scholarly journals Using migrating cells as probes to illuminate features in live embryonic tissues

2020 ◽  
Vol 6 (49) ◽  
pp. eabc5546
Author(s):  
Sargon Gross-Thebing ◽  
Lukasz Truszkowski ◽  
Daniel Tenbrinck ◽  
Héctor Sánchez-Iranzo ◽  
Carolina Camelo ◽  
...  
Keyword(s):  
Zebrafish Embryo ◽  
Three Dimensional ◽  
Biochemical Properties ◽  
Physical Barrier ◽  
Tissue Properties ◽  
Embryonic Tissues ◽  
Amoeboid Cell ◽  
Unique Approach ◽  
Multiple Samples ◽  
Migrating Cells

The biophysical and biochemical properties of live tissues are important in the context of development and disease. Methods for evaluating these properties typically involve destroying the tissue or require specialized technology and complicated analyses. Here, we present a novel, noninvasive methodology for determining the spatial distribution of tissue features within embryos, making use of nondirectionally migrating cells and software we termed “Landscape,” which performs automatized high-throughput three-dimensional image registration. Using the live migrating cells as bioprobes, we identified structures within the zebrafish embryo that affect the distribution of the cells and studied one such structure constituting a physical barrier, which, in turn, influences amoeboid cell polarity. Overall, this work provides a unique approach for detecting tissue properties without interfering with animal’s development. In addition, Landscape allows for integrating data from multiple samples, providing detailed and reliable quantitative evaluation of variable biological phenotypes in different organisms.

scholarly journals Evaluation of BMP-mediated patterning in a 3D mathematical model of the zebrafish blastula embryo

2019 ◽  
Author(s):  
Linlin Li ◽  
Xu Wang ◽  
Mary C. Mullins ◽  
David M. Umulis
Keyword(s):  
Bone Morphogenetic Proteins ◽  
Zebrafish Embryo ◽  
Three Dimensional ◽  
Bmp Signaling ◽  
Multiple Time ◽  
Blastula Stage ◽  
Starting Point ◽  
Gene And Protein Expression ◽  
Multiple Time Points ◽  
Source Sink

AbstractBone Morphogenetic Proteins (BMPs) play an important role in dorsal-ventral (DV) patterning of the early zebrafish embryo. BMP signaling is regulated by a network of extracellular and intracellular factors that impact the range and signaling of BMP ligands. Recent advances in understanding the mechanism of pattern formation support a source-sink mechanism, however it is not clear how the source-sink mechanism shapes patterns in 3D, nor how sensitive the pattern is to biophysical rates and boundary conditions along both the anteroposterior (AP) and DV axes of the embryo. We propose a new three-dimensional growing Partial Differential Equation (PDE)-based model to simulate the BMP patterning process during the blastula stage. This model provides a starting point to elucidate how different mechanisms and components work together in 3D to create and maintain the BMP gradient in the embryo. We also show how the 3D model fits the BMP signaling gradient data at multiple time points along both axes. Furthermore, sensitivity analysis of the model suggests that the spatiotemporal patterns of Chordin and BMP ligand gene expression are dominant drivers of shape in 3D and more work is needed to quantify the spatiotemporal profiles of gene and protein expression to further refine the models.

scholarly journals On the utilization of novel spectral laser scanning for three-dimensional classification of vegetation elements

2018 ◽  
Vol 8 (2) ◽  
pp. 20170039 ◽  
Author(s):  
Zhan Li ◽  
Michael Schaefer ◽  
Alan Strahler ◽  
Crystal Schaaf ◽  
David Jupp
Keyword(s):  
Laser Scanning ◽  
Spatial Information ◽  
Information Source ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Biochemical Properties ◽  
Dual Wavelength ◽  
Wavelength Scanning ◽  
Spatial Attributes

The Dual-Wavelength Echidna Lidar (DWEL), a full waveform terrestrial laser scanner (TLS), has been used to scan a variety of forested and agricultural environments. From these scanning campaigns, we summarize the benefits and challenges given by DWEL's novel coaxial dual-wavelength scanning technology, particularly for the three-dimensional (3D) classification of vegetation elements. Simultaneous scanning at both 1064 nm and 1548 nm by DWEL instruments provides a new spectral dimension to TLS data that joins the 3D spatial dimension of lidar as an information source. Our point cloud classification algorithm explores the utilization of both spectral and spatial attributes of individual points from DWEL scans and highlights the strengths and weaknesses of each attribute domain. The spectral and spatial attributes for vegetation element classification each perform better in different parts of vegetation (canopy interior, fine branches, coarse trunks, etc.) and under different vegetation conditions (dead or live, leaf-on or leaf-off, water content, etc.). These environmental characteristics of vegetation, convolved with the lidar instrument specifications and lidar data quality, result in the actual capabilities of spectral and spatial attributes to classify vegetation elements in 3D space. The spectral and spatial information domains thus complement each other in the classification process. The joint use of both not only enhances the classification accuracy but also reduces its variance across the multiple vegetation types we have examined, highlighting the value of the DWEL as a new source of 3D spectral information. Wider deployment of the DWEL instruments is in practice currently held back by challenges in instrument development and the demands of data processing required by coaxial dual- or multi-wavelength scanning. But the simultaneous 3D acquisition of both spectral and spatial features, offered by new multispectral scanning instruments such as the DWEL, opens doors to study biophysical and biochemical properties of forested and agricultural ecosystems at more detailed scales.

Determination of Mechanical Stresses in Vibration and Contact During Flow-Structure-Interaction in Vocal Folds

2011 ◽  
Author(s):  
Pinaki Bhattacharya ◽  
Thomas H. Siegmund
Keyword(s):  
Surface Deformation ◽  
Three Dimensional ◽  
Vocal Folds ◽  
Biomechanical Properties ◽  
Mechanical Stresses ◽  
Physical Models ◽  
Tissue Properties ◽  
Transient Nature ◽  
Superior Surface ◽  
Glottal Flow

Mechanical stresses in vocal folds (VFs) developed during self-oscillation — due to interaction with the glottal flow — play an important role in tissue damage and healing. Contact stresses occurring due to collision between VFs modify both self-oscillation characteristics, as well as stresses. The complexity of the problem is increased due to other factors acting in combination: transient nature of the flow, non-linear and anisotropic biomechanical properties of the VFs, and acoustic loading. Experiments with physical models [1] have attempted to deduce the state of stress in the interior through measurement of superior surface deformation. However, these methods pose challenges in data acquisition. on the other hand, full three-dimensional transient computational analysis of a self-oscillating and contacting VF model requires highly sophisticated algorithms as well as prohibitive resource usage. Not surprisingly, therefore, it has not been conducted until now. We hypothesize that a high-fidelity numerical simulation incorporating realistic tissue properties is essential to accurately determine stresses within VFs during self-oscillation and contact.

scholarly journals Strength-duration relationship as a tool to prioritize cardiac tissue properties that govern electrical excitability

2019 ◽  
Vol 317 (1) ◽  
pp. H13-H25 ◽  
Author(s):  
Michael N. Sayegh ◽  
Natasha Fernandez ◽  
Hee Cheol Cho
Keyword(s):  
Cardiac Tissue ◽  
Three Dimensional ◽  
Assessment Tools ◽  
Electrical Strength ◽  
Design Parameters ◽  
Electrical Excitability ◽  
Cell Alignment ◽  
Tissue Properties ◽  
Duration Relationship

Gaps exist in the availability of in vitro functional assessment tools that can emulate the integration of regenerative cells and tissues to the host myocardium. We use strength-duration relationships of electrically stimulated two- and three-dimensional myocardial constructs to study the effects of pacing frequency, culture dimensions, anisotropic cell alignment, fibroblast content, and pacemaker phenotype on electrical excitability. Our study delivers electrical strength-duration as a quantifiable parameter to evaluate design parameters of engineered cardiac tissue constructs.

scholarly journals Elastography Method for Reconstruction of Nonlinear Breast Tissue Properties

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Z. G. Wang ◽  
Y. Liu ◽  
G. Wang ◽  
L. Z. Sun
Keyword(s):  
Breast Tissue ◽  
Three Dimensional ◽  
Material Model ◽  
Nonlinear Material ◽  
Fatty Tissue ◽  
Nonlinear Method ◽  
Tissue Properties ◽  
Breast Cancer Study ◽  
Breast Phantom ◽  
The Difference

Elastography is developed as a quantitative approach to imaging linear elastic properties of tissues to detect suspicious tumors. In this paper a nonlinear elastography method is introduced for reconstruction of complex breast tissue properties. The elastic parameters are estimated by optimally minimizing the difference between the computed forces and experimental measures. A nonlinear adjoint method is derived to calculate the gradient of the objective function, which significantly enhances the numerical efficiency and stability. Simulations are conducted on a three-dimensional heterogeneous breast phantom extracting from real imaging including fatty tissue, glandular tissue, and tumors. An exponential-form of nonlinear material model is applied. The effect of noise is taken into account. Results demonstrate that the proposed nonlinear method opens the door toward nonlinear elastography and provides guidelines for future development and clinical application in breast cancer study.

scholarly journals ATP synthase from bovine heart mitochondria: reconstitution into unilamellar phospholipid vesicles of the pure enzyme in a functional state

1996 ◽  
Vol 318 (1) ◽  
pp. 351-357 ◽  
Author(s):  
Georg GROTH ◽  
John E. WALKER
Keyword(s):  
Atp Hydrolysis ◽  
Three Dimensional ◽  
Biochemical Properties ◽  
Proton Gradient ◽  
Heart Mitochondria ◽  
Phospholipid Vesicles ◽  
Dependent Manner ◽  
Biological Functions ◽  
Bovine Heart ◽  
F1fo Atpase

A highly purified and monodisperse preparation of proton-translocating F1Fo-ATPase from bovine heart mitochondria is an assembly of 16 unlike polypeptides. This preparation has been reconstituted in the presence of various detergents into unilamellar phospholipid vesicles. Incorporation of the enzyme into vesicles increases the ATP hydrolase activity of the enzyme by 10–20-fold, depending on the detergent, and the highest activities of ATP hydrolysis, 70 units/mg, were obtained by reconstitution from dodecylmaltoside or CHAPS. This activity is mostly sensitive to inhibitors that act on the Fo membrane sector of the complex. From the quenching of the pH-sensitive probe, 9-amino-6-chloro-2-methoxyacridine, it was shown that the reconstituted enzyme was able to form a transmembrane proton gradient in an ATP-dependent manner. By co-reconstitution of the enzyme with bacteriorhodopsin, it was demonstrated that in the presence of a light-induced proton gradient the enzyme can synthesize ATP from ADP and phosphate. Therefore, the characteristic biological functions of the F1Fo-ATPase in mitochondria have been demonstrated with the purified enzyme. Thus, in terms of both its physical and biochemical properties, the purified enzyme fulfils important pre-requisites for formation of two- and three-dimensional crystals.

scholarly journals Microarray Embedding/Sectioning for Parallel Analysis of 3D Cell Spheroids

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jonathan Gabriel ◽  
David Brennan ◽  
Jennifer H. Elisseeff ◽  
Vince Beachley
Keyword(s):  
High Throughput ◽  
Three Dimensional ◽  
Experimental Conditions ◽  
Spheroid Culture ◽  
Cell Spheroid ◽  
Multiple Biomarkers ◽  
Immunohistochemical Techniques ◽  
Multiple Samples ◽  
Single Slide ◽  
Dimensional Cell

Abstract Three-dimensional cell spheroid models can be used to predict the effect of drugs and therapeutics and to model tissue development and regeneration. The utility of these models is enhanced by high throughput 3D spheroid culture technologies allowing researchers to efficiently culture numerous spheroids under varied experimental conditions. Detailed analysis of high throughput spheroid culture is much less efficient and generally limited to narrow outputs, such as metabolic viability. We describe a microarray approach that makes traditional histological embedding/sectioning/staining feasible for large 3D cell spheroid sample sets. Detailed methodology to apply this technology is provided. Analysis of the technique validates the potential for efficient histological analysis of up to 96 spheroids in parallel. By integrating high throughput 3D spheroid culture technologies with advanced immunohistochemical techniques, this approach will allow researchers to efficiently probe expression of multiple biomarkers with spatial localization within 3D structures. Quantitative comparison of staining will have improved inter- and intra-experimental reproducibility as multiple samples are collectively processed, stained, and imaged on a single slide.

scholarly journals An Interpenetrating Alginate/Gelatin Network for Three-Dimensional (3D) Cell Cultures and Organ Bioprinting

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 756 ◽  
Author(s):  
Qiuhong Chen ◽  
Xiaohong Tian ◽  
Jun Fan ◽  
Hao Tong ◽  
Qiang Ao ◽  
...  
Keyword(s):  
Cell Cultures ◽  
Structural Integrity ◽  
Polymer Network ◽  
Three Dimensional ◽  
Biochemical Properties ◽  
Interpenetrating Polymer Network ◽  
3D Cell Cultures ◽  
Wide Range ◽  
The Individual

Crosslinking is an effective way to improve the physiochemical and biochemical properties of hydrogels. In this study, we describe an interpenetrating polymer network (IPN) of alginate/gelatin hydrogels (i.e., A-G-IPN) in which cells can be encapsulated for in vitro three-dimensional (3D) cultures and organ bioprinting. A double crosslinking model, i.e., using Ca2+ to crosslink alginate molecules and transglutaminase (TG) to crosslink gelatin molecules, is exploited to improve the physiochemical, such as water holding capacity, hardness and structural integrity, and biochemical properties, such as cytocompatibility, of the alginate/gelatin hydrogels. For the sake of convenience, the individual ionic (i.e., only treatment with Ca2+) or enzymatic (i.e., only treatment with TG) crosslinked alginate/gelatin hydrogels are referred as alginate-semi-IPN (i.e., A-semi-IPN) or gelatin-semi-IPN (i.e., G-semi-IPN), respectively. Tunable physiochemical and biochemical properties of the hydrogels have been obtained by changing the crosslinking sequences and polymer concentrations. Cytocompatibilities of the obtained hydrogels are evaluated through in vitro 3D cell cultures and bioprinting. The double crosslinked A-G-IPN hydrogel is a promising candidate for a wide range of biomedical applications, including bioartificial organ manufacturing, high-throughput drug screening, and pathological mechanism analyses.

scholarly journals Biomechanical Evaluations of Ocular Injury Risk for Blast Loading

2017 ◽  
Vol 139 (8) ◽  
Author(s):  
Bahram Notghi ◽  
Rajneesh Bhardwaj ◽  
Shantanu Bailoor ◽  
Kimberly A. Thompson ◽  
Ashley A. Weaver ◽  
...  
Keyword(s):  
Intraocular Pressure ◽  
Injury Risk ◽  
Animal Studies ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Blast Loading ◽  
Ocular Injury ◽  
Tissue Properties ◽  
Primary Blast ◽  
Combat Injuries

Ocular trauma is one of the most common types of combat injuries resulting from the exposure of military personnel with improvised explosive devices. The injury mechanism associated with the primary blast wave is poorly understood. We employed a three-dimensional computational model, which included the main internal ocular structures of the eye, spatially varying thickness of the cornea-scleral shell, and nonlinear tissue properties, to calculate the intraocular pressure and stress state of the eye wall and internal ocular structure caused by the blast. The intraocular pressure and stress magnitudes were applied to estimate the injury risk using existing models for blunt impact and blast loading. The simulation results demonstrated that blast loading can induce significant stresses in the different components of the eyes that correlate with observed primary blast injuries in animal studies. Different injury models produced widely different injury risk predictions, which highlights the need for experimental studies evaluating mechanical and functional damage to the ocular structures caused by the blast loading.

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