scholarly journals Simulating intervertebral disc cell behaviour within 3D multifactorial environments

2020 ◽  
Author(s):  
L Baumgartner ◽  
J J Reagh ◽  
M A González Ballester ◽  
J Noailly
Keyword(s):  
Experimental Data ◽  
Intervertebral Disc ◽  
Cell Viability ◽  
Mrna Expression ◽  
Collagen Type ◽  
Supplementary Information ◽  
Model Parameters ◽  
Type I ◽  
Cell Behaviour ◽  
Model Predictions

Abstract Motivation Low back pain is responsible for more global disability than any other condition. Its incidence is closely related to intervertebral disc (IVD) failure, which is likely caused by an accumulation of microtrauma within the IVD. Crucial factors in microtrauma development are not entirely known yet, probably because their exploration in vivo or in vitro remains tremendously challenging. In silico modelling is, therefore, definitively appealing, and shall include approaches to integrate influences of multiple cell stimuli at the microscale. Accordingly, this study introduces a hybrid Agent-based (AB) model in IVD research and exploits network modelling solutions in systems biology to mimic the cellular behaviour of Nucleus Pulposus cells exposed to a 3D multifactorial biochemical environment, based on mathematical integrations of existing experimental knowledge. Cellular activity reflected by mRNA expression of Aggrecan, Collagen type I, Collagen type II, MMP-3 and ADAMTS were calculated for inflamed and non-inflamed cells. mRNA expression over long periods of time is additionally determined including cell viability estimations. Model predictions were eventually validated with independent experimental data. Results As it combines experimental data to simulate cell behaviour exposed to a multifactorial environment, the present methodology was able to reproduce cell death within 3 days under glucose deprivation and a 50% decrease in cell viability after 7 days in an acidic environment. Cellular mRNA expression under non-inflamed conditions simulated a quantifiable catabolic shift under an adverse cell environment, and model predictions of mRNA expression of inflamed cells provide new explanation possibilities for unexpected results achieved in experimental research. Availabilityand implementation The AB model as well as used mathematical functions were built with open source software. Final functions implemented in the AB model and complete AB model parameters are provided as Supplementary Material. Experimental input and validation data were provided through referenced, published papers. The code corresponding to the model can be shared upon request and shall be reused after proper training. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Simulating intervertebral disc cell behavior within 3D multifactorial environments

2019 ◽  
Author(s):  
L. Baumgartner ◽  
J.J. Reagh ◽  
M.A. González Ballester ◽  
J. Noailly
Keyword(s):  
Experimental Data ◽  
Intervertebral Disc ◽  
Cell Viability ◽  
Mrna Expression ◽  
Type I Collagen ◽  
Collagen Type ◽  
Cell Behavior ◽  
Type I ◽  
Nucleus Pulposus Cells ◽  
Model Predictions

AbstractMotivationLow back pain is responsible for more global disability than any other condition. Its incidence is closely related to intervertebral disc (IVD) failure, which is likely caused by an accumulation of microtrauma within the IVD. Crucial factors in microtrauma development are not entirely known yet, probably because their exploration in vivo or in vitro remains tremendously challenging. In-silico modelling is, therefore, definitively appealing, and shall include approaches to integrate influences of multiple cell stimuli at the microscale. Accordingly, this study introduces a hybrid Agent-based (AB) model in IVD research and exploits network modelling solutions in systems biology to mimic the cellular behavior of Nucleus Pulposus cells exposed to a 3D multifactorial biochemical environment, based on mathematical integrations of existing experimental knowledge. Cellular activity reflected by mRNA expression of Aggrecan, Collagen type I, Collagen type II, MMP-3 and ADAMTS were calculated for inflamed and non-inflamed cells. mRNA expression over long periods of time is additionally determined including cell viability estimations. Model predictions were eventually validated with independent experimental data.ResultsAs it combines experimental data to simulate cell behavior exposed to a multifactorial environment, the present methodology was able to reproduce cell death within 3 days under glucose deprivation and a 50% decrease in cell viability after 7 days in an acidic environment. Cellular mRNA expression under non-inflamed conditions simulated a quantifiable catabolic shift under an adverse cell environment, and model predictions of mRNA expression of inflamed cells provide new explanation possibilities for unexpected results achieved in experimental [email protected]

scholarly journals 14 Characterization of adipose tissue extracellular matrix component mRNA expression during porcine adipogenesis using real-time PCR

2020 ◽  
Vol 98 (Supplement_2) ◽  
pp. 35-35
Author(s):  
Maegan A Reeves ◽  
Courtney E Charlton ◽  
Terry D Brandebourg
Keyword(s):  
Extracellular Matrix ◽  
Adipose Tissue ◽  
Mrna Expression ◽  
Real Time ◽  
Real Time Pcr ◽  
Collagen Type ◽  
Primary Cultures ◽  
Collagen Type I ◽  
Type I ◽  
Matrix Metallopeptidase

Abstract Given adipose tissue is histologically classified as connective tissue, we hypothesized expression of extracellular matrix (ECM) components are significantly altered during adipogenesis. However, little is known about the regulation of the ECM during adipose tissue development in the pig. Therefore, the objective of this study was to characterize expression of ECM components during porcine adipogenesis. Primary cultures of adipose tissue stromal-vascular cells were harvested from 3-day-old neonatal pigs (n=6) and preadipocytes induced to differentiate in vitro for 8 days in the presence of insulin, hydrocortisone, and rosiglitazone. Total RNA was extracted from these cultures on days 0 and 8 post-induction. Real-time PCR was then utilized to determine changes in mRNA expression for collagen type I alpha 1 chain (COL1A), collagen type I alpha 2 chain (COL2A), collagen type I alpha 3 chain (COL3A), collagen type I alpha 4 chain (COL4A), collagen type I alpha 6 chain (COL6A), biglycan, fibronectin, laminin, nitogen-1 (NID1), matrix metallopeptidase 2 (MMP2), matrix metallopeptidase 9 (MMP9), metallopeptidase inhibitor 3 (TIMP3). The mRNA abundances of COL1A, COL3A and MMP2 were significantly downregulated 2.86-fold (P < 0.05), 16.7-fold (P < 0.01) and 3.1-fold (P < 0.05) respectively in day 8 (differentiated) compared to day 0 (undifferentiated) cultures. Meanwhile, mRNA abundances were significantly upregulated during adipogenesis for the COL2A (2.82-fold; P < 0.05), COL4A (2.01-fold; P < 0.05), COL6A (2.8-fold; P < 0.05), biglycan (49.9- fold; P < 0.001), fibronectin (452-fold; P < 0.001), laminin (6.1-fold; P < 0.05), NID1(47.4-fold; P < 0.01), MMP9 (76.8- fold; P < 0.01), and TIMP3(3.04-fold; P < 0.05) genes. These data support the hypothesis that significant changes in ECM components occur during porcine adipogenesis. Modulating adipose tissue ECM remodeling might be a novel strategy to manipulate adiposity in the pig.

Electromagnetic fields enhance chondrogenesis of human adipose-derived stem cells in a chondrogenic microenvironment in vitro

2013 ◽  
Vol 114 (5) ◽  
pp. 647-655 ◽  
Author(s):  
Chung-Hwan Chen ◽  
Yi-Shan Lin ◽  
Yin-Chih Fu ◽  
Chih-Kuang Wang ◽  
Shun-Cheng Wu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Electromagnetic Field ◽  
Cell Viability ◽  
Chondrogenic Differentiation ◽  
Collagen Type ◽  
Cartilage Tissue ◽  
Pulse Electromagnetic Field ◽  
Type I ◽  
Adipose Derived Stem Cells ◽  
Pemf Treatment

We tested the hypothesis that electromagnetic field (EMF) stimulation enhances chondrogenesis in human adipose-derived stem cells (ADSCs) in a chondrogenic microenvironment. A two-dimensional hyaluronan (HA)-coated well (2D-HA) and a three-dimensional pellet culture system (3D-pellet) were used as chondrogenic microenvironments. The ADSCs were cultured in 2D-HA or 3D-pellet, and then treated with clinical-use pulse electromagnetic field (PEMF) or the innovative single-pulse electromagnetic field (SPEMF) stimulation. The cytotoxicity, cell viability, and chondrogenic and osteogenic differentiations were analyzed after PEMF or SPEMF treatment. The modules of PEMF and SPEMF stimulations used in this study did not cause cytotoxicity or alter cell viability in ADSCs. Both PEMF and SPEMF enhanced the chondrogenic gene expression (SOX-9, collagen type II, and aggrecan) of ADSCs cultured in 2D-HA and 3D-pellet. The expressions of bone matrix genes (osteocalcin and collagen type I) of ADSCs were not changed after SPEMF treatment in 2D-HA and 3D-pellet; however, they were enhanced by PEMF treatment. Both PEMF and SPEMF increased the cartilaginous matrix (sulfated glycosaminoglycan) deposition of ADSCs. However, PEMF treatment also increased mineralization of ADSCs, but SPEMF treatment did not. Both PEMF and SPEMF enhanced chondrogenic differentiation of ADSCs cultured in a chondrogenic microenvironment. SPEMF treatment enhanced ADSC chondrogenesis, but not osteogenesis, when the cells were cultured in a chondrogenic microenvironment. However, PEMF enhanced both osteogenesis and chondrogenesis under the same conditions. Thus the combination of a chondrogenic microenvironment with SPEMF stimulation can promote chondrogenic differentiation of ADSCs and may be applicable to articular cartilage tissue engineering.

P0672CALPAINS 1 AND 2 ARE INCREASED DURING THE DEVELOPMENT OF CHRONIC KIDNEY DAMAGE IN MICE FED WITH AN ADENINE RICH DIET

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Elena Gutiérrez-Calabrés ◽  
Sofía Campillo de Blas ◽  
Lourdes Bohorquez Magro ◽  
Mercedes Griera-Merino ◽  
Diego García Ayuso ◽  
...  
Keyword(s):  
Renal Function ◽  
Mrna Expression ◽  
Protein Content ◽  
Experimental Model ◽  
Collagen Type ◽  
Critical Role ◽  
Cysteine Proteases ◽  
Collagen Type I ◽  
Standard Diet ◽  
Type I

Abstract Background and Aims Calpains are intracellular cysteine proteases that play a critical role in cell remodeling, being involved in multiple biological processes linked to tissue damage and repair mechanisms. In addition, they are released into the circulation, being able to carry out systemic actions with pathological consequences. The aim of this study was to investigate the role of calpains in the progression of chronic kidney disease (CKD) in an experimental model of chronic renal damage induced by adenine. Method We induced an experimental model of CKD, in mice fed for 2 weeks with an adenine-supplemented diet (0.2% adenine) (A). Animals receiving this diet develop a tubulointerstitial damage resembling that is observed in human CKD. Mice with standard diet were used as controls (C). Renal function was assessed by measuring serum blood urea nitrogen (BUN) and creatinine (mg/dl). Fibrosis markers (collagen type I and fibronectin) were determined by RT-qPCR. Changes in the renal content of calpains 1 and 2 were analyzed by western blot (protein content), and RT-qPCR (mRNA expression). Results Our results show functional and structural changes at renal level in the adenine-fed mice, with increased BUN (A: 72 mg/dl, C: 28 mg/dl, p < 0.05), creatinine (A: 0.58 mg/dl, C: 0.25 mg/dl, p < 0.05), collagen type I mRNA expression (A: 12.9 units, C: 1.2 units, p < 0.05) and fibronectin mRNA expression (A: 3.46 units, C: 1.3 units, p < 0.05). Furthermore, protein content of calpains 1 (A: 1.27 units, C: 0.78 units, p < 0.05) and 2 (A: 1.30 units, C: 0.66 units, p < 0.05) was significantly higher in adenine-fed mice when compared to control. At the same time, we observed a significant increase in gene expression of both calpain 1 (A: 4.21 units, C: 0.51 units, p < 0.05) and 2 (A: 4.93 units, C: 0.56 units, p < 0.05) in the adenine model regarding to mice with standard diet. Our results demonstrate that calpain 1 and 2 expression in renal tissue increases as CKD progresses. Interestingly, we found statistically significant correlations between renal calpains 1 and 2 protein and mRNA content and plasma BUN and creatinine (p < 0.05, r between 0.79 and 0.92), as well as protein expression of calpain 2 and mRNA expression of collagen type I (p < 0.05, r = 0.76). These data suggest a potential direct relationship between renal calpain 1 and 2 content and loss of renal function, in part due probably to the modulation of the fibrotic changes, in adenine fed mice. Conclusion We suggest an implication of calpains 1 and 2 in the development of CKD. Thus, effective calpain blockade or downregulation could be useful as a therapeutic strategy to prevent CKD. Further experiments will be necessary to establish the relationship between these factors.

Losartan attenuates paraquat-induced pulmonary fibrosis in rats

2014 ◽  
Vol 34 (5) ◽  
pp. 497-505 ◽  
Author(s):  
F Guo ◽  
YB Sun ◽  
L Su ◽  
S Li ◽  
ZF Liu ◽  
...  
Keyword(s):  
Pulmonary Fibrosis ◽  
Lung Injury ◽  
Mrna Expression ◽  
Collagen Type ◽  
Collagen Type I ◽  
Control Group ◽  
Type I ◽  
Expression Levels ◽  
Relative Expression ◽  
Tgf Β1

Paraquat (PQ) is one of the most widely used herbicides in the world and can cause pulmonary fibrosis in the cases with intoxication. Losartan, an angiotensin II type 1 receptor antagonist, has beneficial effects on the treatment of fibrosis. The aim of this study was to examine the effect of losartan on pulmonary fibrosis in PQ-intoxicated rats. Adult male Sprague Dawley rats ( n = 32, 180–220 g) were randomly assigned to four groups: (i) control group; (ii) PQ group; (iii) PQ + losartan 7d group; and (iv) PQ + losartan 14d group. Losartan treatment (intragastrically (i.g.), 10 mg/kg) was performed for 7 and 14 days after a single i.g. dose of 40 mg/kg PQ. All rats were killed on the 16th day, and hematoxylin–eosin and Masson’s trichrome staining were used to examine lung injury and fibrosis. The levels of hydroxyproline and transforming growth factor β1 (TGF-β1), matrix metallopeptidase 9 (Mmp9), and tissue inhibitor of metalloproteinase 1 (TIMP-1) messenger RNA (mRNA) expression and relative expression levels of collagen type I and III were also detected. PQ caused a significant increase in hydroxyproline content, mRNA expression of TGF-β1, Mmp9, and TIMP-1, and relative expression levels of collagen type I and III (  p < 0.05), while losartan significantly decreased the amount of hydroxyproline and downregulated TGF-β1, Mmp9, and TIMP-1 mRNA and collagen type I and III expressions (  p < 0.05). Histological examination of PQ-treated rats showed lung injury and widespread inflammatory cell infiltration in the alveolar space and pulmonary fibrosis, while losartan could markedly reduce such damage and prevent pulmonary fibrosis. The results of this study indicated that losartan could reduce lung damage and prevent pulmonary fibrosis induced by PQ.

scholarly journals Simulating tubulin-associated unit transport in an axon: using bootstrapping for estimating confidence intervals of best-fit parameter values obtained from indirect experimental data

2017 ◽  
Vol 473 (2201) ◽  
pp. 20170045 ◽  
Author(s):  
I. A. Kuznetsov ◽  
A. V. Kuznetsov
Keyword(s):  
Experimental Data ◽  
Confidence Intervals ◽  
Surrogate Data ◽  
Model Parameters ◽  
Model Predictions ◽  
Estimate Parameter ◽  
Minimum Number ◽  
Percentile Bootstrap ◽  
Parameter Values ◽  
Best Fit

In this paper, we first develop a model of axonal transport of tubulin-associated unit (tau) protein. We determine the minimum number of parameters necessary to reproduce published experimental results, reducing the number of parameters from 18 in the full model to eight in the simplified model. We then address the following questions: Is it possible to estimate parameter values for this model using the very limited amount of published experimental data? Furthermore, is it possible to estimate confidence intervals for the determined parameters? The idea that is explored in this paper is based on using bootstrapping. Model parameters were estimated by minimizing the objective function that simulates the discrepancy between the model predictions and experimental data. Residuals were then identified by calculating the differences between the experimental data and model predictions. New, surrogate ‘experimental’ data were generated by randomly resampling residuals. By finding sets of best-fit parameters for a large number of surrogate data the histograms for the model parameters were produced. These histograms were then used to estimate confidence intervals for the model parameters, by using the percentile bootstrap. Once the model was calibrated, we applied it to analysing some features of tau transport that are not accessible to current experimental techniques.

scholarly journals Effect of acute resistance exercise and sex on human patellar tendon structural and regulatory mRNA expression

2009 ◽  
Vol 106 (2) ◽  
pp. 468-475 ◽  
Author(s):  
Bridget E. Sullivan ◽  
Chad C. Carroll ◽  
Bozena Jemiolo ◽  
Scott W. Trappe ◽  
S. Peter Magnusson ◽  
...  
Keyword(s):  
Resistance Exercise ◽  
Mrna Expression ◽  
Patellar Tendon ◽  
Type I Collagen ◽  
Collagen Type ◽  
Collagen Type I ◽  
Tissue Inhibitors Of Metalloproteinases ◽  
Type I ◽  
Collagen Type Iii ◽  
Type Iii

Tendon is mainly composed of collagen and an aqueous matrix of proteoglycans that are regulated by enzymes called matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). Although it is known that resistance exercise (RE) and sex influence tendon metabolism and mechanical properties, it is uncertain what structural and regulatory components contribute to these responses. We measured the mRNA expression of tendon's main fibrillar collagens (type I and type III) and the main proteoglycans (decorin, biglycan, fibromodulin, and versican) and the regulatory enzymes MMP-2, MMP-9, MMP-3, and TIMP-1 at rest and after RE. Patellar tendon biopsy samples were taken from six individuals (3 men and 3 women) before and 4 h after a bout of RE and from a another six individuals (3 men and 3 women) before and 24 h after RE. Resting mRNA expression was used for sex comparisons (6 men and 6 women). Collagen type I, collagen type III, and MMP-2 were downregulated ( P < 0.05) 4 h after RE but were unchanged ( P > 0.05) 24 h after RE. All other genes remained unchanged ( P > 0.05) after RE. Women had higher resting mRNA expression ( P < 0.05) of collagen type III and a trend ( P = 0.08) toward lower resting expression of MMP-3 than men. All other genes were not influenced ( P > 0.05) by sex. Acute RE appears to stimulate a change in collagen type I, collagen type III, and MMP-2 gene regulation in the human patellar tendon. Sex influences the structural and regulatory mRNA expression of tendon.

scholarly journals Model-Based Design and Optimization of Blood Oxygenators

2020 ◽  
Vol 14 (4) ◽  
Author(s):  
Ge He ◽  
Tao Zhang ◽  
Jiafeng Zhang ◽  
Bartley P. Griffith ◽  
Zhongjun J. Wu
Keyword(s):  
Experimental Data ◽  
Carbon Dioxide ◽  
Fiber Bundle ◽  
Cfd Modeling ◽  
Design Parameters ◽  
Model Parameters ◽  
Transfer Rates ◽  
Design And Optimization ◽  
Model Based ◽  
Model Predictions

Abstract Blood oxygenators, also known as artificial lungs, are widely used in cardiopulmonary bypass surgery to maintain physiologic oxygen (O2) and carbon dioxide (CO2) levels in blood, and also serve as respiratory assist devices to support patients with lung failure. The time- and cost-consuming method of trial and error is initially used to optimize the oxygenator design, and this method is followed by the introduction of the computational fluid dynamics (CFD) that is employed to reduce the number of prototypes that must be built as the design is optimized. The CFD modeling method, while having progress in recent years, still requires complex three-dimensional (3D) modeling and experimental data to identify the model parameters and validate the model. In this study, we sought to develop an easily implemented mathematical models to predict and optimize the performance (oxygen partial pressure/saturation, oxygen/carbon dioxide transfer rates, and pressure loss) of hollow fiber membrane-based oxygenators and this model can be then used in conjunction with CFD to reduce the number of 3D CFD iteration for further oxygenator design and optimization. The model parameters are first identified by fitting the model predictions to the experimental data obtained from a mock flow loop experimental test on a mini fiber bundle. The models are then validated through comparing the theoretical results with the experimental data of seven full-size oxygenators. The comparative analysis show that the model predictions and experimental results are in good agreement. Based on the verified models, the design curves showing the effects of parameters on the performance of oxygenators and the guidelines detailing the optimization process are established to determine the optimal design parameters (fiber bundle dimensions and its porosity) under specific system design requirements (blood pressure drop, oxygen pressure/saturation, oxygen/carbon dioxide transfer rates, and priming volume). The results show that the model-based optimization method is promising to derive the optimal parameters in an efficient way and to serve as an intermediate modeling approach prior to complex CFD modeling.

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