scholarly journals Models of tendon development and injury

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Sophia K. Theodossiou ◽  
Nathan R. Schiele
Keyword(s):  
Computational Models ◽  
Ex Vivo ◽  
Current Model ◽  
Stem Cell Differentiation ◽  
Tendon Injury ◽  
Model Systems ◽  
Tendon Development ◽  
Key Aspects

AbstractTendons link muscle to bone and transfer forces necessary for normal movement. Tendon injuries can be debilitating and their intrinsic healing potential is limited. These challenges have motivated the development of model systems to study the factors that regulate tendon formation and tendon injury. Recent advances in understanding of embryonic and postnatal tendon formation have inspired approaches that aimed to mimic key aspects of tendon development. Model systems have also been developed to explore factors that regulate tendon injury and healing. We highlight current model systems that explore developmentally inspired cellular, mechanical, and biochemical factors in tendon formation and tenogenic stem cell differentiation. Next, we discuss in vivo, in vitro, ex vivo, and computational models of tendon injury that examine how mechanical loading and biochemical factors contribute to tendon pathologies and healing. These tendon development and injury models show promise for identifying the factors guiding tendon formation and tendon pathologies, and will ultimately improve regenerative tissue engineering strategies and clinical outcomes.

scholarly journals Considerations to Model Heart Disease in Women with Preeclampsia and Cardiovascular Disease

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 899
Author(s):  
Clara Liu Chung Ming ◽  
Kimberly Sesperez ◽  
Eitan Ben-Sefer ◽  
David Arpon ◽  
Kristine McGrath ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Cardiovascular Disease ◽  
Ex Vivo ◽  
Myocardial Damage ◽  
Cardiovascular Disorder ◽  
Model Systems ◽  
Ex Vivo Model ◽  
Disease Manifestation

Preeclampsia is a multifactorial cardiovascular disorder diagnosed after 20 weeks of gestation, and is the leading cause of death for both mothers and babies in pregnancy. The pathophysiology remains poorly understood due to the variability and unpredictability of disease manifestation when studied in animal models. After preeclampsia, both mothers and offspring have a higher risk of cardiovascular disease (CVD), including myocardial infarction or heart attack and heart failure (HF). Myocardial infarction is an acute myocardial damage that can be treated through reperfusion; however, this therapeutic approach leads to ischemic/reperfusion injury (IRI), often leading to HF. In this review, we compared the current in vivo, in vitro and ex vivo model systems used to study preeclampsia, IRI and HF. Future studies aiming at evaluating CVD in preeclampsia patients could benefit from novel models that better mimic the complex scenario described in this article.

scholarly journals Considerations to Model Heart Disease in Women with Preeclampsia and Cardiovascular Disease

2021 ◽  
Author(s):  
Clara Liu Chung Ming ◽  
Kimberly Sesperez ◽  
Eitan Ben-Sefer ◽  
David Arpon ◽  
Kristine McGrath ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Cardiovascular Disease ◽  
Ex Vivo ◽  
Myocardial Damage ◽  
Cardiovascular Disorder ◽  
Model Systems ◽  
Ex Vivo Model ◽  
Disease Manifestation

Preeclampsia is a multifactorial cardiovascular disorder diagnosed after 20 weeks of gestation that is the leading cause of death for both mothers and babies in pregnancy. The pathophysiology remains poorly understood due to variability and unpredictability of disease manifestation when studied in animal models. After preeclampsia, both mothers and offspring have a higher risk of cardiovascular disease (CVD) including myocardial infarction or heart attack and heart failure (HF). Myocardial infarction is an acute myocardial damage that can be treated through reperfusion, however, that therapeutic approach leads to ischemic/reperfusion injury (IRI) often leading to HF. In this review, we compared the current in vivo, in vitro and ex vivo model systems used to study preeclampsia, IRI and HF. Future studies aiming at evaluating CVD in preeclampsia patients could benefit from novel models that better mimic the complex scenario described in this article.

scholarly journals The MEMIC: An ex vivo system to model the complexity of the tumor microenvironment

2021 ◽  
Author(s):  
Libuše Janská ◽  
Libi Anandi ◽  
Nell C. Kirchberger ◽  
Zoran S. Marinkovic ◽  
Logan T. Schachtner ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Tumor Cells ◽  
Ex Vivo ◽  
Tumor Stroma ◽  
Stem Cell Differentiation ◽  
Blood Stream ◽  
Direct Access ◽  
Ex Vivo Model

There is an urgent need for accurate, scalable, and cost-efficient experimental systems to model the complexity of the tumor microenvironment. Here, we detail how to fabricate and use the Metabolic Microenvironment Chamber (MEMIC) – a 3D-printed ex vivo model of intratumoral heterogeneity. A major driver of the cellular and molecular diversity in tumors is the accessibility to the blood stream that provides key resources such as oxygen and nutrients. While some tumor cells have direct access to these resources, many others must survive under progressively more ischemic environments as they reside further from the vasculature. The MEMIC is designed to simulate the differential access to nutrients and allows co-culturing different cell types, such as tumor and immune cells. This system is optimized for live imaging and other microscopy-based approaches, and it is a powerful tool to study tumor features such as the effect of nutrient scarcity on tumor-stroma interactions. Due to its adaptable design and full experimental control, the MEMIC provide insights into the tumor microenvironment that would be difficult to obtain via other methods. As a proof of principle, we show that cells sense gradual changes in metabolite concentration resulting in multicellular spatial patterns of signal activation and cell proliferation. To illustrate the ease of studying cell-cell interactions in the MEMIC, we show that ischemic macrophages reduce epithelial features in neighboring tumor cells. We propose the MEMIC as a complement to standard in vitro and in vivo experiments, diversifying the tools available to accurately model, perturb, and monitor the tumor microenvironment, as well as to understand how extracellular metabolites affect other processes such as wound healing and stem cell differentiation.

scholarly journals Alzheimer’s Disease: Current Perspectives and Advances in Physiological Modeling

2021 ◽  
Vol 8 (12) ◽  
pp. 211
Author(s):  
E. Josephine Boder ◽  
Ipsita A. Banerjee
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cell Culture ◽  
Stem Cell Differentiation ◽  
Experimental Manipulation ◽  
Model Systems ◽  
Culture Systems ◽  
Cell Culture Systems

Though Alzheimer’s disease (AD) is the most common cause of dementia, complete disease-modifying treatments are yet to be fully attained. Until recently, transgenic mice constituted most in vitro model systems of AD used for preclinical drug screening; however, these models have so far failed to adequately replicate the disease’s pathophysiology. However, the generation of humanized APOE4 mouse models has led to key discoveries. Recent advances in stem cell differentiation techniques and the development of induced pluripotent stem cells (iPSCs) have facilitated the development of novel in vitro devices. These “microphysiological” systems—in vitro human cell culture systems designed to replicate in vivo physiology—employ varying levels of biomimicry and engineering control. Spheroid-based organoids, 3D cell culture systems, and microfluidic devices or a combination of these have the potential to replicate AD pathophysiology and pathogenesis in vitro and thus serve as both tools for testing therapeutics and models for experimental manipulation.

scholarly journals iAmideV-Deep: Valine Amidation Site Prediction in Proteins Using Deep Learning and Pseudo Amino Acid Compositions

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 560
Author(s):  
Sheraz Naseer ◽  
Rao Faizan Ali ◽  
Amgad Muneer ◽  
Suliman Mohamed Fati
Keyword(s):  
Amino Acid ◽  
Computational Models ◽  
Ex Vivo ◽  
Biologically Active ◽  
Peptide Sequence ◽  
Post Translational Modification ◽  
Amino Acid Compositions ◽  
Efficient Alternative

Amidation is an important post translational modification where a peptide ends with an amide group (–NH2) rather than carboxyl group (–COOH). These amidated peptides are less sensitive to proteolytic degradation with extended half-life in the bloodstream. Amides are used in different industries like pharmaceuticals, natural products, and biologically active compounds. The in-vivo, ex-vivo, and in-vitro identification of amidation sites is a costly and time-consuming but important task to study the physiochemical properties of amidated peptides. A less costly and efficient alternative is to supplement wet lab experiments with accurate computational models. Hence, an urgent need exists for efficient and accurate computational models to easily identify amidated sites in peptides. In this study, we present a new predictor, based on deep neural networks (DNN) and Pseudo Amino Acid Compositions (PseAAC), to learn efficient, task-specific, and effective representations for valine amidation site identification. Well-known DNN architectures are used in this contribution to learn peptide sequence representations and classify peptide chains. Of all the different DNN based predictors developed in this study, Convolutional neural network-based model showed the best performance surpassing all other DNN based models and reported literature contributions. The proposed model will supplement in-vivo methods and help scientists to determine valine amidation very efficiently and accurately, which in turn will enhance understanding of the valine amidation in different biological processes.

scholarly journals Discovery of tumoricidal DNA oligonucleotides by effect-directedin-vitroevolution

2019 ◽  
Author(s):  
Noam Mamet ◽  
Yaniv Amir ◽  
Erez Lavi ◽  
Liron Bassali ◽  
Gil Harari ◽  
...  
Keyword(s):  
Drug Discovery ◽  
De Novo ◽  
Ex Vivo ◽  
Binding Capacity ◽  
Biological Effects ◽  
Current Model ◽  
Target Cells ◽  
Dna Oligonucleotides

AbstractOur current model of drug discovery is challenged by the relative ineffectiveness of drugs against highly variable and rapidly evolving diseases and their relatively high incidence of adverse effects due to poor selectivity. Here we describe a robust and reproducible platform which could potentially address these limitations. The platform enables rapid,de-novodiscovery of DNA oligonucleotides evolvedin-vitroto exert specific biological effects on target cells. Unlike aptamers, which are selected by their ligand binding capacity, this platform is driven directly by therapeutic effect and selectivity towards target vs negative target cells. The process could, therefore, operate without anya-prioriknowledge (e.g. mutations, biomarker expression, or known drug resistance) of the target. We report the discovery of DNA oligonucleotides with direct and selective cytotoxicity towards several tumor cell lines as well as primary, patient-derived solid and hematological tumors, some with chemotherapy resistance. Oligonucleotides discovered by this platform exhibited favorable biodistribution in animals, persistence in target tumors up to 48 hours after injection, and safety in human blood. These oligonucleotides showed remarkable efficacyin-vivoas well asex-vivoin freshly obtained, 3D cultured human tumors resistant to multiple chemotherapies. With further improvement, these findings could lead to a drug discovery model which is target-tailored, mechanism-flexible, and nearly on-demand.

scholarly journals Nanoscale patterning of in vitro neuronal circuits

2021 ◽  
Author(s):  
János Vörös ◽  
Sean Weaver ◽  
Jose C. Mateus ◽  
Paulo Aguiar ◽  
Dirk van Swaay ◽  
...  
Keyword(s):  
Computational Models ◽  
Synapse Formation ◽  
Ex Vivo ◽  
Axon Growth ◽  
Neuronal Circuits ◽  
Calcium Indicator ◽  
The Difference ◽  
Pass Through

Methods for patterning neurons in vitro have gradually improved and are used to investigate questions difficult to address in or ex vivo. Though these techniques guide axons between groups of neurons, multiscale control of neuronal connectivity, from circuits to synapses, is yet to be achieved in vitro. As studying neuronal circuits with synaptic resolution in vivo poses significant challenges, an in vitro alternative could serve as a testbed for in vivo experiments or as a platform for validating biophysical and computational models. In this work we use a combination of electron beam and photolithography to create polydimethylsiloxane (PDMS) structures with features ranging from 150 nanometers to a few millimeters. Leveraging the difference between average axon and dendritic spine diameters, we restrict axon growth while allowing spines to pass through nanochannels to guide synapse formation between small groups of neurons (i.e. nodes). We show this technique can be used to generate large numbers of isolated feed-forward circuits where connections between nodes are restricted to regions connected by nanochannels. Using a genetically encoded calcium indicator in combination with fluorescently tagged post synaptic protein, PSD-95, we demonstrate functional synapses can form in this region. Although more work needs to be done to control connectivity in vitro, we believe this is a significant step in that direction.

scholarly journals c-di-AMP is essential for the virulence of Enterococcus faecalis

2021 ◽  
Author(s):  
Shivani Kundra ◽  
Ling Ning Lam ◽  
Jessica K. Kajfasz ◽  
Leila Casella ◽  
Marissa J Andersen ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
Galleria Mellonella ◽  
Ex Vivo ◽  
Biological Significance ◽  
Opportunistic Pathogen ◽  
Bacterial Fitness ◽  
Key Aspects

Second messenger nucleotides are produced by bacteria in response to environmental stimuli and play a major role in the regulation of processes associated with bacterial fitness, including but not limited to osmoregulation, envelope homeostasis, central metabolism, and biofilm formation. In this study, we uncovered the biological significance of c-di-AMP in the opportunistic pathogen Enterococcus faecalis by isolating and characterizing strains lacking genes responsible for c-di-AMP synthesis (cdaA) and degradation (dhhP and gdpP). Using complementary approaches, we demonstrated that either complete loss of c-di-AMP (ΔcdaA strain) or c-di-AMP accumulation (ΔdhhP, ΔgdpP and ΔdhhPΔgdpP strains) drastically impaired general cell fitness and virulence of E. faecalis. In particular, the ΔcdaA strain was highly sensitive to envelope-targeting antibiotics, was unable to multiply and quickly lost viability in human serum or urine ex vivo, and was avirulent in an invertebrate (Galleria mellonella) and in two catheter-associated mouse infection models that recapitulate key aspects of enterococcal infections in humans. In addition to evidence linking these phenotypes to altered activity of metabolite and peptide transporters and inability to maintain osmobalance, we found that the attenuated virulence of ΔcdaA could be also attributed to a defect in Ebp pilus production and activity that severely impaired biofilm formation under both in vitro and in vivo conditions. Collectively, these results reveal that c-di-AMP signaling is essential for E. faecalis pathogenesis and a desirable target for drug development.

scholarly journals Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids

2021 ◽  
Author(s):  
Dilara Sen ◽  
Alexis Voulgaropoulos ◽  
Albert J. Keung
Keyword(s):  
Stem Cell Differentiation ◽  
Cell Types ◽  
Brain Regions ◽  
Embryoid Bodies ◽  
Model Systems ◽  
Human Model ◽  
Spatial Factors ◽  
Neural Lineage

ABSTRACTBackgroundBiophysical factors such as shape and mechanical forces are known to play crucial roles in stem cell differentiation, embryogenesis and neurodevelopment. However, the complexity and experimental challenges capturing such early stages of development, and ethical concerns associated with human embryo and fetal research, limit our understanding of how these factors affect human brain organogenesis. Human cerebral organoids (hCO) are attractive models due to their ability to model important brain regions and transcriptomics of early in vivo brain development. Furthermore, they provide three-dimensional environments that better mimic the in vivo environment. To date, they have been used to understand the effects of genetics and soluble factors on neurodevelopment. Establishing links between spatial factors and hCO development will require the development of new approaches.ResultsHere, we investigated the effects of early geometric confinements on transcriptomic changes during hCO differentiation. Using a custom and tunable agarose microwell platform we generated embryoid bodies (EB) of diverse shapes and then further differentiated those EBs to whole brain hCOs. Our results showed that the microwells did not have negative gross impacts on the ability of the hCOs to differentiate generally towards neural fates, and there were clear shape dependent effects on neural lineage specification. In particular, we observed that non-spherical shapes showed signs of altered neurodevelopmental kinetics and favored the development of medial ganglionic eminence-associated brain regions and cell types over cortical regions.ConclusionsThe findings presented here suggest a role for spatial factors in brain region specification during hCO development. Understanding these spatial patterning factors will not only improve understanding of in vivo development and differentiation, but also provide important handles with which to advance and improve control over human model systems for in vitro applications.

scholarly journals Complementarity of clinical trials, model systems, and metabolomic workflow to unravel the healthy effects of foods: BEBESANO vs MODELSANO: A case study

2021 ◽  
Vol 2 (3) ◽  
Author(s):  
Vicente Agulló ◽  
◽  
Raúl Domínguez-Perles ◽  
Cristina García-Viguera ◽  
◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
Ex Vivo ◽  
In Vitro Models ◽  
Experimental Models ◽  
Model Systems ◽  
Food Science ◽  
Clinical Models ◽  
Safe Condition

Nowadays, the health benefits associated with the consumption of plant-based food constitute a hot topic. To further demonstrate such benefits, related to antioxidant, anti-microbial, and anti-inflammatory activities, as well as the reduction of the risk of several pathophysiological conditions, the study of bioaccessibility and bioavailability of specific food’s constituents, which require interdisciplinary networks, is essential. In this frame, although different experimental models can be developed, the workflow described in the present work support the application of intervention trials in humans as the first option to study the truly effects on health of foods (e.g., plant-based foods), due to the safe condition of them and the realistic approach of this kind of studies, later explored in depth resorting to in vitro, ex vivo, and pre-clinical models, as the most appropriate workflow to get reliable results in the field of Food Science and Nutrition, regarding mechanisms of actions and molecular interactions. Thereby, the work described in the present review is developed in the frame of two consecutive and interconnected projects: BEBESANO (concluded) and MODELSANO (in process) that demonstrate the efficiency of the workflow proposed for research in the Food Science and Nutrition fields. In this regard, in the frame of BEBESANO, acute and longitudinal interventions in humans, devoted to set-up bioavailability of bioactive compounds, followed by functional studies in vivo upon pre-clinical models were conducted to unravel the relationship between bioactive compounds in plant-based beverages and the use of sweetener replacer. Now, most relevant findings from BEBESANO are being further explored in the newly granted project MODELSANO, which is aimed to uncover gaps of knowledge about the mechanisms behind the descriptive results obtained in BEBESANO, using more restrictive in vitro models (allowing the development of studies on the cellular and molecular pathways involved), and integrative cutting edge mathematical modelling alternatives. Keywords: In vivo; in vitro; bioavailability; bioaccessibility; bioactivity; health-promoting foods; metabolomic; mechanistic studies

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