentum imaging of electrons and ions in all three spatial dimensions that employs two-color femtosecond laser pulses in the vacuum and extreme ultraviolet (VUV, XUV) for probing molecular dynamics. Our COLTRIMS style reaction microscope can measure electrons and ions in coincidence and reconstruct the momenta of the reaction fragments in 3D. We use a high power 800 nm laser in a loose focusing geometry gas cell to efficinetly drive High Harmonic Generation. The resulting photon flux is sufficient to perform 2-photon pump-probe experiments using VUV and XUV pulses for both pump and probe. With this setup we investigate non-Born-Oppenheimer dynamics in small molecules such as C2H4 and CO2 on a femtosecond time scale. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  18. Investigation of Dynamic Crack Coalescence Using a Gypsum-Like 3D Printing Material

    NASA Astrophysics Data System (ADS)

    Jiang, Chao; Zhao, Gao-Feng; Zhu, Jianbo; Zhao, Yi-Xin; Shen, Luming

    2016-10-01

    Dynamic crack coalescence attracts great attention in rock mechanics. However, specimen preparation in experimental study is a time-consuming and difficult procedure. In this work, a gypsum-like material by powder bed and inkjet 3D printing technique was applied to produce specimens with preset cracks for split Hopkinson pressure bar (SHPB) test. From micro X-ray CT test, it was found that the 3D printing technique could successfully prepare specimens that contain preset cracks with width of 0.2 mm. Basic mechanical properties of the 3D printing material, i.e., the elastic modulus, the Poisson's ratio, the density, the compressive strength, the indirect tensile strength, and the fracture toughness, were obtained and reported. Unlike 3D printed specimens using polylactic acid, these gypsum-like specimens can produce failure patterns much closer to those observed in classical rock mechanical tests. Finally, the dynamic crack coalescence of the 3D printed specimens with preset cracks were captured using a high-speed camera during SHPB tests. Failure patterns of these 3D printed specimens are similar to the specimens made by Portland cement concrete. Our results indicate that sample preparation by 3D printing is highly competitive due to its quickness in prototyping, precision and flexibility on the geometry, and high material homogeneity.

  19. Nonrigid registration and classification of the kidneys in 3D dynamic contrast enhanced (DCE) MR images

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Ghafourian, Pegah; Sharma, Puneet; Salman, Khalil; Martin, Diego; Fei, Baowei

    2012-02-01

    We have applied image analysis methods in the assessment of human kidney perfusion based on 3D dynamic contrast-enhanced (DCE) MRI data. This approach consists of 3D non-rigid image registration of the kidneys and fuzzy C-mean classification of kidney tissues. The proposed registration method reduced motion artifacts in the dynamic images and improved the analysis of kidney compartments (cortex, medulla, and cavities). The dynamic intensity curves show the successive transition of the contrast agent through kidney compartments. The proposed method for motion correction and kidney compartment classification may be used to improve the validity and usefulness of further model-based pharmacokinetic analysis of kidney function.

  20. Parallel contact detection algorithm for transient solid dynamics simulations using PRONTO3D

    SciTech Connect

    Attaway, S.W.; Hendrickson, B.A.; Plimpton, S.J.

    1996-09-01

    An efficient, scalable, parallel algorithm for treating material surface contacts in solid mechanics finite element programs has been implemented in a modular way for MIMD parallel computers. The serial contact detection algorithm that was developed previously for the transient dynamics finite element code PRONTO3D has been extended for use in parallel computation by devising a dynamic (adaptive) processor load balancing scheme.

  1. Evolution, Interaction, and Intrinsic Properties of Dislocations in Intermetallics: Anisotropic 3D Dislocation Dynamics Approach

    SciTech Connect

    Chen, Qian

    2008-01-01

    The generation, motion, and interaction of dislocations play key roles during the plastic deformation process of crystalline solids. 3D Dislocation Dynamics has been employed as a mesoscale simulation algorithm to investigate the collective and cooperative behavior of dislocations. Most current research on 3D Dislocation Dynamics is based on the solutions available in the framework of classical isotropic elasticity. However, due to some degree of elastic anisotropy in almost all crystalline solids, it is very necessary to extend 3D Dislocation Dynamics into anisotropic elasticity. In this study, first, the details of efficient and accurate incorporation of the fully anisotropic elasticity into 3D discrete Dislocation Dynamics by numerically evaluating the derivatives of Green's functions are described. Then the intrinsic properties of perfect dislocations, including their stability, their core properties and disassociation characteristics, in newly discovered rare earth-based intermetallics and in conventional intermetallics are investigated, within the framework of fully anisotropic elasticity supplemented with the atomistic information obtained from the ab initio calculations. Moreover, the evolution and interaction of dislocations in these intermetallics as well as the role of solute segregation are presented by utilizing fully anisotropic 3D dislocation dynamics. The results from this work clearly indicate the role and the importance of elastic anisotropy on the evolution of dislocation microstructures, the overall ductility and the hardening behavior in these systems.

  2. 3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

    ERIC Educational Resources Information Center

    Rodenbough, Philip P.; Vanti, William B.; Chan, Siu-Wai

    2015-01-01

    Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of…

  3. 3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

    ERIC Educational Resources Information Center

    Rodenbough, Philip P.; Vanti, William B.; Chan, Siu-Wai

    2015-01-01

    Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of…

  4. Multiscale cytometry and regulation of 3D cell cultures on a chip.

    PubMed

    Sart, Sébastien; Tomasi, Raphaël F-X; Amselem, Gabriel; Baroud, Charles N

    2017-09-07

    Three-dimensional cell culture is emerging as a more relevant alternative to the traditional two-dimensional format. Yet the ability to perform cytometry at the single cell level on intact three-dimensional spheroids or together with temporal regulation of the cell microenvironment remains limited. Here we describe a microfluidic platform to perform high-density three-dimensional culture, controlled stimulation, and observation in a single chip. The method extends the capabilities of droplet microfluidics for performing long-term culture of adherent cells. Using arrays of 500 spheroids per chip, in situ immunocytochemistry and image analysis provide multiscale cytometry that we demonstrate at the population scale, on 10(4) single spheroids, and over 10(5) single cells, correlating functionality with cellular location within the spheroids. Also, an individual spheroid can be extracted for further analysis or culturing. This will enable a shift towards quantitative studies on three-dimensional cultures, under dynamic conditions, with implications for stem cells, organs-on-chips, or cancer research.3D cell culture is more relevant than the two-dimensional format, but methods for parallel analysis and temporal regulation of the microenvironment are limited. Here the authors develop a droplet microfluidics system to perform long-term culture of 3D spheroids, enabling multiscale cytometry of individual cells within the spheroid.

  5. Lensfree diffractive tomography for the imaging of 3D cell cultures

    PubMed Central

    Momey, F.; Berdeu, A.; Bordy, T.; Dinten, J.-M.; Marcel, F. Kermarrec; Picollet-D’hahan, N.; Gidrol, X.; Allier, C.

    2016-01-01

    New microscopes are needed to help realize the full potential of 3D organoid culture studies. In order to image large volumes of 3D organoid cultures while preserving the ability to catch every single cell, we propose a new imaging platform based on lensfree microscopy. We have built a lensfree diffractive tomography setup performing multi-angle acquisitions of 3D organoid culture embedded in Matrigel and developed a dedicated 3D holographic reconstruction algorithm based on the Fourier diffraction theorem. With this new imaging platform, we have been able to reconstruct a 3D volume as large as 21.5 mm3 of a 3D organoid culture of prostatic RWPE1 cells showing the ability of these cells to assemble in 3D intricate cellular network at the mesoscopic scale. Importantly, comparisons with 2D images show that it is possible to resolve single cells isolated from the main cellular structure with our lensfree diffractive tomography setup. PMID:27231600

  6. The AFDD International Dynamic Stall Workshop on Correlation of Dynamic Stall Models with 3-D Dynamic Stall Data

    NASA Technical Reports Server (NTRS)

    Tan, C. M.; Carr, L. W.

    1996-01-01

    A variety of empirical and computational fluid dynamics two-dimensional (2-D) dynamic stall models were compared to recently obtained three-dimensional (3-D) dynamic stall data in a workshop on modeling of 3-D dynamic stall of an unswept, rectangular wing, of aspect ratio 10. Dynamic stall test data both below and above the static stall angle-of-attack were supplied to the participants, along with a 'blind' case where only the test conditions were supplied in advance, with results being compared to experimental data at the workshop itself. Detailed graphical comparisons are presented in the report, which also includes discussion of the methods and the results. The primary conclusion of the workshop was that the 3-D effects of dynamic stall on the oscillating wing studied in the workshop can be reasonably reproduced by existing semi-empirical models once 2-D dynamic stall data have been obtained. The participants also emphasized the need for improved quantification of 2-D dynamic stall.

  7. A 3D microfluidic model for preclinical evaluation of TCR-engineered T cells against solid tumors.

    PubMed

    Pavesi, Andrea; Tan, Anthony T; Koh, Sarene; Chia, Adeline; Colombo, Marta; Antonecchia, Emanuele; Miccolis, Carlo; Ceccarello, Erica; Adriani, Giulia; Raimondi, Manuela T; Kamm, Roger D; Bertoletti, Antonio

    2017-06-15

    The tumor microenvironment imposes physical and functional constraints on the antitumor efficacy of adoptive T cell immunotherapy. Preclinical testing of different T cell preparations can help in the selection of efficient immune therapies, but in vivo models are expensive and cumbersome to develop, while classical in vitro 2D models cannot recapitulate the spatiotemporal dynamics experienced by T cells targeting cancer. Here, we describe an easily customizable 3D model, in which the tumor microenvironment conditions are modulated and the functionality of different T cell preparations is tested. We incorporate human cancer hepatocytes as a single cell or as tumor cell aggregates in a 3D collagen gel region of a microfluidic device. Human T cells engineered to express tumor-specific T cell receptors (TCR-T cells) are then added in adjacent channels. The TCR-T cells' ability to migrate and kill the tumor target and the profile of soluble factors were investigated under conditions of varying oxygen levels and in the presence of inflammatory cytokines. We show that only the 3D model detects the effect that oxygen levels and the inflammatory environment impose on engineered TCR-T cell function, and we also used the 3D microdevice to analyze the TCR-T cell efficacy in an immunosuppressive scenario. Hence, we show that our microdevice platform enables us to decipher the factors that can alter T cell function in 3D and can serve as a preclinical assay to tailor the most efficient immunotherapy configuration for a specific therapeutic goal.

  8. Mesenchymal stem cell interactions with 3D ECM modules fabricated via multiphoton excited photochemistry.

    PubMed

    Su, Ping-Jung; Tran, Quyen A; Fong, Jimmy J; Eliceiri, Kevin W; Ogle, Brenda M; Campagnola, Paul J

    2012-09-10

    To understand complex micro/nanoscale ECM stem cell interactions, reproducible in vitro models are needed that can strictly recapitulate the relative content and spatial arrangement of native tissue. Additionally, whole ECM proteins are required to most accurately reflect native binding dynamics. To address this need, we use multiphoton excited photochemistry to create 3D whole protein constructs or "modules" to study how the ECM governs stem cell migration. The constructs were created from mixtures of BSA/laminin (LN) and BSA alone, whose comparison afforded studying how the migration dynamics are governed from the combination of morphological and ECM cues. We found that mesenchymal stem cells interacted for significantly longer durations with the BSA/LN constructs than pure BSA, pointing to the importance of binding cues of the LN. Critical to this work was the development of an automated system with feedback based on fluorescence imaging to provide quality control when synthesizing multiple identical constructs.

  9. Contractility of the cell rear drives invasion of breast tumor cells in 3D Matrigel

    PubMed Central

    Poincloux, Renaud; Collin, Olivier; Lizárraga, Floria; Romao, Maryse; Debray, Marcel; Piel, Matthieu; Chavrier, Philippe

    2011-01-01

    Cancer cells use different modes of migration, including integrin-dependent mesenchymal migration of elongated cells along elements of the 3D matrix as opposed to low-adhesion-, contraction-based amoeboid motility of rounded cells. We report that MDA-MB-231 human breast adenocarcinoma cells invade 3D Matrigel with a characteristic rounded morphology and with F-actin and myosin-IIa accumulating at the cell rear in a uropod-like structure. MDA-MB-231 cells display neither lamellipodia nor bleb extensions at the leading edge and do not require Arp2/3 complex activity for 3D invasion in Matrigel. Accumulation of phospho-MLC and blebbing activity were restricted to the uropod as reporters of actomyosin contractility, and velocimetric analysis of fluorescent beads embedded within the 3D matrix showed that pulling forces exerted to the matrix are restricted to the side and rear of cells. Inhibition of actomyosin contractility or β1 integrin function interferes with uropod formation, matrix deformation, and invasion through Matrigel. These findings support a model whereby actomyosin-based uropod contractility generates traction forces on the β1 integrin adhesion system to drive cell propulsion within the 3D matrix, with no contribution of lamellipodia extension or blebbing to movement. PMID:21245302

  10. 3D-printed microfluidic chips with patterned, cell-laden hydrogel constructs.

    PubMed

    Knowlton, Stephanie; Yu, Chu Hsiang; Ersoy, Fulya; Emadi, Sharareh; Khademhosseini, Ali; Tasoglu, Savas

    2016-06-20

    Three-dimensional (3D) printing offers potential to fabricate high-throughput and low-cost fabrication of microfluidic devices as a promising alternative to traditional techniques which enables efficient design iterations in the development stage. In this study, we demonstrate a single-step fabrication of a 3D transparent microfluidic chip using two alternative techniques: a stereolithography-based desktop 3D printer and a two-step fabrication using an industrial 3D printer based on polyjet technology. This method, compared to conventional fabrication using relatively expensive materials and labor-intensive processes, presents a low-cost, rapid prototyping technique to print functional 3D microfluidic chips. We enhance the capabilities of 3D-printed microfluidic devices by coupling 3D cell encapsulation and spatial patterning within photocrosslinkable gelatin methacryloyl (GelMA). The platform presented here serves as a 3D culture environment for long-term cell culture and growth. Furthermore, we have demonstrated the ability to print complex 3D microfluidic channels to create predictable and controllable fluid flow regimes. Here, we demonstrate the novel use of 3D-printed microfluidic chips as controllable 3D cell culture environments, advancing the applicability of 3D printing to engineering physiological systems for future applications in bioengineering.

  11. Reconstruction and Visualization of Coordinated 3D Cell Migration Based on Optical Flow.

    PubMed

    Kappe, Christopher P; Schütz, Lucas; Gunther, Stefan; Hufnagel, Lars; Lemke, Steffen; Leitte, Heike

    2016-01-01

    Animal development is marked by the repeated reorganization of cells and cell populations, which ultimately determine form and shape of the growing organism. One of the central questions in developmental biology is to understand precisely how cells reorganize, as well as how and to what extent this reorganization is coordinated. While modern microscopes can record video data for every cell during animal development in 3D+t, analyzing these videos remains a major challenge: reconstruction of comprehensive cell tracks turned out to be very demanding especially with decreasing data quality and increasing cell densities. In this paper, we present an analysis pipeline for coordinated cellular motions in developing embryos based on the optical flow of a series of 3D images. We use numerical integration to reconstruct cellular long-term motions in the optical flow of the video, we take care of data validation, and we derive a LIC-based, dense flow visualization for the resulting pathlines. This approach allows us to handle low video quality such as noisy data or poorly separated cells, and it allows the biologists to get a comprehensive understanding of their data by capturing dynamic growth processes in stills. We validate our methods using three videos of growing fruit fly embryos.

  12. Dynamics of Capillary-Driven Flow in 3D Printed Open Microchannels.

    PubMed

    Lade, Robert K; Hippchen, Erik J; Macosko, Christopher W; Francis, Lorraine F

    2017-03-28

    Microchannels have applications in microfluidic devices, patterns for micromolding, and even flexible electronic devices. Three-dimensional (3D) printing presents a promising alternative manufacturing route for these microchannels due to the technology's relative speed and the design freedom it affords its users. However, the roughness of 3D printed surfaces can significantly influence flow dynamics inside of a microchannel. In this work, open microchannels are fabricated using four different 3D printing techniques: fused deposition modeling (FDM), stereolithography (SLA), selective laser sintering, and multi jet modeling. Microchannels printed with each technology are evaluated with respect to their surface roughness, morphology, and how conducive they are to spontaneous capillary filling. Based on this initial assessment, microchannels printed with FDM and SLA are chosen as models to study spontaneous, capillary-driven flow dynamics in 3D printed microchannels. Flow dynamics are investigated over short (∼10(-3) s), intermediate (∼1 s), and long (∼10(2) s) time scales. Surface roughness causes a start-stop motion down the channel due to contact line pinning, while the cross-sectional shape imparted onto the channels during the printing process is shown to reduce the expected filling velocity. A significant delay in the onset of Lucas-Washburn dynamics (a long-time equilibrium state where meniscus position advances proportionally to the square root of time) is also observed. Flow dynamics are assessed as a function of printing technology, print orientation, channel dimensions, and liquid properties. This study provides the first in-depth investigation of the effect of 3D printing on microchannel flow dynamics as well as a set of rules on how to account for these effects in practice. The extension of these effects to closed microchannels and microchannels fabricated with other 3D printing technologies is also discussed.

  13. Analysis of Wnt signalling dynamics during colon crypt development in 3D culture

    PubMed Central

    Tan, Chin Wee; Hirokawa, Yumiko; Burgess, Antony W.

    2015-01-01

    Many systems biology studies lack context-relevant data and as a consequence the predictive capabilities can be limited in developing targeted cancer therapeutics. Production of colon crypt in vitro is ideal for studying colon systems biology. This report presents the first production of, to our knowledge, physiologically-shaped, functional colon crypts in vitro (i.e. single crypts with cells expressing Mucin 2 and Chromogranin A). Time-lapsed monitoring of crypt formation revealed an increased frequency of single-crypt formation in the absence of noggin. Using quantitative 3D immunofluorescence of β-catenin and E-cadherin, spatial-temporal dynamics of these proteins in normal colon crypt cells stimulated with Wnt3A or inhibited by cycloheximide has been measured. Colon adenoma cultures established from APCmin/+ mouse have developmental differences and β-catenin spatial localization compared to normal crypts. Quantitative data describing the effects of signalling pathways and proteins dynamics for both normal and adenomatous colon crypts is now within reach to inform a systems approach to colon crypt biology. PMID:26087250

  14. Numerical simulations and vorticity dynamics of self-propelled swimming of 3D bionic fish

    NASA Astrophysics Data System (ADS)

    Xin, ZhiQiang; Wu, ChuiJie

    2012-02-01

    Numerical simulations and the control of self-propelled swimming of three-dimensional bionic fish in a viscous flow and the mechanism of fish swimming are carried out in this study, with a 3D computational fluid dynamics package, which includes the immersed boundary method and the volume of fluid method, the adaptive multi-grid finite volume method, and the control strategy of fish swimming. Firstly, the mechanism of 3D fish swimming was studied and the vorticity dynamics root was traced to the moving body surface by using the boundary vorticity-flux theory. With the change of swimming speed, the contributions of the fish body and caudal fin to thrust are analyzed quantitatively. The relationship between vortex structures of fish swimming and the forces exerted on the fish body are also given in this paper. Finally, the 3D wake structure of self-propelled swimming of 3D bionic fish is presented. The in-depth analysis of the 3D vortex structure in the role of 3D biomimetic fish swimming is also performed.

  15. The integration of 3-D cell printing and mesoscopic fluorescence molecular tomography of vascular constructs within thick hydrogel scaffolds.

    PubMed

    Zhao, Lingling; Lee, Vivian K; Yoo, Seung-Schik; Dai, Guohao; Intes, Xavier

    2012-07-01

    Developing methods that provide adequate vascular perfusion is an important step toward engineering large functional tissues. Meanwhile, an imaging modality to assess the three-dimensional (3-D) structures and functions of the vascular channels is lacking for thick matrices (>2 ≈ 3 mm). Herein, we report on an original approach to construct and image 3-D dynamically perfused vascular structures in thick hydrogel scaffolds. In this work, we integrated a robotic 3-D cell printing technology with a mesoscopic fluorescence molecular tomography imaging system, and demonstrated the capability of the platform to construct perfused collagen scaffolds with endothelial lining and to image both the fluid flow and fluorescent-labeled living endothelial cells at high-frame rates, with high sensitivity and accuracy. These results establish the potential of integrating both 3-D cell printing and fluorescence mesoscopic imaging for functional and molecular studies in complex tissue-engineered tissues.

  16. The Integration of 3-D Cell-Printing and Mesoscopic Fluorescence Molecular Tomography of Vascular Constructs within Thick Hydrogel Scaffolds

    PubMed Central

    Zhao, Lingling; Lee, Vivian K.; Yoo, Seung-Schik; Dai, Guohao; Intes, Xavier

    2012-01-01

    Developing methods that provide adequate vascular perfusion is an important step toward engineering large functional tissues. Meanwhile, an imaging modality to assess the three-dimensional (3-D) structures and functions of the vascular channels is lacking for thick matrices (>2~3mm). Herein, we report on an original approach to construct and image 3-D dynamically perfused vascular structures in thick hydrogel scaffolds. In this work, we integrated a robotic 3-D cell-printing technology with a mesoscopic fluorescence molecular tomography imaging system, and demonstrated the capability of the platform to construct perfused collagen scaffolds with endothelial lining and to image both the fluid flow and fluorescent-labeled living endothelial cells at high-frame rates, with high sensitivity and accuracy. These results establish the potential of integrating both 3-D cell-printing and fluorescence mesoscopic imaging for functional and molecular studies in complex tissue engineered tissues. PMID:22531221

  17. Filopodia in cell adhesion, 3D migration and cancer cell invasion.

    PubMed

    Jacquemet, Guillaume; Hamidi, Hellyeh; Ivaska, Johanna

    2015-10-01

    This review discusses recent advances in our understanding of the role filopodia and filopodia-like structures in cell adhesion and three dimensional (3D) cell migration both in vitro and in vivo. In particular, we focus on recent advances demonstrating that filopodia are involved in substrate tethering and environment sensing in vivo. We further discuss the emerging role of filopodia and filopodial proteins in tumor dissemination as mounting in vitro, in vivo and clinical evidence suggest that filopodia drive cancer cell invasion and highlight filopodia proteins as attractive therapeutic targets. Finally, we outline outstanding questions that remain to be addressed to elucidate the role of filopodia during 3D cell migration.

  18. 3D Cell Printed Tissue Analogues: A New Platform for Theranostics

    PubMed Central

    Choi, Yeong-Jin; Yi, Hee-Gyeong; Kim, Seok-Won; Cho, Dong-Woo

    2017-01-01

    Stem cell theranostics has received much attention for noninvasively monitoring and tracing transplanted therapeutic stem cells through imaging agents and imaging modalities. Despite the excellent regenerative capability of stem cells, their efficacy has been limited due to low cellular retention, low survival rate, and low engraftment after implantation. Three-dimensional (3D) cell printing provides stem cells with the similar architecture and microenvironment of the native tissue and facilitates the generation of a 3D tissue-like construct that exhibits remarkable regenerative capacity and functionality as well as enhanced cell viability. Thus, 3D cell printing can overcome the current concerns of stem cell therapy by delivering the 3D construct to the damaged site. Despite the advantages of 3D cell printing, the in vivo and in vitro tracking and monitoring of the performance of 3D cell printed tissue in a noninvasive and real-time manner have not been thoroughly studied. In this review, we explore the recent progress in 3D cell technology and its applications. Finally, we investigate their potential limitations and suggest future perspectives on 3D cell printing and stem cell theranostics. PMID:28839468

  19. First application of the 3D-MHB on dynamic compressive behavior of UHPC

    NASA Astrophysics Data System (ADS)

    Cadoni, Ezio; Dotta, Matteo; Forni, Daniele; Riganti, Gianmario; Albertini, Carlo

    2015-09-01

    In order to study the dynamic behaviour of material in confined conditions a new machine was conceived and called 3D-Modified Hopkinson Bar (3D-MHB). It is a Modified Hopkinson Bar apparatus designed to apply dynamic loading in materials having a tri-axial stress state. It consists of a pulse generator system (with pre-tensioned bar and brittle joint), 1 input bar, and 5 output bars. The first results obtained on Ultra High Performance Concrete in compression with three different mono-axial compression states are presented. The results show how the pre-stress states minimize the boundary condition and a more uniform response is obtained.

  20. Development and applications of 4-D ultrasound (dynamic 3-D) in neurosonology.

    PubMed

    Delcker, A; Schürks, M; Polz, H

    1999-10-01

    The development and application of color-coded data in three-dimensional (3-D) reconstruction or four-dimensional (4-D) imaging (equal to dynamic 3-D) are demonstrated. In 4-D imaging, electrocardiography-triggered data acquisition of consecutive phases during the heart cycle are stored to form a multiphase 3-D data set. The option of color-coded data gives a new insight into such hemodynamic information. In the past, 3-D reconstructions were simple unicolor images, as in power mode, and the color-coded hemodynamic information was lost. These new options are presented here, along with color-coded data in examples of angiographically controlled pathologic results in extracranial and intracranial vessels.

  1. Dynamic 3d Modeling of a Canal-Tunnel Using Photogrammetric and Bathymetric Data

    NASA Astrophysics Data System (ADS)

    Moisan, E.; Heinkele, C.; Charbonnier, P.; Foucher, P.; Grussenmeyer, P.; Guillemin, S.; Koehl, M.

    2017-02-01

    This contribution introduces an original method for dynamically surveying the vault and underwater parts of a canal-tunnel for 3D modeling. The recording system, embedded on a barge, is composed of cameras that provide images of the above-water part of the tunnel, and a sonar that acquires underwater 3D profiles. In this contribution we propose to fully exploit the capacities of photogrammetry to deal with the issue of geo-referencing data in the absence of global positioning system (GPS) data. More specifically, we use it both for reconstructing the vault and side walls of the tunnel in 3D and for estimating the trajectory of the boat, which is necessary to rearrange sonar profiles to form the 3D model of the canal. We report on a first experimentation carried out inside a canal-tunnel and show promising preliminary results that illustrate the potentialities of the proposed approach.

  2. Optimization of a 3D Dynamic Culturing System for In Vitro Modeling of Frontotemporal Neurodegeneration-Relevant Pathologic Features.

    PubMed

    Tunesi, Marta; Fusco, Federica; Fiordaliso, Fabio; Corbelli, Alessandro; Biella, Gloria; Raimondi, Manuela T

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) is a severe neurodegenerative disorder that is diagnosed with increasing frequency in clinical setting. Currently, no therapy is available and in addition the molecular basis of the disease are far from being elucidated. Consequently, it is of pivotal importance to develop reliable and cost-effective in vitro models for basic research purposes and drug screening. To this respect, recent results in the field of Alzheimer's disease have suggested that a tridimensional (3D) environment is an added value to better model key pathologic features of the disease. Here, we have tried to add complexity to the 3D cell culturing concept by using a microfluidic bioreactor, where cells are cultured under a continuous flow of medium, thus mimicking the interstitial fluid movement that actually perfuses the body tissues, including the brain. We have implemented this model using a neuronal-like cell line (SH-SY5Y), a widely exploited cell model for neurodegenerative disorders that shows some basic features relevant for FTLD modeling, such as the release of the FTLD-related protein progranulin (PRGN) in specific vesicles (exosomes). We have efficiently seeded the cells on 3D scaffolds, optimized a disease-relevant oxidative stress experiment (by targeting mitochondrial function that is one of the possible FTLD-involved pathological mechanisms) and evaluated cell metabolic activity in dynamic culture in comparison to static conditions, finding that SH-SY5Y cells cultured in 3D scaffold are susceptible to the oxidative damage triggered by a mitochondrial-targeting toxin (6-OHDA) and that the same cells cultured in dynamic conditions kept their basic capacity to secrete PRGN in exosomes once recovered from the bioreactor and plated in standard 2D conditions. We think that a further improvement of our microfluidic system may help in providing a full device where assessing basic FTLD-related features (including PRGN dynamic secretion) that may be

  3. Impact of dimensionality and network disruption on microrheology of cancer cells in 3D environments.

    PubMed

    Mak, Michael; Kamm, Roger D; Zaman, Muhammad H

    2014-11-01

    Dimensionality is a fundamental component that can have profound implications on the characteristics of physical systems. In cell biology, however, the majority of studies on cell physical properties, from rheology to force generation to migration, have been performed on 2D substrates, and it is not clear how a more realistic 3D environment influences cell properties. Here, we develop an integrated approach and demonstrate the combination of mitochondria-tracking microrheology, microfluidics, and Brownian dynamics simulations to explore the impact of dimensionality on intracellular mechanics and on the effects of intracellular disruption. Additionally, we consider both passive thermal and active motor-driven processes within the cell and demonstrate through modeling how active internal fluctuations are modulated via dimensionality. Our results demonstrate that metastatic breast cancer cells (MDA-MB-231) exhibit more solid-like internal motions in 3D compared to 2D, and actin network disruption via Cytochalasin D has a more pronounced effect on internal cell fluctuations in 2D. Our computational results and modeling show that motor-induced active stress fluctuations are enhanced in 2D, leading to increased local intracellular particle fluctuations and apparent fluid-like behavior.

  4. Vinculin is required for cell polarization, migration, and extracellular matrix remodeling in 3D collagen.

    PubMed

    Thievessen, Ingo; Fakhri, Nikta; Steinwachs, Julian; Kraus, Viola; McIsaac, R Scott; Gao, Liang; Chen, Bi-Chang; Baird, Michelle A; Davidson, Michael W; Betzig, Eric; Oldenbourg, Rudolf; Waterman, Clare M; Fabry, Ben

    2015-11-01

    Vinculin is filamentous (F)-actin-binding protein enriched in integrin-based adhesions to the extracellular matrix (ECM). Whereas studies in 2-dimensional (2D) tissue culture models have suggested that vinculin negatively regulates cell migration by promoting cytoskeleton-ECM coupling to strengthen and stabilize adhesions, its role in regulating cell migration in more physiologic, 3-dimensional (3D) environments is unclear. To address the role of vinculin in 3D cell migration, we analyzed the morphodynamics, migration, and ECM remodeling of primary murine embryonic fibroblasts (MEFs) with cre/loxP-mediated vinculin gene disruption in 3D collagen I cultures. We found that vinculin promoted 3D cell migration by increasing directional persistence. Vinculin was necessary for persistent cell protrusion, cell elongation, and stable cell orientation in 3D collagen, but was dispensable for lamellipodia formation, suggesting that vinculin-mediated cell adhesion to the ECM is needed to convert actin-based cell protrusion into persistent cell shape change and migration. Consistent with this finding, vinculin was necessary for efficient traction force generation in 3D collagen without affecting myosin II activity and promoted 3D collagen fiber alignment and macroscopical gel contraction. Our results suggest that vinculin promotes directionally persistent cell migration and tension-dependent ECM remodeling in complex 3D environments by increasing cell-ECM adhesion and traction force generation.

  5. Guiding Cell Attachment in 3D Microscaffolds Selectively Functionalized with Two Distinct Adhesion Proteins.

    PubMed

    Richter, Benjamin; Hahn, Vincent; Bertels, Sarah; Claus, Tanja K; Wegener, Martin; Delaittre, Guillaume; Barner-Kowollik, Christopher; Bastmeyer, Martin

    2017-02-01

    The combination of three different photoresists into a single direct laser written 3D microscaffold permits functionalization with two bioactive full-length proteins. The cell-instructive microscaffolds consist of a passivating framework equipped with light activatable constituents featuring distinct protein-binding properties. This allows directed cell attachment of epithelial or fibroblast cells in 3D.

  6. Reprogramming mediated radio-resistance of 3D-grown cancer cells.

    PubMed

    Xue, Gang; Ren, Zhenxin; Grabham, Peter W; Chen, Yaxiong; Zhu, Jiayun; Du, Yarong; Pan, Dong; Li, Xiaoman; Hu, Burong

    2015-07-01

    In vitro 3D growth of tumors is a new cell culture model that more closely mimics the features of the in vivo environment and is being used increasingly in the field of biological and medical research. It has been demonstrated that cancer cells cultured in 3D matrices are more radio-resistant compared with cells in monolayers. However, the mechanisms causing this difference remain unclear. Here we show that cancer cells cultured in a 3D microenvironment demonstrated an increase in cells with stem cell properties. This was confirmed by the finding that cells in 3D cultures upregulated the gene and protein expression of the stem cell reprogramming factors such as OCT4, SOX2, NANOG, LIN28 and miR-302a, compared with cells in monolayers. Moreover, the expression of β-catenin, a regulating molecule of reprogramming factors, also increased in 3D-grown cancer cells. These findings suggest that cancer cells were reprogrammed to become stem cell-like cancer cells in a 3D growth culture microenvironment. Since cancer stem cell-like cells demonstrate an increased radio-resistance and chemo-resistance, our results offer a new perspective as to why. Our findings shed new light on understanding the features of the 3D growth cell model and its application in basic research into clinical radiotherapy and medicine. © The Author 2015. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

  7. 3D timelapse analysis of muscle satellite cell motility.

    PubMed

    Siegel, Ashley L; Atchison, Kevin; Fisher, Kevin E; Davis, George E; Cornelison, D D W

    2009-10-01

    Skeletal muscle repair and regeneration requires the activity of satellite cells, a population of myogenic stem cells scattered throughout the tissue and activated to proliferate and differentiate in response to myotrauma or disease. While it seems likely that satellite cells would need to navigate local muscle tissue to reach damaged areas, relatively little data on such motility exist, and most studies have been with immortalized cell lines. We find that primary satellite cells are significantly more motile than myoblast cell lines, and that adhesion to laminin promotes primary cell motility more than fourfold over other substrates. Using timelapse videomicroscopy to assess satellite cell motility on single living myofibers, we have identified a requirement for the laminin-binding integrin alpha 7 beta 1 in satellite cell motility, as well as a role for hepatocyte growth factor in promoting directional persistence. The extensive migratory behavior of satellite cells resident on muscle fibers suggests caution when determining, based on fixed specimens, whether adjacent cells are daughters from the same mother cell. We also observed more persistent long-term contact between individual satellite cells than has been previously supposed, potential cell-cell attractive and repulsive interactions, and migration between host myofibers. Based on such activity, we assayed for expression of "pathfinding" cues, and found that satellite cells express multiple guidance ligands and receptors. Together, these data suggest that satellite cell migration in vivo may be more extensive than currently thought, and could be regulated by combinations of signals, including adhesive haptotaxis, soluble factors, and guidance cues.

  8. XML-based 3D model visualization and simulation framework for dynamic models

    NASA Astrophysics Data System (ADS)

    Kim, Taewoo; Fishwick, Paul A.

    2002-07-01

    Relatively recent advances in computer technology enable us to create three-dimensional (3D) dynamic models and simulate them within a 3D web environment. The use of such models is especially valuable when teaching simulation, and the concepts behind dynamic models, since the models are made more accessible to the students. Students tend to enjoy a construction process in which they are able to employ their own cultural and aesthetic forms. The challenge is to create a language that allows for a grammar for modeling, while simultaneously permitting arbitrary presentation styles. For further flexibility, we need an effective way to represent and simulate dynamic models that can be shared by modelers over the Internet. We present an Extensible Markup Language (XML)-based framework that will guide a modeler in creating personalized 3D models, visualizing its dynamic behaviors, and simulating the created models. A model author will use XML files to represent geometries and topology of a dynamic model. Model Fusion Engine, written in Extensible Stylesheet Language Transformation (XSLT), expedites the modeling process by automating the creation of dynamic models with the user-defined XML files. Modelers can also link simulation programs with a created model to analyze the characteristics of the model. The advantages of this system lie in the education of modeling and simulating dynamic models, and in the exploitation of visualizing the dynamic model behaviors.

  9. Fluorescence fluctuation microscopy to reveal 3D architecture and function in the cell nucleus.

    PubMed

    Lenser, Thorsten; Weisshart, Klaus; Ulbricht, Tobias; Klement, Karolin; Hemmerich, Peter

    2010-01-01

    The three-dimensional (3D) architecture of the cell nucleus is determined not only by the presence of subnuclear domains, such as the nuclear envelope, chromosome territories, and nuclear bodies, but also by smaller domains which form in response to specific functions, such as RNA transcription, DNA replication, and DNA repair. Since both stable and dynamic structures contribute to nuclear morphology, it is important to study the biophysical principles of the formation of macromolecular assemblies within the nucleus. For this purpose, a variety of fluorescence fluctuation microscopy techniques can be applied. Here, we summarize our current knowledge on the 3D architecture of the mammalian cell nucleus and describe in detail how the assembly of functional nuclear protein complexes can be analyzed in living cells using fluorescence bleaching techniques, fluorescence correlation spectroscopy, raster image correlation spectroscopy, and mathematical modeling. In conclusion, the application of all these techniques in combination is a powerful tool to assess the full spectrum of nuclear protein dynamics and to understand the biophysical principles underlying nuclear structure and function.

  10. Regulation of mesenchymal stem cell 3D microenvironment: From macro to microfluidic bioreactors.

    PubMed

    Sart, Sébastien; Agathos, Spiros N; Li, Yan; Ma, Teng

    2016-01-01

    Human mesenchymal stem cells (hMSCs) have emerged as an important cell type in cell therapy and tissue engineering. In these applications, maintaining the therapeutic properties of hMSCs requires tight control of the culture environments and the structural cell organizations. Bioreactor systems are essential tools to achieve these goals in the clinical-scale expansion and tissue engineering applications. This review summarizes how different bioreactors provide cues to regulate the structure and the chemico-mechanical microenvironment of hMSCs with a focus on 3D organization. In addition to conventional bioreactors, recent advances in microfluidic bioreactors as a novel approach to better control the hMSC microenvironment are also discussed. These advancements highlight the key role of bioreactor systems in preserving hMSC's functional properties by providing dynamic and temporal regulation of in vitro cellular microenvironment.

  11. Network dynamics of 3D engineered neuronal cultures: a new experimental model for in-vitro electrophysiology

    PubMed Central

    Frega, Monica; Tedesco, Mariateresa; Massobrio, Paolo; Pesce, Mattia; Martinoia, Sergio

    2014-01-01

    Despite the extensive use of in-vitro models for neuroscientific investigations and notwithstanding the growing field of network electrophysiology, all studies on cultured cells devoted to elucidate neurophysiological mechanisms and computational properties, are based on 2D neuronal networks. These networks are usually grown onto specific rigid substrates (also with embedded electrodes) and lack of most of the constituents of the in-vivo like environment: cell morphology, cell-to-cell interaction and neuritic outgrowth in all directions. Cells in a brain region develop in a 3D space and interact with a complex multi-cellular environment and extracellular matrix. Under this perspective, 3D networks coupled to micro-transducer arrays, represent a new and powerful in-vitro model capable of better emulating in-vivo physiology. In this work, we present a new experimental paradigm constituted by 3D hippocampal networks coupled to Micro-Electrode-Arrays (MEAs) and we show how the features of the recorded network dynamics differ from the corresponding 2D network model. Further development of the proposed 3D in-vitro model by adding embedded functionalized scaffolds might open new prospects for manipulating, stimulating and recording the neuronal activity to elucidate neurophysiological mechanisms and to design bio-hybrid microsystems. PMID:24976386

  12. Network dynamics of 3D engineered neuronal cultures: a new experimental model for in-vitro electrophysiology.

    PubMed

    Frega, Monica; Tedesco, Mariateresa; Massobrio, Paolo; Pesce, Mattia; Martinoia, Sergio

    2014-06-30

    Despite the extensive use of in-vitro models for neuroscientific investigations and notwithstanding the growing field of network electrophysiology, all studies on cultured cells devoted to elucidate neurophysiological mechanisms and computational properties, are based on 2D neuronal networks. These networks are usually grown onto specific rigid substrates (also with embedded electrodes) and lack of most of the constituents of the in-vivo like environment: cell morphology, cell-to-cell interaction and neuritic outgrowth in all directions. Cells in a brain region develop in a 3D space and interact with a complex multi-cellular environment and extracellular matrix. Under this perspective, 3D networks coupled to micro-transducer arrays, represent a new and powerful in-vitro model capable of better emulating in-vivo physiology. In this work, we present a new experimental paradigm constituted by 3D hippocampal networks coupled to Micro-Electrode-Arrays (MEAs) and we show how the features of the recorded network dynamics differ from the corresponding 2D network model. Further development of the proposed 3D in-vitro model by adding embedded functionalized scaffolds might open new prospects for manipulating, stimulating and recording the neuronal activity to elucidate neurophysiological mechanisms and to design bio-hybrid microsystems.

  13. 3D dynamic simulation of crack propagation in extracorporeal shock wave lithotripsy

    NASA Astrophysics Data System (ADS)

    Wijerathne, M. L. L.; Hori, Muneo; Sakaguchi, Hide; Oguni, Kenji

    2010-06-01

    Some experimental observations of Shock Wave Lithotripsy(SWL), which include 3D dynamic crack propagation, are simulated with the aim of reproducing fragmentation of kidney stones with SWL. Extracorporeal shock wave lithotripsy (ESWL) is the fragmentation of kidney stones by focusing an ultrasonic pressure pulse onto the stones. 3D models with fine discretization are used to accurately capture the high amplitude shear shock waves. For solving the resulting large scale dynamic crack propagation problem, PDS-FEM is used; it provides numerically efficient failure treatments. With a distributed memory parallel code of PDS-FEM, experimentally observed 3D photoelastic images of transient stress waves and crack patterns in cylindrical samples are successfully reproduced. The numerical crack patterns are in good agreement with the experimental ones, quantitatively. The results shows that the high amplitude shear waves induced in solid, by the lithotriptor generated shock wave, play a dominant role in stone fragmentation.

  14. Tunable nonuniform sampling method for fast calculation and intensity modulation in 3D dynamic holographic display.

    PubMed

    Zhang, Zhao; Liu, Juan; Jia, Jia; Li, Xin; Han, Jian; Hu, Bin; Wang, Yongtian

    2013-08-01

    Heavy computational load of computer-generated hologram (CGH) and imprecise intensity modulation of 3D images are crucial problems in dynamic holographic display. The nonuniform sampling method is proposed to speed up CGH generation and precisely modulate the reconstructed intensities of phase-only CGH. The proposed method can eliminate the redundant information properly, where 70% reduction in the storage amount can be reached when it is combined with the novel lookup table method. Multigrayscale modulation of reconstructed 3D images can be achieved successfully. Numerical simulations and optical experiments are performed, and both are in good agreement. It is believed that the proposed method can be used in 3D dynamic holographic display.

  15. Introducing a Public Stereoscopic 3D High Dynamic Range (SHDR) Video Database

    NASA Astrophysics Data System (ADS)

    Banitalebi-Dehkordi, Amin

    2017-03-01

    High dynamic range (HDR) displays and cameras are paving their ways through the consumer market at a rapid growth rate. Thanks to TV and camera manufacturers, HDR systems are now becoming available commercially to end users. This is taking place only a few years after the blooming of 3D video technologies. MPEG/ITU are also actively working towards the standardization of these technologies. However, preliminary research efforts in these video technologies are hammered by the lack of sufficient experimental data. In this paper, we introduce a Stereoscopic 3D HDR database of videos that is made publicly available to the research community. We explain the procedure taken to capture, calibrate, and post-process the videos. In addition, we provide insights on potential use-cases, challenges, and research opportunities, implied by the combination of higher dynamic range of the HDR aspect, and depth impression of the 3D aspect.

  16. The optimizations of CGH generation algorithms based on multiple GPUs for 3D dynamic holographic display

    NASA Astrophysics Data System (ADS)

    Yang, Dan; Liu, Juan; Zhang, Yingxi; Li, Xin; Wang, Yongtian

    2016-10-01

    Holographic display has been considered as a promising display technology. Currently, low-speed generation of holograms with big holographic data is one of crucial bottlenecks for three dimensional (3D) dynamic holographic display. To solve this problem, the acceleration method computation platform is presented based on look-up table point source method. The computer generated holograms (CGHs) acquisition is sped up by offline file loading and inline calculation optimization, where a pure phase CGH with gigabyte data is encoded to record an object with 10 MB sampling data. Both numerical simulation and optical experiment demonstrate that the CGHs with 1920×1080 resolution by the proposed method can be applied to the 3D objects reconstruction with high quality successfully. It is believed that the CGHs with huge data can be generated by the proposed method with high speed for 3D dynamic holographic display in near future.

  17. From competency to dormancy: a 3D model to study cancer cells and drug responsiveness.

    PubMed

    Fang, Josephine Y; Tan, Shih-Jye; Wu, Yi-Chen; Yang, Zhi; Hoang, Ba X; Han, Bo

    2016-02-04

    The heterogeneous and dynamic tumor microenvironment has significant impact on cancer cell proliferation, invasion, drug response, and is probably associated with entering dormancy and recurrence. However, these complex settings are hard to recapitulate in vitro. In this study, we mimic different restriction forces that tumor cells are exposed to using a physiologically relevant 3D model with tunable mechanical stiffness. Breast cancer MDA-MB-231, colon cancer HCT-116 and pancreatic cancer CFPAC cells embedded in the stiffer gels exhibit a changed morphology and cluster formation, prolonged doubling time, and a slower metabolism rate, recapitulating the pathway from competency to dormancy. Altering environmental restriction allows them to re-enter and exit dormant conditions and change their sensitivities to drugs such as paclitaxol and gemcitabine. Cells surviving drug treatments can still regain competent growth and form tumors in vivo. We have successfully developed an in vitro 3D model to mimic the effects of matrix restriction on tumor cells and this high throughput model can be used to study tumor cellular functions and their drug responses in their different states. This all in one platform may aid effective drug development.

  18. In Situ "Clickable" Zwitterionic Starch-Based Hydrogel for 3D Cell Encapsulation.

    PubMed

    Dong, Dianyu; Li, Junjie; Cui, Man; Wang, Jinmei; Zhou, Yuhang; Luo, Liu; Wei, Yufei; Ye, Lei; Sun, Hong; Yao, Fanglian

    2016-02-01

    Three-dimensional (3D) cell encapsulation in hydrogel provides superb methods to investigate the biochemical cues in directing cellular fate and behaviors outside the organism, the primary step of which is to establish suitable "blank platform" to mimic and simplify native ECM microenvironment. In this study, zwitterionic starch-based "clickable" hydrogels were fabricated via a "copper- and light- free" Michael-type "thiol-ene" addition reaction between acylated-modified sulfobetaine-derived starch (SB-ST-A) and dithiol-functionalized poly(ethylene glycol) (PEG-SH). By incorporating antifouling SB-ST and PEG, the hydrogel system would be excellently protected from nontarget protein adsorption to act as a "blank platform". The hydrogels could rapidly gel under physiological conditions in less than 7 min. Dynamic rheology experiments suggested the stiffness of the hydrogel was close to the native tissues, and the mechanical properties as well as the gelation times and swelling behaviors could be easily tuned by varying the precursor proportions. The protein and cell adhesion assays demonstrated that the hydrogel surface could effectively resist nonspecific protein and cell adhesion. The degradation study in vitro confirmed that the hydrogel was biodegradable. A549 cells encapsulated in the hydrogel maintained high viability (up to 93%) and started to proliferate in number and extend in morphology after 2 days' culture. These results indicated the hydrogel presented here could be a potential candidate as "blank platform" for 3D cell encapsulation and biochemical cues induced cellular behavior investigation in vitro.

  19. Reprogramming mediated radio-resistance of 3D-grown cancer cells

    PubMed Central

    Xue, Gang; Ren, Zhenxin; Grabham, Peter W.; Chen, Yaxiong; Zhu, Jiayun; Du, Yarong; Pan, Dong; Li, Xiaoman; Hu, Burong

    2015-01-01

    In vitro 3D growth of tumors is a new cell culture model that more closely mimics the features of the in vivo environment and is being used increasingly in the field of biological and medical research. It has been demonstrated that cancer cells cultured in 3D matrices are more radio-resistant compared with cells in monolayers. However, the mechanisms causing this difference remain unclear. Here we show that cancer cells cultured in a 3D microenvironment demonstrated an increase in cells with stem cell properties. This was confirmed by the finding that cells in 3D cultures upregulated the gene and protein expression of the stem cell reprogramming factors such as OCT4, SOX2, NANOG, LIN28 and miR-302a, compared with cells in monolayers. Moreover, the expression of β-catenin, a regulating molecule of reprogramming factors, also increased in 3D-grown cancer cells. These findings suggest that cancer cells were reprogrammed to become stem cell–like cancer cells in a 3D growth culture microenvironment. Since cancer stem cell–like cells demonstrate an increased radio-resistance and chemo-resistance, our results offer a new perspective as to why. Our findings shed new light on understanding the features of the 3D growth cell model and its application in basic research into clinical radiotherapy and medicine. PMID:25883172

  20. Integrating protein structural dynamics and evolutionary analysis with Bio3D.

    PubMed

    Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

    2014-12-10

    Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

  1. Dynamic 3D ultrasound and MR image registration of the beating heart.

    PubMed

    Huang, Xishi; Hill, Nicholas A; Ren, Jing; Guiraudon, Gerard; Boughner, Derek; Peters, Terry M

    2005-01-01

    Real-time three-dimensional ultrasound (RT3D US) is an ideal imaging modality for the diagnosis of cardiac disease. RT3D US is a flexible, inexpensive, non-invasive tool that provides important diagnostic information related to cardiac function. Unfortunately, RT3D US suffers from inherent shortcomings, such as low signal-to-noise ratio and limited field of view, producing images that are difficult to interpret. Multi-modal dynamic cardiac image registration is a well-recognized approach that compensates for these deficiencies while retaining the advantages of RT3D US imaging. The clinical application of multi-modal image registration methods is difficult, and there are a number of implementation issues to be resolved. In this work, we present a method for the rapid registration of RT3D US images of the beating heart to high-resolution magnetic resonance (MR) images. This method was validated using a volunteer image set. Validation results demonstrate that this approach can achieve rapid registration of images of the beating heart with fiducial landmark and registration errors of 1.25 +/- 0.63 and 1.76 mm respectively. This technique can potentially be used to improve the diagnosis of cardiac disease by augmenting RT3D US images with high-resolution MR images and to facilitate intra-operative image fusion for minimally invasive cardio-thoracic surgical navigation.

  2. Trans3D: a free tool for dynamical visualization of EEG activity transmission in the brain.

    PubMed

    Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

    2014-08-01

    The problem of functional connectivity in the brain is in the focus of attention nowadays, since it is crucial for understanding information processing in the brain. A large repertoire of measures of connectivity have been devised, some of them being capable of estimating time-varying directed connectivity. Hence, there is a need for a dedicated software tool for visualizing the propagation of electrical activity in the brain. To this aim, the Trans3D application was developed. It is an open access tool based on widely available libraries and supporting both Windows XP/Vista/7(™), Linux and Mac environments. Trans3D can create animations of activity propagation between electrodes/sensors, which can be placed by the user on the scalp/cortex of a 3D model of the head. Various interactive graphic functions for manipulating and visualizing components of the 3D model and input data are available. An application of the Trans3D tool has helped to elucidate the dynamics of the phenomena of information processing in motor and cognitive tasks, which otherwise would have been very difficult to observe. Trans3D is available at: http://www.eeg.pl/.

  3. Effect of Ductile Agents on the Dynamic Behavior of SiC3D Network Composites

    NASA Astrophysics Data System (ADS)

    Zhu, Jingbo; Wang, Yangwei; Wang, Fuchi; Fan, Qunbo

    2016-10-01

    Co-continuous SiC ceramic composites using pure aluminum, epoxy, and polyurethane (PU) as ductile agents were developed. The dynamic mechanical behavior and failure mechanisms were investigated experimentally using the split Hopkinson pressure bar (SHPB) method and computationally by finite element (FE) simulations. The results show that the SiC3D/Al composite has the best overall performance in comparison with SiC3D/epoxy and SiC3D/PU composites. FE simulations are generally consistent with experimental data. These simulations provide valuable help in predicting mechanical strength and in interpreting the experimental results and failure mechanisms. They may be combined with micrographs for fracture characterizations of the composites. We found that interactions between the SiC phase and ductile agents under dynamic compression in the SHPB method are complex, and that interfacial condition is an important parameter that determines the mechanical response of SiC3D composites with a characteristic interlocking structure during dynamic compression. However, the effect of the mechanical properties of ductile agents on dynamic behavior of the composites is a second consideration in the production of the composites.

  4. How Spatial Abilities and Dynamic Visualizations Interplay When Learning Functional Anatomy with 3D Anatomical Models

    ERIC Educational Resources Information Center

    Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

    2015-01-01

    The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material…

  5. On the Dynamic Programming Approach for the 3D Navier-Stokes Equations

    SciTech Connect

    Manca, Luigi

    2008-06-15

    The dynamic programming approach for the control of a 3D flow governed by the stochastic Navier-Stokes equations for incompressible fluid in a bounded domain is studied. By a compactness argument, existence of solutions for the associated Hamilton-Jacobi-Bellman equation is proved. Finally, existence of an optimal control through the feedback formula and of an optimal state is discussed.

  6. How Spatial Abilities and Dynamic Visualizations Interplay When Learning Functional Anatomy with 3D Anatomical Models

    ERIC Educational Resources Information Center

    Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

    2015-01-01

    The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material…

  7. Hydrogels as extracellular matrix mimics for 3D cell culture.

    PubMed

    Tibbitt, Mark W; Anseth, Kristi S

    2009-07-01

    Methods for culturing mammalian cells ex vivo are increasingly needed to study cell and tissue physiology and to grow replacement tissue for regenerative medicine. Two-dimensional culture has been the paradigm for typical in vitro cell culture; however, it has been demonstrated that cells behave more natively when cultured in three-dimensional environments. Permissive, synthetic hydrogels and promoting, natural hydrogels have become popular as three-dimensional cell culture platforms; yet, both of these systems possess limitations. In this perspective, we discuss the use of both synthetic and natural hydrogels as scaffolds for three-dimensional cell culture as well as synthetic hydrogels that incorporate sophisticated biochemical and mechanical cues as mimics of the native extracellular matrix. Ultimately, advances in synthetic-biologic hydrogel hybrids are needed to provide robust platforms for investigating cell physiology and fabricating tissue outside of the organism. (c) 2009 Wiley Periodicals, Inc.

  8. Verification of real sensor motion for a high-dynamic 3D measurement inspection system

    NASA Astrophysics Data System (ADS)

    Breitbarth, Andreas; Correns, Martin; Zimmermann, Manuel; Zhang, Chen; Rosenberger, Maik; Schambach, Jörg; Notni, Gunther

    2017-06-01

    Inline three-dimensional measurements are a growing part of optical inspection. Considering increasing production capacities and economic aspects, dynamic measurements under motion are inescapable. Using a sequence of different pattern, like it is generally done in fringe projection systems, relative movements of the measurement object with respect to the 3d sensor between the images of one pattern sequence have to be compensated. Based on the application of fully automated optical inspection of circuit boards at an assembly line, the knowledge of the relative speed of movement between the measurement object and the 3d sensor system should be used inside the algorithms of motion compensation. Optimally, this relative speed is constant over the whole measurement process and consists of only one motion direction to avoid sensor vibrations. The quantified evaluation of this two assumptions and the error impact on the 3d accuracy are content of the research project described by this paper. For our experiments we use a glass etalon with non-transparent circles and transmitted light. Focused on the circle borders, this is one of the most reliable methods to determine subpixel positions using a couple of searching rays. The intersection point of all rays characterize the center of each circle. Based on these circle centers determined with a precision of approximately 1=50 pixel, the motion vector between two images could be calculated and compared with the input motion vector. Overall, the results are used to optimize the weight distribution of the 3d sensor head and reduce non-uniformly vibrations. Finally, there exists a dynamic 3d measurement system with an error of motion vectors about 4 micrometer. Based on this outcome, simulations result in a 3d standard deviation at planar object regions of 6 micrometers. The same system yields a 3d standard deviation of 9 µm without the optimization of weight distribution.

  9. Modeling cell migration on filamentous tracks in 3D

    NASA Astrophysics Data System (ADS)

    Schwarz, J. M.

    2014-03-01

    Cell motility is integral to a number of physiological processes ranging from wound healing to immune response to cancer metastasis. Many studies of cell migration, both experimental and theoretical, have addressed various aspects of it in two dimensions, including protrusion and retraction at the level of single cells. However, the in vivo environment for a crawling cell is typically a three-dimensional environment, consisting of the extracellular matrix (ECM) and surrounding cells. Recent experiments demonstrate that some cells crawling along fibers of the ECM mimic the geometry of the fibers to become long and thin, as opposed to fan-like in two dimensions, and can remodel the ECM. Inspired by these experiments, a model cell consisting of beads and springs that moves along a tense semiflexible filamentous track is constructed and studied, paying particular attention to the mechanical feedback between the model cell and the track, as mediated by the active myosin-driven contractility and the catch/slip bond behavior of the focal adhesions, as the model cell crawls. This simple construction can then be scaled up to a model cell moving along a three-dimensional filamentous network, with a prescribed microenvironment, in order to make predictions for proposed experiments.

  10. Dynamic stress-strain states for metal foams using a 3D cellular model

    NASA Astrophysics Data System (ADS)

    Zheng, Zhijun; Wang, Changfeng; Yu, Jilin; Reid, Stephen R.; Harrigan, John J.

    2014-12-01

    Dynamic uniaxial impact behaviour of metal foams using a 3D cell-based finite element model is examined. At sufficiently high loading rates, these materials respond by forming ‘shock or consolidation waves' (Tan et al., 2005a, 2005b). However, the existing dynamic experimental methods have limitations in fully informing this behaviour, particularly for solving boundary/initial value problems. Recently, the problem of the shock-like response of an open-cell foam has been examined by Barnes et al. (2014) using the Hugoniot-curve representations. The present study is somewhat complementary to that approach and additionally aims to provide insight into the ‘rate sensitivity' mechanism applicable to cellular materials. To assist our understanding of the ‘loading rate sensitivity' behaviour of cellular materials, a virtual ‘test' method based on the direct impact technique is explored. Following a continuum representation of the response, the strain field calculation method is employed to determine the local strains ahead of and behind the resulting ‘shock front'. The dynamic stress-strain states in the densification stage are found to be different from the quasi-static ones. It is evident that the constitutive behaviour of the cellular material is deformation-mode dependent. The nature of the ‘rate sensitivity' revealed for cellular materials in this paper is different from the strain-rate sensitivity of dense metals. It is shown that the dynamic stress-strain states behind a shock front of the cellular material lie on a unique curve and each point on the curve corresponds to a particular ‘impact velocity', referred as the velocity upstream of the shock in this study. The dynamic stress-strain curve is related to a layer-wise collapse mode, whilst the equivalent quasi-static curve is related to a random shear band collapse mode. The findings herein are aimed at improving the experimental test techniques used to characterise the rate-sensitivity behaviour

  11. Modulation measuring profilometry with cross grating projection and single shot for dynamic 3D shape measurement

    NASA Astrophysics Data System (ADS)

    Lu, Mingteng; Su, Xianyu; Cao, Yiping; You, Zhisheng; Zhong, Min

    2016-12-01

    In order to determine Dynamic 3-D shape with vertical measurement mode, a fast modulation measuring profilometry (MMP) with a cross grating projection and single shot is proposed. Unlike the previous methods, in our current projection system, one cross grating is projected by a special projection lens consisting of a common projection lens and a cylindrical lens. Due to the characteristics of cylindrical lens, the image of the vertical component and the horizontal component of the cross grating is separated in the image space, and the measuring range is just the space between the two image planes. Through a beam splitter, the CCD camera can coaxially capture the fringe pattern of the cross grating modulated by the testing object's shape. In one fringe pattern, by applying Fourier transform, filtering and inverse Fourier transform, the modulation corresponding to the vertical and horizontal components of the cross grating can be obtained respectively. Then the 3-D shape of the object can be reconstructed according to the mapping relationship between modulation and height, which was established by calibration process in advance. So the 3-D shape information can be recorded at the same speed of the frame rate of the CCD camera. This paper gives the principle of the proposed method and the set-up for measuring experiment and system calibration. The 3-D shape of a still object and a dynamic process of liquid vortex were measured and reconstructed in the experiments, and the results proved the method's feasibility. The advantage of the proposed method is that only one fringe pattern is needed to extract the modulation distribution and to reconstruct the 3-D shape of the object. Therefore, the proposed method can achieve high speed measurement and vertical measurement without shadow and occlusion. It can be used in the dynamic 3-D shape measurement and vibration analysis.

  12. A porous 3D cell culture micro device for cell migration study.

    PubMed

    Ma, Liang; Zhou, Changchun; Lin, Biaoyang; Li, Wei

    2010-08-01

    Cell migration under chemoattractant is an important biological step in cancer metastasis that causes the spread of malignant tumor cells. Porous polymeric materials are widely used to mimic the extracellular matrix (ECM) environment for applications such as three dimensional (3D) cell culturing and tissue engineering. In this paper we report a novel 3D cell culture device based on porous polymeric material to study cancer migration. We fabricated a porous channel on a polymeric chip using a selective ultrasonic foaming method. We demonstrate that a chemical concentration gradient could be established through the porous channel due to the slow diffusion process. We show that significant cell migration could be observed through the porous channel within 1-2 weeks of cell culturing when metastatic M4A4-GFP breast cancer cells were induced by 20% fetal bovine serum (FBS).We also developed a mathematical model to evaluate the diffusivity and concentration gradient through the fabricated porous structure.

  13. Biofabrication of cell-loaded 3D spider silk constructs.

    PubMed

    Schacht, Kristin; Jüngst, Tomasz; Schweinlin, Matthias; Ewald, Andrea; Groll, Jürgen; Scheibel, Thomas

    2015-02-23

    Biofabrication is an emerging and rapidly expanding field of research in which additive manufacturing techniques in combination with cell printing are exploited to generate hierarchical tissue-like structures. Materials that combine printability with cytocompatibility, so called bioinks, are currently the biggest bottleneck. Since recombinant spider silk proteins are non-immunogenic, cytocompatible, and exhibit physical crosslinking, their potential as a new bioink system was evaluated. Cell-loaded spider silk constructs can be printed by robotic dispensing without the need for crosslinking additives or thickeners for mechanical stabilization. Cells are able to adhere and proliferate with good viability over at least one week in such spider silk scaffolds. Introduction of a cell-binding motif to the spider silk protein further enables fine-tuned control over cell-material interactions. Spider silk hydrogels are thus a highly attractive novel bioink for biofabrication. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. 3D dynamic computer model of the head-neck complex.

    PubMed

    Sierra, Daniel A; Enderle, John D

    2006-01-01

    A 3D dynamic computer model for the movement of the head is presented that incorporates anatomically correct information about the diverse elements forming the system. The skeleton is considered as a set of interconnected rigid 3D bodies following the Newton-Euler laws of movement. The muscles are modeled using Enderle's linear model. Finally, the soft tissues, namely the ligaments, intervertebral disks, and zigapophysial joints, are modeled using the finite elements approach. The model is intended to study the neural network that controls movement and maintains the balance of the head-neck complex during eye movements.

  15. Hydrogels for 3D mammalian cell culture: a starting guide for laboratory practice.

    PubMed

    Ruedinger, Ferdinand; Lavrentieva, Antonina; Blume, Cornelia; Pepelanova, Iliyana; Scheper, Thomas

    2015-01-01

    Hydrogels have become one of the most popular platforms for three-dimensional (3D) cultivation of mammalian cells. The enormous versatility of hydrogel materials makes it possible to design scaffolds with predefined mechanical properties, as well as with desired biofunctionality. 3D hydrogel constructs have been used for a variety of applications, including tissue engineering of microorgan systems, drug delivery, cytotoxicity testing, and drug screening. Moreover, 3D culture is applied for investigating cellular physiology, stem cell differentiation, and tumor models and for studying interaction mechanisms between the extracellular matrix and cells. In this paper, we review current examples of performance-based hydrogel design for 3D cell culture applications. A major emphasis is placed on a description of how standard analytical protocols and imaging techniques are being adapted to analysis of 3D cell culture in hydrogel systems.

  16. Dynamic inversion time for improved 3D late gadolinium enhancement imaging in patients with atrial fibrillation.

    PubMed

    Keegan, Jennifer; Gatehouse, Peter D; Haldar, Shouvik; Wage, Ricardo; Babu-Narayan, Sonya V; Firmin, David N

    2015-02-01

    High resolution three-dimensional (3D) late gadolinium enhancement (LGE) imaging is performed with single R-wave gating to minimize lengthy acquisition durations. In patients with atrial fibrillation (AF), heart rate variability results in variable magnetization recovery between sequence repeats, and image quality is often poor. In this study, we implemented and tested a dynamic inversion time (dynamic-TI) scheme designed to reduce sequence sensitivity to heart rate variations. An inversion-prepared 3D segmented gradient echo sequence was modified so that the TI varied automatically from beat-to-beat (dynamic-TI) based on the time since the last sequence repeat. 3D LGE acquisitions were performed in 17 patients prior to radio frequency ablation of persistent AF both with and without dynamic-TI. Qualitative image quality scores, blood signal-to-ghosting ratios (SGRs). and blood-myocardium contrast-to-ghosting ratios (CGRs) were compared. Image quality scores were higher with dynamic-TI than without dynamic-TI (2.2 ± 0.9 vs. 1.8 ± 1.1, P = 0.008), as were blood-myocardium CGRs (13.8 ± 7.6 vs. 8.3 ± 6.1, P = 0.003) and blood SGRs (19.6 ± 8.5 vs. 13.1 ± 8.0, P = 0.003). The dynamic-TI algorithm improves image quality of 3D LGE imaging in this difficult patient population by reducing the sequence sensitivity to RR interval variations © 2014 Wiley Periodicals, Inc.

  17. Engineering muscle cell alignment through 3D bioprinting.

    PubMed

    Mozetic, Pamela; Giannitelli, Sara Maria; Gori, Manuele; Trombetta, Marcella; Rainer, Alberto

    2017-09-01

    Processing of hydrogels represents a main challenge for the prospective application of additive manufacturing (AM) to soft tissue engineering. Furthermore, direct manufacturing of tissue precursors with a cell density similar to native tissues has the potential to overcome the extensive in vitro culture required for conventional cell-seeded scaffolds seeking to fabricate constructs with tailored structural and functional properties. In this work, we present a simple AM methodology that exploits the thermoresponsive behavior of a block copolymer (Pluronic(®) ) as a means to obtain good shape retention at physiological conditions and to induce cellular alignment. Pluronic/alginate blends have been investigated as a model system for the processing of C2C12 murine myoblast cell line. Interestingly, C2C12 cell model demonstrated cell alignment along the deposition direction, potentially representing a new avenue to tailor the resulting cell histoarchitecture during AM process. Furthermore, the fabricated constructs exhibited high cell viability, as well as a significantly improved expression of myogenic genes vs. conventional 2D cultures. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2582-2588, 2017. © 2017 Wiley Periodicals, Inc.

  18. Directed 3D Cell Alignment and Elongation in Microengineered Hydrogels

    DTIC Science & Technology

    2010-01-01

    Immortalized human liver carcinoma cells (Hep-G2) were maintained in DMEM supplemented with 10% FBS, 1% P/S and were passaged twice per week. 2.4. Prepolymer ... prepolymer (20% (w/v) in DPBS) was used to coat TMSPMA treated glass slides as previously described [28]. 2.5. Cell encapsulation and micropatterning Cell... prepolymer was pipetted between a TMSPMA coated glass slide and an untreated coverslip (18 mm (w) 18 mm (l)), then exposed to 6.9 mW/cm2 UV light

  19. A 3D Hydrodynamic Model for Cytokinesis of Eukaryotic Cells

    DTIC Science & Technology

    2014-08-01

    goes wrong may lead to a catastrophe or failure, which may lead to an unwelcome outcome for instance cancer . Thus, a detailed understanding on... biofilm - drug interaction. Discrete and Continuous Dynamical Systems Series B, 15:417–456, March 2011. 13 [17] Brandon Lindley, Qi Wang, and Tianyu Zhang...Multicomponent hydrodynamic model for heterogeneous biofilms : Two-dimensional numerical simulations of growth and in- teraction with flows. Physical

  20. 2D µ-Particle Image Velocimetry and Computational Fluid Dynamics Study Within a 3D Porous Scaffold.

    PubMed

    Campos Marin, A; Grossi, T; Bianchi, E; Dubini, G; Lacroix, D

    2017-05-01

    Transport properties of 3D scaffolds under fluid flow are critical for tissue development. Computational fluid dynamics (CFD) models can resolve 3D flows and nutrient concentrations in bioreactors at the scaffold-pore scale with high resolution. However, CFD models can be formulated based on assumptions and simplifications. μ-Particle image velocimetry (PIV) measurements should be performed to improve the reliability and predictive power of such models. Nevertheless, measuring fluid flow velocities within 3D scaffolds is challenging. The aim of this study was to develop a μPIV approach to allow the extraction of velocity fields from a 3D additive manufacturing scaffold using a conventional 2D μPIV system. The μ-computed tomography scaffold geometry was included in a CFD model where perfusion conditions were simulated. Good agreement was found between velocity profiles from measurements and computational results. Maximum velocities were found at the centre of the pore using both techniques with a difference of 12% which was expected according to the accuracy of the μPIV system. However, significant differences in terms of velocity magnitude were found near scaffold substrate due to scaffold brightness which affected the μPIV measurements. As a result, the limitations of the μPIV system only permits a partial validation of the CFD model. Nevertheless, the combination of both techniques allowed a detailed description of velocity maps within a 3D scaffold which is crucial to determine the optimal cell and nutrient transport properties.

  1. Gyrotactic cells subject to imposed 3D flows

    NASA Astrophysics Data System (ADS)

    Hill, Nicholas; Richardson, Scott; Baggaley, Andrew

    2014-11-01

    We examine the effect of imposed 3-dimensional test flows, specifically a Taylor-Green Vortex flow and an ABC flow, on the patterns and mixing of suspensions of gyrotactic swimming cells. Numerically solving the deterministic swimming trajectory equations for individual cells with random starting positions, we explore how the surrounding flow and the cell shape determine the long-time patterns. For certain parameter ranges these patterns often take the form of braided ``plume-lie'' structures, even when using the chaotic ABC flow. For various pattern configurations, analysis of the governing equations of motion reveals why they are formed, as analytical solutions of the equations for the swimming cell trajectories can be obtained. These patterns persist when small random perturbations (noise) are added to individual trajectories.

  2. 3-D Microwell Array System for Culturing Virus Infected Tumor Cells.

    PubMed

    El Assal, Rami; Gurkan, Umut A; Chen, Pu; Juillard, Franceline; Tocchio, Alessandro; Chinnasamy, Thiruppathiraja; Beauchemin, Chantal; Unluisler, Sebnem; Canikyan, Serli; Holman, Alyssa; Srivatsa, Srikar; Kaye, Kenneth M; Demirci, Utkan

    2016-12-22

    Cancer cells have been increasingly grown in pharmaceutical research to understand tumorigenesis and develop new therapeutic drugs. Currently, cells are typically grown using two-dimensional (2-D) cell culture approaches, where the native tumor microenvironment is difficult to recapitulate. Thus, one of the main obstacles in oncology is the lack of proper infection models that recount main features present in tumors. In recent years, microtechnology-based platforms have been employed to generate three-dimensional (3-D) models that better mimic the native microenvironment in cell culture. Here, we present an innovative approach to culture Kaposi's sarcoma-associated herpesvirus (KSHV) infected human B cells in 3-D using a microwell array system. The results demonstrate that the KSHV-infected B cells can be grown up to 15 days in a 3-D culture. Compared with 2-D, cells grown in 3-D had increased numbers of KSHV latency-associated nuclear antigen (LANA) dots, as detected by immunofluorescence microscopy, indicating a higher viral genome copy number. Cells in 3-D also demonstrated a higher rate of lytic reactivation. The 3-D microwell array system has the potential to improve 3-D cell oncology models and allow for better-controlled studies for drug discovery.

  3. 3-D Microwell Array System for Culturing Virus Infected Tumor Cells

    PubMed Central

    El Assal, Rami; Gurkan, Umut A.; Chen, Pu; Juillard, Franceline; Tocchio, Alessandro; Chinnasamy, Thiruppathiraja; Beauchemin, Chantal; Unluisler, Sebnem; Canikyan, Serli; Holman, Alyssa; Srivatsa, Srikar; Kaye, Kenneth M.; Demirci, Utkan

    2016-01-01

    Cancer cells have been increasingly grown in pharmaceutical research to understand tumorigenesis and develop new therapeutic drugs. Currently, cells are typically grown using two-dimensional (2-D) cell culture approaches, where the native tumor microenvironment is difficult to recapitulate. Thus, one of the main obstacles in oncology is the lack of proper infection models that recount main features present in tumors. In recent years, microtechnology-based platforms have been employed to generate three-dimensional (3-D) models that better mimic the native microenvironment in cell culture. Here, we present an innovative approach to culture Kaposi’s sarcoma-associated herpesvirus (KSHV) infected human B cells in 3-D using a microwell array system. The results demonstrate that the KSHV-infected B cells can be grown up to 15 days in a 3-D culture. Compared with 2-D, cells grown in 3-D had increased numbers of KSHV latency-associated nuclear antigen (LANA) dots, as detected by immunofluorescence microscopy, indicating a higher viral genome copy number. Cells in 3-D also demonstrated a higher rate of lytic reactivation. The 3-D microwell array system has the potential to improve 3-D cell oncology models and allow for better-controlled studies for drug discovery. PMID:28004818

  4. Label free cell tracking in 3D tissue engineering constructs with high resolution imaging

    NASA Astrophysics Data System (ADS)

    Smith, W. A.; Lam, K.-P.; Dempsey, K. P.; Mazzocchi-Jones, D.; Richardson, J. B.; Yang, Y.

    2014-02-01

    Within the field of tissue engineering there is an emphasis on studying 3-D live tissue structures. Consequently, to investigate and identify cellular activities and phenotypes in a 3-D environment for all in vitro experiments, including shape, migration/proliferation and axon projection, it is necessary to adopt an optical imaging system that enables monitoring 3-D cellular activities and morphology through the thickness of the construct for an extended culture period without cell labeling. This paper describes a new 3-D tracking algorithm developed for Cell-IQ®, an automated cell imaging platform, which has been equipped with an environmental chamber optimized to enable capturing time-lapse sequences of live cell images over a long-term period without cell labeling. As an integral part of the algorithm, a novel auto-focusing procedure was developed for phase contrast microscopy equipped with 20x and 40x objectives, to provide a more accurate estimation of cell growth/trajectories by allowing 3-D voxels to be computed at high spatiotemporal resolution and cell density. A pilot study was carried out in a phantom system consisting of horizontally aligned nanofiber layers (with precise spacing between them), to mimic features well exemplified in cellular activities of neuronal growth in a 3-D environment. This was followed by detailed investigations concerning axonal projections and dendritic circuitry formation in a 3-D tissue engineering construct. Preliminary work on primary animal neuronal cells in response to chemoattractant and topographic cue within the scaffolds has produced encouraging results.

  5. Generation of compartmentalized pressure by a nuclear piston governs cell motility in a 3D matrix.

    PubMed

    Petrie, Ryan J; Koo, Hyun; Yamada, Kenneth M

    2014-08-29

    Cells use actomyosin contractility to move through three-dimensional (3D) extracellular matrices. Contractility affects the type of protrusions cells use to migrate in 3D, but the mechanisms are unclear. In this work, we found that contractility generated high-pressure lobopodial protrusions in human cells migrating in a 3D matrix. In these cells, the nucleus physically divided the cytoplasm into forward and rear compartments. Actomyosin contractility with the nucleoskeleton-intermediate filament linker protein nesprin-3 pulled the nucleus forward and pressurized the front of the cell. Reducing expression of nesprin-3 decreased and equalized the intracellular pressure. Thus, the nucleus can act as a piston that physically compartmentalizes the cytoplasm and increases the hydrostatic pressure between the nucleus and the leading edge of the cell to drive lamellipodia-independent 3D cell migration. Copyright © 2014, American Association for the Advancement of Science.

  6. Compact and field-portable 3D printed shearing digital holographic microscope for automated cell identification.

    PubMed

    Rawat, Siddharth; Komatsu, Satoru; Markman, Adam; Anand, Arun; Javidi, Bahram

    2017-03-20

    We propose a low-cost, compact, and field-portable 3D printed holographic microscope for automated cell identification based on a common path shearing interferometer setup. Once a hologram is captured from the portable setup, a 3D reconstructed height profile of the cell is created. We extract several morphological cell features from the reconstructed 3D height profiles, including mean physical cell thickness, coefficient of variation, optical volume (OV) of the cell, projected area of the cell (PA), ratio of PA to OV, cell thickness kurtosis, cell thickness skewness, and the dry mass of the cell for identification using the random forest (RF) classifier. The 3D printed prototype can serve as a low-cost alternative for the developing world, where access to laboratory facilities for disease diagnosis are limited. Additionally, a cell phone sensor is used to capture the digital holograms. This enables the user to send the acquired holograms over the internet to a computational device located remotely for cellular identification and classification (analysis). The 3D printed system presented in this paper can be used as a low-cost, stable, and field-portable digital holographic microscope as well as an automated cell identification system. To the best of our knowledge, this is the first research paper presenting automatic cell identification using a low-cost 3D printed digital holographic microscopy setup based on common path shearing interferometry.

  7. Local 3D matrix confinement determines division axis through cell shape

    PubMed Central

    He, Lijuan; Chen, Weitong; Wu, Pei-Hsun; Jimenez, Angela; Wong, Bin Sheng; San, Angela; Konstantopoulos, Konstantinos; Wirtz, Denis

    2016-01-01

    How the division axis is determined in mammalian cells embedded in three-dimensional (3D) matrices remains elusive, despite that many types of cells divide in 3D environments. Cells on two-dimensional (2D) substrates typically round up completely to divide. Here, we show that in 3D collagen matrices, mammalian cells such as HT1080 human fibrosarcoma and MDA-MB-231 breast cancer cells exhibit division modes distinct from their Counterparts on 2D substrates, with a markedly higher fraction of cells remaining highly elongated through mitosis in 3D matrices. The long axis of elongated mitotic cells accurately predicts the division axis, independently of matrix density and cell-matrix interactions. This 3D-specific elongated division mode is determined by the local confinement produced by the matrix and the ability of cells to protrude and locally remodel the matrix via β1 integrin. Elongated division is readily recapitulated using collagen-coated microfabricated channels. Cells depleted of β1 integrin still divide in the elongated mode in microchannels, suggesting that 3D confinement is sufficient to induce the elongated cell-division phenotype. PMID:26515603

  8. Local 3D matrix confinement determines division axis through cell shape.

    PubMed

    He, Lijuan; Chen, Weitong; Wu, Pei-Hsun; Jimenez, Angela; Wong, Bin Sheng; San, Angela; Konstantopoulos, Konstantinos; Wirtz, Denis

    2016-02-09

    How the division axis is determined in mammalian cells embedded in three-dimensional (3D) matrices remains elusive, despite that many types of cells divide in 3D environments. Cells on two-dimensional (2D) substrates typically round up completely to divide. Here, we show that in 3D collagen matrices, mammalian cells such as HT1080 human fibrosarcoma and MDA-MB-231 breast cancer cells exhibit division modes distinct from their Counterparts on 2D substrates, with a markedly higher fraction of cells remaining highly elongated through mitosis in 3D matrices. The long axis of elongated mitotic cells accurately predicts the division axis, independently of matrix density and cell-matrix interactions. This 3D-specific elongated division mode is determined by the local confinement produced by the matrix and the ability of cells to protrude and locally remodel the matrix via β1 integrin. Elongated division is readily recapitulated using collagen-coated microfabricated channels. Cells depleted of β1 integrin still divide in the elongated mode in microchannels, suggesting that 3D confinement is sufficient to induce the elongated cell-division phenotype.

  9. Screening for Stromal and Matrix Effects in 3D Microenvironments of Breast Cancer Cells

    NASA Astrophysics Data System (ADS)

    Montanez-Sauri, Sara I.

    Breast cancer progression ensures through the acquisition of genetic mutations, the uncontrollable growth of cells, and their progression to invasion. Studies have shown that the surrounding three-dimensional (3D) microenvironment can also influence breast cancer cell progression by controlling the morphology, differentiation, proliferation, and migration of cells. However, most of the currently available in vitro screening platforms are based on the two-dimensional (2D) culture of cells, and do not provide cells with the complex 3D microenvironment that exists in vivo. Therefore, there is a need for more biologically relevant in vitro platforms to help decipher the complexity of the microenvironment and its influence in breast cancer. In this dissertation we present an automated microfluidic platform that allows to efficiently screen for the effect of multiple matrix and stromal microenvironment in 3D cultures of breast cancer cells. Several extracellular matrix (ECM) compositions and stromal cells are included in the 3D microenvironments to examine their influence on breast cancer cell behavior. The screening results suggest that collagen gels with fibronectin might be influencing paracrine signals between breast cancer cells and stromal cells. The ability of the platform to culture and treat cells in 3D microenvironments offers a powerful screening tool for the identification of compounds and interactions using more in vivo-like 3D microenvironments. The identification of these mechanisms will increase our current understanding of breast cancer, and will aid in the identification of potential therapeutics.

  10. Polysaccharide matrices used in 3D in vitro cell culture systems.

    PubMed

    Diekjürgen, Dorina; Grainger, David W

    2017-10-01

    Polysaccharides comprise a diverse class of polymeric materials with a history of proven biocompatibility and continual use as biomaterials. Recent focus on new matrices appropriate for three-dimensional (3D) cell culture offers new opportunities to apply polysaccharides as extracellular matrix mimics. However, chemical and structural bases for specific cell-polysaccharide interactions essential for their utility as 3-D cell matrices are not well defined. This review describes how these naturally sourced biomaterials satisfy several key properties for current 3D cell culture needs and can also be synthetically modified or blended with additional components to tailor their cell engagement properties. Beyond their benign interactions with many cell types in cultures, their economical and high quality sourcing, optical clarity for ex situ analytical interrogation and in situ gelation represent important properties of these polymers for 3D cell culture applications. Continued diversification of their versatile glycan chemistry, new bio-synthetic sourcing strategies and elucidation of new cell-specific properties are attractive to expand the polysaccharide polymer utility for cell culture needs. Many 3D cell culture priorities are addressed with the portfolio of polysaccharide materials available and under development. This review provides a critical analysis of their properties, capabilities and challenges in 3D cell culture applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Fluid and cell behaviors along a 3D printed alginate/gelatin/fibrin channel.

    PubMed

    Xu, Yufan; Wang, Xiaohong

    2015-08-01

    Three-dimensional (3D) cell manipulation is available with the integration of microfluidic technology and rapid prototyping techniques. High-Fidelity (Hi-Fi) constructs hold enormous therapeutic potential for organ manufacturing and regenerative medicine. In the present paper we introduced a quasi-three-dimensional (Q3D) model with parallel biocompatible alginate/gelatin/fibrin hurdles. The behaviors of fluids and cells along the microfluidic channels with various widths were studied. Cells inside the newly designed microfluidic channels attached and grew well. Morphological changes of adipose-derived stem cells (ADSCs) in both two-dimensional (2D) and 3D milieu were found on the printed constructs. Endothelialization occurred with the co-cultures of ADSCs and hepatocytes. This study provides insights into the interactions among fluids, cells and biomaterials, the behaviors of fluids and cells along the microfluidic channels, and the applications of Q3D techniques.

  12. Laser irradiated fluorescent perfluorocarbon microparticles in 2-D and 3-D breast cancer cell models

    PubMed Central

    Niu, Chengcheng; Wang, Long; Wang, Zhigang; Xu, Yan; Hu, Yihe; Peng, Qinghai

    2017-01-01

    Perfluorocarbon (PFC) droplets were studied as new generation ultrasound contrast agents via acoustic or optical droplet vaporization (ADV or ODV). Little is known about the ODV irradiated vaporization mechanisms of PFC-microparticle complexs and the stability of the new bubbles produced. In this study, fluorescent perfluorohexane (PFH) poly(lactic-co-glycolic acid) (PLGA) particles were used as a model to study the process of particle vaporization and bubble stability following excitation in two-dimensional (2-D) and three-dimensional (3-D) cell models. We observed localization of the fluorescent agent on the microparticle coating material initially and after vaporization under fluorescence microscopy. Furthermore, the stability and growth dynamics of the newly created bubbles were observed for 11 min following vaporization. The particles were co-cultured with 2-D cells to form 3-D spheroids and could be vaporized even when encapsulated within the spheroids via laser irradiation, which provides an effective basis for further work. PMID:28262671

  13. A Bio-Inspired Approach to Task Assignment of Swarm Robots in 3-D Dynamic Environments.

    PubMed

    Xin Yi; Anmin Zhu; Yang, Simon X; Chaomin Luo

    2017-04-01

    Intending to mimic the operating mechanism of biological neural systems, a self organizing map-based approach to task assignment of a swarm of robots in 3-D dynamic environments is proposed in this paper. This approach integrates the advantages and characteristics of biological neural systems. It is capable of dynamically planning the paths of a swarm of robots in 3-D environments under uncertain situations, such as when some robots are presented in or broken down or when more than one robot is needed for some special task locations. A Bezier path optimizing algorithm and a parameter adjusting algorithm are integrated in this paper. It is capable of reducing the complexity of the robot navigation control and limiting the number of convergence iterations. The simulation results with different environments demonstrate the effectiveness of the proposed approach.

  14. Supply-demand 3D dynamic model in water resources evaluation: taking Lebanon as an example

    NASA Astrophysics Data System (ADS)

    Fang, Hong; Hou, Zhimin

    2017-05-01

    In this paper, supply-demand 3D dynamic model is adopted to create a measurement of a region’s capacity to provide available water to meet the needs of its population. First of all, we draw a diagram between supply and demand. Then taking the main dynamic factors into account, we establish an index to evaluate the balance of supply and demand. The three dimension vector reflects the scarcity of industrial, agricultural and residential water. Lebanon is chosen as the object of case study, and we do quantitative analysis of its current situation. After data collecting and processing, we calculate the 3D vector in 2012, which reveals that agriculture is susceptible to water scarcity. Water resources of Lebanon are “physical rich” but “economic scarcity” according to the correlation chart and other statistical analysis.

  15. Dynamic 3D shape measurement based on digital speckle projection and temporal sequence correlation

    NASA Astrophysics Data System (ADS)

    Xu, Renchao; Zhou, Fangyan; Zhang, Qican

    2016-11-01

    Based on digital speckle temporal sequence correlation and speckle projection, an experimental platform was developed to measure the dynamic 3D shape measurement in this paper. Speckle patterns generated by computer were projected onto the quartz clock surface by a white-light projector, and the deformed speckle patterns were acquired by a camera. Programming was written to implement the algorithm to reconstruct every motion of the running clock's pointers. Beyond that, a simple Newton's cradle was established, and the collision course between three steel balls was reconstructed. These experimental results show that the method can be used for dynamic 3D shape measurement, which has an effect on the reconstruction of objects with characteristics of steep variation, isolation and small details.

  16. A Bio-Inspired Approach to Task Assignment of Swarm Robots in 3-D Dynamic Environments.

    PubMed

    Yi, Xin; Zhu, Anmin; Yang, Simon X; Luo, Chaomin

    2016-03-15

    Intending to mimic the operating mechanism of biological neural systems, a self organizing map-based approach to task assignment of a swarm of robots in 3-D dynamic environments is proposed in this paper. This approach integrates the advantages and characteristics of biological neural systems. It is capable of dynamically planning the paths of a swarm of robots in 3-D environments under uncertain situations, such as when some robots are presented in or broken down or when more than one robot is needed for some special task locations. A Bezier path optimizing algorithm and a parameter adjusting algorithm are integrated in this paper. It is capable of reducing the complexity of the robot navigation control and limiting the number of convergence iterations. The simulation results with different environments demonstrate the effectiveness of the proposed approach.

  17. The use of catalytic carbon deposits as 3D carriers for human bone marrow stromal cells.

    PubMed

    Petrenko, Yu A; Gurin, I V; Volkova, N A; Mazur, S P; Sandomirskii, B P

    2011-08-01

    We studied the possibility of using 3D structures based on carbon catalytic deposits as carriers for human bone marrow stromal cells. It was found that carbon catalytic deposits obtained by gas deposition method using FeCl(3) × 6H(2)O as the catalyst are a biocompatible material for human bone marrow stromal cells promoting adhesion, proliferation, and distribution of cells within the 3D carrier, and therefore can be used for tissue engineering.

  18. N-cadherin as a key regulator of collective cell migration in a 3D environment.

    PubMed

    Shih, Wenting; Yamada, Soichiro

    2012-01-01

    Cell migration is a critical step of normal developmental processes and disease progression. Often, migrating cells interact and maintain contact with neighboring cells. However, the precise roles of cell-cell adhesion in cell migration have thus far been poorly defined. Often in aggressive cancers, N-cadherin is prominently upregulated, yet, these highly motile cells have limited cell-cell adhesion when plated on a stiff 2D substrate. But, the same cells in a 3D matrix migrate as a multicellular cluster. This new observation suggests that N-cadherin-mediated cell-cell adhesion supports cell interactions between migrating cells in a more physiologically relevant 3D matrix, but not on a 2D substrate. While N-cadherin is an integral part of neural synapses, the ectopic expression of N-cadherin in transformed epithelial cells plays an equally important part in initiating pro-migratory signaling, and providing strong yet flexible cell cohesion essential for persistent cell migration in a 3D matrix. The 3D cell migration analysis for studying cell-to-cell interactions exposes the roles of N-cadherin in multicellular migration, and reveals novel insights into cell migration-dependent normal and pathological processes.

  19. Nonpolarized signaling reveals two distinct modes of 3D cell migration

    PubMed Central

    Gavara, Núria; Chadwick, Richard S.

    2012-01-01

    We search in this paper for context-specific modes of three-dimensional (3D) cell migration using imaging for phosphatidylinositol (3,4,5)-trisphosphate (PIP3) and active Rac1 and Cdc42 in primary fibroblasts migrating within different 3D environments. In 3D collagen, PIP3 and active Rac1 and Cdc42 were targeted to the leading edge, consistent with lamellipodia-based migration. In contrast, elongated cells migrating inside dermal explants and the cell-derived matrix (CDM) formed blunt, cylindrical protrusions, termed lobopodia, and Rac1, Cdc42, and PIP3 signaling was nonpolarized. Reducing RhoA, Rho-associated protein kinase (ROCK), or myosin II activity switched the cells to lamellipodia-based 3D migration. These modes of 3D migration were regulated by matrix physical properties. Specifically, experimentally modifying the elasticity of the CDM or collagen gels established that nonlinear elasticity supported lamellipodia-based migration, whereas linear elasticity switched cells to lobopodia-based migration. Thus, the relative polarization of intracellular signaling identifies two distinct modes of 3D cell migration governed intrinsically by RhoA, ROCK, and myosin II and extrinsically by the elastic behavior of the 3D extracellular matrix. PMID:22547408

  20. Design of 3D printed insert for hanging culture of Caco-2 cells.

    PubMed

    Shen, Chong; Meng, Qin; Zhang, Guoliang

    2014-12-17

    A Caco-2 cell culture on Transwell, an alternative testing to animal or human testing used in evaluating drug intestinal permeability, incorrectly estimated the absorption of actively transported drugs due to the low expression of membrane transporters. Similarly, three-dimensional (3D) cultures of Caco-2 cells, which have been recommended to be more physiological relevant, were not superior to the Transwell culture in either accuracy or convenience in drug permeability testing. Using rapid 3D printing prototyping techniques, this study proposed a hanging culture of Caco-2 cells that performed with high accuracy in predicting drug permeability in humans. As found, hanging cultured Caco-2 cells formed a confluent monolayer and maintained high cell viability on the 3D printed insert. Compared with the normal culture on Transwell, the Caco-2 cells on the 3D printed insert presented ∼30-100% higher brush border enzyme activity and ∼2-7 folds higher activity of P-glycoprotein/multidrug resistance-associated protein 2 during 21 days of incubation. For the eight membrane transporter substrates, the predictive curve of the 3D printing culture exhibited better linearity (R(2) = 0.92) to the human oral adsorption than that of the Transwell culture (R(2) = 0.84), indicating better prediction by the 3D printing culture. In this regard, the 3D printed insert for hanging culture could be potentially developed as a convenient and low-cost tool for testing drug oral absorption.

  1. Nonpolarized signaling reveals two distinct modes of 3D cell migration.

    PubMed

    Petrie, Ryan J; Gavara, Núria; Chadwick, Richard S; Yamada, Kenneth M

    2012-04-30

    We search in this paper for context-specific modes of three-dimensional (3D) cell migration using imaging for phosphatidylinositol (3,4,5)-trisphosphate (PIP3) and active Rac1 and Cdc42 in primary fibroblasts migrating within different 3D environments. In 3D collagen, PIP3 and active Rac1 and Cdc42 were targeted to the leading edge, consistent with lamellipodia-based migration. In contrast, elongated cells migrating inside dermal explants and the cell-derived matrix (CDM) formed blunt, cylindrical protrusions, termed lobopodia, and Rac1, Cdc42, and PIP3 signaling was nonpolarized. Reducing RhoA, Rho-associated protein kinase (ROCK), or myosin II activity switched the cells to lamellipodia-based 3D migration. These modes of 3D migration were regulated by matrix physical properties. Specifically, experimentally modifying the elasticity of the CDM or collagen gels established that nonlinear elasticity supported lamellipodia-based migration, whereas linear elasticity switched cells to lobopodia-based migration. Thus, the relative polarization of intracellular signaling identifies two distinct modes of 3D cell migration governed intrinsically by RhoA, ROCK, and myosin II and extrinsically by the elastic behavior of the 3D extracellular matrix.

  2. Real-Time Modeling and 3D Visualization of Source Dynamics and Connectivity Using Wearable EEG

    PubMed Central

    Mullen, Tim; Kothe, Christian; Chi, Yu Mike; Ojeda, Alejandro; Kerth, Trevor; Makeig, Scott; Cauwenberghs, Gert; Jung, Tzyy-Ping

    2014-01-01

    This report summarizes our recent efforts to deliver real-time data extraction, preprocessing, artifact rejection, source reconstruction, multivariate dynamical system analysis (including spectral Granger causality) and 3D visualization as well as classification within the open-source SIFT and BCILAB toolboxes. We report the application of such a pipeline to simulated data and real EEG data obtained from a novel wearable high-density (64-channel) dry EEG system. PMID:24110155

  3. Improving segmentation of 3D touching cell nuclei using flow tracking on surface meshes.

    PubMed

    Li, Gang; Guo, Lei

    2012-01-01

    Automatic segmentation of touching cell nuclei in 3D microscopy images is of great importance in bioimage informatics and computational biology. This paper presents a novel method for improving 3D touching cell nuclei segmentation. Given binary touching nuclei by the method in Li et al. (2007), our method herein consists of several steps: surface mesh reconstruction and curvature information estimation; direction field diffusion on surface meshes; flow tracking on surface meshes; and projection of surface mesh segmentation to volumetric images. The method is validated on both synthesised and real 3D touching cell nuclei images, demonstrating its validity and effectiveness.

  4. Melanoma cells undergo aggressive coalescence in a 3D Matrigel model that is repressed by anti-CD44

    PubMed Central

    Voss, Edward; Kuhl, Spencer; Buchele, Emma C.; Klemme, Michael R.; Russell, Kanoe B.; Ambrose, Joseph; Soll, Benjamin A.; Bossler, Aaron; Milhem, Mohammed; Goldman, Charles

    2017-01-01

    Using unique computer-assisted 3D reconstruction software, it was previously demonstrated that tumorigenic cell lines derived from breast tumors, when seeded in a 3D Matrigel model, grew as clonal aggregates which, after approximately 100 hours, underwent coalescence mediated by specialized cells, eventually forming a highly structured large spheroid. Non-tumorigenic cells did not undergo coalescence. Because histological sections of melanomas forming in patients suggest that melanoma cells migrate and coalesce to form tumors, we tested whether they also underwent coalescence in a 3D Matrigel model. Melanoma cells exiting fragments of three independent melanomas or from secondary cultures derived from them, and cells from the melanoma line HTB-66, all underwent coalescence mediated by specialized cells in the 3D model. Normal melanocytes did not. However, coalescence of melanoma cells differed from that of breast-derived tumorigenic cell lines in that they 1) coalesced immediately, 2) underwent coalescence as individual cells as well as aggregates, 3) underwent coalescence far faster and 4) ultimately formed long, flat, fenestrated aggregates that were extremely dynamic. A screen of 51 purified monoclonal antibodies (mAbs) targeting cell surface-associated molecules revealed that two mAbs, anti-beta 1 integrin/(CD29) and anti-CD44, blocked melanoma cell coalescence. They also blocked coalescence of tumorigenic cells derived from a breast tumor. These results add weight to the commonality of coalescence as a characteristic of tumorigenic cells, as well as the usefulness of the 3D Matrigel model and software for both investigating the mechanisms regulating tumorigenesis and screening for potential anti-tumorigenesis mAbs. PMID:28264026

  5. Melanoma cells undergo aggressive coalescence in a 3D Matrigel model that is repressed by anti-CD44.

    PubMed

    Wessels, Deborah; Lusche, Daniel F; Voss, Edward; Kuhl, Spencer; Buchele, Emma C; Klemme, Michael R; Russell, Kanoe B; Ambrose, Joseph; Soll, Benjamin A; Bossler, Aaron; Milhem, Mohammed; Goldman, Charles; Soll, David R

    2017-01-01

    Using unique computer-assisted 3D reconstruction software, it was previously demonstrated that tumorigenic cell lines derived from breast tumors, when seeded in a 3D Matrigel model, grew as clonal aggregates which, after approximately 100 hours, underwent coalescence mediated by specialized cells, eventually forming a highly structured large spheroid. Non-tumorigenic cells did not undergo coalescence. Because histological sections of melanomas forming in patients suggest that melanoma cells migrate and coalesce to form tumors, we tested whether they also underwent coalescence in a 3D Matrigel model. Melanoma cells exiting fragments of three independent melanomas or from secondary cultures derived from them, and cells from the melanoma line HTB-66, all underwent coalescence mediated by specialized cells in the 3D model. Normal melanocytes did not. However, coalescence of melanoma cells differed from that of breast-derived tumorigenic cell lines in that they 1) coalesced immediately, 2) underwent coalescence as individual cells as well as aggregates, 3) underwent coalescence far faster and 4) ultimately formed long, flat, fenestrated aggregates that were extremely dynamic. A screen of 51 purified monoclonal antibodies (mAbs) targeting cell surface-associated molecules revealed that two mAbs, anti-beta 1 integrin/(CD29) and anti-CD44, blocked melanoma cell coalescence. They also blocked coalescence of tumorigenic cells derived from a breast tumor. These results add weight to the commonality of coalescence as a characteristic of tumorigenic cells, as well as the usefulness of the 3D Matrigel model and software for both investigating the mechanisms regulating tumorigenesis and screening for potential anti-tumorigenesis mAbs.

  6. RV functional imaging: 3-D echo-derived dynamic geometry and flow field simulations.

    PubMed

    Pasipoularides, Ares D; Shu, Ming; Womack, Michael S; Shah, Ashish; Von Ramm, Olaf; Glower, Donald D

    2003-01-01

    We describe a novel functional imaging approach for quantitative analysis of right ventricular (RV) blood flow patterns in specific experimental animals (or humans) using real-time, three-dimensional (3-D) echocardiography (RT3D). The method is independent of the digital imaging modality used. It comprises three parts. First, a semiautomated segmentation aided by intraluminal contrast medium locates the RV endocardial surface. Second, a geometric scheme for dynamic RV chamber reconstruction applies a time interpolation procedure to the RT3D data to quantify wall geometry and motion at 400 Hz. A volumetric prism method validated the dynamic geometric reconstruction against simultaneous sonomicrometric canine measurements. Finally, the RV endocardial border motion information is used for mesh generation on a computational fluid dynamics solver to simulate development of the early RV diastolic inflow field. Boundary conditions (tessellated endocardial surface nodal velocities) for the solver are directly derived from the endocardial geometry and motion information. The new functional imaging approach may yield important kinematic information on the distribution of instantaneous velocities in the RV diastolic flow field of specific normal or diseased hearts.

  7. Dynamical D4-D8 and D3-D7 branes in supergravity

    SciTech Connect

    Binetruy, Pierre; Sasaki, Misao; Uzawa, Kunihito

    2009-07-15

    We present a class of dynamical solutions for intersecting D4-D8 and D3-D7 brane systems in ten-dimensional type IIA and IIB supergravity. We discuss if these solutions can be recovered in lower-dimensional effective theories for the warped compactification of a general p-brane system. It is found that an effective p+1-dimensional description is not possible in general due to the entanglement of the transverse coordinates and the p+1-dimensional coordinates in the metric components. For the D4-D8 brane system, the dynamical solutions reduces to a static warped AdS{sub 6}xS{sup 4} geometry in a certain spacetime region. For the D3-D7 brane system, we find a dynamical solution whose metric form is similar to that of a D3-brane solution. The main difference is the existence of a nontrivial dilaton configuration in the D3-D7 solution. Then we discuss cosmology of these solutions. We find that they behave like a Kasner-type cosmological solution at {tau}{yields}{infinity}, while it reduces to a warped static solution at {tau}{yields}0, where {tau} is the cosmic time.

  8. Automatic detection of endothelial cells in 3D angiogenic sprouts from experimental phase contrast images

    NASA Astrophysics Data System (ADS)

    Wang, MengMeng; Ong, Lee-Ling Sharon; Dauwels, Justin; Asada, H. Harry

    2015-03-01

    Cell migration studies in 3D environments become more popular, as cell behaviors in 3D are more similar to the behaviors of cells in a living organism (in vivo). We focus on the 3D angiogenic sprouting in microfluidic devices, where Endothelial Cells (ECs) burrow into the gel matrix and form solid lumen vessels. Phase contrast microscopy is used for long-term observation of the unlabeled ECs in the 3D microfluidic devices. Two template matching based approaches are proposed to automatically detect the unlabeled ECs in the angiogenic sprouts from the acquired experimental phase contrast images. Cell and non-cell templates are obtained from these phase contrast images as the training data. The first approach applies Partial Least Square Regression (PLSR) to find the discriminative features and their corresponding weight to distinguish cells and non-cells, whereas the second approach relies on Principal Component Analysis (PCA) to reduce the template feature dimension and Support Vector Machine (SVM) to find their corresponding weight. Through a sliding window manner, the cells in the test images are detected. We then validate the detection accuracy by comparing the results with the same images acquired with a confocal microscope after cells are fixed and their nuclei are stained. More accurate numerical results are obtained for approach I (PLSR) compared to approach II (PCA & SVM) for cell detection. Automatic cell detection will aid in the understanding of cell migration in 3D environment and in turn result in a better understanding of angiogenesis.

  9. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    SciTech Connect

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A.; Zadoks, R.I.

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  10. Characteristics of tumor and host cells in 3-D simulated microgravity environment

    NASA Astrophysics Data System (ADS)

    Chopra, V.; Dinh, T.; Wood, T.; Pellis, N.; Hannigan, E.

    Co-cultures of three-dimensional (3-D) constructs of one cell type with dispersed cells of a second cell type in low-shear rotating suspension cultures in simulated microgravity environment have been used to investigate invasive properties of normal and malignant cell types. We have shown that the epithelial and endothelial cells undergo a switch in characteristics when grown in an in vitro 3-D environment, that mimics the in vivo host environment as compared with conventional two-dimensional (2-D) monolayer cultures. Histological preparations and immunohistochemical staining procedures of cocultured harvests demonstrated various markers of interest: like collagen vimentin, mucin, elastin, fibrin, fibrinogen, cytokeratin, adhesion molecules and various angiogenic factors by tumor cells from gynecological cancer patients along with fibroblasts, endothelial cells and patient-derived mononuclear cells (n=8). The growth rate was enhanced 10-15 folds by 3-D cocultures of patient-derived cells as compared with 2-D monolayer cultures and 3-D monocultures. The production of interleukin-2, interleukin-6, interleukin -8, vascular endothelial cell growth factor, basic fibroblast growth factor, and angiogenin was studied by using ELISA and RT- PCR. Human umbilical vein-derived endothelial cell (HUVEC) were used to study the mitogenic response of the conditioned medium collected from 3-D monocultures and cocultures during proliferation and migration assays. The conditioned medium collected from 3-D cocultures of cancer cells also 1) increased the expression of message levels of vascular endothelial growth factor and its receptor flt-1 and KDR was observed by HUVEC, and 2) increased the expression of intracellular and vascular cell adhesion molecules on the surface of HUVEC, when measured by using Live cell ELISA assays and immunofluorescent staining as compared with 3-D monocultures of normal epithelial cells. There was an increase in production of 1) enzymatic activity that

  11. Micro-well arrays for 3D shape control and high resolution analysis of single cells.

    PubMed

    Ochsner, Mirjam; Dusseiller, Marc R; Grandin, H Michelle; Luna-Morris, Sheila; Textor, Marcus; Vogel, Viola; Smith, Michael L

    2007-08-01

    In addition to rigidity, matrix composition, and cell shape, dimensionality is now considered an important property of the cell microenvironment which directs cell behavior. However, available tools for cell culture in two-dimensional (2D) versus three-dimensional (3D) environments are difficult to compare, and no tools exist which provide 3D shape control of single cells. We developed polydimethylsiloxane (PDMS) substrates for the culture of single cells in 3D arrays which are compatible with high-resolution microscopy. Cell adhesion was limited to within microwells by passivation of the flat upper surface through 'wet-printing' of a non-fouling polymer and backfilling of the wells with specific adhesive proteins or lipid bilayers. Endothelial cells constrained within microwells were viable, and intracellular features could be imaged with high resolution objectives. Finally, phalloidin staining of actin stress fibers showed that the cytoskeleton of cells in microwells was 3D and not limited to the cell-substrate interface. Thus, microwells can be used to produce microenvironments for large numbers of single cells with 3D shape control and can be added to a repertoire of tools which are ever more sought after for both fundamental biological studies as well as high throughput cell screening assays.

  12. 3D cell-printing of large-volume tissues: Application to ear regeneration.

    PubMed

    Lee, Jung-Seob; Kim, Byung Soo; Seo, Dong Hwan; Park, Jeong Hun; Cho, Dong-Woo

    2017-01-17

    The three-dimensional (3D) printing of large-volume cells, printed in a clinically relevant size, is one of the most important challenges in the field of tissue engineering. However, few studies have reported the fabrication of large-volume cell-printed constructs (LCCs). To create LCCs, appropriate fabrication conditions should be established: factors involved include fabrication time, residence time, and temperature control of the cell-laden hydrogel in the syringe to ensure high cell viability and functionality. The prolonged time required for 3D printing of LCCs can reduce cell viability and result in insufficient functionality of the construct, because the cells are exposed to a harsh environment during the printing process. In this regard, we present an advanced 3D cell-printing system composed of a clean air workstation, humidifier, and Peltier system, which provides a suitable printing environment for production of LCCs with high cell viability. We confirmed that the advanced 3D cell-printing system was capable of providing enhanced printability of hydrogels and fabricating an ear-shaped LCC with high cell viability. In vivo results for the ear-shaped LCC also showed that printed chondrocytes proliferated sufficiently and differentiated into cartilage tissue. Thus, we conclude that the advanced 3D cell-printing system is a versatile tool to create cell-printed constructs for the generation of large-volume tissues.

  13. Dynamic WIFI-Based Indoor Positioning in 3D Virtual World

    NASA Astrophysics Data System (ADS)

    Chan, S.; Sohn, G.; Wang, L.; Lee, W.

    2013-11-01

    A web-based system based on the 3DTown project was proposed using Google Earth plug-in that brings information from indoor positioning devices and real-time sensors into an integrated 3D indoor and outdoor virtual world to visualize the dynamics of urban life within the 3D context of a city. We addressed limitation of the 3DTown project with particular emphasis on video surveillance camera used for indoor tracking purposes. The proposed solution was to utilize wireless local area network (WLAN) WiFi as a replacement technology for localizing objects of interest due to the wide spread availability and large coverage area of WiFi in indoor building spaces. Indoor positioning was performed using WiFi without modifying existing building infrastructure or introducing additional access points (AP)s. A hybrid probabilistic approach was used for indoor positioning based on previously recorded WiFi fingerprint database in the Petrie Science and Engineering building at York University. In addition, we have developed a 3D building modeling module that allows for efficient reconstruction of outdoor building models to be integrated with indoor building models; a sensor module for receiving, distributing, and visualizing real-time sensor data; and a web-based visualization module for users to explore the dynamic urban life in a virtual world. In order to solve the problems in the implementation of the proposed system, we introduce approaches for integration of indoor building models with indoor positioning data, as well as real-time sensor information and visualization on the web-based system. In this paper we report the preliminary results of our prototype system, demonstrating the system's capability for implementing a dynamic 3D indoor and outdoor virtual world that is composed of discrete modules connected through pre-determined communication protocols.

  14. Real-Time Cell Cycle Imaging in a 3D Cell Culture Model of Melanoma.

    PubMed

    Spoerri, Loredana; Beaumont, Kimberley A; Anfosso, Andrea; Haass, Nikolas K

    2017-01-01

    Aberrant cell cycle progression is a hallmark of solid tumors; therefore, cell cycle analysis is an invaluable technique to study cancer cell biology. However, cell cycle progression has been most commonly assessed by methods that are limited to temporal snapshots or that lack spatial information. Here, we describe a technique that allows spatiotemporal real-time tracking of cell cycle progression of individual cells in a multicellular context. The power of this system lies in the use of 3D melanoma spheroids generated from melanoma cells engineered with the fluorescent ubiquitination-based cell cycle indicator (FUCCI). This technique allows us to gain further and more detailed insight into several relevant aspects of solid cancer cell biology, such as tumor growth, proliferation, invasion, and drug sensitivity.

  15. A 3D microfluidic model for preclinical evaluation of TCR-engineered T cells against solid tumors

    PubMed Central

    Tan, Anthony T.; Koh, Sarene; Chia, Adeline; Colombo, Marta; Antonecchia, Emanuele; Miccolis, Carlo; Raimondi, Manuela T.; Kamm, Roger D.

    2017-01-01

    The tumor microenvironment imposes physical and functional constraints on the antitumor efficacy of adoptive T cell immunotherapy. Preclinical testing of different T cell preparations can help in the selection of efficient immune therapies, but in vivo models are expensive and cumbersome to develop, while classical in vitro 2D models cannot recapitulate the spatiotemporal dynamics experienced by T cells targeting cancer. Here, we describe an easily customizable 3D model, in which the tumor microenvironment conditions are modulated and the functionality of different T cell preparations is tested. We incorporate human cancer hepatocytes as a single cell or as tumor cell aggregates in a 3D collagen gel region of a microfluidic device. Human T cells engineered to express tumor-specific T cell receptors (TCR–T cells) are then added in adjacent channels. The TCR–T cells’ ability to migrate and kill the tumor target and the profile of soluble factors were investigated under conditions of varying oxygen levels and in the presence of inflammatory cytokines. We show that only the 3D model detects the effect that oxygen levels and the inflammatory environment impose on engineered TCR–T cell function, and we also used the 3D microdevice to analyze the TCR–T cell efficacy in an immunosuppressive scenario. Hence, we show that our microdevice platform enables us to decipher the factors that can alter T cell function in 3D and can serve as a preclinical assay to tailor the most efficient immunotherapy configuration for a specific therapeutic goal. PMID:28614795

  16. Parallel 3D Finite Element Particle-in-Cell Simulations with Pic3P

    SciTech Connect

    Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; Ko, K.; Ben-Zvi, I.; Kewisch, J.; /Brookhaven

    2009-06-19

    SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic Particle-In-Cell code Pic3P. Designed for simulations of beam-cavity interactions dominated by space charge effects, Pic3P solves the complete set of Maxwell-Lorentz equations self-consistently and includes space-charge, retardation and boundary effects from first principles. Higher-order Finite Element methods with adaptive refinement on conformal unstructured meshes lead to highly efficient use of computational resources. Massively parallel processing with dynamic load balancing enables large-scale modeling of photoinjectors with unprecedented accuracy, aiding the design and operation of next-generation accelerator facilities. Applications include the LCLS RF gun and the BNL polarized SRF gun.

  17. Quantitative Proteomic and Phosphoproteomic Comparison of 2D and 3D Colon Cancer Cell Culture Models.

    PubMed

    Yue, Xiaoshan; Lukowski, Jessica K; Weaver, Eric M; Skube, Susan B; Hummon, Amanda B

    2016-12-02

    Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined, and notable differences in both the proteome and the phosphoproteome were determined by nanoliquid chromatography tandem mass spectrometry (LC-MS/MS) to assess how growth configuration affects molecular expression. A total of 5867 protein groups, including 2523 phosphoprotein groups and 8733 phosphopeptides were identified in the samples. The Gene Ontology analysis revealed enriched GO terms in the 3D samples for RNA binding, nucleic acid binding, enzyme binding, cytoskeletal protein binding, and histone binding for their molecular functions (MF) and in the process of cell cycle, cytoskeleton organization, and DNA metabolic process for the biological process (BP). The KEGG pathway analysis indicated that 3D cultures are enriched for oxidative phosphorylation pathways, metabolic pathways, peroxisome pathways, and biosynthesis of amino acids. In contrast, analysis of the phosphoproteomes indicated that 3D cultures have decreased phosphorylation correlating with slower growth rates and lower cell-to-extracellular matrix interactions. In sum, these results provide quantitative assessments of the effects on the proteome and phosphoproteome of culturing cells in 2D versus 3D cell culture configurations.

  18. BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models

    PubMed Central

    Bilgin, Cemal Cagatay; Fontenay, Gerald; Cheng, Qingsu; Chang, Hang; Han, Ju; Parvin, Bahram

    2016-01-01

    BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation. PMID:26978075

  19. BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models.

    PubMed

    Bilgin, Cemal Cagatay; Fontenay, Gerald; Cheng, Qingsu; Chang, Hang; Han, Ju; Parvin, Bahram

    2016-01-01

    BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation.

  20. Migration of bone marrow stromal cells in 3D: 4 color methodology reveals spatially and temporally coordinated events.

    PubMed

    Thibault, Marc M; Buschmann, Michael D

    2006-12-01

    The cytoskeleton plays a central role in many cell processes including directed cell migration. Since most previous work has investigated cell migration in two dimensions (2D), new methods are required to study movement in three dimensions (3D) while preserving 3D structure of the cytoskeleton. Most previous studies have labeled two cytoskeletal networks simultaneously, impeding an appreciation of their complex and dynamic interconnections. Here we report the development of a 4 color method to simultaneously image vimentin, actin, tubulin and the nucleus for high-resolution confocal microscopy of bone-marrow stromal cells (BMSCs) migrating through a porous membrane. Several methods were tested for structural preservation and labeling intensity resulting in identification of an optimized simultaneous fixation and permeabilization method using glutaraldehyde, paraformaldehyde and Triton X-100 followed by a quadruple fluorescent labeling method. This procedure was then applied at a sequence of time points to migrating cells, allowing temporal progression of migration to be assessed by visualizing all three networks plus the nucleus, providing new insights into 3D directed cell migration including processes such as leading edge structure, cytoskeletal distribution and nucleokinesis. Colocalization of actin and microtubules with distinct spatial arrangements at the cellular leading edge during migration, together with microtubule axial polarization supports recent reports indicating the pivotal role of microtubules in directed cell migration. This study also provides a foundation for 3D migration studies versus 2D studies, providing precise and robust methods to attain new insights into the cellular mechanisms of motility.

  1. 3D dosimetric validation of motion compensation concepts in radiotherapy using an anthropomorphic dynamic lung phantom

    NASA Astrophysics Data System (ADS)

    Mann, P.; Witte, M.; Moser, T.; Lang, C.; Runz, A.; Johnen, W.; Berger, M.; Biederer, J.; Karger, C. P.

    2017-01-01

    In this study, we developed a new setup for the validation of clinical workflows in adaptive radiation therapy, which combines a dynamic ex vivo porcine lung phantom and three-dimensional (3D) polymer gel dosimetry. The phantom consists of an artificial PMMA-thorax and contains a post mortem explanted porcine lung to which arbitrary breathing patterns can be applied. A lung tumor was simulated using the PAGAT (polyacrylamide gelatin gel fabricated at atmospheric conditions) dosimetry gel, which was evaluated in three dimensions by magnetic resonance imaging (MRI). To avoid bias by reaction with oxygen and other materials, the gel was collocated inside a BAREX™ container. For calibration purposes, the same containers with eight gel samples were irradiated with doses from 0 to 7 Gy. To test the technical feasibility of the system, a small spherical dose distribution located completely within the gel volume was planned. Dose delivery was performed under static and dynamic conditions of the phantom with and without motion compensation by beam gating. To verify clinical target definition and motion compensation concepts, the entire gel volume was homogeneously irradiated applying adequate margins in case of the static phantom and an additional internal target volume in case of dynamically operated phantom without and with gated beam delivery. MR-evaluation of the gel samples and comparison of the resulting 3D dose distribution with the planned dose distribution revealed a good agreement for the static phantom. In case of the dynamically operated phantom without motion compensation, agreement was very poor while additional application of motion compensation techniques restored the good agreement between measured and planned dose. From these experiments it was concluded that the set up with the dynamic and anthropomorphic lung phantom together with 3D-gel dosimetry provides a valuable and versatile tool for geometrical and dosimetrical validation of motion compensated

  2. 3D-VAS--initial results from computerized visualization of dynamic occlusion.

    PubMed

    Ruge, S; Kordass, B

    2008-01-01

    Visualization of the dynamic occlusion is one of the central tasks in both clinical dentistry and dental engineering. Many aspects of dynamic occlusion, such as the interocclusal function in the posterior region, cannot be seen directly clinically and at best can be recorded with contact paper. Therefore, analyses of the dynamic occlusion using mounted models in the articulator are unavoidable in many cases for reproduction of dynamic occlusion. However, the reproduction of dynamic occlusion in the mechanical articulator has clear restrictions inherent to the process, but also caused by biological variability. Virtual articulators can expediently supplement mechanical articulators, since with them it is possible to display in relation to time unusual and extraordinary perspectives, such as sectional images and flowing, sliding contact points. One of the latest developments in the field of virtual articulation is the 3D virtual articulation system module of the Zebris company, D-Isny. By means of a specially developed coupling tray, 3D-scanned rows of teeth can be matched with computerized motion recordings of mandibular function. The software displays the movements of the 3D-scanned rows of teeth not only with jaw motion but also with chewing motion--therefore movements under chewing pressure--in real time and facilitates special analytical methods transcending mechanical occlusion analysis in conventional articulators: This includes displays of the strength of the contact points and surfaces, the occurrence of the contact points in relation to time, sectional images of the dentition, analyses of the interocclusal gap in the occlusal region, etc. This software and its possibilities are described and explained by reference to individual cases.

  3. 3D dosimetric validation of motion compensation concepts in radiotherapy using an anthropomorphic dynamic lung phantom.

    PubMed

    Mann, P; Witte, M; Moser, T; Lang, C; Runz, A; Johnen, W; Berger, M; Biederer, J; Karger, C P

    2017-01-21

    In this study, we developed a new setup for the validation of clinical workflows in adaptive radiation therapy, which combines a dynamic ex vivo porcine lung phantom and three-dimensional (3D) polymer gel dosimetry. The phantom consists of an artificial PMMA-thorax and contains a post mortem explanted porcine lung to which arbitrary breathing patterns can be applied. A lung tumor was simulated using the PAGAT (polyacrylamide gelatin gel fabricated at atmospheric conditions) dosimetry gel, which was evaluated in three dimensions by magnetic resonance imaging (MRI). To avoid bias by reaction with oxygen and other materials, the gel was collocated inside a BAREX(™) container. For calibration purposes, the same containers with eight gel samples were irradiated with doses from 0 to 7 Gy. To test the technical feasibility of the system, a small spherical dose distribution located completely within the gel volume was planned. Dose delivery was performed under static and dynamic conditions of the phantom with and without motion compensation by beam gating. To verify clinical target definition and motion compensation concepts, the entire gel volume was homogeneously irradiated applying adequate margins in case of the static phantom and an additional internal target volume in case of dynamically operated phantom without and with gated beam delivery. MR-evaluation of the gel samples and comparison of the resulting 3D dose distribution with the planned dose distribution revealed a good agreement for the static phantom. In case of the dynamically operated phantom without motion compensation, agreement was very poor while additional application of motion compensation techniques restored the good agreement between measured and planned dose. From these experiments it was concluded that the set up with the dynamic and anthropomorphic lung phantom together with 3D-gel dosimetry provides a valuable and versatile tool for geometrical and dosimetrical validation of motion compensated

  4. The Natural and Engineered 3D Microenvironment as a Regulatory Cue During Stem Cell Fate Determination

    PubMed Central

    Lund, Amanda W.; Yener, Bülent; Stegemann, Jan P.

    2009-01-01

    The concept of using stem cells as self-renewing sources of healthy cells in regenerative medicine has existed for decades, but most applications have yet to achieve clinical success. A main reason for the lack of successful stem cell therapies is the difficulty in fully recreating the maintenance and control of the native stem cell niche. Improving the performance of transplanted stem cells therefore requires a better understanding of the cellular mechanisms guiding stem cell behavior in both native and engineered three-dimensional (3D) microenvironments. Most techniques, however, for uncovering mechanisms controlling cell behavior in vitro have been developed using 2D cell cultures and are of limited use in 3D environments such as engineered tissue constructs. Deciphering the mechanisms controlling stem cell fate in native and engineered 3D environments, therefore, requires rigorous quantitative techniques that permit mechanistic, hypothesis-driven studies of cell–microenvironment interactions. Here, we review the current understanding of 2D and 3D stem cell control mechanisms and propose an approach to uncovering the mechanisms that govern stem cell behavior in 3D. PMID:19505193

  5. Pico-projector-based optical sectioning microscopy for 3D chlorophyll fluorescence imaging of mesophyll cells

    NASA Astrophysics Data System (ADS)

    Chen, Szu-Yu; Hsu, Yu John; Yeh, Chia-Hua; Chen, S.-Wei; Chung, Chien-Han

    2015-03-01

    A pico-projector-based optical sectioning microscope (POSM) was constructed using a pico-projector to generate structured illumination patterns. A net rate of 5.8 × 106 pixel/s and sub-micron spatial resolution in three-dimensions (3D) were achieved. Based on the pico-projector’s flexibility in pattern generation, the characteristics of POSM with different modulation periods and at different imaging depths were measured and discussed. With the application of different modulation periods, 3D chlorophyll fluorescence imaging of mesophyll cells was carried out in freshly plucked leaves of four species without sectioning or staining. For each leaf, an average penetration depth of 120 μm was achieved. Increasing the modulation period along with the increment of imaging depth, optical sectioning images can be obtained with a compromise between the axial resolution and signal-to-noise ratio. After ∼30 min imaging on the same area, photodamage was hardly observed. Taking the advantages of high speed and low damages of POSM, the investigation of the dynamic fluorescence responses to temperature changes was performed under three different treatment temperatures. The three embedded blue, green and red light-emitting diode light sources were applied to observe the responses of the leaves with different wavelength excitation.

  6. TRICE - A program for reconstructing 3D reciprocal space and determining unit-cell parameters.

    PubMed

    Zou, X D Xiaodong; Hovmöller, Anders; Hovmöller, Sven

    2004-01-01

    A program system-Trice-for reconstructing the 3D reciprocal lattice from an electron diffraction tilt series is described. The unit-cell parameters can be determined from electron diffraction patterns directly by Trice. The unit cell can be checked and the lattice type and crystal system can be determined from the 3D reciprocal lattice. Trice can be applied to all crystal systems and lattice types.

  7. Examination of 1D Solar Cell Model Limitations Using 3D SPICE Modeling: Preprint

    SciTech Connect

    McMahon, W. E.; Olson, J. M.; Geisz, J. F.; Friedman, D. J.

    2012-06-01

    To examine the limitations of one-dimensional (1D) solar cell modeling, 3D SPICE-based modeling is used to examine in detail the validity of the 1D assumptions as a function of sheet resistance for a model cell. The internal voltages and current densities produced by this modeling give additional insight into the differences between the 1D and 3D models.

  8. How spatial abilities and dynamic visualizations interplay when learning functional anatomy with 3D anatomical models.

    PubMed

    Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

    2015-01-01

    The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material presentation formats, spatial abilities, and anatomical tasks. First, to understand the cognitive challenges a novice learner would be faced with when first exposed to 3D anatomical content, a six-step cognitive task analysis was developed. Following this, an experimental study was conducted to explore how presentation formats (dynamic vs. static visualizations) support learning of functional anatomy, and affect subsequent anatomical tasks derived from the cognitive task analysis. A second aim was to investigate the interplay between spatial abilities (spatial visualization and spatial relation) and presentation formats when the functional anatomy of a 3D scapula and the associated shoulder flexion movement are learned. Findings showed no main effect of the presentation formats on performances, but revealed the predictive influence of spatial visualization and spatial relation abilities on performance. However, an interesting interaction between presentation formats and spatial relation ability for a specific anatomical task was found. This result highlighted the influence of presentation formats when spatial abilities are involved as well as the differentiated influence of spatial abilities on anatomical tasks. © 2015 American Association of Anatomists.

  9. Dynamics of tokamak plasma surface current in 3D ideal MHD model

    NASA Astrophysics Data System (ADS)

    Galkin, Sergei A.; Svidzinski, V. A.; Zakharov, L. E.

    2013-10-01

    Interest in the surface current which can arise on perturbed sharp plasma vacuum interface in tokamaks was recently generated by a few papers (see and references therein). In dangerous disruption events with plasma-touching-wall scenarios, the surface current can be shared with the wall leading to the strong, damaging forces acting on the wall A relatively simple analytic definition of δ-function surface current proportional to a jump of tangential component of magnetic field nevertheless leads to a complex computational problem on the moving plasma-vacuum interface, requiring the incorporation of non-linear 3D plasma dynamics even in one-fluid ideal MHD. The Disruption Simulation Code (DSC), which had recently been developed in a fully 3D toroidal geometry with adaptation to the moving plasma boundary, is an appropriate tool for accurate self-consistent δfunction surface current calculation. Progress on the DSC-3D development will be presented. Self-consistent surface current calculation under non-linear dynamics of low m kink mode and VDE will be discussed. Work is supported by the US DOE SBIR grant #DE-SC0004487.

  10. Characterisation of dynamic couplings at lower limb residuum/socket interface using 3D motion capture.

    PubMed

    Tang, Jinghua; McGrath, Michael; Laszczak, Piotr; Jiang, Liudi; Bader, Dan L; Moser, David; Zahedi, Saeed

    2015-12-01

    Design and fitting of artificial limbs to lower limb amputees are largely based on the subjective judgement of the prosthetist. Understanding the science of three-dimensional (3D) dynamic coupling at the residuum/socket interface could potentially aid the design and fitting of the socket. A new method has been developed to characterise the 3D dynamic coupling at the residuum/socket interface using 3D motion capture based on a single case study of a trans-femoral amputee. The new model incorporated a Virtual Residuum Segment (VRS) and a Socket Segment (SS) which combined to form the residuum/socket interface. Angular and axial couplings between the two segments were subsequently determined. Results indicated a non-rigid angular coupling in excess of 10° in the quasi-sagittal plane and an axial coupling of between 21 and 35 mm. The corresponding angular couplings of less than 4° and 2° were estimated in the quasi-coronal and quasi-transverse plane, respectively. We propose that the combined experimental and analytical approach adopted in this case study could aid the iterative socket fitting process and could potentially lead to a new socket design.

  11. Optimization of a 3D Dynamic Culturing System for In Vitro Modeling of Frontotemporal Neurodegeneration-Relevant Pathologic Features

    PubMed Central

    Tunesi, Marta; Fusco, Federica; Fiordaliso, Fabio; Corbelli, Alessandro; Biella, Gloria; Raimondi, Manuela T.

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) is a severe neurodegenerative disorder that is diagnosed with increasing frequency in clinical setting. Currently, no therapy is available and in addition the molecular basis of the disease are far from being elucidated. Consequently, it is of pivotal importance to develop reliable and cost-effective in vitro models for basic research purposes and drug screening. To this respect, recent results in the field of Alzheimer’s disease have suggested that a tridimensional (3D) environment is an added value to better model key pathologic features of the disease. Here, we have tried to add complexity to the 3D cell culturing concept by using a microfluidic bioreactor, where cells are cultured under a continuous flow of medium, thus mimicking the interstitial fluid movement that actually perfuses the body tissues, including the brain. We have implemented this model using a neuronal-like cell line (SH-SY5Y), a widely exploited cell model for neurodegenerative disorders that shows some basic features relevant for FTLD modeling, such as the release of the FTLD-related protein progranulin (PRGN) in specific vesicles (exosomes). We have efficiently seeded the cells on 3D scaffolds, optimized a disease-relevant oxidative stress experiment (by targeting mitochondrial function that is one of the possible FTLD-involved pathological mechanisms) and evaluated cell metabolic activity in dynamic culture in comparison to static conditions, finding that SH-SY5Y cells cultured in 3D scaffold are susceptible to the oxidative damage triggered by a mitochondrial-targeting toxin (6-OHDA) and that the same cells cultured in dynamic conditions kept their basic capacity to secrete PRGN in exosomes once recovered from the bioreactor and plated in standard 2D conditions. We think that a further improvement of our microfluidic system may help in providing a full device where assessing basic FTLD-related features (including PRGN dynamic secretion) that may

  12. A pump-free microfluidic 3D perfusion platform for the efficient differentiation of human hepatocyte-like cells.

    PubMed

    Ong, Louis Jun Ye; Chong, Lor Huai; Jin, Lin; Singh, Pawan Kumar; Lee, Poh Seng; Yu, Hanry; Ananthanarayanan, Abhishek; Leo, Hwa Liang; Toh, Yi-Chin

    2017-10-01

    The practical application of microfluidic liver models for in vitro drug testing is partly hampered by their reliance on human primary hepatocytes, which are limited in number and have batch-to-batch variation. Human stem cell-derived hepatocytes offer an attractive alternative cell source, although their 3D differentiation and maturation in a microfluidic platform have not yet been demonstrated. We develop a pump-free microfluidic 3D perfusion platform to achieve long-term and efficient differentiation of human liver progenitor cells into hepatocyte-like cells (HLCs). The device contains a micropillar array to immobilize cells three-dimensionally in a central cell culture compartment flanked by two side perfusion channels. Constant pump-free medium perfusion is accomplished by controlling the differential heights of horizontally orientated inlet and outlet media reservoirs. Computational fluid dynamic simulation is used to estimate the hydrostatic pressure heads required to achieve different perfusion flow rates, which are experimentally validated by micro-particle image velocimetry, as well as viability and functional assessments in a primary rat hepatocyte model. We perform on-chip differentiation of HepaRG, a human bipotent progenitor cell, and discover that 3D microperfusion greatly enhances the hepatocyte differentiation efficiency over static 2D and 3D cultures. However, HepaRG progenitor cells are highly sensitive to the time-point at which microperfusion is applied. Isolated HepaRG cells that are primed as static 3D spheroids before being subjected to microperfusion yield a significantly higher proportion of HLCs (92%) than direct microperfusion of isolated HepaRG cells (62%). This platform potentially offers a simple and efficient means to develop highly functional microfluidic liver models incorporating human stem cell-derived HLCs. Biotechnol. Bioeng. 2017;114: 2360-2370. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. Effects of 1D and 3D Thermal Radiation on Cloud Dynamics and Microphysics

    NASA Astrophysics Data System (ADS)

    Klinger, C.; Mayer, B. C.; Jakub, F.; Zinner, T.

    2016-12-01

    Radiation is a key driver for the development of clouds. Solar radiation heats the surface and causes updrafts to rise, thus initializing cloud formation. In the very moment that a cloud forms, absorption and emission of thermal radiation at the cloud itself cause heating and cooling rates of several hundred K/d at the interface between cloud and cloudless sky. The magnitude of the cooling rates, compared to the commonly known clear sky cooling of 1-2 K/d, can alter cloud dynamics and microphysics and thus cloud development or lifetime. In cloud resolving numerical simulations, radiation is, if considered at all, usually applied as a 1D approximation, omitting horizontal transport of radiation through the modeling domain. However, it is obvious that radiation is a three dimensional problem. Applying 3D radiative transfer in cloud resolving simulations causes, in addition to cloud top cooling and cloud bottom warming, an additional cooling at cloud sides which is completely neglected by common 1D radiative transfer solutions. Here, we examine the effects of 1D and 3D thermal radiative transfer in cloud resolving simulation, by applying the newly developed "Neighboring Column Approximation" (NCA) - a fast 3D approximation for thermal radiative transfer in cloud resolving simulations. The NCA accurately represents 3D effects at moderate computational cost which make it an ideal tool to explore how 1D and 3D radiative transfer modify cloud development in numerical models. Thermal radiation can modify clouds in terms of cloud lifetime, cloud size and cloud circulation. These effects on cloud development will be analyzed in a set of cumulus cloud simulations.

  14. Development of a 3D cell printed construct considering angiogenesis for liver tissue engineering.

    PubMed

    Lee, Jin Woo; Choi, Yeong-Jin; Yong, Woon-Jae; Pati, Falguni; Shim, Jin-Hyung; Kang, Kyung Shin; Kang, In-Hye; Park, Jaesung; Cho, Dong-Woo

    2016-01-12

    Several studies have focused on the regeneration of liver tissue in a two-dimensional (2D) planar environment, whereas actual liver tissue is three-dimensional (3D). Cell printing technology has been successfully utilized for building 3D structures; however, the poor mechanical properties of cell-laden hydrogels are a major concern. Here, we demonstrate the printing of a 3D cell-laden construct and its application to liver tissue engineering using 3D cell printing technology through a multi-head tissue/organ building system. Polycaprolactone (PCL) was used as a framework material because of its excellent mechanical properties. Collagen bioink containing three different types of cells-hepatocytes (HCs), human umbilical vein endothelial cells , and human lung fibroblasts--was infused into the canals of a PCL framework to induce the formation of capillary--like networks and liver cell growth. A co-cultured 3D microenvironment of the three types of cells was successfully established and maintained. The vascular formation and functional abilities of HCs (i.e., albumin secretion and urea synthesis) demonstrated that the heterotypic interaction among HCs and nonparenchymal cells increased the survivability and functionality of HCs within the collagen gel. Therefore, our results demonstrate the prospect of using cell printing technology for the creation of heterotypic cellular interaction within a structure for liver tissue engineering.

  15. The computer simulation of 3d gas dynamics in a gas centrifuge

    NASA Astrophysics Data System (ADS)

    Borman, V. D.; Bogovalov, S. V.; Borisevich, V. D.; Tronin, I. V.; Tronin, V. N.

    2016-09-01

    We argue on the basis of the results of 2D analysis of the gas flow in gas centrifuges that a reliable calculation of the circulation of the gas and gas content in the gas centrifuge is possible only in frameworks of 3D numerical simulation of gas dynamics in the gas centrifuge (hereafter GC). The group from National research nuclear university, MEPhI, has created a computer code for 3D simulation of the gas flow in GC. The results of the computer simulations of the gas flows in GC are presented. A model Iguassu centrifuge is explored for the simulations. A nonaxisymmetric gas flow is produced due to interaction of the hypersonic rotating flow with the scoops for extraction of the product and waste flows from the GC. The scoops produce shock waves penetrating into a working camera of the GC and form spiral waves there.

  16. User's manuals for DYNA3D and DYNAP: nonlinear dynamic analysis of solids in three dimensions

    SciTech Connect

    Hallquist, J.O.

    1981-07-01

    This report provides a user's manual for DYNA3D, an explicit three-dimensional finite element code for analyzing the large deformation dynamic response of inelastic solids. A contact-impact algorithm permits gaps and sliding along material interfaces. By a specialization of this algorithm, such interfaces can be rigidly tied to admit variable zoning without the need of transition regions. Spatial discretization is achieved by the use of 8-node solid elements, and the equations-of-motion are integrated by the central difference method. Post-processors for DYNA3D include GRAPE for plotting deformed shapes and stress contours and DYNAP for plotting time histories. A user's manual for DYNAP is also provided in this report.

  17. Blob Dynamics in 3D BOUT Simulations of Tokamak Edge Turbulence

    SciTech Connect

    Russell, D; D'Ippolito, D; Myra, J; Nevins, W; Xu, X

    2004-08-23

    Propagating filaments of enhanced plasma density, or blobs, observed in 3D numerical simulations of a diverted, neutral-fueled tokamak are studied. Fluctuations of vorticity, electrical potential {phi}, temperature T{sub e} and current density J{sub {parallel}} associated with the blobs have a dipole structure perpendicular to the magnetic field and propagate radially with large E {center_dot} B drift velocities (> 1 km/s). The simulation results are consistent with a 3D blob dynamics model that incorporates increased parallel plasma resistivity (from neutral cooling of the X-point region), blob disconnection from the divertor sheath, X-point closure of the current loops, and collisional physics to sustain the {phi}, T{sub e}, J{sub {parallel}} dipoles.

  18. Inverse compositional estimation of 3D pose and lighting in dynamic scenes.

    PubMed

    Xu, Yilei; Roy-Chowdhury, Amit

    2008-07-01

    In this paper, we show how to estimate, accurately and efficiently, the 3D motion of a rigid object and time-varying lighting in a dynamic scene. This is achieved in an inverse compositional tracking framework with a novel warping function that involves a 2D --> 3D --> 2D transformation. This also allows us to extend traditional two frame inverse compositional tracking to a sequence of frames, leading to even higher computational savings. We prove the theoretical convergence of this method and show that it leads to significant reduction in computational burden. Experimental analysis on multiple video sequences shows impressive speed-up over existing methods while retaining a high level of accuracy.

  19. Dynamic 3D measurement of modulated radiotherapy: a scintillator-based approach

    NASA Astrophysics Data System (ADS)

    Archambault, Louis; Rilling, Madison; Roy-Pomerleau, Xavier; Thibault, Simon

    2017-05-01

    With the rise of high-conformity dynamic radiotherapy, such as volumetric modulated arc therapy and robotic radiosurgery, the temporal dimension of dose measurement is becoming increasingly important. It must be possible to tell both ‘where’ and ‘when’ a discrepancy occurs between the plan and its delivery. A 3D scintillation-based dosimetry system could be ideal for such a thorough, end-to-end verification; however, the challenge lies in retrieving the volumetric information of the light-emitting volume. This paper discusses the motivation, from an optics point of view, of using the images acquired with a plenoptic camera, or light field imager, of an irradiated plastic scintillator volume to reconstruct the delivered 3D dose distribution. Current work focuses on the optimization of the optical design as well as the data processing that is involved in the ongoing development of a clinically viable, second generation dosimetry system.

  20. Radial electric field 3D modeling for wire arrays driving dynamic hohlraums on Z.

    SciTech Connect

    Mock, Raymond Cecil

    2007-06-01

    The anode-cathode structure of the Z-machine wire array results in a higher negative radial electric field (Er) on the wires near the cathode relative to the anode. The magnitude of this field has been shown to anti-correlate with the axial radiation top/bottom symmetry in the DH (Dynamic Hohlraum). Using 3D modeling, the structure of this field is revealed for different wire-array configurations and for progressive mechanical alterations, providing insight for minimizing the negative Er on the wire array in the anode-to-cathode region of the DH. Also, the 3D model is compared to Sasorov's approximation, which describes Er at the surface of the wire in terms of wire-array parameters.

  1. Chaotic electroconvection near ion-selective membranes: investigation of transport dynamics from a 3D DNS

    NASA Astrophysics Data System (ADS)

    Druzgalski, Clara; Mani, Ali

    2014-11-01

    We have investigated the transport dynamics of an electrokinetic instability that occurs when ions are driven from bulk fluids to ion-selective membranes due to externally applied electric fields. This phenomenon is relevant to a wide range of electrochemical applications including electrodialysis for fresh water production. Using data from our 3D DNS, we show how electroconvective instability, arising from concentration polarization, results in a chaotic flow that significantly alters the net ion transport rate across the membrane surface. The 3D DNS results, which fully resolve the spatiotemporal scales including the electric double layers, enable visualization of instantaneous snapshots of current density directly on the membrane surface, as well as analysis of transport statistics such as concentration variance and fluctuating advective fluxes. Furthermore, we present a full spectral analysis revealing broadband spectra in both concentration and flow fields and deduce the key parameter controlling the range of contributing scales.

  2. 3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells

    PubMed Central

    Felts, Richard L.; Narayan, Kedar; Estes, Jacob D.; Shi, Dan; Trubey, Charles M.; Fu, Jing; Hartnell, Lisa M.; Ruthel, Gordon T.; Schneider, Douglas K.; Nagashima, Kunio; Bess, Julian W.; Bavari, Sina; Lowekamp, Bradley C.; Bliss, Donald; Lifson, Jeffrey D.; Subramaniam, Sriram

    2010-01-01

    The efficiency of HIV infection is greatly enhanced when the virus is delivered at conjugates between CD4+ T cells and virus-bearing antigen-presenting cells such as macrophages or dendritic cells via specialized structures known as virological synapses. Using ion abrasion SEM, electron tomography, and superresolution light microscopy, we have analyzed the spatial architecture of cell-cell contacts and distribution of HIV virions at virological synapses formed between mature dendritic cells and T cells. We demonstrate the striking envelopment of T cells by sheet-like membrane extensions derived from mature dendritic cells, resulting in a shielded region for formation of virological synapses. Within the synapse, filopodial extensions emanating from CD4+ T cells make contact with HIV virions sequestered deep within a 3D network of surface-accessible compartments in the dendritic cell. Viruses are detected at the membrane surfaces of both dendritic cells and T cells, but virions are not released passively at the synapse; instead, virus transfer requires the engagement of T-cell CD4 receptors. The relative seclusion of T cells from the extracellular milieu, the burial of the site of HIV transfer, and the receptor-dependent initiation of virion transfer by T cells highlight unique aspects of cell-cell HIV transmission. PMID:20624966

  3. 3D Microfluidic model for evaluating immunotherapy efficacy by tracking dendritic cell behaviour toward tumor cells.

    PubMed

    Parlato, Stefania; De Ninno, Adele; Molfetta, Rosa; Toschi, Elena; Salerno, Debora; Mencattini, Arianna; Romagnoli, Giulia; Fragale, Alessandra; Roccazzello, Lorenzo; Buoncervello, Maria; Canini, Irene; Bentivegna, Enrico; Falchi, Mario; Bertani, Francesca Romana; Gerardino, Annamaria; Martinelli, Eugenio; Natale, Corrado; Paolini, Rossella; Businaro, Luca; Gabriele, Lucia

    2017-04-24

    Immunotherapy efficacy relies on the crosstalk within the tumor microenvironment between cancer and dendritic cells (DCs) resulting in the induction of a potent and effective antitumor response. DCs have the specific role of recognizing cancer cells, taking up tumor antigens (Ags) and then migrating to lymph nodes for Ag (cross)-presentation to naïve T cells. Interferon-α-conditioned DCs (IFN-DCs) exhibit marked phagocytic activity and the special ability of inducing Ag-specific T-cell response. Here, we have developed a novel microfluidic platform recreating tightly interconnected cancer and immune systems with specific 3D environmental properties, for tracking human DC behaviour toward tumor cells. By combining our microfluidic platform with advanced microscopy and a revised cell tracking analysis algorithm, it was possible to evaluate the guided efficient motion of IFN-DCs toward drug-treated cancer cells and the succeeding phagocytosis events. Overall, this platform allowed the dissection of IFN-DC-cancer cell interactions within 3D tumor spaces, with the discovery of major underlying factors such as CXCR4 involvement and underscored its potential as an innovative tool to assess the efficacy of immunotherapeutic approaches.

  4. Rapid 3-D delineation of cell nuclei for high-content screening platforms.

    PubMed

    Gertych, Arkadiusz; Ma, Zhaoxuan; Tajbakhsh, Jian; Velásquez-Vacca, Adriana; Knudsen, Beatrice S

    2016-02-01

    High-resolution three-dimensional (3-D) microscopy combined with multiplexing of fluorescent labels allows high-content analysis of large numbers of cell nuclei. The full automation of 3-D screening platforms necessitates image processing algorithms that can accurately and robustly delineate nuclei in images with little to no human intervention. Imaging-based high-content screening was originally developed as a powerful tool for drug discovery. However, cell confluency, complexity of nuclear staining as well as poor contrast between nuclei and background result in slow and unreliable 3-D image processing and therefore negatively affect the performance of studying a drug response. Here, we propose a new method, 3D-RSD, to delineate nuclei by means of 3-D radial symmetries and test it on high-resolution image data of human cancer cells treated by drugs. The nuclei detection performance was evaluated by means of manually generated ground truth from 2351 nuclei (27 confocal stacks). When compared to three other nuclei segmentation methods, 3D-RSD possessed a better true positive rate of 83.3% and F-score of 0.895±0.045 (p-value=0.047). Altogether, 3D-RSD is a method with a very good overall segmentation performance. Furthermore, implementation of radial symmetries offers good processing speed, and makes 3D-RSD less sensitive to staining patterns. In particular, the 3D-RSD method performs well in cell lines, which are often used in imaging-based HCS platforms and are afflicted by nuclear crowding and overlaps that hinder feature extraction.

  5. Rapid 3-D delineation of cell nuclei for high-content screening platforms

    PubMed Central

    Gertych, Arkadiusz; Ma, Zhaoxuan; Tajbakhsh, Jian; Velásquez-Vacca, Adriana; Knudsen, Beatrice S.

    2015-01-01

    High-resolution three-dimensional (3-D) microscopy combined with multiplexing of fluorescent labels allows high-content analysis of large numbers of cell nuclei. The full automation of 3-D screening platforms necessitates image processing algorithms that can accurately and robustly delineate nuclei in images with little to no human intervention. Imaging-based high-content screening was originally developed as a powerful tool for drug discovery. However, cell confluency, complexity of nuclear staining as well as poor contrast between nuclei and background result in slow and unreliable 3-D image processing and therefore negatively affect the performance of studying a drug response. Here, we propose a new method, 3D-RSD, to delineate nuclei by means of 3-D radial symmetries and test it on high-resolution image data of human cancer cells treated by drugs. The nuclei detection performance was evaluated by means of manually generated ground truth from 2351 nuclei (27 confocal stacks). When compared to three other nuclei segmentation methods, 3D-RSD possessed a better true positive rate of 83.3% and F-score of 0.895+/-0.045 (p- value=0.047). Altogether, 3D-RSD is a method with a very good overall segmentation performance. Furthermore, implementation of radial symmetries offers good processing speed, and makes 3D-RSD less sensitive to staining patterns. In particular the 3D-RSG method performs well in cell lines, which are often used in imaging-based HCS platforms and are afflicted by nuclear crowding and overlaps that hinder feature extraction. PMID:25982066

  6. Cells in 3D matrices under interstitial flow: effects of extracellular matrix alignment on cell shear stress and drag forces.

    PubMed

    Pedersen, John A; Lichter, Seth; Swartz, Melody A

    2010-03-22

    Interstitial flow is an important regulator of various cell behaviors both in vitro and in vivo, yet the forces that fluid flow imposes on cells embedded in a 3D extracellular matrix (ECM), and the effects of matrix architecture on those forces, are not well understood. Here, we demonstrate how fiber alignment can affect the shear and pressure forces on the cell and ECM. Using computational fluid dynamics simulations, we show that while the solutions of the Brinkman equation accurately estimate the average fluid shear stress and the drag forces on a cell within a 3D fibrous medium, the distribution of shear stress on the cellular surface as well as the peak shear stresses remain intimately related to the pericellular fiber architecture and cannot be estimated using bulk-averaged properties. We demonstrate that perpendicular fiber alignment of the ECM yields lower shear stress and pressure forces on the cells and higher stresses on the ECM, leading to decreased permeability, while parallel fiber alignment leads to higher stresses on cells and increased permeability, as compared to a cubic lattice arrangement. The Spielman-Goren permeability relationships for fibrous media agreed well with CFD simulations of flow with explicitly considered fibers. These results suggest that the experimentally observed active remodeling of ECM fibers by fibroblasts under interstitial flow to a perpendicular alignment could serve to decrease the shear and drag forces on the cell.

  7. Quantitative 3D analysis of complex single border cell behaviors in coordinated collective cell migration.

    PubMed

    Cliffe, Adam; Doupé, David P; Sung, HsinHo; Lim, Isaac Kok Hwee; Ong, Kok Haur; Cheng, Li; Yu, Weimiao

    2017-04-04

    Understanding the mechanisms of collective cell migration is crucial for cancer metastasis, wound healing and many developmental processes. Imaging a migrating cluster in vivo is feasible, but the quantification of individual cell behaviours remains challenging. We have developed an image analysis toolkit, CCMToolKit, to quantify the Drosophila border cell system. In addition to chaotic motion, previous studies reported that the migrating cells are able to migrate in a highly coordinated pattern. We quantify the rotating and running migration modes in 3D while also observing a range of intermediate behaviours. Running mode is driven by cluster external protrusions. Rotating mode is associated with cluster internal cell extensions that could not be easily characterized. Although the cluster moves slower while rotating, individual cells retain their mobility and are in fact slightly more active than in running mode. We also show that individual cells may exchange positions during migration.

  8. Quantitative 3D analysis of complex single border cell behaviors in coordinated collective cell migration

    PubMed Central

    Cliffe, Adam; Doupé, David P.; Sung, HsinHo; Lim, Isaac Kok Hwee; Ong, Kok Haur; Cheng, Li; Yu, Weimiao

    2017-01-01

    Understanding the mechanisms of collective cell migration is crucial for cancer metastasis, wound healing and many developmental processes. Imaging a migrating cluster in vivo is feasible, but the quantification of individual cell behaviours remains challenging. We have developed an image analysis toolkit, CCMToolKit, to quantify the Drosophila border cell system. In addition to chaotic motion, previous studies reported that the migrating cells are able to migrate in a highly coordinated pattern. We quantify the rotating and running migration modes in 3D while also observing a range of intermediate behaviours. Running mode is driven by cluster external protrusions. Rotating mode is associated with cluster internal cell extensions that could not be easily characterized. Although the cluster moves slower while rotating, individual cells retain their mobility and are in fact slightly more active than in running mode. We also show that individual cells may exchange positions during migration. PMID:28374738

  9. 3D inverted colloidal crystals in realistic cell migration assays for drug screening applications.

    PubMed

    da Silva, Joakim; Lautenschläger, Franziska; Kuo, Cheng-Hwa R; Guck, Jochen; Sivaniah, Easan

    2011-12-01

    Screening drugs for their specific impact on cell mechanics, in addition to targeting adhesion and proteolysis, will be important for successfully moderating migration in infiltrative disorders including cancer metastasis. We present 3D inverted colloidal crystals made of hydrogel as a realistic cell migration assay, where the geometry and stiffness can be set independently to mimic the tissue requirements in question. We show the utility of this 3D assay for drug screening purposes, specifically in contrast to conventional 2D migration studies, by surveying the effects of commonly used cytoskeletal toxins that impact cell mechanics. This assay allows studying large cell numbers for good statistics but at single-cell resolution.

  10. Phage as versatile nanoink for printing 3-D cell-laden scaffolds.

    PubMed

    Lee, Doe-Young; Lee, Hyeongjin; Kim, YongBok; Yoo, So Young; Chung, Woo-Jae; Kim, GeunHyung

    2016-01-01

    Bioprinting is an emerging technology for producing tissue-mimetic 3-D structures using cell-containing hydrogels (bioink). Various synthetic and natural hydrogels with key characteristics, including biocompatibility, biodegradability, printability and crosslinkability, have been employed as ink materials in bioprinting. Choosing the right cell-containing "bioink" material is the most essential step for fabricating 3-D constructs with a controlled mechanical and biochemical microenvironment that can lead to successful tissue regeneration and repair. Here, we demonstrate that the genetically engineered M13 phage holds great potential for use as a versatile nanoink for printing 3-D cell-laden matrices. In particular, M13 phages displaying integrin-binding (GRGDS) and calcium-binding (DDYD) domains on their surface were blended with alginate to successfully form Ca(2+)-crosslinked hydrogels. Furthermore, 3-D cell-laden scaffolds with high cell viability were generated after optimizing the printing process. The MC3T3-E1 cells within these scaffolds showed enhanced proliferation and differentiation rates that increased proportionally with the concentration of phages in the 3-D matrices compared with the rates of cells in pure alginate scaffolds. Bioprinting is an emerging technology for producing tissue-mimetic 3-D structures using cell-containing hydrogels called bioink. Choosing the right bioink is essential for fabricating 3-D structures with controlled mechanical and biochemical properties which lead to successful tissue regeneration. Therefore, there is a growing demand for a new bioink material that can be designed from molecular level. Here, we demonstrate that genetically engineered M13 phage holds great potential for use as versatile bioink. The phage-based bioink benefits from its replicability, self-assembling property, and tunable molecular design and enables bioprinted scaffolds to exhibit improved cell viability, proliferation and differentiation. This

  11. Development of Islet Organoids from H9 Human Embryonic Stem Cells in Biomimetic 3D Scaffolds.

    PubMed

    Wang, Weiwei; Jin, Sha; Ye, Kaiming

    2017-03-15

    Success in the differentiating human embryonic stem cells (hESCs) into insulin-secreting β cells raises new hopes for diabetes treatment. In this work, we demonstrated the feasibility of developing islet organoids from hESCs within biomimetic 3D scaffolds. We showed that such a 3D microenvironment is critical to the generation of pancreatic endoderm and endocrine from hESCs. The organoids formed consisted of pancreatic α, β, δ, and pancreatic polypeptide (PP) cells. A high-level co-expression of PDX1, NKX6.1, and NGN3 in these cells suggests the characteristics of pancreatic β cells. More importantly, most insulin-secreting cells generated did not express glucagon, somatostatin, or PP. The expression of mature β cell marker genes such as Pdx1, Ngn3, Insulin, MafA, and Glut2 was detected in these 3D-induced cell clusters. A high-level expression of C-peptide confirmed the de novo endogenous insulin production in these 3D induced cells. Insulin-secretory granules, an indication of β cell maturity, were detected in these cells as well. Glucose challenging experiments suggested that these cells are sensitive to glucose levels due to their elevated maturity. Exposing the cells to a high concentration of glucose induced a sharp increase in insulin secretion.

  12. A modular segmented-flow platform for 3D cell cultivation.

    PubMed

    Lemke, Karen; Förster, Tobias; Römer, Robert; Quade, Mandy; Wiedemeier, Stefan; Grodrian, Andreas; Gastrock, Gunter

    2015-07-10

    In vitro 3D cell cultivation is promised to equate tissue in vivo more realistically than 2D cell cultivation corresponding to cell-cell and cell-matrix interactions. Therefore, a scalable 3D cultivation platform was developed. This platform, called pipe-based bioreactors (pbb), is based on the segmented-flow technology: aqueous droplets are embedded in a water-immiscible carrier fluid. The droplet volumes range from 60 nL to 20 μL and are used as bioreactors lined up in a tubing like pearls on a string. The modular automated platform basically consists of several modules like a fluid management for a high throughput droplet generation for self-assembly or scaffold-based 3D cell cultivation, a storage module for incubation and storage, and an analysis module for monitoring cell aggregation and proliferation basing on microscopy or photometry. In this report, the self-assembly of murine embryonic stem cells (mESCs) to uniformly sized embryoid bodies (EBs), the cell proliferation, the cell viability as well as the influence on the cell differentiation to cardiomyocytes are described. The integration of a dosage module for medium exchange or agent addition will enable pbb as long-term 3D cell cultivation system for studying stem cell differentiation, e.g. cardiac myogenesis or for diagnostic and therapeutic testing in personalized medicine.

  13. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  14. Optical µ-Printing of Cellular-Scale Microscaffold Arrays for 3D Cell Culture.

    PubMed

    Ouyang, Xia; Zhang, Kunyu; Wu, Jushuai; Wong, Dexter Siu-Hong; Feng, Qian; Bian, Liming; Zhang, A Ping

    2017-08-21

    Guiding cell culture via engineering extracellular microenvironment has attracted tremendous attention due to its appealing potentials in the repair, maintenance, and development of tissues or even whole organs. However, conventional biofabrication technologies are usually less productive in fabricating microscale three-dimensional (3D) constructs because of the strident requirements in processing precision and complexity. Here we present an optical µ-printing technology to rapidly fabricate 3D microscaffold arrays for 3D cell culture and cell-scaffold interaction studies on a single chip. Arrays of 3D cubic microscaffolds with cubical sizes matching the single-cell size were fabricated to facilitate cell spreading on suspended microbeams so as to expose both apical and basal cell membranes. We further showed that the increasing of the cubical size of the microscaffolds led to enhanced spreading of the seeded human mesenchymal stem cells and activation of mechanosensing signaling, thereby promoting osteogenesis. Moreover, we demonstrated that the spatially selective modification of the surfaces of suspended beams with a bioactive coating (gelatin methacrylate) via an in-situ printing process allowed tailorable cell adhesion and spreading on the 3D microscaffolds.

  15. Modeling Physiological Events in 2D vs. 3D Cell Culture.

    PubMed

    Duval, Kayla; Grover, Hannah; Han, Li-Hsin; Mou, Yongchao; Pegoraro, Adrian F; Fredberg, Jeffery; Chen, Zi

    2017-07-01

    Cell culture has become an indispensable tool to help uncover fundamental biophysical and biomolecular mechanisms by which cells assemble into tissues and organs, how these tissues function, and how that function becomes disrupted in disease. Cell culture is now widely used in biomedical research, tissue engineering, regenerative medicine, and industrial practices. Although flat, two-dimensional (2D) cell culture has predominated, recent research has shifted toward culture using three-dimensional (3D) structures, and more realistic biochemical and biomechanical microenvironments. Nevertheless, in 3D cell culture, many challenges remain, including the tissue-tissue interface, the mechanical microenvironment, and the spatiotemporal distributions of oxygen, nutrients, and metabolic wastes. Here, we review 2D and 3D cell culture methods, discuss advantages and limitations of these techniques in modeling physiologically and pathologically relevant processes, and suggest directions for future research. Copyright © 2017 the American Physiological Society.

  16. Modeling Physiological Events in 2D vs. 3D Cell Culture

    PubMed Central

    Duval, Kayla; Grover, Hannah; Han, Li-Hsin; Mou, Yongchao; Pegoraro, Adrian F.; Fredberg, Jeffery

    2017-01-01

    Cell culture has become an indispensable tool to help uncover fundamental biophysical and biomolecular mechanisms by which cells assemble into tissues and organs, how these tissues function, and how that function becomes disrupted in disease. Cell culture is now widely used in biomedical research, tissue engineering, regenerative medicine, and industrial practices. Although flat, two-dimensional (2D) cell culture has predominated, recent research has shifted toward culture using three-dimensional (3D) structures, and more realistic biochemical and biomechanical microenvironments. Nevertheless, in 3D cell culture, many challenges remain, including the tissue-tissue interface, the mechanical microenvironment, and the spatiotemporal distributions of oxygen, nutrients, and metabolic wastes. Here, we review 2D and 3D cell culture methods, discuss advantages and limitations of these techniques in modeling physiologically and pathologically relevant processes, and suggest directions for future research. PMID:28615311

  17. 1-integrin and MT1-MMP promote tumor cell migration in 2D but not in 3D fibronectin microenvironments

    NASA Astrophysics Data System (ADS)

    Corall, Silke; Haraszti, Tamas; Bartoschik, Tanja; Spatz, Joachim Pius; Ludwig, Thomas; Cavalcanti-Adam, Elisabetta Ada

    2014-03-01

    Cell migration is a crucial event for physiological processes, such as embryonic development and wound healing, as well as for pathological processes, such as cancer dissemination and metastasis formation. Cancer cell migration is a result of the concerted action of matrix metalloproteinases (MMPs), expressed by cancer cells to degrade the surrounding matrix, and integrins, the transmembrane receptors responsible for cell binding to matrix proteins. While it is known that cell-microenvironment interactions are essential for migration, the role of the physical state of such interactions remains still unclear. In this study we investigated human fibrosarcoma cell migration in two-dimensional (2D) and three-dimensional (3D) fibronectin (FN) microenvironments. By using antibody blocking approach and cell-binding site mutation, we determined that -integrin is the main mediator of fibrosarcoma cell migration in 2D FN, whereas in 3D fibrillar FN, the binding of - and -integrins is not necessary for cell movement in the fibrillar network. Furthermore, while the general inhibition of MMPs with GM6001 has no effect on cell migration in both 2D and 3D FN matrices, we observed opposing effect after targeted silencing of a membrane-bound MMP, namely MT1-MMP. In 2D fibronectin, silencing of MT1-MMP results in decreased migration speed and loss of directionality, whereas in 3D FN matrices, cell migration speed is increased and integrin-mediated signaling for actin dynamics is promoted. Our results suggest that the fibrillar nature of the matrix governs the migratory behavior of fibrosarcoma cells. Therefore, to hinder migration and dissemination of diseased cells, matrix molecules should be directly targeted, rather than specific subtypes of receptors at the cell membrane.

  18. More Dynamical Properties Revealed from a 3D Lorenz-like System

    NASA Astrophysics Data System (ADS)

    Wang, Haijun; Li, Xianyi

    After a 3D Lorenz-like system has been revisited, more rich hidden dynamics that was not found previously is clearly revealed. Some more precise mathematical work, such as for the complete distribution and the local stability and bifurcation of its equilibrium points, the existence of singularly degenerate heteroclinic cycles as well as homoclinic and heteroclinic orbits, and the dynamics at infinity, is carried out in this paper. In particular, another possible new mechanism behind the creation of chaotic attractors is presented. Based on this mechanism, some different structure types of chaotic attractors are numerically found in the case of small b > 0. All theoretical results obtained are further illustrated by numerical simulations. What we formulate in this paper is to not only show those dynamical properties hiding in this system, but also (more mainly) present a kind of way and means — both "locally" and "globally" and both "finitely" and "infinitely" — to comprehensively explore a given system.

  19. Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI

    PubMed Central

    Mogalle, Katja; Perez-Rovira, Adria; Ciet, Pierluigi; Wens, Stephan C. A.; van Doorn, Pieter A.; Tiddens, Harm A. W. M.; van der Ploeg, Ans T.; de Bruijne, Marleen

    2016-01-01

    Background Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness. Methods The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle. Results Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls. Conclusion Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response. PMID:27391236

  20. Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI.

    PubMed

    Mogalle, Katja; Perez-Rovira, Adria; Ciet, Pierluigi; Wens, Stephan C A; van Doorn, Pieter A; Tiddens, Harm A W M; van der Ploeg, Ans T; de Bruijne, Marleen

    2016-01-01

    Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness. The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle. Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls. Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response.

  1. Semi-automatic segmentation for 3D motion analysis of the tongue with dynamic MRI.

    PubMed

    Lee, Junghoon; Woo, Jonghye; Xing, Fangxu; Murano, Emi Z; Stone, Maureen; Prince, Jerry L

    2014-12-01

    Dynamic MRI has been widely used to track the motion of the tongue and measure its internal deformation during speech and swallowing. Accurate segmentation of the tongue is a prerequisite step to define the target boundary and constrain the tracking to tissue points within the tongue. Segmentation of 2D slices or 3D volumes is challenging because of the large number of slices and time frames involved in the segmentation, as well as the incorporation of numerous local deformations that occur throughout the tongue during motion. In this paper, we propose a semi-automatic approach to segment 3D dynamic MRI of the tongue. The algorithm steps include seeding a few slices at one time frame, propagating seeds to the same slices at different time frames using deformable registration, and random walker segmentation based on these seed positions. This method was validated on the tongue of five normal subjects carrying out the same speech task with multi-slice 2D dynamic cine-MR images obtained at three orthogonal orientations and 26 time frames. The resulting semi-automatic segmentations of a total of 130 volumes showed an average dice similarity coefficient (DSC) score of 0.92 with less segmented volume variability between time frames than in manual segmentations.

  2. Salinity effects on cracking morphology and dynamics in 3-D desiccating clays

    NASA Astrophysics Data System (ADS)

    DeCarlo, Keita F.; Shokri, Nima

    2014-04-01

    Saline conditions induce not only chemical but physical changes in swelling clays, and have a significant influence on the crack dynamics and morphology of desiccating clays. In this study, we used X-ray microtomography to experimentally investigate the effects of sodium chloride on the morphology and dynamics of desiccation cracks in three-dimensional mixtures of sand-bentonite slurry under varying rheological conditions. Rectangular glass containers were packed with slurries of different salt concentrations, with the top boundary exposed to air for evaporation. The growth and propagation of the cracking network that subsequently formed was visualized in 3-D at multiple intervals. The characterization of cracking and branching behavior shows a high extent of localized surficial crack networks at low salinity, with a transition to less extensive but more centralized crack networks with increased salinity. The observed behavior was described in the context of the physicochemical properties of the montmorillonite clay, where shifts from an "entangled" (large platelet spacing, small pore structure) to a "stacked" (small platelet spacing, open pore structure) network influence fluid distribution and thus extent of cracking and branching behavior. This is further corroborated by vertical profiles of water distribution, which shows localized desiccation fronts that shift to uniform desaturation with increasing salt concentration. Our results provide new insights regarding the formation, dynamics, and patterns of desiccation cracks formed during evaporation from 3-D saline clay structures, which will be useful in hydrological applications including water management, land surface evaporation, and subsurface contaminant transport.

  3. Semi-automatic segmentation for 3D motion analysis of the tongue with dynamic MRI

    PubMed Central

    Lee, Junghoon; Woo, Jonghye; Xing, Fangxu; Murano, Emi Z.; Stone, Maureen; Prince, Jerry L.

    2014-01-01

    Dynamic MRI has been widely used to track the motion of the tongue and measure its internal deformation during speech and swallowing. Accurate segmentation of the tongue is a prerequisite step to define the target boundary and constrain the tracking to tissue points within the tongue. Segmentation of 2D slices or 3D volumes is challenging because of the large number of slices and time frames involved in the segmentation, as well as the incorporation of numerous local deformations that occur throughout the tongue during motion. In this paper, we propose a semi-automatic approach to segment 3D dynamic MRI of the tongue. The algorithm steps include seeding a few slices at one time frame, propagating seeds to the same slices at different time frames using deformable registration, and random walker segmentation based on these seed positions. This method was validated on the tongue of five normal subjects carrying out the same speech task with multi-slice 2D dynamic cine-MR images obtained at three orthogonal orientations and 26 time frames. The resulting semi-automatic segmentations of a total of 130 volumes showed an average dice similarity coefficient (DSC) score of 0.92 with less segmented volume variability between time frames than in manual segmentations. PMID:25155697

  4. Magnetic resonance velocity mapping of 3D cerebrospinal fluid flow dynamics in hydrocephalus: preliminary results.

    PubMed

    Stadlbauer, Andreas; Salomonowitz, Erich; Brenneis, Christian; Ungersböck, Karl; van der Riet, Wilma; Buchfelder, Michael; Ganslandt, Oliver

    2012-01-01

    To investigate the detectability of CSF flow alterations in the ventricular system of patients with hydrocephalus using time-resolved 3D MR velocity mapping. MR velocity mapping was performed in 21 consecutive hydrocephalus patients and 21 age-matched volunteers using a 3D phase-contrast (PC) sequence. Velocity vectors and particle path lines were calculated for visualisation of flow dynamics. CSF flow was classified as "hypomotile flow" if it showed attenuated dynamics and as "hypermotile flow" if it showed increased dynamics compared with volunteers. Diagnostic efficacy was compared with routine 2D cine PC-MRI. Seven patients showed hypomotile CSF flow: six had non-communicating hydrocephalus due to aqueductal stenosis. One showed oscillating flow between the lateral ventricles after craniotomy for intracranial haemorrhage. Seven patients showed normal flow: six had hydrocephalus ex vacuo due to brain atrophy. One patient who underwent ventriculostomy 10 years ago showed a flow path through the opening. Seven patients showed hypermotile flow: three had normal pressure hydrocephalus, three had dementia, and in one the diagnosis remained unclear. The diagnostic efficacy of velocity mapping was significantly higher except for that of aqueductal stenosis. Our approach may be useful for diagnosis, therapy planning, and follow-up of different kinds of hydrocephalus.

  5. Simulating 3-D lung dynamics using a programmable graphics processing unit.

    PubMed

    Santhanam, Anand P; Hamza-Lup, Felix G; Rolland, Jannick P

    2007-09-01

    Medical simulations of lung dynamics promise to be effective tools for teaching and training clinical and surgical procedures related to lungs. Their effectiveness may be greatly enhanced when visualized in an augmented reality (AR) environment. However, the computational requirements of AR environments limit the availability of the central processing unit (CPU) for the lung dynamics simulation for different breathing conditions. In this paper, we present a method for computing lung deformations in real time by taking advantage of the programmable graphics processing unit (GPU). This will save the CPU time for other AR-associated tasks such as tracking, communication, and interaction management. An approach for the simulations of the three-dimensional (3-D) lung dynamics using Green's formulation in the case of upright position is taken into consideration. We extend this approach to other orientations as well as the subsequent changes in breathing. Specifically, the proposed extension presents a computational optimization and its implementation in a GPU. Results show that the computational requirements for simulating the deformation of a 3-D lung model are significantly reduced for point-based rendering.

  6. Representation and coding of large-scale 3D dynamic maps

    NASA Astrophysics Data System (ADS)

    Cohen, Robert A.; Tian, Dong; Krivokuća, Maja; Sugimoto, Kazuo; Vetro, Anthony; Wakimoto, Koji; Sekiguchi, Shunichi

    2016-09-01

    combined with depth and color measurements of the surrounding environment. Localization could be achieved with GPS, inertial measurement units (IMU), cameras, or combinations of these and other devices, while the depth measurements could be achieved with time-of-flight, radar or laser scanning systems. The resulting 3D maps, which are composed of 3D point clouds with various attributes, could be used for a variety of applications, including finding your way around indoor spaces, navigating vehicles around a city, space planning, topographical surveying or public surveying of infrastructure and roads, augmented reality, immersive online experiences, and much more. This paper discusses application requirements related to the representation and coding of large-scale 3D dynamic maps. In particular, we address requirements related to different types of acquisition environments, scalability in terms of progressive transmission and efficiently rendering different levels of details, as well as key attributes to be included in the representation. Additionally, an overview of recently developed coding techniques is presented, including an assessment of current performance. Finally, technical challenges and needs for future standardization are discussed.

  7. Obstacle avoidance using predictive vision based on a dynamic 3D world model

    NASA Astrophysics Data System (ADS)

    Benjamin, D. Paul; Lyons, Damian; Achtemichuk, Tom

    2006-10-01

    We have designed and implemented a fast predictive vision system for a mobile robot based on the principles of active vision. This vision system is part of a larger project to design a comprehensive cognitive architecture for mobile robotics. The vision system represents the robot's environment with a dynamic 3D world model based on a 3D gaming platform (Ogre3D). This world model contains a virtual copy of the robot and its environment, and outputs graphics showing what the virtual robot "sees" in the virtual world; this is what the real robot expects to see in the real world. The vision system compares this output in real time with the visual data. Any large discrepancies are flagged and sent to the robot's cognitive system, which constructs a plan for focusing on the discrepancies and resolving them, e.g. by updating the position of an object or by recognizing a new object. An object is recognized only once; thereafter its observed data are monitored for consistency with the predictions, greatly reducing the cost of scene understanding. We describe the implementation of this vision system and how the robot uses it to locate and avoid obstacles.

  8. Signatures of topological phase transition in 3 d topological insulators from dynamical axion response

    NASA Astrophysics Data System (ADS)

    Makhfudz, Imam

    2016-04-01

    Axion electrodynamics, first proposed in the context of particle physics, manifests itself in condensed matter physics in the topological field theory description of 3 d topological insulators and gives rise to magnetoelectric effect, where applying magnetic (electric) field B (E ) induces polarization (magnetization) p (m ) . We use linear response theory to study the associated topological current using the Fu-Kane-Mele model of 3 d topological insulators in the presence of time-dependent uniform weak magnetic field. By computing the dynamical current susceptibility χij jpjp(ω ) , we discover from its static limit an `order parameter' of the topological phase transition between weak topological (or ordinary) insulator and strong topological insulator, found to be continuous. The χij jpjp(ω ) shows a sign-changing singularity at a critical frequency with suppressed strength in the topological insulating state. Our results can be verified in current noise experiment on 3 d TI candidate materials for the detection of such topological phase transition.

  9. Label-free characterization of white blood cells by measuring 3D refractive index maps

    PubMed Central

    Yoon, Jonghee; Kim, Kyoohyun; Park, HyunJoo; Choi, Chulhee; Jang, Seongsoo; Park, YongKeun

    2015-01-01

    The characterization of white blood cells (WBCs) is crucial for blood analyses and disease diagnoses. However, current standard techniques rely on cell labeling, a process which imposes significant limitations. Here we present three-dimensional (3D) optical measurements and the label-free characterization of mouse WBCs using optical diffraction tomography. 3D refractive index (RI) tomograms of individual WBCs are constructed from multiple two-dimensional quantitative phase images of samples illuminated at various angles of incidence. Measurements of the 3D RI tomogram of WBCs enable the separation of heterogeneous populations of WBCs using quantitative morphological and biochemical information. Time-lapse tomographic measurements also provide the 3D trajectory of micrometer-sized beads ingested by WBCs. These results demonstrate that optical diffraction tomography can be a useful and versatile tool for the study of WBCs. PMID:26504637

  10. Label-free characterization of white blood cells by measuring 3D refractive index maps.

    PubMed

    Yoon, Jonghee; Kim, Kyoohyun; Park, HyunJoo; Choi, Chulhee; Jang, Seongsoo; Park, YongKeun

    2015-10-01

    The characterization of white blood cells (WBCs) is crucial for blood analyses and disease diagnoses. However, current standard techniques rely on cell labeling, a process which imposes significant limitations. Here we present three-dimensional (3D) optical measurements and the label-free characterization of mouse WBCs using optical diffraction tomography. 3D refractive index (RI) tomograms of individual WBCs are constructed from multiple two-dimensional quantitative phase images of samples illuminated at various angles of incidence. Measurements of the 3D RI tomogram of WBCs enable the separation of heterogeneous populations of WBCs using quantitative morphological and biochemical information. Time-lapse tomographic measurements also provide the 3D trajectory of micrometer-sized beads ingested by WBCs. These results demonstrate that optical diffraction tomography can be a useful and versatile tool for the study of WBCs.

  11. Static versus dynamic kinematics in cyclists: A comparison of goniometer, inclinometer and 3D motion capture.

    PubMed

    Holliday, W; Fisher, J; Theo, R; Swart, J

    2017-07-27

    Kinematic measurements conducted during bike set-ups utilise either static or dynamic measures. There is currently limited data on reliability of static and dynamic measures nor consensus on which is the optimal method. The aim of the study was to assess the difference between static and dynamic measures of the ankle, knee, hip, shoulder and elbow. Nineteen subjects performed three separate trials for a 10-min duration at a fixed workload (70% of peak power output). Static measures were taken with a standard goniometer (GM), an inclinometer (IM) and dynamic three-dimensional motion capture (3DMC) using an eight camera motion capture system. Static and dynamic joint angles were compared over the three trials to assess repeatability of the measurements and differences between static and dynamic values. There was a positive correlation between GM and IM measures for all joints. Only the knee, shoulder and elbow were positively correlated between GM and 3DMC, and IM and 3DMC. Although all three instruments were reliable, 3D motion analysis utilised different landmarks for most joints and produced different means. Changes in knee flexion angle from static to dynamic are attributable to changes in the positioning of the foot. Controlling for this factor, the differences are negated. It was demonstrated that 3DMC is not interchangeable with GM and IM, and it is recommended that 3DMC develop independent reference values for bicycle configuration.

  12. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  13. Time resolved 3D momentum imaging of ultrafast dynamics by coherent VUV-XUV radiation

    NASA Astrophysics Data System (ADS)

    Sturm, F. P.; Wright, T. W.; Ray, D.; Zalyubovskaya, I.; Shivaram, N.; Slaughter, D. S.; Ranitovic, P.; Belkacem, A.; Weber, Th.

    2016-06-01

    We present a new experimental setup for measuring ultrafast nuclear and electron dynamics of molecules after photo-excitation and ionization. We combine a high flux femtosecond vacuum ultraviolet (VUV) and extreme ultraviolet (XUV) source with an internally cold molecular beam and a 3D momentum imaging particle spectrometer to measure electrons and ions in coincidence. We describe a variety of tools developed to perform pump-probe studies in the VUV-XUV spectrum and to modify and characterize the photon beam. First benchmark experiments are presented to demonstrate the capabilities of the system.

  14. Time resolved 3D momentum imaging of ultrafast dynamics by coherent VUV-XUV radiation.

    PubMed

    Sturm, F P; Wright, T W; Ray, D; Zalyubovskaya, I; Shivaram, N; Slaughter, D S; Ranitovic, P; Belkacem, A; Weber, Th

    2016-06-01

    We present a new experimental setup for measuring ultrafast nuclear and electron dynamics of molecules after photo-excitation and ionization. We combine a high flux femtosecond vacuum ultraviolet (VUV) and extreme ultraviolet (XUV) source with an internally cold molecular beam and a 3D momentum imaging particle spectrometer to measure electrons and ions in coincidence. We describe a variety of tools developed to perform pump-probe studies in the VUV-XUV spectrum and to modify and characterize the photon beam. First benchmark experiments are presented to demonstrate the capabilities of the system.

  15. Time resolved 3D momentum imaging of ultrafast dynamics by coherent VUV-XUV radiation

    SciTech Connect

    Sturm, F. P.; Wright, T. W.; Ray, D.; Zalyubovskaya, I.; Shivaram, N.; Slaughter, D. S.; Ranitovic, P.; Belkacem, A.; Weber, Th.

    2016-06-14

    Have we present a new experimental setup for measuring ultrafast nuclear and electron dynamics of molecules after photo-excitation and ionization. We combine a high flux femtosecond vacuum ultraviolet (VUV) and extreme ultraviolet (XUV) source with an internally cold molecular beam and a 3D momentum imaging particle spectrometer to measure electrons and ions in coincidence. We describe a variety of tools developed to perform pump-probe studies in the VUV-XUV spectrum and to modify and characterize the photon beam. First benchmark experiments are presented to demonstrate the capabilities of the system.

  16. Determination of the material fracture toughness by numerical analysis of 3D elastoplastic dynamic deformation

    NASA Astrophysics Data System (ADS)

    Bogdanov, V. R.; Sulim, G. T.

    2016-03-01

    We develop a technique for calculating the plastic strain and fracture toughness fields of a material by solving dynamical 3D problems of determining the stress-strain state in the elastoplastic statement with possible unloading of the material taken into account. The numerical solution was obtained by a finite difference scheme applied to the three-point shock bending tests of parallelepiped-shaped bars made of different materials with plane crack-notches in the middle. The fracture toughness coefficient was determined for reactor steel. The numerically calculated stress tensor components, mean stresses, the Odquist parameter characterizing the accumulated plastic strain, and the fracture toughness are illustrated by graphs.

  17. Stem cells catalyze cartilage formation by neonatal articular chondrocytes in 3D biomimetic hydrogels

    NASA Astrophysics Data System (ADS)

    Lai, Janice H.; Kajiyama, Glen; Smith, Robert Lane; Maloney, William; Yang, Fan

    2013-12-01

    Cartilage loss is a leading cause of disability among adults and effective therapy remains elusive. Neonatal chondrocytes (NChons) are an attractive allogeneic cell source for cartilage repair, but their clinical translation has been hindered by scarce donor availability. Here we examine the potential for catalyzing cartilage tissue formation using a minimal number of NChons by co-culturing them with adipose-derived stem cells (ADSCs) in 3D hydrogels. Using three different co-culture models, we demonstrated that the effects of co-culture on cartilage tissue formation are dependent on the intercellular distance and cell distribution in 3D. Unexpectedly, increasing ADSC ratio in mixed co-culture led to increased synergy between NChons and ADSCs, and resulted in the formation of large neocartilage nodules. This work raises the potential of utilizing stem cells to catalyze tissue formation by neonatal chondrocytes via paracrine signaling, and highlights the importance of controlling cell distribution in 3D matrices to achieve optimal synergy.

  18. An Experimental Study of Mixing Dynamics in 3D Granular Flows

    NASA Astrophysics Data System (ADS)

    Zaman, Zafir

    Compared with the mixing of fluids, the mixing and segregation of granular materials remains one of the big questions of science. Unlike fluids, granular materials segregate based on differences in particle properties, such as density and size. For 2D granular flows, a dynamical systems framework has been effective in describing regions of mixing and segregation. However, computational and theoretical results are just starting to form a framework for 3D granular flows, such as the bi-axial spherical tumbler (BST) flow. This thesis builds on this emerging framework through a series of experimental studies with theoretical and model support with the goal of better understanding 3D mixing. The first study tests the commonly used assumption in continuum models of granular flow that single axis tumbler flow is two dimensional. Utilizing both surface and destructive subsurface imaging, this study shows that weak 3D deviations occur in the form of an axial drift within single axis tumbler flow of varying material spanwise depth. Afterward, this thesis focuses on the development of a custom-built X-ray imaging system to non-destructively visualize the tumbler subsurface. The second study revisits the axial drift and demonstrates that wall roughness impacts the curvature and overall displacement of particle trajectories throughout the tumbler domain using subsurface particle trajectories provided by the X-ray imaging system. Finally, mixing in the fully 3D BST flow is studied. In particular, 3D persistent mixing barriers that are predicted by the dynamical systems framework are shown to exist. Some barriers are remarkably persistent for as much as 500 protocol iterations despite the presence of collisional diffusion. The structures arise from two competing effects, the cutting and shuffling action of the protocol and the stretching from the flowing layer. The tumbling protocol controls the mixing behavior as well as the types of non-mixing barriers observed. Supplementary

  19. High sensitivity plasmonic biosensor based on nanoimprinted quasi 3D nanosquares for cell detection

    NASA Astrophysics Data System (ADS)

    Zhu, Shuyan; Li, Hualin; Yang, Mengsu; Pang, Stella W.

    2016-07-01

    Quasi three-dimensional (3D) plasmonic nanostructures consisting of Au nanosquares on top of SU-8 nanopillars and Au nanoholes on the bottom were developed and fabricated using nanoimprint lithography with simultaneous thermal and UV exposure. These 3D plasmonic nanostructures were used to detect cell concentration of lung cancer A549 cells, retinal pigment epithelial (RPE) cells, and breast cancer MCF-7 cells. Nanoimprint technology has the advantage of producing high uniformity plasmonic nanostructures for such biosensors. Multiple resonance modes were observed in these quasi 3D plasmonic nanostructures. The hybrid coupling of localized surface plasmon resonances and Fabry-Perot cavity modes in the quasi 3D nanostructures resulted in high sensitivity of 496 nm/refractive index unit. The plasmonic resonance peak wavelength and sensitivity could be tuned by varying the Au thickness. Resonance peak shifts for different cells at the same concentration were distinct due to their different cell area and confluency. The cell concentration detection limit covered a large range of 5 × 102 to 1 × 107 cells ml-1 with these new plasmonic nanostructures. They also provide a large resonance peak shift of 51 nm for as little as 0.08 cells mm-2 of RPE cells for high sensitivity cell detection.

  20. Computational efficient segmentation of cell nuclei in 2D and 3D fluorescent micrographs

    NASA Astrophysics Data System (ADS)

    De Vylder, Jonas; Philips, Wilfried

    2011-02-01

    This paper proposes a new segmentation technique developed for the segmentation of cell nuclei in both 2D and 3D fluorescent micrographs. The proposed method can deal with both blurred edges as with touching nuclei. Using a dual scan line algorithm its both memory as computational efficient, making it interesting for the analysis of images coming from high throughput systems or the analysis of 3D microscopic images. Experiments show good results, i.e. recall of over 0.98.

  1. Live-cell 3D super-resolution imaging in thick biological samples.

    PubMed

    Cella Zanacchi, Francesca; Lavagnino, Zeno; Perrone Donnorso, Michela; Del Bue, Alessio; Furia, Laura; Faretta, Mario; Diaspro, Alberto

    2011-10-09

    We demonstrate three-dimensional (3D) super-resolution live-cell imaging through thick specimens (50-150 μm), by coupling far-field individual molecule localization with selective plane illumination microscopy (SPIM). The improved signal-to-noise ratio of selective plane illumination allows nanometric localization of single molecules in thick scattering specimens without activating or exciting molecules outside the focal plane. We report 3D super-resolution imaging of cellular spheroids.

  2. Efficient light harvesting with micropatterned 3D pyramidal photoanodes in dye-sensitized solar cells.

    PubMed

    Wooh, Sanghyuk; Yoon, Hyunsik; Jung, Jae-Hyun; Lee, Yong-Gun; Koh, Jai Hyun; Lee, Byoungho; Kang, Yong Soo; Char, Kookheon

    2013-06-11

    3D TiO2 photoanodes in dye-sensitized solar cells (DSCs) are fabricated by the soft lithographic technique for efficient light trapping. An extended strategy to the construction of randomized pyramid structure is developed by the conventional wet-etching of a silicon wafer for low-cost fabrication. Moreover, the futher enhancement of light absorption resulting in photocurrent increase is achieved by combining the 3D photoanode with a conventional scattering layer.

  3. Spontaneous Electroless Galvanic Cell Deposition of 3D Hierarchical and Interlaced S-M-S Heterostructures.

    PubMed

    Tan, Chuan Fu; Azmansah, Siti Aishah Bte; Zhu, Hai; Xu, Qing-Hua; Ho, Ghim Wei

    2017-01-01

    One-pot electroless galvanic cell deposition of a 3D hierarchical semiconductor-metal-semiconductor interlaced nanoarray is demonstrated. The fabricated 3D photoanode deviates from the typical planar geometry, and aims to optimize the effective surface area for light harvesting and long-range charge transfer-collection pathways. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Quantitative 3D magnetic resonance elastography: Comparison with dynamic mechanical analysis

    PubMed Central

    Rossman, Phillip J.; Arani, Arvin; Lake, David S.; Glaser, Kevin J.; Trzasko, Joshua D.; Manduca, Armando; McGee, Kiaran P.; Ehman, Richard L.; Araoz, Philip A.

    2016-01-01

    Purpose Magnetic resonance elastography (MRE) is a rapidly growing noninvasive imaging technique for measuring tissue mechanical properties in vivo. Previous studies have compared two‐dimensional MRE measurements with material properties from dynamic mechanical analysis (DMA) devices that were limited in frequency range. Advanced DMA technology now allows broad frequency range testing, and three‐dimensional (3D) MRE is increasingly common. The purpose of this study was to compare 3D MRE stiffness measurements with those of DMA over a wide range of frequencies and shear stiffnesses. Methods 3D MRE and DMA were performed on eight different polyvinyl chloride samples over 20–205 Hz with stiffness between 3 and 23 kPa. Driving frequencies were chosen to create 1.1, 2.2, 3.3, 4.4, 5.5, and 6.6 effective wavelengths across the diameter of the cylindrical phantoms. Wave images were analyzed using direct inversion and local frequency estimation algorithm with the curl operator and compared with DMA measurements at each corresponding frequency. Samples with sufficient spatial resolution and with an octahedral shear strain signal‐to‐noise ratio > 3 were compared. Results Consistency between the two techniques was measured with the intraclass correlation coefficient (ICC) and was excellent with an overall ICC of 0.99. Conclusions 3D MRE and DMA showed excellent consistency over a wide range of frequencies and stiffnesses. Magn Reson Med 77:1184–1192, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made. PMID:27016276

  5. Dynamic lens and monovision 3D displays to improve viewer comfort

    PubMed Central

    Johnson, Paul V.; Parnell, Jared AQ.; Kim, Joohwan; Saunter, Christopher D.; Love, Gordon D.; Banks, Martin S.

    2016-01-01

    Stereoscopic 3D (S3D) displays provide an additional sense of depth compared to non-stereoscopic displays by sending slightly different images to the two eyes. But conventional S3D displays do not reproduce all natural depth cues. In particular, focus cues are incorrect causing mismatches between accommodation and vergence: The eyes must accommodate to the display screen to create sharp retinal images even when binocular disparity drives the eyes to converge to other distances. This mismatch causes visual discomfort and reduces visual performance. We propose and assess two new techniques that are designed to reduce the vergence-accommodation conflict and thereby decrease discomfort and increase visual performance. These techniques are much simpler to implement than previous conflict-reducing techniques. The first proposed technique uses variable-focus lenses between the display and the viewer’s eyes. The power of the lenses is yoked to the expected vergence distance thereby reducing the mismatch between vergence and accommodation. The second proposed technique uses a fixed lens in front of one eye and relies on the binocularly fused percept being determined by one eye and then the other, depending on simulated distance. We conducted performance tests and discomfort assessments with both techniques and compared the results to those of a conventional S3D display. The first proposed technique, but not the second, yielded clear improvements in performance and reductions in discomfort. This dynamic-lens technique therefore offers an easily implemented technique for reducing the vergence-accommodation conflict and thereby improving viewer experience. PMID:27410105

  6. Development and validation of a 3-D model to predict knee joint loading during dynamic movement.

    PubMed

    McLean, S G; Su, A; van den Bogert, A J

    2003-12-01

    The purpose of this study was to develop a subject-specific 3-D model of the lower extremity to predict neuromuscular control effects on 3-D knee joint loading during movements that can potentially cause injury to the anterior cruciate ligament (ACL) in the knee. The simulation consisted of a forward dynamic 3-D musculoskeletal model of the lower extremity, scaled to represent a specific subject. Inputs of the model were the initial position and velocity of the skeletal elements, and the muscle stimulation patterns. Outputs of the model were movement and ground reaction forces, as well as resultant 3-D forces and moments acting across the knee joint. An optimization method was established to find muscle stimulation patterns that best reproduced the subject's movement and ground reaction forces during a sidestepping task. The optimized model produced movements and forces that were generally within one standard deviation of the measured subject data. Resultant knee joint loading variables extracted from the optimized model were comparable to those reported in the literature. The ability of the model to successfully predict the subject's response to altered initial conditions was quantified and found acceptable for use of the model to investigate the effect of altered neuromuscular control on knee joint loading during sidestepping. Monte Carlo simulations (N = 100,000) using randomly perturbed initial kinematic conditions, based on the subject's variability, resulted in peak anterior force, valgus torque and internal torque values of 378 N, 94 Nm and 71 Nm, respectively, large enough to cause ACL rupture. We conclude that the procedures described in this paper were successful in creating valid simulations of normal movement, and in simulating injuries that are caused by perturbed neuromuscular control.

  7. Statistical analysis of cell migration in 3D using the anisotropic persistent random walk model.

    PubMed

    Wu, Pei-Hsun; Giri, Anjil; Wirtz, Denis

    2015-03-01

    Cell migration through 3D extracellular matrices (ECMs) is crucial to the normal development of tissues and organs and in disease processes, yet adequate analytical tools to characterize 3D migration are lacking. The motility of eukaryotic cells on 2D substrates in the absence of gradients has long been described using persistent random walks (PRWs). Recent work shows that 3D migration is anisotropic and features an exponential mean cell velocity distribution, rendering the PRW model invalid. Here we present a protocol for the analysis of 3D cell motility using the anisotropic PRW model. The software, which is implemented in MATLAB, enables statistical profiling of experimentally observed 2D and 3D cell trajectories, and it extracts the persistence and speed of cells along primary and nonprimary directions and an anisotropic index of migration. Basic computer skills and experience with MATLAB software are recommended for successful use of the protocol. This protocol is highly automated and fast, taking <30 min to analyze trajectory data per biological condition.

  8. Automatic 3D Cell Analysis in High-Throughput Microarray Using Micropillar and Microwell Chips.

    PubMed

    Lee, Dong Woo; Lee, Moo-Yeal; Ku, Bosung; Nam, Do-Hyun

    2015-10-01

    Area-based and intensity-based 3D cell viability measurement methods are compared in high-throughput screening in order to analyze their effects on the assay results (doubling time and IC50) and their repeatability. Many other 3D cell-based high-throughput screening platforms had been previously introduced, but these had not clearly addressed the effects of the two methods on the assay results and assay repeatability. In this study, the optimal way to analyze 3D cultured cells is achieved by comparing day-to-day data of doubling times and IC50 values obtained from the two methods. In experiments, the U251 cell line is grown in chips. The doubling time, based on the area of the 3D cells, was 27.8 ± 1.8 h (standard deviation: 6.6%) and 27.8 ± 3.8 h (standard deviation: 13.7%) based on the intensity of the 3D cells. The doubling time calculated by area shows a smaller standard deviation than one calculated by intensity. IC50 values calculated by both methods are very similar. The standard deviations of IC50 values for the two methods were within ± 3-fold. The IC50 variations of the 12 compounds were similar regardless of the viability measurement methods and were highly related to the shape of the dose-response curves.

  9. 3D cell culture to determine in vitro biocompatibility of bioactive glass in association with chitosan.

    PubMed

    Bédouin, Y; Pellen Mussi, P; Tricot-Doleux, S; Chauvel-Lebret, D; Auroy, P; Ravalec, X; Oudadesse, H; Perez, F

    2015-01-01

    This study reports the in vitro biocompatibility of a composite biomaterial composed of 46S6 bioactive glass in association with chitosan (CH) by using 3D osteoblast culture of SaOS2. The 46S6 and CH composite (46S6-CH) forms small hydroxyapatite crystals on its surface after only three days immersion in the simulated body fluid. For 2D osteoblast culture, a significant increase in cell proliferation was observed after three days of contact with 46S6 or 46S6-CH-immersed media. After six days, 46S6-CH led to a significant increase in cell proliferation (128%) compared with pure 46S6 (113%) and pure CH (122%). For 3D osteoblast culture, after six days of culture, there was an increase in gene expression of markers of the early osteoblastic differentiation (RUNX2, ALP, COL1A1). Geometric structures corresponding to small apatite clusters were observed by SEM on the surface of the spheroids cultivated with 46S6 or 46S6-CH-immersed media. We showed different cellular responses depending on the 2D and 3D cell culture model. The induction of osteoblast differentiation in the 3D cell culture explained the differences of cell proliferation in contact with 46S6, CH or 46S6-CH-immersed media. This study confirmed that the 3D cell culture model is a very promising tool for in vitro biological evaluation of bone substitutes' properties.

  10. Enhancement of neurite outgrowth in neuron cancer stem cells by growth on 3-D collagen scaffolds

    SciTech Connect

    Chen, Chih-Hao; Kuo, Shyh Ming; Liu, Guei-Sheung; Chen, Wan-Nan U.; Chuang, Chin-Wen; Liu, Li-Feng

    2012-11-09

    Highlights: Black-Right-Pointing-Pointer Neuron cancer stem cells (NCSCs) behave high multiply of growth on collagen scaffold. Black-Right-Pointing-Pointer Enhancement of NCSCs neurite outgrowth on porous collagen scaffold. Black-Right-Pointing-Pointer 3-D collagen culture of NCSCs shows an advance differentiation than 2-D culture. -- Abstract: Collagen is one component of the extracellular matrix that has been widely used for constructive remodeling to facilitate cell growth and differentiation. The 3-D distribution and growth of cells within the porous scaffold suggest a clinical significance for nerve tissue engineering. In the current study, we investigated proliferation and differentiation of neuron cancer stem cells (NCSCs) on a 3-D porous collagen scaffold that mimics the natural extracellular matrix. We first generated green fluorescence protein (GFP) expressing NCSCs using a lentiviral system to instantly monitor the transitions of morphological changes during growth on the 3-D scaffold. We found that proliferation of GFP-NCSCs increased, and a single cell mass rapidly grew with unrestricted expansion between days 3 and 9 in culture. Moreover, immunostaining with neuronal nuclei (NeuN) revealed that NCSCs grown on the 3-D collagen scaffold significantly enhanced neurite outgrowth. Our findings confirmed that the 80 {mu}m porous collagen scaffold could enhance attachment, viability and differentiation of the cancer neural stem cells. This result could provide a new application for nerve tissue engineering and nerve regeneration.

  11. 3D texture analysis in renal cell carcinoma tissue image grading.

    PubMed

    Kim, Tae-Yun; Cho, Nam-Hoon; Jeong, Goo-Bo; Bengtsson, Ewert; Choi, Heung-Kook

    2014-01-01

    One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM) and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system.

  12. 3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading

    PubMed Central

    Cho, Nam-Hoon; Choi, Heung-Kook

    2014-01-01

    One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM) and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system. PMID:25371701

  13. 3D Lifetime Tomography Reveals How CdCl 2 Improves Recombination Throughout CdTe Solar Cells

    SciTech Connect

    Barnard, Edward S.; Ursprung, Benedikt; Colegrove, Eric; Moutinho, Helio R.; Borys, Nicholas J.; Hardin, Brian E.; Peters, Craig H.; Metzger, Wyatt K.; Schuck, P. James

    2016-11-15

    When using two-photon tomography, carrier lifetimes are mapped in polycrystalline CdTe photovoltaic devices. These 3D maps probe subsurface carrier dynamics that are inaccessible with traditional optical techniques. They reveal that CdCl2 treatment of CdTe solar cells suppresses nonradiative recombination and enhances carrier lifetimes throughout the film with substantial improvements particularly near subsurface grain boundaries and the critical buried p-n junction.

  14. 3D Lifetime Tomography Reveals How CdCl 2 Improves Recombination Throughout CdTe Solar Cells

    DOE PAGES

    Barnard, Edward S.; Ursprung, Benedikt; Colegrove, Eric; ...

    2016-11-15

    When using two-photon tomography, carrier lifetimes are mapped in polycrystalline CdTe photovoltaic devices. These 3D maps probe subsurface carrier dynamics that are inaccessible with traditional optical techniques. They reveal that CdCl2 treatment of CdTe solar cells suppresses nonradiative recombination and enhances carrier lifetimes throughout the film with substantial improvements particularly near subsurface grain boundaries and the critical buried p-n junction.

  15. 3D Lifetime Tomography Reveals How CdCl2 Improves Recombination Throughout CdTe Solar Cells.

    PubMed

    Barnard, Edward S; Ursprung, Benedikt; Colegrove, Eric; Moutinho, Helio R; Borys, Nicholas J; Hardin, Brian E; Peters, Craig H; Metzger, Wyatt K; Schuck, P James

    2017-01-01

    Using two-photon tomography, carrier lifetimes are mapped in polycrystalline CdTe photovoltaic devices. These 3D maps probe subsurface carrier dynamics that are inaccessible with traditional optical techniques. They reveal that CdCl2 treatment of CdTe solar cells suppresses nonradiative recombination and enhances carrier lifetimes throughout the film with substantial improvements particularly near subsurface grain boundaries and the critical buried p-n junction.

  16. Rapid 3D dynamic arterial spin labeling with a sparse model-based image reconstruction.

    PubMed

    Zhao, Li; Fielden, Samuel W; Feng, Xue; Wintermark, Max; Mugler, John P; Meyer, Craig H

    2015-11-01

    Dynamic arterial spin labeling (ASL) MRI measures the perfusion bolus at multiple observation times and yields accurate estimates of cerebral blood flow in the presence of variations in arterial transit time. ASL has intrinsically low signal-to-noise ratio (SNR) and is sensitive to motion, so that extensive signal averaging is typically required, leading to long scan times for dynamic ASL. The goal of this study was to develop an accelerated dynamic ASL method with improved SNR and robustness to motion using a model-based image reconstruction that exploits the inherent sparsity of dynamic ASL data. The first component of this method is a single-shot 3D turbo spin echo spiral pulse sequence accelerated using a combination of parallel imaging and compressed sensing. This pulse sequence was then incorporated into a dynamic pseudo continuous ASL acquisition acquired at multiple observation times, and the resulting images were jointly reconstructed enforcing a model of potential perfusion time courses. Performance of the technique was verified using a numerical phantom and it was validated on normal volunteers on a 3-Tesla scanner. In simulation, a spatial sparsity constraint improved SNR and reduced estimation errors. Combined with a model-based sparsity constraint, the proposed method further improved SNR, reduced estimation error and suppressed motion artifacts. Experimentally, the proposed method resulted in significant improvements, with scan times as short as 20s per time point. These results suggest that the model-based image reconstruction enables rapid dynamic ASL with improved accuracy and robustness.

  17. Insights from 3D numerical simulations on the dynamics of the India-Asia collision zone

    NASA Astrophysics Data System (ADS)

    Pusok, A. E.; Kaus, B.; Popov, A.

    2013-12-01

    The dynamics of the India-Asia collision zone remains one of the most remarkable topics of the current research interest: the transition from subduction to collision and uplift, followed by the rise of the abnormally thick Tibetan plateau, and the deformation at its Eastern and Western syntaxes, are processes still not fully understood. Models that have addressed this topic include wholescale underthrusting of Indian lithospheric mantle under Tibet, distributed homogeneous shortening or the thin-sheet model, slip-line field model for lateral extrusion or lower crustal flow models for the exhumation of the Himalayan units and lateral spreading of the Tibetan plateau. Of these, the thin-sheet model has successfully illustrated some of the basic physics of continental collision and has the advantage of a 3D model being reduced to 2D, but one of its major shortcomings is that it cannot simultaneously represent channel flow and gravitational collapse of the mantle lithosphere, since these mechanisms require the lithosphere to interact with the underlying mantle, or to have a vertically non-homogeneous rheology. As a consequence, 3D models are emerging as powerful tools to understand the dynamics of coupled systems. However, because of yet recent developments and various complexities, the current 3D models simulating the dynamics of continent collision zones have relied on certain explicit assumptions, such as replacing part of the asthenosphere with various types of boundary conditions that mimic the effect of mantle flow, in order to focus on the lithospheric/crustal deformation. Here, we employ the parallel 3D code LaMEM (Lithosphere and Mantle Evolution Model), with a finite difference staggered grid solver, which is capable of simulating lithospheric deformation while simultaneously taking mantle flow and a free surface into account. We present qualitative results on lithospheric and upper-mantle scale simulations in which the Indian lithosphere is subducted and

  18. Adipose tissue-derived stem cells display a proangiogenic phenotype on 3D scaffolds.

    PubMed

    Neofytou, Evgenios A; Chang, Edwin; Patlola, Bhagat; Joubert, Lydia-Marie; Rajadas, Jayakumar; Gambhir, Sanjiv S; Cheng, Zhen; Robbins, Robert C; Beygui, Ramin E

    2011-09-01

    Ischemic heart disease is the leading cause of death worldwide. Recent studies suggest that adipose tissue-derived stem cells (ASCs) can be used as a potential source for cardiovascular tissue engineering due to their ability to differentiate along the cardiovascular lineage and to adopt a proangiogenic phenotype. To understand better ASCs' biology, we used a novel 3D culture device. ASCs' and b.END-3 endothelial cell proliferation, migration, and vessel morphogenesis were significantly enhanced compared to 2D culturing techniques. ASCs were isolated from inguinal fat pads of 6-week-old GFP+/BLI+ mice. Early passage ASCs cells (P3-P4), PKH26-labeled murine b.END-3 cells or a co-culture of ASCs and b.END-3 cells were seeded at a density of 1 × 10(5) on three different surface configurations: (a) a 2D surface of tissue culture plastic, (b) Matrigel, and (c) a highly porous 3D scaffold fabricated from inert polystyrene. VEGF expression, cell proliferation, and tubulization, were assessed using optical microscopy, fluorescence microscopy, 3D confocal microscopy, and SEM imaging (n = 6). Increased VEGF levels were seen in conditioned media harvested from co-cultures of ASCs and b.END-3 on either Matrigel or a 3D matrix. Fluorescence, confocal, SEM, bioluminescence revealed improved cell, proliferation, and tubule formation for cells seeded on the 3D polystyrene matrix. Collectively, these data demonstrate that co-culturing ASCs with endothelial cells in a 3D matrix environment enable us to generate prevascularized tissue-engineered constructs. This can potentially help us to surpass the tissue thickness limitations faced by the tissue engineering community today.

  19. A 3D sphere culture system containing functional polymers for large-scale human pluripotent stem cell production.

    PubMed

    Otsuji, Tomomi G; Bin, Jiang; Yoshimura, Azumi; Tomura, Misayo; Tateyama, Daiki; Minami, Itsunari; Yoshikawa, Yoshihiro; Aiba, Kazuhiro; Heuser, John E; Nishino, Taito; Hasegawa, Kouichi; Nakatsuji, Norio

    2014-05-06

    Utilizing human pluripotent stem cells (hPSCs) in cell-based therapy and drug discovery requires large-scale cell production. However, scaling up conventional adherent cultures presents challenges of maintaining a uniform high quality at low cost. In this regard, suspension cultures are a viable alternative, because they are scalable and do not require adhesion surfaces. 3D culture systems such as bioreactors can be exploited for large-scale production. However, the limitations of current suspension culture methods include spontaneous fusion between cell aggregates and suboptimal passaging methods by dissociation and reaggregation. 3D culture systems that dynamically stir carrier beads or cell aggregates should be refined to reduce shearing forces that damage hPSCs. Here, we report a simple 3D sphere culture system that incorporates mechanical passaging and functional polymers. This setup resolves major problems associated with suspension culture methods and dynamic stirring systems and may be optimal for applications involving large-scale hPSC production.

  20. Bridging the gap: from 2D cell culture to 3D microengineered extracellular matrices

    PubMed Central

    Li, Yanfen

    2016-01-01

    Historically the culture of mammalian cells in the laboratory has been performed on planar substrates with media cocktails that are optimized to maintain phenotype. However, it is becoming increasingly clear that much of biology discerned from 2D studies does not translate well to the 3D microenvironment. Over the last several decades, 2D and 3D microengineering approaches have been developed that better recapitulate the complex architecture and properties of in vivo tissue. Inspired by the infrastructure of the microelectronics industry, lithographic patterning approaches have taken center stage because of the ease in which cell-sized features can be engineered on surfaces and within a broad range of biocompatible materials. Patterning and templating techniques enable precise control over extracellular matrix properties including: composition, mechanics, geometry, cell-cell contact, and diffusion. In this review article we will explore how the field of engineered extracellular matrices has evolved with the development of new hydrogel chemistry and the maturation of micro- and nano- fabrication. Guided by the spatiotemporal regulation of cell state in developing tissues, we will review the maturation of micropatterning in 2D, pseudo-3D systems, and patterning within 3D hydrogels in the context of translating the information gained from 2D systems to synthetic engineered 3D tissues. PMID:26592366

  1. 3D Cell Printing of Functional Skeletal Muscle Constructs Using Skeletal Muscle-Derived Bioink.

    PubMed

    Choi, Yeong-Jin; Kim, Taek Gyoung; Jeong, Jonghyeon; Yi, Hee-Gyeong; Park, Ji Won; Hwang, Woonbong; Cho, Dong-Woo

    2016-10-01

    Engineered skeletal muscle tissues that mimic the structure and function of native muscle have been considered as an alternative strategy for the treatment of various muscular diseases and injuries. Here, it is demonstrated that 3D cell-printing of decellularized skeletal muscle extracellular matrix (mdECM)-based bioink facilitates the fabrication of functional skeletal muscle constructs. The cellular alignment and the shape of the tissue constructs are controlled by 3D cell-printing technology. mdECM bioink provides the 3D cell-printed muscle constructs with a myogenic environment that supports high viability and contractility as well as myotube formation, differentiation, and maturation. More interestingly, the preservation of agrin is confirmed in the mdECM, and significant increases in the formation of acetylcholine receptor clusters are exhibited in the 3D cell-printed muscle constructs. In conclusion, mdECM bioink and 3D cell-printing technology facilitate the mimicking of both the structural and functional properties of native muscle and hold great promise for producing clinically relevant engineered muscle for the treatment of muscular injuries.

  2. A cell-instructive hydrogel to regulate malignancy of 3D tumor spheroids with matrix rigidity.

    PubMed

    Liang, Youyun; Jeong, Jaehyun; DeVolder, Ross J; Cha, Chaenyung; Wang, Fei; Tong, Yen Wah; Kong, Hyunjoon

    2011-12-01

    Three dimensional (3D) tumor spheroid models are becoming important biomedical tools for both fundamental and applied cancer studies, but current models do not account for different levels of cancer malignancy. Several studies have reported that the mechanical rigidity of a hydrogel plays a significant role in regulating the phenotypes of cancer cells adhered to the gel surface. This finding suggests that matrix rigidity should also modulate the malignancy of 3D tumor spheroids. However, the role of matrix stiffness is often confounded by concurrent changes in 3D matrix permeability. This study reports an advanced strategy to assemble 3D liver tumor spheroids with controlled intercellular organization, phenotypes, and angiogenic activities using hydrogels with controlled stiffness and minimal differences in molecular diffusivity. The elastic moduli of cell-encapsulated collagen gels were increased by stiffening interconnected collagen fibers with varied amounts of poly(ethylene glycol) di-(succinic acid N-hydroxysuccinimidyl ester). Interestingly, hepatocellular carcinoma cells encapsulated in a fat-like, softer hydrogel formed malignant cancer spheroids, while cells cultured in a liver-like, stiffer gel formed compact hepatoids with suppressed malignancy. Overall, both the hydrogel and the 3D tumor spheroids developed in this study will be greatly useful to better understand and regulate the emergent behaviors of various cancer cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

  3. 3D Models of the NCI60 Cell Lines for Screening Oncology Compounds.

    PubMed

    Selby, Mike; Delosh, Rene; Laudeman, Julie; Ogle, Chad; Reinhart, Russell; Silvers, Thomas; Lawrence, Scott; Kinders, Robert; Parchment, Ralph; Teicher, Beverly A; Evans, David M

    2017-03-01

    The NCI60 cell line panel screen includes 60 human tumor cell lines derived from nine tumor types that has been used over the past 20+ years to screen small molecules, biologics, and natural products for activity. Cells in monolayer culture in 96-well plates are exposed to compounds for 48 h, and Sulforhodamine B is used to determine cell viability. Data analysis tools such as COMPARE allow classification of compounds based on the pattern of cell line response. However, many compounds highly active in monolayer cell culture fail to show efficacy in vivo. Therefore, we explored 3D culture of the NCI60 panel as a strategy to improve the predictive accuracy of the screen. 3D cultures more closely resemble tumors than monolayer cultures with tighter cell-cell contact and nutrient and oxygen gradients between the periphery and the center. We optimized the NCI60 cell line panel for generating 3D spheroids of a prespecified diameter (300-500 µm) in ultra-low attachment (ULA) plates. Spheroids were classified into four categories based on imaging, and concentration response of select agents in 2D and 3D models is presented.

  4. Paper/PMMA Hybrid 3D Cell Culture Microfluidic Platform for the Study of Cellular Crosstalk.

    PubMed

    Lei, Kin Fong; Chang, Chih-Hsuan; Chen, Ming-Jie

    2017-04-06

    Studying cellular crosstalk is important for understanding tumor initiation, progression, metastasis, and therapeutic resistance. Moreover, a three-dimensional (3D) cell culture model can provide a more physiologically meaningful culture microenvironment. However, studying cellular crosstalk in a 3D cell culture model involves tedious processing. In this study, a paper/poly(methyl methacrylate) (PMMA) hybrid 3D cell culture microfluidic platform was successfully developed for the study of cellular crosstalk. The platform was a paper substrate with culture microreactors placed on a PMMA substrate with hydrogel-infused channels. Different types of cells were directly seeded and cultured in the microreactors. Aberrant cell proliferation of the affected cells was induced by secretions from transfected cells, and the proliferation ratios were investigated using a colorimetric method. The results showed that the responses of cellular crosstalk were different in different types of cells. Moreover, neutralizing and competitive assays were performed to show the functionality of the platform. Additionally, the triggered signaling pathways of the affected cells were directly analyzed by a subsequent immunoassay. The microfluidic platform provides a simple method for studying cellular crosstalk and the corresponding signaling pathways in a 3D culture model.

  5. A novel 3D human glioblastoma cell culture system for modeling drug and radiation responses

    PubMed Central

    Stevenson, Katrina; Gilmour, Lesley; Hamilton, Graham; Chalmers, Anthony J

    2017-01-01

    Abstract Background. Glioblastoma (GBM) is the most common primary brain tumor, with dismal prognosis. The failure of drug–radiation combinations with promising preclinical data to translate into effective clinical treatments may relate to the use of simplified 2-dimensional in vitro GBM cultures. Methods. We developed a customized 3D GBM culture system based on a polystyrene scaffold (Alvetex) that recapitulates key histological features of GBM and compared it with conventional 2D cultures with respect to their response to radiation and to molecular targeted agents for which clinical data are available. Results. In 3 patient-derived GBM lines, no difference in radiation sensitivity was observed between 2D and 3D cultures, as measured by clonogenic survival. Three different molecular targeted agents, for which robust clinical data are available were evaluated in 2D and 3D conditions: (i) temozolomide, which improves overall survival and is standard of care for GBM, exhibited statistically significant effects on clonogenic survival in both patient-derived cell lines when evaluated in the 3D model compared with only one cell line in 2D cells; (ii) bevacizumab, which has been shown to increase progression-free survival when added to standard chemoradiation in phase III clinical trials, exhibited marked radiosensitizing activity in our 3D model but had no effect on 2D cells; and (iii) erlotinib, which had no efficacy in clinical trials, displayed no activity in our 3D GBM model, but radiosensitized 2D cells. Conclusions. Our 3D model reliably predicted clinical efficacy, strongly supporting its clinical relevance and potential value in preclinical evaluation of drug–radiation combinations for GBM. PMID:27576873

  6. A novel 3D human glioblastoma cell culture system for modeling drug and radiation responses.

    PubMed

    Gomez-Roman, Natividad; Stevenson, Katrina; Gilmour, Lesley; Hamilton, Graham; Chalmers, Anthony J

    2017-02-01

    Glioblastoma (GBM) is the most common primary brain tumor, with dismal prognosis. The failure of drug-radiation combinations with promising preclinical data to translate into effective clinical treatments may relate to the use of simplified 2-dimensional in vitro GBM cultures. We developed a customized 3D GBM culture system based on a polystyrene scaffold (Alvetex) that recapitulates key histological features of GBM and compared it with conventional 2D cultures with respect to their response to radiation and to molecular targeted agents for which clinical data are available. In 3 patient-derived GBM lines, no difference in radiation sensitivity was observed between 2D and 3D cultures, as measured by clonogenic survival. Three different molecular targeted agents, for which robust clinical data are available were evaluated in 2D and 3D conditions: (i) temozolomide, which improves overall survival and is standard of care for GBM, exhibited statistically significant effects on clonogenic survival in both patient-derived cell lines when evaluated in the 3D model compared with only one cell line in 2D cells; (ii) bevacizumab, which has been shown to increase progression-free survival when added to standard chemoradiation in phase III clinical trials, exhibited marked radiosensitizing activity in our 3D model but had no effect on 2D cells; and (iii) erlotinib, which had no efficacy in clinical trials, displayed no activity in our 3D GBM model, but radiosensitized 2D cells. Our 3D model reliably predicted clinical efficacy, strongly supporting its clinical relevance and potential value in preclinical evaluation of drug-radiation combinations for GBM.

  7. Quantification by SIFT-MS of acetaldehyde released by lung cells in a 3D model.

    PubMed

    Rutter, Abigail V; Chippendale, Thomas W E; Yang, Ying; Španěl, Patrik; Smith, David; Sulé-Suso, Josep

    2013-01-07

    Our previous studies have shown that both lung cancer cells and non-malignant lung cells release acetaldehyde in vitro. However, data from other laboratories have produced conflicting results. Furthermore, all these studies have been carried out in 2D models which are less physiological cell growth systems when compared to 3D models. Therefore, we have carried out further work on the release of acetaldehyde by lung cells in 3D collagen hydrogels. Lung cancer cells CALU-1 and non-malignant lung cells NL20 were seeded in these hydrogels at different cell concentrations and the release of acetaldehyde was measured with the Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) technique. The data obtained showed that the amount of acetaldehyde released by both cell types grown in a 3D model is higher when compared to that of the same cells grown in 2D models. More importantly, acetaldehyde from the headspace of lung cancer cells could be measured even at a low cell concentration (10(5) cells per hydrogel). The differential of acetaldehyde release could be, depending on the cell concentration, more than 3 fold higher for cancer cells when compared to non-malignant lung cells. This pilot study is the first to study acetaldehyde emission from albeit only two cell types cultured in 3D scaffolds. Clearly, from such limited data the behaviour of other cell types and of tumour cells in vivo cannot be predicted with confidence. Nevertheless, this work represents another step in the search for volatile biomarkers of tumour cells, the ultimate goal of which is to exploit volatile compounds in exhaled breath and other biological fluids as biomarkers of tumours in vivo.

  8. 3D Nanochannel Array Platform for High-throughput Cell Manipulation and Nano-electroporation

    NASA Astrophysics Data System (ADS)

    Chang, Lingqian

    Electroporation is one of the most common non-viral methods for gene delivery. Recent progress in gene therapy has offered special opportunities to electroporation for in vitro and in vivo applications. However, conventional bulk electroporation (BEP) inevitably causes serious cell damage and stochastic transfection between cells. Microfluidic electroporation (MEP) has been claimed to provide benign single cell transfection for the last decade. Nevertheless, the intracellular transport in both MEP and BEP systems is highly diffusion-dominant, which prevents precise dose control and high uniformity. In this Ph.D. research, we developed a 3D nanochannel-electroporation (3D NEP) platform for mass cell transfection. A silicon-based nanochannel array (3D NEP) chip was designed and fabricated for cell manipulation and electroporation. The chip, designed as Z-directional microchannel - nanochannel array, was fabricated by clean room techniques including projection photolithography and deep reactive-ion etching (DRIE). The fabricated 3D NEP chip is capable of handling 40,000 cells per 1 cm2, up to 1 million per wafer (100 mm diameter). High-throughput cell manipulation technologies were investigated for precise alignment of individual cells to the nanochannel array, a key step for NEP to achieve dose control. We developed three techniques for cell trapping in this work. (1) Magnetic tweezers (MTs) were integrated on the chip to remotely control cells under a programmed magnetic field. (2) A positive dielectrophoresis (pDEP) power system was built as an alternative to trap cells onto the nanochannel array using DEP force. (3) A novel yet simple 'dipping-trap' method was used to rapidly trap cells onto a nanochannel array, aligned by a micro-cap array pattern on the 3D NEP chip, which eventually offered 70 - 90 % trapping efficiency and 90 % specificity. 3D NEP platforms were assembled for cell transfection based on the Si-based nanochannel array chip and cell manipulation

  9. Innovative LIDAR 3D Dynamic Measurement System to Estimate Fruit-Tree Leaf Area

    PubMed Central

    Sanz-Cortiella, Ricardo; Llorens-Calveras, Jordi; Escolà, Alexandre; Arnó-Satorra, Jaume; Ribes-Dasi, Manel; Masip-Vilalta, Joan; Camp, Ferran; Gràcia-Aguilá, Felip; Solanelles-Batlle, Francesc; Planas-DeMartí, Santiago; Pallejà-Cabré, Tomàs; Palacin-Roca, Jordi; Gregorio-Lopez, Eduard; Del-Moral-Martínez, Ignacio; Rosell-Polo, Joan R.

    2011-01-01

    In this work, a LIDAR-based 3D Dynamic Measurement System is presented and evaluated for the geometric characterization of tree crops. Using this measurement system, trees were scanned from two opposing sides to obtain two three-dimensional point clouds. After registration of the point clouds, a simple and easily obtainable parameter is the number of impacts received by the scanned vegetation. The work in this study is based on the hypothesis of the existence of a linear relationship between the number of impacts of the LIDAR sensor laser beam on the vegetation and the tree leaf area. Tests performed under laboratory conditions using an ornamental tree and, subsequently, in a pear tree orchard demonstrate the correct operation of the measurement system presented in this paper. The results from both the laboratory and field tests confirm the initial hypothesis and the 3D Dynamic Measurement System is validated in field operation. This opens the door to new lines of research centred on the geometric characterization of tree crops in the field of agriculture and, more specifically, in precision fruit growing. PMID:22163926

  10. Dynamic 3-D virtual fixtures for minimally invasive beating heart procedures.

    PubMed

    Ren, Jing; Patel, Rajni V; McIsaac, Kenneth A; Guiraudon, Gerard; Peters, Terry M

    2008-08-01

    Two-dimensional or 3-D visual guidance is often used for minimally invasive cardiac surgery and diagnosis. This visual guidance suffers from several drawbacks such as limited field of view, loss of signal from time to time, and in some cases, difficulty of interpretation. These limitations become more evident in beating-heart procedures when the surgeon has to perform a surgical procedure in the presence of heart motion. In this paper, we propose dynamic 3-D virtual fixtures (DVFs) to augment the visual guidance system with haptic feedback, to provide the surgeon with more helpful guidance by constraining the surgeon's hand motions thereby protecting sensitive structures. DVFs can be generated from preoperative dynamic magnetic resonance (MR) or computed tomograph (CT) images and then mapped to the patient during surgery. We have validated the feasibility of the proposed method on several simulated surgical tasks using a volunteer's cardiac image dataset. Validation results show that the integration of visual and haptic guidance can permit a user to perform surgical tasks more easily and with reduced error rate. We believe this is the first work presented in the field of virtual fixtures that explicitly considers heart motion.

  11. A high dynamic range structured light means for the 3D measurement of specular surface

    NASA Astrophysics Data System (ADS)

    Song, Zhan; Jiang, Hualie; Lin, Haibo; Tang, Suming

    2017-08-01

    This paper presents a novel structured light approach for the 3D reconstruction of specular surface. The binary shifting strip is adopted as structured light pattern instead of conventional sinusoidal pattern. Based on the framework of conventional High Dynamic Range (HDR) imaging technique, an efficient means is first introduced to estimate the camera response function. And then, dynamic range of the generated radiance map is compressed in the gradient domain by introducing an attenuation function. Subject to the change of lighting conditions caused by projecting different structured light patterns, the structure light image with middle exposure level is selected as the reference image and used for the slight adjustment of the primary fused image. Finally, the regenerated structured light images with well exposing condition are used for 3D reconstruction of the specular surface. To evaluate performance of the method, some stainless stamping parts with strong reflectivity are used for the experiments. And the results showed that, different specular targets with various shapes can be precisely reconstructed by the proposed method.

  12. Stability and 3-D spatial dynamics analysis of a three cable crane

    NASA Technical Reports Server (NTRS)

    Yang, Li-Farn; Mikulas, Martin M., Jr.; Chiou, Jin-Chern

    1992-01-01

    A 3-cable crane mechanism has been designed for incorporation into a highly loaded Lunar crane for planetary construction. This 3-cable crane must maintain a positive stability margin in all phases of the loading/unloading, assembly, or installation operations. A 2D kinematic curvature theory is applied to: (1) derive a general stability criterion to prevent the 3-cable crane from instability; and (2) determine a simple equation of natural frequency for two planar models of 3-cable crane. Investigation of the 2D vibrational characteristics of the planar models provides valuable insight toward understanding of 3D dynamic behavior of the 3-cable crane. Also, precision in natural frequency from this simple kinematic equation due to the exclusion of the radius-of-gyration of a suspended article is discussed. Multibody dynamics of the 3D 3-cable crane is presented and simulated to study the resulting vibrational characteristics under external disturbances and to verify the feasibility of the stability criterion for the 3-cable crane.

  13. Innovative LIDAR 3D Dynamic Measurement System to estimate fruit-tree leaf area.

    PubMed

    Sanz-Cortiella, Ricardo; Llorens-Calveras, Jordi; Escolà, Alexandre; Arnó-Satorra, Jaume; Ribes-Dasi, Manel; Masip-Vilalta, Joan; Camp, Ferran; Gràcia-Aguilá, Felip; Solanelles-Batlle, Francesc; Planas-DeMartí, Santiago; Pallejà-Cabré, Tomàs; Palacin-Roca, Jordi; Gregorio-Lopez, Eduard; Del-Moral-Martínez, Ignacio; Rosell-Polo, Joan R

    2011-01-01

    In this work, a LIDAR-based 3D Dynamic Measurement System is presented and evaluated for the geometric characterization of tree crops. Using this measurement system, trees were scanned from two opposing sides to obtain two three-dimensional point clouds. After registration of the point clouds, a simple and easily obtainable parameter is the number of impacts received by the scanned vegetation. The work in this study is based on the hypothesis of the existence of a linear relationship between the number of impacts of the LIDAR sensor laser beam on the vegetation and the tree leaf area. Tests performed under laboratory conditions using an ornamental tree and, subsequently, in a pear tree orchard demonstrate the correct operation of the measurement system presented in this paper. The results from both the laboratory and field tests confirm the initial hypothesis and the 3D Dynamic Measurement System is validated in field operation. This opens the door to new lines of research centred on the geometric characterization of tree crops in the field of agriculture and, more specifically, in precision fruit growing.

  14. Stability and 3-D spatial dynamics analysis of a three cable crane

    NASA Technical Reports Server (NTRS)

    Yang, Li-Farn; Mikulas, Martin M., Jr.; Chiou, Jin-Chern

    1992-01-01

    A 3-cable crane mechanism has been designed for incorporation into a highly loaded Lunar crane for planetary construction. This 3-cable crane must maintain a positive stability margin in all phases of the loading/unloading, assembly, or installation operations. A 2D kinematic curvature theory is applied to: (1) derive a general stability criterion to prevent the 3-cable crane from instability; and (2) determine a simple equation of natural frequency for two planar models of 3-cable crane. Investigation of the 2D vibrational characteristics of the planar models provides valuable insight toward understanding of 3D dynamic behavior of the 3-cable crane. Also, precision in natural frequency from this simple kinematic equation due to the exclusion of the radius-of-gyration of a suspended article is discussed. Multibody dynamics of the 3D 3-cable crane is presented and simulated to study the resulting vibrational characteristics under external disturbances and to verify the feasibility of the stability criterion for the 3-cable crane.

  15. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    NASA Technical Reports Server (NTRS)

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-01

    This paper presents results from an exploratory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected and the resulting steady-state analyses using NASA's FUN3D CFD software.

  16. A portable instrument for 3-D dynamic robot measurements using triangulation and laser tracking

    SciTech Connect

    Mayer, J.R.R. . Mechanical Engineering Dept.); Parker, G.A. . Dept. of Mechanical Engineering)

    1994-08-01

    The paper describes the development and validation of a 3-D measurement instrument capable of determining the static and dynamic performance of industrial robots to ISO standards. Using two laser beams to track an optical target attached to the robot end-effector, the target position coordinates may be estimated, relative to the instrument coordinate frame, to a high accuracy using triangulation principles. The effect of variations in the instrument geometry from the nominal model is evaluated through a kinematic model of the tracking head. Significant improvements of the measurement accuracy are then obtained by a simple adjustment of the main parameters. Extensive experimental test results are included to demonstrate the instrument performance. Finally typical static and dynamic measurement results for an industrial robot are presented to illustrate the effectiveness and usefulness of the instrument.

  17. A high sensitive 66 dB linear dynamic range receiver for 3-D laser radar

    NASA Astrophysics Data System (ADS)

    Ma, Rui; Zheng, Hao; Zhu, Zhangming

    2017-08-01

    This study presents a CMOS receiver chip realized in 0.18 μm standard CMOS technology and intended for high precision 3-D laser radar. The chip includes an adjustable gain transimpedance pre-amplifier, a post-amplifier and two timing comparators. An additional feedback is employed in the regulated cascode transimpedance amplifier to decrease the input impedance, and a variable gain transimpedance amplifier controlled by digital switches and analog multiplexer is utilized to realize four gain modes, extending the input dynamic range. The measurement shows that the highest transimpedance of the channel is 50 k {{Ω }}, the uncompensated walk error is 1.44 ns in a wide linear dynamic range of 66 dB (1:2000), and the input referred noise current is 2.3 pA/\\sqrt{{Hz}} (rms), resulting in a very low detectable input current of 1 μA with SNR = 5.

  18. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    SciTech Connect

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-04

    This paper presents results from an explanatory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected in the resulting steady-state analyses using NASA's FUN3D CFD software.

  19. Semi-brittle rheology and ice dynamics in DynEarthSol3D

    NASA Astrophysics Data System (ADS)

    Logan, Liz C.; Lavier, Luc L.; Choi, Eunseo; Tan, Eh; Catania, Ginny A.

    2017-01-01

    We present a semi-brittle rheology and explore its potential for simulating glacier and ice sheet deformation using a numerical model, DynEarthSol3D (DES), in simple, idealized experiments. DES is a finite-element solver for the dynamic and quasi-static simulation of continuous media. The experiments within demonstrate the potential for DES to simulate ice failure and deformation in dynamic regions of glaciers, especially at quickly changing boundaries like glacier termini in contact with the ocean. We explore the effect that different rheological assumptions have on the pattern of flow and failure. We find that the use of a semi-brittle constitutive law is a sufficient material condition to form the characteristic pattern of basal crevasse-aided pinch-and-swell geometry, which is observed globally in floating portions of ice and can often aid in eroding the ice sheet margins in direct contact with oceans.

  20. Microchip-based 3D-Cell Culture Using Polymer Nanofibers Generated by Solution Blow Spinning.

    PubMed

    Chen, Chengpeng; Townsend, Alexandra D; Sell, Scott A; Martin, R Scott

    2017-06-14

    Polymer nano/micro fibers have found many applications including 3D cell culture and the creation of wound dressings. The fibers can be produced by a variety of techniques that include electrospinning, the primary disadvantage of which include the requirement for a high voltage supply (which may cause issues such as polymer denaturation) and lack of portability. More recently, solution blow spinning, where a high velocity sheath gas is used instead of high voltage, has been used to generate polymer fibers. In this work, we used blow spinning to create nano/microfibers for microchip-based 3D cell culture. First, we thoroughly investigated fiber generation from a 3D printed gas sheath device using two polymers that are amenable to cell culture (polycaprolactone, PCL and polystyrene, PS) as well as the parameters that can affect PCL and PS fiber quality. Using the 3D printed sheath device, it was found that the pressure of the sheath N2 and the concentration of polymer solutions determine if fibers can be produced as well as the resulting fiber morphology. In addition, we showed how these fibers can be used for 3D cell culture by directly depositing PCL fibers in petri dishes and well plates. It is shown the fibers have good compatibility with RAW 264.7 macrophages and the PCL fiber scaffold can be as thick as 178 ± 14 μm. PCL fibers created from solution blow spinning (with the 3D printed sheath device) were then integrated with a microfluidic device for the first time to fabricate a 3D cell culture scaffold with a flow component. After culturing and stimulating macrophages on the fluidic device, it was found that the integrated 3D fibrous scaffold is a better mimic of the extracellular matrix (as opposed to a flat, 2D substrate), with enhanced nitrite accumulation (product of nitric oxide release) from macrophages stimulated with lipopolysaccharide. PS fibers were also made and integrated in a microfluidic device for 3D culture of endothelial cells, which stayed

  1. Large-scale pharmacological profiling of 3D tumor models of cancer cells.

    PubMed

    Mathews Griner, Lesley A; Zhang, Xiaohu; Guha, Rajarshi; McKnight, Crystal; Goldlust, Ian S; Lal-Nag, Madhu; Wilson, Kelli; Michael, Sam; Titus, Steve; Shinn, Paul; Thomas, Craig J; Ferrer, Marc

    2016-12-01

    The discovery of chemotherapeutic agents for the treatment of cancer commonly uses cell proliferation assays in which cells grow as two-dimensional (2D) monolayers. Compounds identified using 2D monolayer assays often fail to advance during clinical development, most likely because these assays do not reproduce the cellular complexity of tumors and their microenvironment in vivo. The use of three-dimensional (3D) cellular systems have been explored as enabling more predictive in vitro tumor models for drug discovery. To date, small-scale screens have demonstrated that pharmacological responses tend to differ between 2D and 3D cancer cell growth models. However, the limited scope of screens using 3D models has not provided a clear delineation of the cellular pathways and processes that differentially regulate cell survival and death in the different in vitro tumor models. Here we sought to further understand the differences in pharmacological responses between cancer tumor cells grown in different conditions by profiling a large collection of 1912 chemotherapeutic agents. We compared pharmacological responses obtained from cells cultured in traditional 2D monolayer conditions with those responses obtained from cells forming spheres versus cells already in 3D spheres. The target annotation of the compound library screened enabled the identification of those key cellular pathways and processes that when modulated by drugs induced cell death in all growth conditions or selectively in the different cell growth models. In addition, we also show that many of the compounds targeting these key cellular functions can be combined to produce synergistic cytotoxic effects, which in many cases differ in the magnitude of their synergism depending on the cellular model and cell type. The results from this work provide a high-throughput screening framework to profile the responses of drugs both as single agents and in pairwise combinations in 3D sphere models of cancer cells.

  2. Large-scale pharmacological profiling of 3D tumor models of cancer cells

    PubMed Central

    Mathews Griner, Lesley A; Zhang, Xiaohu; Guha, Rajarshi; McKnight, Crystal; Goldlust, Ian S; Lal-Nag, Madhu; Wilson, Kelli; Michael, Sam; Titus, Steve; Shinn, Paul; Thomas, Craig J; Ferrer, Marc

    2016-01-01

    The discovery of chemotherapeutic agents for the treatment of cancer commonly uses cell proliferation assays in which cells grow as two-dimensional (2D) monolayers. Compounds identified using 2D monolayer assays often fail to advance during clinical development, most likely because these assays do not reproduce the cellular complexity of tumors and their microenvironment in vivo. The use of three-dimensional (3D) cellular systems have been explored as enabling more predictive in vitro tumor models for drug discovery. To date, small-scale screens have demonstrated that pharmacological responses tend to differ between 2D and 3D cancer cell growth models. However, the limited scope of screens using 3D models has not provided a clear delineation of the cellular pathways and processes that differentially regulate cell survival and death in the different in vitro tumor models. Here we sought to further understand the differences in pharmacological responses between cancer tumor cells grown in different conditions by profiling a large collection of 1912 chemotherapeutic agents. We compared pharmacological responses obtained from cells cultured in traditional 2D monolayer conditions with those responses obtained from cells forming spheres versus cells already in 3D spheres. The target annotation of the compound library screened enabled the identification of those key cellular pathways and processes that when modulated by drugs induced cell death in all growth conditions or selectively in the different cell growth models. In addition, we also show that many of the compounds targeting these key cellular functions can be combined to produce synergistic cytotoxic effects, which in many cases differ in the magnitude of their synergism depending on the cellular model and cell type. The results from this work provide a high-throughput screening framework to profile the responses of drugs both as single agents and in pairwise combinations in 3D sphere models of cancer cells. PMID

  3. Influence of the 3D inverse dynamic method on the joint forces and moments during gait.

    PubMed

    Dumas, R; Nicol, E; Chèze, L

    2007-10-01

    The joint forces and moments are commonly used in gait analysis. They can be computed by four different 3D inverse dynamic methods proposed in the literature, either based on vectors and Euler angles, wrenches and quaternions, homogeneous matrices, or generalized coordinates and forces. In order to analyze the influence of the inverse dynamic method, the joint forces and moments were computed during gait on nine healthy subjects. A ratio was computed between the relative dispersions (due to the method) and the absolute amplitudes of the gait curves. The influence of the inverse dynamic method was negligible at the ankle (2%) but major at the knee and the hip joints (40%). This influence seems to be due to the dynamic computation rather than the kinematic computation. Compared to the influence of the joint center location, the body segment inertial parameter estimation, and more, the influence of the inverse dynamic method is at least of equivalent importance. This point should be confirmed with other subjects, possibly pathologic, and other movements.

  4. 3D microscale laser dynamic forming: Multiscale modeling and experimental validation

    SciTech Connect

    Gao Huang; Cheng, Gary J.

    2011-05-15

    Microscale laser dynamic forming ({mu}LDF) shows great potential in fabricating robust and high-aspect-ratio metallic microcomponents. Experiments revealed that strain rate and sample size play important roles in determining the dynamic plasticity and final results of {mu}LDF. To further understand these effects, a multiscale modeling methodology is adopted to characterize the microscale dynamic plasticity considering the evolutions of nano-to-submicron dislocations avalanches under shock loading. In this methodology, 3D discrete dislocation dynamics simulations are implemented to derive the yield strength and the initial strain hardening dependence on size and strain rate. It is observed that there exist three dynamic stages during deformation process. The initial strain hardening rate in Stage II increases with strain rate. The mechanical threshold stress model, intrinsically equipped with strain-rate-dependent flow stress and initial hardening, is chosen and modified to incorporate size effect quantitatively. This scale-dependent model, implemented in abaqus/explicit, provides deformation depths and thickness variations in good agreement with experimental results in {mu}LDF.

  5. Mechanosensing of cells in 3D gel matrices based on natural and synthetic materials.

    PubMed

    Shan, Jieling; Chi, Qingjia; Wang, Hongbing; Huang, Qiping; Yang, Li; Yu, Guanglei; Zou, Xiaobing

    2014-11-01

    Cells in vivo typically are found in 3D matrices, the mechanical stiffness of which is important to the cell and tissue-scale biological processes. Although it is well characterized that as to how cells sense matrix stiffness in 2D substrates, the scenario in 3D matrices needs to be explored. Thus, materials that can mimic native 3D environments and possess wide, physiologically relevant elasticity are highly desirable. Natural polymer-based materials and synthetic hydrogels could provide an better 3D platforms to investigate the mechano-response of cells with stiffness comparable to their native environments. However, the limited stiffness range together with interdependence of matrix stiffness and adhesive ligand density are inherent in many kinds of materials, and hinder efforts to demonstrate the true effects contributed by matrix stiffness. These problems have been addressed by the recently emerging exquisitely designed materials based on native matrix components, designer matrices, and synthetic polymers. In this review, a variety of materials with a wide stiffness range that mimic the mechanical environment of native 3D matrices and the independent affection of stiffness for cellular behavior and tissue-level processes are discussed.

  6. Manifold Based Optimization for Single-Cell 3D Genome Reconstruction

    PubMed Central

    Collas, Philippe

    2015-01-01

    The three-dimensional (3D) structure of the genome is important for orchestration of gene expression and cell differentiation. While mapping genomes in 3D has for a long time been elusive, recent adaptations of high-throughput sequencing to chromosome conformation capture (3C) techniques, allows for genome-wide structural characterization for the first time. However, reconstruction of "consensus" 3D genomes from 3C-based data is a challenging problem, since the data are aggregated over millions of cells. Recent single-cell adaptations to the 3C-technique, however, allow for non-aggregated structural assessment of genome structure, but data suffer from sparse and noisy interaction sampling. We present a manifold based optimization (MBO) approach for the reconstruction of 3D genome structure from chromosomal contact data. We show that MBO is able to reconstruct 3D structures based on the chromosomal contacts, imposing fewer structural violations than comparable methods. Additionally, MBO is suitable for efficient high-throughput reconstruction of large systems, such as entire genomes, allowing for comparative studies of genomic structure across cell-lines and different species. PMID:26262780

  7. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation.

  8. Direct cell writing of 3D microorgan for in vitro pharmacokinetic model.

    PubMed

    Chang, Robert; Nam, Jae; Sun, Wei

    2008-06-01

    A novel targeted application of tissue engineering is the development of an in vitro pharmacokinetic model for drug screening and toxicology. An in vitro pharmacokinetic model is needed to realistically and reliably predict in vivo human response to drug administrations and potential toxic exposures. This paper details the fabrication process development and adaptation of microfluidic devices for the creation of such a physiologically relevant pharmacokinetic model. First, an automated syringe-based, layered direct cell writing (DCW) bioprinting process creates a 3D microorgan that biomimics the cell's natural microenvironment with enhanced functionality. Next, soft lithographic micropatterning techniques are used to fabricate a microscale in vitro device to house the 3D microorgan. This paper demonstrates the feasibility of the DCW process for freeform biofabrication of 3D cell-encapsulated hydrogel-based tissue constructs with defined reproducible patterns, direct integration of 3D constructs onto a microfluidic device for continuous perfusion drug flow, and characterization of 3D tissue constructs with predictable cell viability/proliferation outcomes and enhanced functionality over traditional culture methods.

  9. Geological evolution of the North Sea: a dynamic 3D model including petroleum system elements

    NASA Astrophysics Data System (ADS)

    Sabine, Heim; Rüdiger, Lutz; Dirk, Kaufmann; Lutz, Reinhardt

    2013-04-01

    This study investigates the sedimentary basin evolution of the German North Sea with a focus on petroleum generation, migration and accumulation. The study is conducted within the framework of the project "Geoscientific Potential of the German North Sea (GPDN)", a joint project of federal (BGR, BSH) and state authorities (LBEG) with partners from industry and scientific institutions. Based on the structural model of the "Geotektonischer Atlas 3D" (GTA3D, LBEG), this dynamic 3D model contains additionally the northwestern part ("Entenschnabel" area) of the German North Sea. Geological information, e.g. lithostratigraphy, facies and structural data, provided by industry, was taken from published research projects, or literature data such as the Southern Permian Basin Atlas (SPBA; Doornenbal et al., 2010). Numerical modeling was carried out for a sedimentary succession containing 17 stratigraphic layers and several sublayers, representing the sedimentary deposition from the Devonian until Present. Structural details have been considered in terms of simplified faults and salt structures, as well as main erosion and salt movement events. Lithology, facies and the boundary conditions e.g. heat flow, paleo water-depth and sediment water interface temperature were assigned. The system calibration is based on geochemical and petrological data, such as maturity of organic matter (VRr) and present day temperature. Due to the maturity of the sedimentary organic matter Carboniferous layers are the major source rocks for gas generation. Main reservoir rocks are the Rotliegend sandstones, furthermore, sandstones of the Lower Triassic and Jurassic can serve as reservoir rocks in areas where the Zechstein salts are absent. The model provides information on the temperature and maturity distribution within the main source rock layers as well as information of potential hydrocarbon generation based on kinetic data for gas liberation. Finally, this dynamic 3D model offers a first

  10. HUMAN RETINAL ENDOTHELIAL CELLS AND ASTROCYTES CULTURED ON 3-D SCAFFOLDS FOR OCULAR DRUG DISCOVERY AND DEVELOPMENT.

    PubMed

    Beharry, Kay D; Cai, Charles L; Valencia, Gloria B; Lazzaro, Douglas; Valencia, Arwin M; Salomone, Fabrizio; Aranda, Jacob V

    2017-09-15

    Topical ocular ketorolac improves the outcomes of severe retinopathy of prematurity and when administered with systemic caffeine, decreases the severity of oxygen-induced retinopathy. We tested the hypothesis that co-cultures of human retinal endothelial cells (HRECs) and human retinal astrocytes (HRAs) on 3-dimensional (3-D) hydrogel scaffolds is a more representative biomimetic paradigm of the blood-retinal-barrier (BRB) than 2-D cultures, and should be utilized for preclinical drug discovery and development. Mono- and co-cultures of HRECs and HRAs were treated with standard doses of ketorolac, ibuprofen, and/or caffeine, and exposed to hyperoxia, intermittent hypoxia (IH), or normoxia on 2-D surfaces or 3-D biodegradable hydrogel scaffolds (AlgiMatrix or Geltrex). Media and cells were collected at 72hours post treatment for arachidonic acid metabolites. Cells cultured on 3-D scaffolds exhibited less oxidative stress and variability in drug responses. HRAs enhanced the responses of HRECs to drugs and changes in oxygen environment. PGE2 and PGI2 were the predominant prostanoids produced in response to IH, reflecting COX-2 immunoreactivity. We conclude that HRECs and HRAs co-cultured on 3-D scaffolds may recapitulate drug responses of the dynamic BRB and therefore should be implemented for preclinical ocular drug discovery and development. Published by Elsevier Inc.

  11. Automated Identification and Localization of Hematopoietic Stem Cells in 3D Intravital Microscopy Data

    PubMed Central

    Khorshed, Reema A.; Hawkins, Edwin D.; Duarte, Delfim; Scott, Mark K.; Akinduro, Olufolake A.; Rashidi, Narges M.; Spitaler, Martin; Lo Celso, Cristina

    2015-01-01

    Summary Measuring three-dimensional (3D) localization of hematopoietic stem cells (HSCs) within the bone marrow microenvironment using intravital microscopy is a rapidly expanding research theme. This approach holds the key to understanding the detail of HSC-niche interactions, which are critical for appropriate stem cell function. Due to the complex tissue architecture of the bone marrow and to the progressive introduction of scattering and signal loss at increasing imaging depths, there is no ready-made software to handle efficient segmentation and unbiased analysis of the data. To address this, we developed an automated image analysis tool that simplifies and standardizes the biological interpretation of 3D HSC microenvironment images. The algorithm identifies HSCs and measures their localization relative to surrounding osteoblast cells and bone collagen. We demonstrate here the effectiveness, consistency, and accuracy of the proposed approach compared to current manual analysis and its wider applicability to analyze other 3D bone marrow components. PMID:26120058

  12. Nanoscale Analysis of a Hierarchical Hybrid Solar Cell in 3D.

    PubMed

    Divitini, Giorgio; Stenzel, Ole; Ghadirzadeh, Ali; Guarnera, Simone; Russo, Valeria; Casari, Carlo S; Bassi, Andrea Li; Petrozza, Annamaria; Di Fonzo, Fabio; Schmidt, Volker; Ducati, Caterina

    2014-05-01

    A quantitative method for the characterization of nanoscale 3D morphology is applied to the investigation of a hybrid solar cell based on a novel hierarchical nanostructured photoanode. A cross section of the solar cell device is prepared by focused ion beam milling in a micropillar geometry, which allows a detailed 3D reconstruction of the titania photoanode by electron tomography. It is found that the hierarchical titania nanostructure facilitates polymer infiltration, thus favoring intermixing of the two semiconducting phases, essential for charge separation. The 3D nanoparticle network is analyzed with tools from stochastic geometry to extract information related to the charge transport in the hierarchical solar cell. In particular, the experimental dataset allows direct visualization of the percolation pathways that contribute to the photocurrent.

  13. Quantitative analysis of 3D extracellular matrix remodelling by pancreatic stellate cells

    PubMed Central

    Robinson, Benjamin K.; Cortes, Ernesto; Rice, Alistair J.; Sarper, Muge

    2016-01-01

    ABSTRACT Extracellular matrix (ECM) remodelling is integral to numerous physiological and pathological processes in biology, such as embryogenesis, wound healing, fibrosis and cancer. Until recently, most cellular studies have been conducted on 2D environments where mechanical cues significantly differ from physiologically relevant 3D environments, impacting cellular behaviour and masking the interpretation of cellular function in health and disease. We present an integrated methodology where cell-ECM interactions can be investigated in 3D environments via ECM remodelling. Monitoring and quantification of collagen-I structure in remodelled matrices, through designated algorithms, show that 3D matrices can be used to correlate remodelling with increased ECM stiffness observed in fibrosis. Pancreatic stellate cells (PSCs) are the key effectors of the stromal fibrosis associated to pancreatic cancer. We use PSCs to implement our methodology and demonstrate that PSC matrix remodelling capabilities depend on their contractile machinery and β1 integrin-mediated cell-ECM attachment. PMID:27170254

  14. Nanoscale Analysis of a Hierarchical Hybrid Solar Cell in 3D

    PubMed Central

    Divitini, Giorgio; Stenzel, Ole; Ghadirzadeh, Ali; Guarnera, Simone; Russo, Valeria; Casari, Carlo S; Bassi, Andrea Li; Petrozza, Annamaria; Di Fonzo, Fabio; Schmidt, Volker; Ducati, Caterina

    2014-01-01

    A quantitative method for the characterization of nanoscale 3D morphology is applied to the investigation of a hybrid solar cell based on a novel hierarchical nanostructured photoanode. A cross section of the solar cell device is prepared by focused ion beam milling in a micropillar geometry, which allows a detailed 3D reconstruction of the titania photoanode by electron tomography. It is found that the hierarchical titania nanostructure facilitates polymer infiltration, thus favoring intermixing of the two semiconducting phases, essential for charge separation. The 3D nanoparticle network is analyzed with tools from stochastic geometry to extract information related to the charge transport in the hierarchical solar cell. In particular, the experimental dataset allows direct visualization of the percolation pathways that contribute to the photocurrent. PMID:25834481

  15. High Content Imaging (HCI) on Miniaturized Three-Dimensional (3D) Cell Cultures

    PubMed Central

    Joshi, Pranav; Lee, Moo-Yeal

    2015-01-01

    High content imaging (HCI) is a multiplexed cell staining assay developed for better understanding of complex biological functions and mechanisms of drug action, and it has become an important tool for toxicity and efficacy screening of drug candidates. Conventional HCI assays have been carried out on two-dimensional (2D) cell monolayer cultures, which in turn limit predictability of drug toxicity/efficacy in vivo; thus, there has been an urgent need to perform HCI assays on three-dimensional (3D) cell cultures. Although 3D cell cultures better mimic in vivo microenvironments of human tissues and provide an in-depth understanding of the morphological and functional features of tissues, they are also limited by having relatively low throughput and thus are not amenable to high-throughput screening (HTS). One attempt of making 3D cell culture amenable for HTS is to utilize miniaturized cell culture platforms. This review aims to highlight miniaturized 3D cell culture platforms compatible with current HCI technology. PMID:26694477

  16. Development and Validation of a 3D Clinostat for the Study of Cells during Microgravity Simulation.

    PubMed

    Russomano, T; Cardoso, R; Falcao, F; Dalmarco, G; V Dos Santos, C; F Dos Santos, L; G de Azevedo, D; Dos Santos, M; Martinelli, L; Motta, J; Forraz, N; McGuckin, C

    2005-01-01

    The clinostat was originally used to find out why plant roots appear to grow predominantly toward the center of the Earth. Over the last 2-3 decades, slow- and fast-rotating 2D and 3D clinostats have been used to assess cellular adaptation to this environment. A cell culture is placed in a spin module of the clinostat platform and its rotation is set empirically (2-3 rpm). The machine is then allowed to run for a specified period (hours to days) after which the cultures are removed and assayed for specific properties, such as cell growth, size and shape, distribution of receptors, integrity of the cytoskeleton or gene expression. A 3D clinostat was developed by the Microgravity Laboratory/IPCT-PUCRS group and validated by the Stem Cell Group of Kingston University London, which used 4 different types of human cancer cells and cord blood stem cells (CBSC). After rotation for 19h at 37degC, 5%CO2 humidified atmosphere, the 3D clinostat significantly improved proliferation potential of all tested cell populations when compared to static cultures. After only 5 days, high definition microscopic analysis revealed that all CBSC adhered and expanded onto the BDtrade 3D collagen composite scaffolds, and cross-developed into hepatocyte-like cells upon stimulation.

  17. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

    PubMed Central

    2013-01-01

    The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

  18. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation.

    PubMed

    Hodneland, Erlend; Kögel, Tanja; Frei, Dominik Michael; Gerdes, Hans-Hermann; Lundervold, Arvid

    2013-08-09

    : The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.

  19. On-chip clearing of arrays of 3-D cell cultures and micro-tissues.

    PubMed

    Grist, S M; Nasseri, S S; Poon, T; Roskelley, C; Cheung, K C

    2016-07-01

    Three-dimensional (3-D) cell cultures are beneficial models for mimicking the complexities of in vivo tissues, especially in tumour studies where transport limitations can complicate response to cancer drugs. 3-D optical microscopy techniques are less involved than traditional embedding and sectioning, but are impeded by optical scattering properties of the tissues. Confocal and even two-photon microscopy limit sample imaging to approximately 100-200 μm depth, which is insufficient to image hypoxic spheroid cores. Optical clearing methods have permitted high-depth imaging of tissues without physical sectioning, but they are difficult to implement for smaller 3-D cultures due to sample loss in solution exchange. In this work, we demonstrate a microfluidic platform for high-throughput on-chip optical clearing of breast cancer spheroids using the SeeDB, Clear(T2), and ScaleSQ clearing methods. Although all three methods are able to effectively clear the spheroids, we find that SeeDB and ScaleSQ more effectively clear the sample than Clear(T2); however, SeeDB induces green autofluorescence while ScaleS causes sample expansion. Our unique on-chip implementation permits clearing arrays of 3-D cultures using perfusion while monitoring the 3-D cultures throughout the process, enabling visualization of the clearing endpoint as well as monitoring of transient changes that could induce image artefacts. Our microfluidic device is compatible with on-chip 3-D cell culture, permitting the use of on-chip clearing at the endpoint after monitoring the same spheroids during their culture. This on-chip method has the potential to improve readout from 3-D cultures, facilitating their use in cell-based assays for high-content drug screening and other applications.

  20. On-chip clearing of arrays of 3-D cell cultures and micro-tissues

    PubMed Central

    Grist, S. M.; Poon, T.; Roskelley, C.; Cheung, K. C.

    2016-01-01

    Three-dimensional (3-D) cell cultures are beneficial models for mimicking the complexities of in vivo tissues, especially in tumour studies where transport limitations can complicate response to cancer drugs. 3-D optical microscopy techniques are less involved than traditional embedding and sectioning, but are impeded by optical scattering properties of the tissues. Confocal and even two-photon microscopy limit sample imaging to approximately 100–200 μm depth, which is insufficient to image hypoxic spheroid cores. Optical clearing methods have permitted high-depth imaging of tissues without physical sectioning, but they are difficult to implement for smaller 3-D cultures due to sample loss in solution exchange. In this work, we demonstrate a microfluidic platform for high-throughput on-chip optical clearing of breast cancer spheroids using the SeeDB, ClearT2, and ScaleSQ clearing methods. Although all three methods are able to effectively clear the spheroids, we find that SeeDB and ScaleSQ more effectively clear the sample than ClearT2; however, SeeDB induces green autofluorescence while ScaleS causes sample expansion. Our unique on-chip implementation permits clearing arrays of 3-D cultures using perfusion while monitoring the 3-D cultures throughout the process, enabling visualization of the clearing endpoint as well as monitoring of transient changes that could induce image artefacts. Our microfluidic device is compatible with on-chip 3-D cell culture, permitting the use of on-chip clearing at the endpoint after monitoring the same spheroids during their culture. This on-chip method has the potential to improve readout from 3-D cultures, facilitating their use in cell-based assays for high-content drug screening and other applications. PMID:27493703

  1. Lensfree diffractive tomography for the imaging of 3D cell cultures

    NASA Astrophysics Data System (ADS)

    Berdeu, Anthony; Momey, Fabien; Dinten, Jean-Marc; Gidrol, Xavier; Picollet-D'hahan, Nathalie; Allier, Cédric

    2017-02-01

    New microscopes are needed to help reaching the full potential of 3D organoid culture studies by gathering large quantitative and systematic data over extended periods of time while preserving the integrity of the living sample. In order to reconstruct large volumes while preserving the ability to catch every single cell, we propose new imaging platforms based on lens-free microscopy, a technic which is addressing these needs in the context of 2D cell culture, providing label-free and non-phototoxic acquisition of large datasets. We built lens-free diffractive tomography setups performing multi-angle acquisitions of 3D organoid cultures embedded in Matrigel and developed dedicated 3D holographic reconstruction algorithms based on the Fourier diffraction theorem. Nonetheless, holographic setups do not record the phase of the incident wave front and the biological samples in Petri dish strongly limit the angular coverage. These limitations introduce numerous artefacts in the sample reconstruction. We developed several methods to overcome them, such as multi-wavelength imaging or iterative phase retrieval. The most promising technic currently developed is based on a regularised inverse problem approach directly applied on the 3D volume to reconstruct. 3D reconstructions were performed on several complex samples such as 3D networks or spheroids embedded in capsules with large reconstructed volumes up to 25 mm3 while still being able to identify single cells. To our knowledge, this is the first time that such an inverse problem approach is implemented in the context of lens-free diffractive tomography enabling to reconstruct large fully 3D volumes of unstained biological samples.

  2. Growth of human breast tissues from patient cells in 3D hydrogel scaffolds.

    PubMed

    Sokol, Ethan S; Miller, Daniel H; Breggia, Anne; Spencer, Kevin C; Arendt, Lisa M; Gupta, Piyush B

    2016-03-01

    Three-dimensional (3D) cultures have proven invaluable for expanding human tissues for basic research and clinical applications. In both contexts, 3D cultures are most useful when they (1) support the outgrowth of tissues from primary human cells that have not been immortalized through extensive culture or viral infection and (2) include defined, physiologically relevant components. Here we describe a 3D culture system with both of these properties that stimulates the outgrowth of morphologically complex and hormone-responsive mammary tissues from primary human breast epithelial cells. Primary human breast epithelial cells isolated from patient reduction mammoplasty tissues were seeded into 3D hydrogels. The hydrogel scaffolds were composed of extracellular proteins and carbohydrates present in human breast tissue and were cultured in serum-free medium containing only defined components. The physical properties of these hydrogels were determined using atomic force microscopy. Tissue growth was monitored over time using bright-field and fluorescence microscopy, and maturation was assessed using morphological metrics and by immunostaining for markers of stem cells and differentiated cell types. The hydrogel tissues were also studied by fabricating physical models from confocal images using a 3D printer. When seeded into these 3D hydrogels, primary human breast epithelial cells rapidly self-organized in the absence of stromal cells and within 2 weeks expanded to form mature mammary tissues. The mature tissues contained luminal, basal, and stem cells in the correct topological orientation and also exhibited the complex ductal and lobular morphologies observed in the human breast. The expanded tissues became hollow when treated with estrogen and progesterone, and with the further addition of prolactin produced lipid droplets, indicating that they were responding to hormones. Ductal branching was initiated by clusters of cells expressing putative mammary stem cell

  3. Ultrafine fibrous gelatin scaffolds with deep cell infiltration mimicking 3D ECMs for soft tissue repair.

    PubMed

    Jiang, Qiuran; Xu, Helan; Cai, Shaobo; Yang, Yiqi

    2014-07-01

    In this research, ultrafine fibrous scaffolds with deep cell infiltration and sufficient water stability have been developed from gelatin, aiming to mimic the extracellular matrices (ECMs) as three dimensional (3D) stromas for soft tissue repair. The ultrafine fibrous scaffolds produced from the current technologies of electrospinning and phase separation are either lack of 3D oriented fibrous structure or too compact to be penetrated by cells. Whilst electrospun scaffolds are able to emulate two dimensional (2D) ECMs, they cannot mimic the 3D ECM stroma. In this work, ultralow concentration phase separation (ULCPS) has been developed to fabricate gelatin scaffolds with 3D randomly oriented ultrafine fibers and loose structures. Besides, a non-toxic citric acid crosslinking system has been established for the ULCPS method. This system could endow the scaffolds with sufficient water stability, while maintain the fibrous structures of scaffolds. Comparing with electrospun scaffolds, the ULCPS scaffolds showed improved cytocompatibility and more importantly, cell infiltration. This research has proved the possibility of using gelatin ULCPS scaffolds as the substitutes of 3D ECMs.

  4. Comparative analysis of 3D culture methods on human HepG2 cells.

    PubMed

    Luckert, Claudia; Schulz, Christina; Lehmann, Nadja; Thomas, Maria; Hofmann, Ute; Hammad, Seddik; Hengstler, Jan G; Braeuning, Albert; Lampen, Alfonso; Hessel, Stefanie

    2017-01-01

    Human primary hepatocytes represent a gold standard in in vitro liver research. Due to their low availability and high costs alternative liver cell models with comparable morphological and biochemical characteristics have come into focus. The human hepatocarcinoma cell line HepG2 is often used as a liver model for toxicity studies. However, under two-dimensional (2D) cultivation conditions the expression of xenobiotic-metabolizing enzymes and typical liver markers such as albumin is very low. Cultivation for 21 days in a three-dimensional (3D) Matrigel culture system has been reported to strongly increase the metabolic competence of HepG2 cells. In our present study we further compared HepG2 cell cultivation in three different 3D systems: collagen, Matrigel and Alvetex culture. Cell morphology, albumin secretion, cytochrome P450 monooxygenase enzyme activities, as well as gene expression of xenobiotic-metabolizing and liver-specific enzymes were analyzed after 3, 7, 14, and 21 days of cultivation. Our results show that the previously reported increase of metabolic competence of HepG2 cells is not primarily the result of 3D culture but a consequence of the duration of cultivation. HepG2 cells grown for 21 days in 2D monolayer exhibit comparable biochemical characteristics, CYP activities and gene expression patterns as all 3D culture systems used in our study. However, CYP activities did not reach the level of HepaRG cells. In conclusion, the increase of metabolic competence of the hepatocarcinoma cell line HepG2 is not due to 3D cultivation but rather a result of prolonged cultivation time.

  5. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-07

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

  6. Dynamical Monte Carlo Simulations of 3-D Galactic Systems in Axisymmetric and Triaxial Potentials

    NASA Astrophysics Data System (ADS)

    Taani, Ali; Vallejo, Juan C.

    2017-06-01

    We describe the dynamical behavior of isolated old ( ⩾ 1Gyr) objects-like Neutron Stars (NSs). These objects are evolved under smooth, time-independent, gravitational potentials, axisymmetric and with a triaxial dark halo. We analysed the geometry of the dynamics and applied the Poincaré section for comparing the influence of different birth velocities. The inspection of the maximal asymptotic Lyapunov (λ) exponent shows that dynamical behaviors of the selected orbits are nearly the same as the regular orbits with 2-DOF, both in axisymmetric and triaxial when (ϕ, qz )= (0,0). Conversely, a few chaotic trajectories are found with a rotated triaxial halo when (ϕ, qz )= (90, 1.5). The tube orbits preserve direction of their circulation around either the long or short axis as appeared in the triaxial potential, even when every initial condition leads to different orientations. The Poincaré section shows that there are 2-D invariant tori and invariant curves (islands) around stable periodic orbits that bound to the surface of 3-D tori. The regularity of several prototypical orbits offer the means to identify the phase-space regions with localized motions and to determine their environment in different models, because they can occupy significant parts of phase-space depending on the potential. This is of particular importance in Galactic Dynamics.

  7. Modeling spatial distribution of oxygen in 3d culture of islet beta-cells.

    PubMed

    McReynolds, John; Wen, Yu; Li, Xiaofei; Guan, Jianjun; Jin, Sha

    2017-01-01

    Three-dimensional (3D) scaffold culture of pancreatic β-cell has been proven to be able to better mimic physiological conditions in the body. However, one critical issue with culturing pancreatic β-cells is that β-cells consume large amounts of oxygen, and hence insufficient oxygen supply in the culture leads to loss of β-cell mass and functions. This becomes more significant when cells are cultured in a 3D scaffold. In this study, in order to understand the effect of oxygen tension inside a cell-laden collagen culture on β-cell proliferation, a culture model with encapsulation of an oxygen-generator was established. The oxygen-generator was made by embedding hydrogen peroxide into nontoxic polydimethylsiloxane to avoid the toxicity of a chemical reaction in the β-cell culture. To examine the effectiveness of the oxygenation enabled 3D culture, the spatial-temporal distribution of oxygen tension inside a scaffold was evaluated by a mathematical modeling approach. Our simulation results indicated that an oxygenation-aided 3D culture would augment the oxygen supply required for the β-cells. Furthermore, we identified that cell seeding density and the capacity of the oxygenator are two critical parameters in the optimization of the culture. Notably, cell-laden scaffold cultures with an in situ oxygen supply significantly improved the β-cells' biological function. These β-cells possess high insulin secretion capacity. The results obtained in this work would provide valuable information for optimizing and encouraging functional β-cell cultures. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:221-228, 2017. © 2016 American Institute of Chemical Engineers.

  8. Activating the nuclear piston mechanism of 3D migration in tumor cells.

    PubMed

    Petrie, Ryan J; Harlin, Heather M; Korsak, Lulu I T; Yamada, Kenneth M

    2017-01-02

    Primary human fibroblasts have the remarkable ability to use their nucleus like a piston, switching from low- to high-pressure protrusions in response to the surrounding three-dimensional (3D) matrix. Although migrating tumor cells can also change how they migrate in response to the 3D matrix, it is not clear if they can switch between high- and low-pressure protrusions like primary fibroblasts. We report that unlike primary fibroblasts, the nuclear piston is not active in fibrosarcoma cells. Protease inhibition rescued the nuclear piston mechanism in polarized HT1080 and SW684 cells and generated compartmentalized pressure. Achieving compartmentalized pressure required the nucleoskeleton-cytoskeleton linker protein nesprin 3, actomyosin contractility, and integrin-mediated adhesion, consistent with lobopodia-based fibroblast migration. In addition, this activation of the nuclear piston mechanism slowed the 3D movement of HT1080 cells. Together, these data indicate that inhibiting protease activity during polarized tumor cell 3D migration is sufficient to restore the nuclear piston migration mechanism with compartmentalized pressure characteristic of nonmalignant cells.

  9. Developing a 3D neutron tomography method for proton exchange membrane fuel cells

    NASA Astrophysics Data System (ADS)

    Tang, Hong-Yue; Santamaria, Anthony; Kurniawan, Jonathan; Park, Jae Wan; Yang, Tae-Hyun; Sohn, Young-Jun

    Fuel cell visualization is an ongoing challenge in the world of hydrogen-based research. Neutron tomography is a powerful tool for acquiring otherwise unattainable information about the inner workings of a proton exchange membrane fuel cell. Advanced neutron imaging methods allow for validation of both cell design and run methods. The tomography techniques discussed in this paper show how 3D visualization provides a clear view of flow channel activity for water management analysis. A brief intro to tomography is explained via its mathematical construction, outlining how 2D radiographs can be reconstructed and layered to form 3D visualizations. The low attenuation aluminum cell designs used for imaging are described focusing on how they are specifically tailored for neutron tomography. Images of the flow channel and water distributions are shown in cross-sections throughout the cell, both perpendicular and along the channel length. Finally, 3D tomography images of the cell are shown, with the bipolar aluminum plates signal subtracted revealing a 3D water distribution of both cathode and anode layers.

  10. Activating the nuclear piston mechanism of 3D migration in tumor cells

    PubMed Central

    2017-01-01

    Primary human fibroblasts have the remarkable ability to use their nucleus like a piston, switching from low- to high-pressure protrusions in response to the surrounding three-dimensional (3D) matrix. Although migrating tumor cells can also change how they migrate in response to the 3D matrix, it is not clear if they can switch between high- and low-pressure protrusions like primary fibroblasts. We report that unlike primary fibroblasts, the nuclear piston is not active in fibrosarcoma cells. Protease inhibition rescued the nuclear piston mechanism in polarized HT1080 and SW684 cells and generated compartmentalized pressure. Achieving compartmentalized pressure required the nucleoskeleton–cytoskeleton linker protein nesprin 3, actomyosin contractility, and integrin-mediated adhesion, consistent with lobopodia-based fibroblast migration. In addition, this activation of the nuclear piston mechanism slowed the 3D movement of HT1080 cells. Together, these data indicate that inhibiting protease activity during polarized tumor cell 3D migration is sufficient to restore the nuclear piston migration mechanism with compartmentalized pressure characteristic of nonmalignant cells. PMID:27998990

  11. Development of 3-D Hydrogel Culture Systems With On-Demand Cell Separation

    PubMed Central

    Hamilton, Sharon K.; Bloodworth, Nathaniel C.; Massad, Christopher S.; Hammoudi, Taymour M.; Suri, Shalu; Yang, Peter J.; Lu, Hang; Temenoff, Johnna S.

    2013-01-01

    Recently there has been an increased interest in the effects of paracrine signaling between groups of cells, particularly in the context of better understanding how stem cells contribute to tissue repair. Most current 3-D co-culture methods lack the ability to effectively separate 2 cell populations after the culture period, which is important for simultaneously analyzing the reciprocal effects of each cell type on the other. Here, we detail the development of a 3-D hydrogel co-culture system that allows us to culture different cell types for up to 7 days and subsequently separate and isolate the different cell populations using enzyme-sensitive glues. Separable 3-D co-culture laminates were prepared by laminating PEG-based hydrogels with enzyme-degradable hydrogel adhesives. Encapsulated cell populations exhibited good segregation with well-defined interfaces. Furthermore, constructs can be separated on-demand upon addition of the appropriate enzyme and cell viability remains high throughout the culture period, even after laminate separation. This platform offers great potential for a variety of basic cell signaling studies as the incorporation of an enzyme-sensitive adhesive interface allows the on-demand separation of individual cell populations for immediate analysis or further culture to examine persistence of co-culture effects and paracrine signaling on cell populations. PMID:23447378

  12. 3D Silicon Microstructures: A New Tool for Evaluating Biological Aggressiveness of Tumor Cells.

    PubMed

    Mazzini, Giuliano; Carpignano, Francesca; Surdo, Salvatore; Aredia, Francesca; Panini, Nicolò; Torchio, Martina; Erba, Eugenio; Danova, Marco; Scovassi, Anna Ivana; Barillaro, Giuseppe; Merlo, Sabina

    2015-10-01

    In this work, silicon micromachined structures (SMS), consisting of arrays of 3- μ m-thick silicon walls separated by 50- μm-deep, 5- μ m-wide gaps, were applied to investigate the behavior of eight tumor cell lines, with different origins and biological aggressiveness, in a three-dimensional (3D) microenvironment. Several cell culture experiments were performed on 3D-SMS and cells grown on silicon were stained for fluorescence microscopy analyses. Most of the tumor cell lines recognized in the literature as highly aggressive (OVCAR-5, A375, MDA-MB-231, and RPMI-7951) exhibited a great ability to enter and colonize the narrow deep gaps of the SMS, whereas less aggressive cell lines (OVCAR-3, Capan-1, MCF7, and NCI-H2126) demonstrated less penetration capability and tended to remain on top of the SMS. Quantitative image analyses of several fluorescence microscopy fields of silicon samples were performed for automatic cell recognition and count, in order to quantify the fraction of cells inside the gaps, with respect to the total number of cells in the examined field. Our results show that higher fractions of cells in the gaps are obtained with more aggressive cell lines, thus supporting in a quantitative way the observation that the behavior of tumor cells on the 3D-SMS depends on their aggressiveness level.

  13. Bioengineered 3D Glial Cell Culture Systems and Applications for Neurodegeneration and Neuroinflammation.

    PubMed

    Watson, P Marc D; Kavanagh, Edel; Allenby, Gary; Vassey, Matthew

    2017-02-01

    Neurodegeneration and neuroinflammation are key features in a range of chronic central nervous system (CNS) diseases such as Alzheimer's and Parkinson's disease, as well as acute conditions like stroke and traumatic brain injury, for which there remains significant unmet clinical need. It is now well recognized that current cell culture methodologies are limited in their ability to recapitulate the cellular environment that is present in vivo, and there is a growing body of evidence to show that three-dimensional (3D) culture systems represent a more physiologically accurate model than traditional two-dimensional (2D) cultures. Given the complexity of the environment from which cells originate, and their various cell-cell and cell-matrix interactions, it is important to develop models that can be controlled and reproducible for drug discovery. 3D cell models have now been developed for almost all CNS cell types, including neurons, astrocytes, microglia, and oligodendrocyte cells. This review will highlight a number of current and emerging techniques for the culture of astrocytes and microglia, glial cell types with a critical role in neurodegenerative and neuroinflammatory conditions. We describe recent advances in glial cell culture using electrospun polymers and hydrogel macromolecules, and highlight how these novel culture environments influence astrocyte and microglial phenotypes in vitro, as compared to traditional 2D systems. These models will be explored to illuminate current trends in the techniques used to create 3D environments for application in research and drug discovery focused on astrocytes and microglial cells.

  14. Considering 3D topography of endothelial folds to improve cell count of organ cultured corneas.

    PubMed

    Jumelle, Clotilde; Garcin, Thibaud; Gauthier, Anne Sophie; Glasson, Yaël; Bernard, Aurélien; Gavet, Yann; Klossa, Jacques; He, Zhiguo; Acquart, Sophie; Gain, Philippe; Thuret, Gilles

    2017-06-01

    The posterior side of the cornea is covered by the endothelial monolayer, which governs corneal transparency but cannot proliferate. Determination of endothelial cell density (ECD) is therefore the minimal and mandatory quality control in all eye banks. It avoids primary graft failures caused by endothelial insufficiency, and allows allocation of corneas to surgical techniques requiring different numbers of endothelial cells (ECs). Corneas stored in organ culture (17% of grafts worldwide), are characterized by heavy stromal swelling and numerous deep endothelial folds, up to 200 µm high. During microscopic en face observation, flat surfaces are thus exceptional and EC counting is biased by parallax errors, resulting in overestimated eye bank ECD (ebECD). We used a motorized transmitted light microscope to acquire Z-stacks of images every 10 µm, and processed them to reconstruct the 3D surface of the folded endothelium. This method (3D-ECD) takes into account the local point-by-point slope in order to correct ECD. On a set of 30 corneas, we compared 3D-ECD and ebECD determined on five identical zones at the center of the cornea. 3D reconstruction allowed us to visualize twice as many cells, and ebECD was 8.1 ± 4.5% (95%CI 6.4-9.7) higher than 3D-ECD, with 1744 ± 488 versus 1606 ± 473 cells/mm(2). 3D counting makes it possible to increase cell sampling and to correct overestimation by the conventional en face counting still routinely performed in eye banks.

  15. Combined Dynamic Time Warping with Multiple Sensors for 3D Gesture Recognition.

    PubMed

    Choi, Hyo-Rim; Kim, TaeYong

    2017-08-17

    Cyber-physical systems, which closely integrate physical systems and humans, can be applied to a wider range of applications through user movement analysis. In three-dimensional (3D) gesture recognition, multiple sensors are required to recognize various natural gestures. Several studies have been undertaken in the field of gesture recognition; however, gesture recognition was conducted based on data captured from various independent sensors, which rendered the capture and combination of real-time data complicated. In this study, a 3D gesture recognition method using combined information obtained from multiple sensors is proposed. The proposed method can robustly perform gesture recognition regardless of a user's location and movement directions by providing viewpoint-weighted values and/or motion-weighted values. In the proposed method, the viewpoint-weighted dynamic time warping with multiple sensors has enhanced performance by preventing joint measurement errors and noise due to sensor measurement tolerance, which has resulted in the enhancement of recognition performance by comparing multiple joint sequences effectively.

  16. Effects of haptic information on the perception of dynamic 3-D movement.

    PubMed

    Umemura, Hiroyuki

    2014-01-01

    This study examined effects of hand movement on visual perception of 3-D movement. I used an apparatus in which a cursor position in a simulated 3-D space and the position of a stylus on a haptic device could coincide using a mirror. In three experiments, participants touched the center of a rectangle in the visual display with the stylus of the force-feedback device. Then the rectangle's surface stereoscopically either protruded toward a participant or indented away from the participant. Simultaneously, the stylus either pushed back participant's hand, pulled away, or remained static. Visual and haptic information were independently manipulated. Participants judged whether the rectangle visually protruded or dented. Results showed that when the hand was pulled away, subjects were biased to perceive rectangles indented; however, when the hand was pushed back, no effect of haptic information was observed (Experiment 1). This effect persisted even when the cursor position was spatially separated from the hand position (Experiment 2). But, when participants touched an object different from the visual stimulus, this effect disappeared (Experiment 3). These results suggest that the visual system tried to integrate the dynamic visual and haptic information when they coincided cognitively, and the effect of haptic information on visually perceived depth was direction-dependent.

  17. Defragmented image based autostereoscopic 3D displays with dynamic eye tracking

    NASA Astrophysics Data System (ADS)

    Kim, Sung-Kyu; Yoon, Ki-Hyuk; Yoon, Seon Kyu; Ju, Heongkyu

    2015-12-01

    We studied defragmented image based autostereoscopic 3D displays with dynamic eye tracking. Specifically, we examined the impact of parallax barrier (PB) angular orientation on their image quality. The 3D display system required fine adjustment of PB angular orientation with respect to a display panel. This was critical for both image color balancing and minimizing image resolution mismatch between horizontal and vertical directions. For evaluating uniformity of image brightness, we applied optical ray tracing simulations. The simulations took effects of PB orientation misalignment into account. The simulation results were then compared with recorded experimental data. Our optimal simulated system produced significantly enhanced image uniformity at around sweet spots in viewing zones. However this was contradicted by real experimental results. We offer quantitative treatment of illuminance uniformity of view images to estimate misalignment of PB orientation, which could account for brightness non-uniformity observed experimentally. Our study also shows that slight imperfection in the adjustment of PB orientation due to practical restrictions of adjustment accuracy can induce substantial non-uniformity of view images' brightness. We find that image brightness non-uniformity critically depends on misalignment of PB angular orientation, for example, as slight as ≤ 0.01 ° in our system. This reveals that reducing misalignment of PB angular orientation from the order of 10-2 to 10-3 degrees can greatly improve the brightness uniformity.

  18. Description of patellar movement by 3D parameters obtained from dynamic CT acquisition

    NASA Astrophysics Data System (ADS)

    de Sá Rebelo, Marina; Moreno, Ramon Alfredo; Gobbi, Riccardo Gomes; Camanho, Gilberto Luis; de Ávila, Luiz Francisco Rodrigues; Demange, Marco Kawamura; Pecora, Jose Ricardo; Gutierrez, Marco Antonio

    2014-03-01

    The patellofemoral joint is critical in the biomechanics of the knee. The patellofemoral instability is one condition that generates pain, functional impairment and often requires surgery as part of orthopedic treatment. The analysis of the patellofemoral dynamics has been performed by several medical image modalities. The clinical parameters assessed are mainly based on 2D measurements, such as the patellar tilt angle and the lateral shift among others. Besides, the acquisition protocols are mostly performed with the leg laid static at fixed angles. The use of helical multi slice CT scanner can allow the capture and display of the joint's movement performed actively by the patient. However, the orthopedic applications of this scanner have not yet been standardized or widespread. In this work we present a method to evaluate the biomechanics of the patellofemoral joint during active contraction using multi slice CT images. This approach can greatly improve the analysis of patellar instability by displaying the physiology during muscle contraction. The movement was evaluated by computing its 3D displacements and rotations from different knee angles. The first processing step registered the images in both angles based on the femuŕs position. The transformation matrix of the patella from the images was then calculated, which provided the rotations and translations performed by the patella from its position in the first image to its position in the second image. Analysis of these parameters for all frames provided real 3D information about the patellar displacement.

  19. 3D Bioprinting a Cell-Laden Bone Matrix for Breast Cancer Metastasis Study.

    PubMed

    Zhou, Xuan; Zhu, Wei; Nowicki, Margaret; Miao, Shida; Cui, Haitao; Holmes, Benjamin; Glazer, Robert I; Zhang, Lijie Grace

    2016-11-09

    Metastasis is one of the deadliest consequences of breast cancer, with bone being one of the primary sites of occurrence. Insufficient 3D biomimetic models currently exist to replicate this process in vitro. In this study, we developed a biomimetic bone matrix using 3D bioprinting technology to investigate the interaction between breast cancer (BrCa) cells and bone stromal cells (fetal osteoblasts and human bone marrow mesenchymal stem cells (MSCs)). A tabletop stereolithography 3D bioprinter was employed to fabricate a series of bone matrices consisting of osteoblasts or MSCs encapsulated in gelatin methacrylate (GelMA) hydrogel with nanocrystalline hydroxyapatite (nHA). When BrCa cells were introduced into the stromal cell-laden bioprinted matrices, we found that the growth of BrCa cells was enhanced by the presence of osteoblasts or MSCs, whereas the proliferation of the osteoblasts or MSCs was inhibited by the BrCa cells. The BrCa cells co-cultured with MSCs or osteoblasts presented increased vascular endothelial growth factor (VEGF) secretion in comparison to that of monocultured BrCa cells. Additionally, the alkaline phosphatase activity of MSCs or osteoblasts was reduced after BrCa cell co-culture. These results demonstrate that the 3D bioprinted matrix, with BrCa cells and bone stromal cells, provides a suitable model with which to study the interactive effects of cells in the context of an artificial bone microenvironment and thus may serve as a valuable tool for the investigation of postmetastatic breast cancer progression in bone.

  20. Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography

    PubMed Central

    Chen, Lingling; Alexandrov, Yuriy; Kumar, Sunil; Andrews, Natalie; Dallman, Margaret J.; French, Paul M. W.; McGinty, James

    2015-01-01

    We describe an angular multiplexed imaging technique for 3-D in vivo cell tracking of sparse cell distributions and optical projection tomography (OPT) with superior time-lapse resolution and a significantly reduced light dose compared to volumetric time-lapse techniques. We demonstrate that using dual axis OPT, where two images are acquired simultaneously at different projection angles, can enable localization and tracking of features in 3-D with a time resolution equal to the camera frame rate. This is achieved with a 200x reduction in light dose compared to an equivalent volumetric time-lapse single camera OPT acquisition with 2