Generation of a tumor spheroid in a microgravity environment as a 3D model of melanoma

An in vitro 3D model was developed utilizing a synthetic microgravity environment to facilitate studying the cell interactions. 2D monolayer cell culture models have been successfully used to understand various cellular reactions that occur in vivo. There are some limitations to the 2D model that are apparent when compared to cells grown in a 3D matrix. For example, some proteins that are not expressed in a 2D model are found up-regulated in the 3D matrix. In this paper, we discuss techniques used to develop the first known large, free-floating 3D tissue model used to establish tumor spheroids. The bioreactor system known as the High Aspect Ratio Vessel (HARVs) was used to provide a microgravity environment. The HARVs promoted aggregation of keratinocytes (HaCaT) that formed a construct that served as scaffolding for the growth of mouse melanoma. Although there is an emphasis on building a 3D model with the proper extracellular matrix and stroma, we were able to develop a model that excluded the use of matrigel. Immunohistochemistry and apoptosis assays provided evidence that this 3D model supports B16.F10 cell growth, proliferation, and synthesis of extracellular matrix. Immunofluorescence showed that melanoma cells interact with one another displaying observable cellular morphological changes. The goal of engineering a 3D tissue model is to collect new information about cancer development and develop new potential treatment regimens that can be translated to in vivo models while reducing the use of laboratory animals.     

A one-dimensional model of water flow in soil-plant systems based on plant architecture

The estimation of root water uptake and water flow in plants is crucial to quantify transpiration and hence the water exchange between land surface and atmosphere. In particular the soil water extraction by plant roots which provides the water supply of plants is a highly dynamic and non-linear process interacting with soil transport processes that are mainly determined by the natural soil variability at different scales. To better consider this root-soil interaction we extended and further developed a finite element tree hydro-dynamics model based on the one-dimensional (1D) porous media equation. This is achieved by including in addition to the explicit three-dimensional (3D) architectural representation of the tree crown a corresponding 3D characterisation of the root system. This 1D xylem water flow model was then coupled to a soil water flow model derived also from the 1D porous media equation. We apply the new model to conduct sensitivity analysis of root water uptake and transpiration dynamics and compare the results to simulation results obtained by using a 3D model of soil water flow and root water uptake. Based on data from lysimeter experiments with young European beech trees (Fagus silvatica L.) is shown, that the model is able to correctly describe transpiration and soil water flow. In conclusion, compared to a fully 3D model the 1D porous media approach provides a computationally efficient alternative, able to reproduce the main mechanisms of plant hydro-dynamics including root water uptake from soil.     

Identifying novel sequence variants of RNA 3D motifs

Predicting RNA 3D structure from sequence is a major challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochastic Context-Free Grammars and Markov Random Fields (SCFG/MRF). The SCFG/MRF models are constructed using atomic-resolution RNA 3D structures. To parameterize each model, we use all instances of each motif found in the RNA 3D Motif Atlas and annotations of pairwise nucleotide interactions generated by the FR3D software. Isostericity relations between non-Watson–Crick basepairs are used in scoring sequence variants. SCFG techniques model nested pairs and insertions, while MRF ideas handle crossing interactions and base triples. We use test sets of randomly-generated sequences to set acceptance and rejection thresholds for each motif group and thus control the false positive rate. Validation was carried out by comparing results for four motif groups to RMDetect. The software developed for sequence scoring (JAR3D) is structured to automatically incorporate new motifs as they accumulate in the RNA 3D Motif Atlas when new structures are solved and is available free for download.     

Microscopic Mechanism for Experimentally Observed Anomalous Elasticity of DNA in Two Dimensions

By exploring a recent model in which DNA bending elasticity, described by the wormlike chain model, is coupled to basepair denaturation, we demonstrate that small denaturation bubbles lead to anomalies in the flexibility of DNA at the nanometric scale, when confined in two dimensions (2D), as reported in atomic-force microscopy experiments. Our model yields very good fits to experimental data and quantitative predictions that can be tested experimentally. Although such anomalies exist when DNA fluctuates freely in three dimensions (3D), they are too weak to be detected. Interactions between bases in the helical double-stranded DNA are modified by electrostatic adsorption on a 2D substrate, which facilitates local denaturation. This work reconciles the apparent discrepancy between observed 2D and 3D DNA elastic properties and points out that conclusions about the 3D properties of DNA (and its companion proteins and enzymes) do not directly follow from 2D experiments by atomic-force microscopy.     

Modeling cell apoptosis for simulating three-dimensional multicellular morphogenesis based on a reversible network reconnection framework

Morphogenesis in multicellular organisms is accompanied by apoptotic cell behaviors: cell shrinkage and cell disappearance. The mechanical effects of these behaviors are spatiotemporally regulated within multicellular dynamics to achieve proper tissue sizes and shapes in three-dimensional (3D) space. To analyze 3D multicellular dynamics, 3D vertex models have been suggested, in which a reversible network reconnection (RNR) model has successfully expressed 3D cell rearrangements during large deformations. To analyze the effects of apoptotic cell behaviors on 3D multicellular morphogenesis, we modeled cell apoptosis based on the RNR model framework. Cell shrinkage was modeled by the potential energy as a function of individual cell times during the apoptotic phase. Cell disappearance was modeled by merging neighboring polyhedrons at their boundary surface according to the topological rules of the RNR model. To establish that the apoptotic cell behaviors could be expressed as modeled, we simulated morphogenesis driven by cell apoptosis in two types of tissue topology: 3D monolayer cell sheet and 3D compacted cell aggregate. In both types of tissue topology, the numerical simulations successfully illustrated that cell aggregates gradually shrank because of successive cell apoptosis. During tissue shrinkage, the number of cells in aggregates decreased while maintaining individual cell size and shape. Moreover, in case of localizing apoptotic cells within a part of the 3D monolayer cell aggregate, the cell apoptosis caused the global tissue bending by pulling on surrounding cells. In case of localizing apoptotic cells on the surface of the 3D compacted cell aggregate, the cell apoptosis caused successive, directional cell rearrangements from the inside to the surface. Thus, the proposed model successfully provided a basis for expressing apoptotic cell behaviors during 3D multicellular morphogenesis based on an RNR model framework.     

3D model of amphioxus steroid receptor complexed with estradiol

The origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen-binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ERα are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ERα in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR. The 3D model predicts that mutation of Glu-346 to Gln will increase the affinity of testosterone for amphioxus SR and elucidate the evolution of steroid-binding to nuclear receptors.     

Interfacing 3D Engineered Neuronal Cultures to Micro-Electrode Arrays: An Innovative In Vitro Experimental Model

Currently, large-scale networks derived from dissociated neurons growing and developing in vitro on extracellular micro-transducer devices are the gold-standard experimental model to study basic neurophysiological mechanisms involved in the formation and maintenance of neuronal cell assemblies. However, in vitro studies have been limited to the recording of the electrophysiological activity generated by bi-dimensional (2D) neural networks. Nonetheless, given the intricate relationship between structure and dynamics, a significant improvement is necessary to investigate the formation and the developing dynamics of three-dimensional (3D) networks. In this work, a novel experimental platform in which 3D hippocampal or cortical networks are coupled to planar Micro-Electrode Arrays (MEAs) is presented. 3D networks are realized by seeding neurons in a scaffold constituted of glass microbeads (30-40 µm in diameter) on which neurons are able to grow and form complex interconnected 3D assemblies. In this way, it is possible to design engineered 3D networks made up of 5-8 layers with an expected final cell density. The increasing complexity in the morphological organization of the 3D assembly induces an enhancement of the electrophysiological patterns displayed by this type of networks. Compared with the standard 2D networks, where highly stereotyped bursting activity emerges, the 3D structure alters the bursting activity in terms of duration and frequency, as well as it allows observation of more random spiking activity. In this sense, the developed 3D model more closely resembles in vivo neural networks.     

3D reconstruction of the pelvis from bi-planar radiography

3D personalized models are more and more requested for clinical and biomechanical studies. Techniques based on bi-planar X-rays present the advantage of a low radiation dose for the patient. However, up to now, such techniques have shown limited accuracy in the case of pelvis reconstruction. This study proposes and validates a method providing accurate 3D personalized model of the pelvis from bi-planar X-rays. The algorithm is based on the fast computation of an initial solution followed by local deformations based on 2D anatomical points and contours that are digitized in both radiographs. Results were close to CT-scan reconstructions (mean difference 1.6 mm and differences under 4.3 mm for 95% of the points). Moreover, 3D morphometry of the pelvis could be obtained with an accuracy of 5%. This technique provides 3D patient specific model with a low radiation dose.     

Temperature heterogeneity over leaf surfaces: the contribution of the lamina microtopography

Temperature is spatially heterogeneous over leaf surfaces, yet the underlying mechanisms are not fully resolved. We hypothesized that the 3D leaf microtopography determines locally the amount of incoming irradiation flux at leaf surface, thereby driving the temperature gradient over the leaf surface. This hypothesis was tested by developing a model of leaf temperature heterogeneity that includes the development of the leaf boundary layer, the microtopography of the leaf surface and the physiological response of the leaf. Temperature distributions under various irradiation loads (1) over apple leaves based on their 3D microtopography, (2) over simulated flat (2D) apple leaves and (3) over 3D leaves with a transpiration rate distributed as in 2D leaves were simulated. Accuracy of the predictions was quantified by comparing model outputs and thermographic measurements of leaf surface temperature under controlled conditions. Only the model with 3D leaves predicted accurately the spatial heterogeneity of surface temperature over single leaves, whereas the mean temperature was well predicted by both 2D and 3D leaves. We suggest that in these conditions, the 3D leaf microtopography is the primary driver of leaf surface heterogeneity in temperature when the leaf is exposed to a light/heat source.     

The use of three-dimensional model construction of virtual technology in orthopedic treatment

ObjectiveThe objective of this study is to explore the construction of a digital three-dimensional model of virtual technology that plays an auxiliary role in orthopedic treatment.MethodsThree fracture patients were selected, with no abnormality was observed in bone examination, no musculoskeletal disease in the past; and spiral CT scan of the spine and pelvis, upper limbs, and lower limbs was performed. The virtual technology was used to build a digital 3D model, mainly using the editing software Mimics10.0 software. In addition, the virtual three-dimensional model was verified by virtual surgery, data storage security, work efficiency of the model, model validity, three-dimensional characteristics of the model, the interaction mode of the model, and the data accuracy of the model were studied.ResultsThe digital 3D model was successfully established by Mimics10.0 software. The data fitting efficiency was very high. The data storage security of the 3D model was greatly improved compared with the 2D model, and the work efficiency was improved by at least 50%. There was also a significant change in the accuracy and interaction of data acquisition. Therefore, the detection of digital 3D model work through virtual surgery simulation fully demonstrated the positive auxiliary role of 3D model in orthopedic treatment.ConclusionThe digital 3D model based on Mimics10.0 software is efficient and accurate in obtaining data. It is very effective for subsequent adjuvant therapy in the field of orthopedics, reducing the probability of misdiagnosis by doctors, saving time and improving efficiency, reducing patient's physical pain and unnecessary economic expenses.     

neuroConstruct: a tool for modeling networks of neurons in 3D space

Conductance-based neuronal network models can help us understand how synaptic and cellular mechanisms underlie brain function. However, these complex models are difficult to develop and are inaccessible to most neuroscientists. Moreover, even the most biologically realistic network models disregard many 3D anatomical features of the brain. Here, we describe a new software application, neuroConstruct, that facilitates the creation, visualization, and analysis of networks of multicompartmental neurons in 3D space. A graphical user interface allows model generation and modification without programming. Models within neuroConstruct are based on new simulator-independent NeuroML standards, allowing automatic generation of code for NEURON or GENESIS simulators. neuroConstruct was tested by reproducing published models and its simulator independence verified by comparing the same model on two simulators. We show how more anatomically realistic network models can be created and their properties compared with experimental measurements by extending a published 1D cerebellar granule cell layer model to 3D.     

Antibody-antigen interactions measured by surface plasmon resonance: global fitting of numerical integration algorithms

The interactions between adenylate kinase (AK) and a monoclonal antibody against AK (McAb3D3) were examined by means of optical biosensor technology, and the sensograms were fitted to four models using numerical integration algorithms. The interaction of a solution of McAb3D3 with immobilized AK follows a double exponential function and the data fitted well to an inhomogeneous ligand model. The interaction of a solution AK with immobilized McAb3D3 follows a single exponential function and the data fitted well to a pseudo-first order reaction model. The true association constants of AK binding to McAb3D3 in solution were obtained from competition BIAcore measurements. The difference in results obtained with solid-phase BIAcore and competition BIAcore may be due to rebinding of the dissociated analyte to the immobilized surface. The results obtained with BIAcore are compared to those obtained by ELISA methods. We suggest that the best method for analysis of BIAcore data is direct, global fitting of sensorgrams to numerical integration algorithms corresponding to the different possible models for binding.     

Hemodynamic Based Surgical Decision on Sequential Graft and Y-Type Graft in Coronary Artery Bypass Grafting

Purpose: Sequential graft and Y-type graft are two different surgical procedures in coronary artery bypass grafting (CABG). The hemodynamic environment of them are different, that may cause different short-term surgical result and long-term patency. In this study, the short-term and long-term result of sequential and Y-type graft was discussed by comparing the hemodynamics of them. Materials and Methods: Two postoperative 3-dimensional (3D) models were built by applying different graft on a patient-specific 3D model with serious stenosis. Then zero-dimensional (0D)/3D coupled simulation was carried out by coupling the postoperative 3D models with a 0D lumped parameter model of the cardiovascular system. Results: The flow rate of native coronary arteries and grafts are all calculated and illustrated in this paper. No significant difference of the native coronary arteries flow and graft flow exists between two surgical procedures. The wall shear stress (WSS) and streamline were also depicted. The graft WSS of sequential graft is 19.1% higher than Y-type graft. While flow separation appears at the bifurcation of Y-type graft. Conclusion: The short-term outcomes of sequential graft and Y-type graft are almost the same. But it can be found from the hemodynamics factors that the longterm patency of the sequential graft is better.     

基于光学相干层析图像的离体牙三维重建

利用shear-warp算法对离体牙的光学相干层析图像进行三维重建,通过不透明度传递函数的合理设置及光照模型的引入实现牙齿内部组织结构的可视化,便于医生在早期龋齿诊断中定位病变.介绍了shear-warp算法的原理、用于龋齿检测的全光纤光学相干层析成像系统及其二维层析图,以及利用离体牙牙冠的二维层析图重建获得三维结构图.     

Effect of geometrical assumptions on numerical modeling of coronary blood flow under normal and disease conditions

Shear stress plays a pivotal role in pathogenesis of coronary heart disease. The spatial and temporal variation in hemodynamics of blood flow, especially shear stress, is dominated by the vessel geometry. The goal of the present study was to investigate the effect of 2D and 3D geometries on the numerical modeling of coronary blood flow and shear stress distribution. We developed physiologically realistic 2D and 3D models (with similar geometries) of the human left coronary artery under normal and stenosis conditions (30%, 60%, and 80%) using PROE (WF 3). Transient blood flows in these models were solved using laminar and turbulent (k-ω) models using a computational fluid dynamics solver, FLUENT (v6.3.26). As the stenosis severity increased, both models predicted a similar pattern of increased shear stress at the stenosis throat, and in recirculation zones formed downstream of the stenosis. The 2D model estimated a peak shear stress value of 0.91, 2.58, 5.21, and 10.09 Pa at the throat location under normal, 30%, 60%, and 80% stenosis severity. The peak shear stress values at the same location estimated by the 3D model were 1.41, 2.56, 3.15, and 13.31 Pa, respectively. The 2D model underestimated the shear stress distribution inside the recirculation zone compared with that of 3D model. The shear stress estimation between the models diverged as the stenosis severity increased. Hence, the 2D model could be sufficient for analyzing coronary blood flow under normal conditions, but under disease conditions (especially 80% stenosis) the 3D model was more suitable.     

Proteomic Analysis of Stromal and Epithelial Cell Communications in Human Endometrial Cancer Using a Unique 3D Co‐Culture Model

Epithelial and stromal communications are essential for normal uterine functions and their dysregulation contributes to the pathogenesis of many diseases including infertility, endometriosis, and cancer. Although many studies have highlighted the advantages of culturing cells in 3D compared to the conventional 2D culture system, one of the major limitations of these systems is the lack of incorporation of cells from non‐epithelial lineages. In an effort to develop a culture system incorporating both stromal and epithelial cells, 3D endometrial cancer spheroids are developed by co‐culturing endometrial stromal cells with cancerous epithelial cells. The spheroids developed by this method are phenotypically comparable to in vivo endometrial cancer tissue. Proteomic analysis of the co‐culture spheroids comparable to human endometrial tissue revealed 591 common proteins and canonical pathways that are closely related to endometrium biology. To determine the feasibility of using this model for drug screening, the efficacy of tamoxifen and everolimus is tested. In summary, a unique 3D model system of human endometrial cancer is developed that will serve as the foundation for the further development of 3D culture systems incorporating different cell types of the human uterus for deciphering the contributions of non‐epithelial cells present in cancer microenvironment.     

A tool to model 3D coarse-root development with annual resolution

Dynamic root-development models are indispensable for biomechanical and biomass allocation studies, and also play an important role in understanding slope stability. There are few root-development models in the literature, and there is a specific lack of dynamic models. Therefore, the aim of this study is to develop a 3D growth-development model for coarse roots, which is species independent, as long as annual rings are formed. In order to implement this model, the objectives are (I) to interpolate annual growth layers, and (II) to evaluate the interpolations and annual volume computations. The model developed is a combination of 3D laser scans and 2D tree-ring data. A FARO laser ScanArm is used to acquire the coarse-root structure. A MATLAB program then integrates the ring-width measurements into the 3D model. A weighted interpolation algorithm is used to compute cross sections at any point within the model to obtain growth layers. The algorithm considers both the root structure and the ring-width data. The model reconstructed ring profiles with a mean absolute error for mean ring chronologies of <9% and for single radii of <20%. The interpolation accuracy was dependent on the number of input sections and root curvature. Total volume computations deviated by 3.5?C6.6% from the reference model. A new robust root-modelling tool was developed which allows for annual volume computations and sophisticated root-development analyses.     

Muscle function may depend on model selection in forward simulation of normal walking

The purpose of this study was to quantify how the predicted muscle function would change in a muscle-driven forward simulation of normal walking when changing the number of degrees of freedom in the model. Muscle function was described by individual muscle contributions to the vertical acceleration of the center of mass (COM). We built a two-dimensional (2D) sagittal plane model and a three-dimensional (3D) model in OpenSim and used both models to reproduce the same normal walking data. Perturbation analysis was applied to deduce muscle function in each model. Muscle excitations and contributions to COM support were compared between the 2D and 3D models. We found that the 2D model was able to reproduce similar joint kinematics and kinetics patterns as the 3D model. Individual muscle excitations were different for most of the hip muscles but ankle and knee muscles were able to attain similar excitations. Total induced vertical COM acceleration by muscles and gravity was the same for both models. However, individual muscle contributions to COM support varied, especially for hip muscles. Although there is currently no standard way to validate muscle function predictions, a 3D model seems to be more appropriate for estimating individual hip muscle function.     

Molecular docking and 3D QSAR studies on 1-amino-2-phenyl-4-(piperidin-1-yl)-butanes based on the structural modeling of human CCR5 receptor

In the present study, we have used an approach combining protein structure modeling, molecular dynamics (MD) simulation, automated docking, and 3D QSAR analyses to investigate the detailed interactions of CCR5 with their antagonists. Homology modeling and MD simulation were used to build the 3D model of CCR5 receptor based on the high-resolution X-ray structure of bovine rhodopsin. A series of 64 CCR5 antagonists, 1-amino-2-phenyl-4-(piperidin-1-yl)-butanes, were docked into the putative binding site of the 3D model of CCR5 using the docking method, and the probable interaction model between CCR5 and the antagonists were obtained. The predicted binding affinities of the antagonists to CCR5 correlate well with the antagonist activities, and the interaction model could be used to explain many mutagenesis results. All these indicate that the 3D model of antagonist-CCR5 interaction is reliable. Based on the binding conformations and their alignment inside the binding pocket of CCR5, three-dimensional structure-activity relationship (3D QSAR) analyses were performed on these antagonists using comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) methods. Both CoMFA and CoMSIA provide statistically valid models with good correlation and predictive power. The q(2)(r(cross)(2)) values are 0.568 and 0.587 for CoMFA and CoMSIA, respectively. The predictive ability of these models was validated by six compounds that were not included in the training set. Mapping these models back to the topology of the active site of CCR5 leads to a better understanding of antagonist-CCR5 interaction. These results suggest that the 3D model of CCR5 can be used in structure-based drug design and the 3D QSAR models provide clear guidelines and accurate activity predictions for novel antagonist design.