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Naletova I, Greco V, Sciuto S, Attanasio F, Rizzarelli E. Ionophore Ability of Carnosine and Its Trehalose Conjugate Assists Copper Signal in Triggering Brain-Derived Neurotrophic Factor and Vascular Endothelial Growth Factor Activation In Vitro. Int J Mol Sci 2021; 22:13504. [PMID: 34948299 PMCID: PMC8706131 DOI: 10.3390/ijms222413504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022] Open
Abstract
l-carnosine (β-alanyl-l-histidine) (Car hereafter) is a natural dipeptide widely distributed in mammalian tissues and reaching high concentrations (0.7-2.0 mM) in the brain. The molecular features of the dipeptide underlie the antioxidant, anti-aggregating and metal chelating ability showed in a large number of physiological effects, while the biological mechanisms involved in the protective role found against several diseases cannot be explained on the basis of the above-mentioned properties alone, requiring further research efforts. It has been reported that l-carnosine increases the secretion and expression of various neurotrophic factors and affects copper homeostasis in nervous cells inducing Cu cellular uptake in keeping with the key metal-sensing system. Having in mind this l-carnosine ability, here we report the copper-binding and ionophore ability of l-carnosine to activate tyrosine kinase cascade pathways in PC12 cells and stimulate the expression of BDNF. Furthermore, the study was extended to verify the ability of the dipeptide to favor copper signaling inducing the expression of VEGF. Being aware that the potential protective action of l-carnosine is drastically hampered by its hydrolysis, we also report on the behavior of a conjugate of l-carnosine with trehalose that blocks the carnosinase degradative activity. Overall, our findings describe a copper tuning effect on the ability of l-carnosine and, particularly its conjugate, to activate tyrosine kinase cascade pathways.
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Affiliation(s)
- Irina Naletova
- Institute of Crystallography, National Council of Research—CNR, Via Paolo Gaifami 18, 95126 Catania, Italy;
- National Inter-University Consortium Metals Chemistry in Biological Systems (CIRCMSB), Via Celso Ulpiani 27, 70126 Bari, Italy
| | - Valentina Greco
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (V.G.); (S.S.)
| | - Sebastiano Sciuto
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (V.G.); (S.S.)
| | - Francesco Attanasio
- Institute of Crystallography, National Council of Research—CNR, Via Paolo Gaifami 18, 95126 Catania, Italy;
| | - Enrico Rizzarelli
- Institute of Crystallography, National Council of Research—CNR, Via Paolo Gaifami 18, 95126 Catania, Italy;
- National Inter-University Consortium Metals Chemistry in Biological Systems (CIRCMSB), Via Celso Ulpiani 27, 70126 Bari, Italy
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (V.G.); (S.S.)
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Hebisz P, Hebisz R, Murawska-Ciałowicz E, Zatoń M. Changes in exercise capacity and serum BDNF following long-term sprint interval training in well-trained cyclists. Appl Physiol Nutr Metab 2018; 44:499-506. [PMID: 30286300 DOI: 10.1139/apnm-2018-0427] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The study determined the effects of sprint interval training on the acute and chronic changes of serum brain-derived neurotrophic factor (BDNF) and aerobic capacity. Twenty-six cyclists were divided into experimental (E) and control groups. Both groups executed a 6-month exercise intervention involving high-intensity interval training (HIIT) and continuous endurance training (CET) with group E replacing HIIT and CET sessions with sprint interval training (SIT) that was executed twice a week. Two exercise tests were administered prior to the intervention and at 2 and 6 months after study outset. Incremental exercise test assessed aerobic capacity by measuring maximal oxygen uptake and work output; the sprint interval exercise test (SIXT) comprises 3 sets of four 30-s all-out repetitions interspersed with 90 s of rest with sets separated by 25-40 min of active recovery. Oxygen uptake, work output, BDNF, and vascular endothelial growth factor A (VEGF-A) concentrations (baseline, 10 min after first set, and 10 and 60 min after third SIXT set) were taken during the SIXT. Significant decreases in BDNF relative to baseline values were observed 10 min after the first set and 60 min after the third set in group E at the 2- and 6-month assessments. Increases in baseline VEGF-A after 2 and 6 months of training and increases in maximal oxygen uptake after 2 months of training were also observed only in group E. The inclusion of SIT with HIIT and CET shows positive long-term effects, including increased maximal oxygen uptake and baseline VEGF-A and a reduction in BDNF below baseline levels during and after SIXT.
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Affiliation(s)
- Paulina Hebisz
- Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland.,Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland
| | - Rafał Hebisz
- Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland.,Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland
| | - Eugenia Murawska-Ciałowicz
- Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland.,Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland
| | - Marek Zatoń
- Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland.,Department of Physiology and Biochemistry, University School of Physical Education in Wroclaw, 35 J.I. Paderewski Avenue, 51-612 Wroclaw, Poland
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Palm MM, Dallinga MG, van Dijk E, Klaassen I, Schlingemann RO, Merks RMH. Computational Screening of Tip and Stalk Cell Behavior Proposes a Role for Apelin Signaling in Sprout Progression. PLoS One 2016; 11:e0159478. [PMID: 27828952 PMCID: PMC5102492 DOI: 10.1371/journal.pone.0159478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/24/2016] [Indexed: 12/30/2022] Open
Abstract
Angiogenesis involves the formation of new blood vessels by sprouting or splitting of existing blood vessels. During sprouting, a highly motile type of endothelial cell, called the tip cell, migrates from the blood vessels followed by stalk cells, an endothelial cell type that forms the body of the sprout. To get more insight into how tip cells contribute to angiogenesis, we extended an existing computational model of vascular network formation based on the cellular Potts model with tip and stalk differentiation, without making a priori assumptions about the differences between tip cells and stalk cells. To predict potential differences, we looked for parameter values that make tip cells (a) move to the sprout tip, and (b) change the morphology of the angiogenic networks. The screening predicted that if tip cells respond less effectively to an endothelial chemoattractant than stalk cells, they move to the tips of the sprouts, which impacts the morphology of the networks. A comparison of this model prediction with genes expressed differentially in tip and stalk cells revealed that the endothelial chemoattractant Apelin and its receptor APJ may match the model prediction. To test the model prediction we inhibited Apelin signaling in our model and in an in vitro model of angiogenic sprouting, and found that in both cases inhibition of Apelin or of its receptor APJ reduces sprouting. Based on the prediction of the computational model, we propose that the differential expression of Apelin and APJ yields a "self-generated" gradient mechanisms that accelerates the extension of the sprout.
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Affiliation(s)
- Margriet M. Palm
- Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, the Netherlands
| | | | - Erik van Dijk
- Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, the Netherlands
| | - Ingeborg Klaassen
- Ocular Angiogenesis Group, Academic Medical Center, Amsterdam, the Netherlands
| | | | - Roeland M. H. Merks
- Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, the Netherlands
- Mathematical Institute, Leiden University, Leiden, the Netherlands
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Mehdizadeh H, Bayrak ES, Lu C, Somo SI, Akar B, Brey EM, Cinar A. Agent-based modeling of porous scaffold degradation and vascularization: Optimal scaffold design based on architecture and degradation dynamics. Acta Biomater 2015; 27:167-178. [PMID: 26363375 DOI: 10.1016/j.actbio.2015.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 08/26/2015] [Accepted: 09/08/2015] [Indexed: 12/11/2022]
Abstract
A multi-layer agent-based model (ABM) of biomaterial scaffold vascularization is extended to consider the effects of scaffold degradation kinetics on blood vessel formation. A degradation model describing the bulk disintegration of porous hydrogels is incorporated into the ABM. The combined degradation-angiogenesis model is used to investigate growing blood vessel networks in the presence of a degradable scaffold structure. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support results in failure for the material. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as a way to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric parameters and degradation behavior of scaffolds, and enables easy refinement of the model as new knowledge about the underlying biological phenomena becomes available. STATEMENT OF SIGNIFICANCE This paper proposes a multi-layer agent-based model (ABM) of biomaterial scaffold vascularization integrated with a structural-kinetic model describing bulk degradation of porous hydrogels to consider the effects of scaffold degradation kinetics on blood vessel formation. This enables the assessment of scaffold characteristics and in particular the disintegration characteristics of the scaffold on angiogenesis. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support by scaffold disintegration results in failure of the material and disruption of angiogenesis. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as away to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric and degradation characteristics of tissue engineering scaffolds.
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Affiliation(s)
- Hamidreza Mehdizadeh
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA
| | - Elif S Bayrak
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA
| | - Chenlin Lu
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA
| | - Sami I Somo
- Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA
| | - Banu Akar
- Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA
| | - Eric M Brey
- Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA; Research Service, Hines Veterans Administration Hospital, Hines, IL, USA
| | - Ali Cinar
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA; Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA.
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5
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Walpole J, Chappell JC, Cluceru JG, Mac Gabhann F, Bautch VL, Peirce SM. Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks. Integr Biol (Camb) 2015; 7:987-97. [PMID: 26158406 PMCID: PMC4558383 DOI: 10.1039/c5ib00024f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many biological processes are controlled by both deterministic and stochastic influences. However, efforts to model these systems often rely on either purely stochastic or purely rule-based methods. To better understand the balance between stochasticity and determinism in biological processes a computational approach that incorporates both influences may afford additional insight into underlying biological mechanisms that give rise to emergent system properties. We apply a combined approach to the simulation and study of angiogenesis, the growth of new blood vessels from existing networks. This complex multicellular process begins with selection of an initiating endothelial cell, or tip cell, which sprouts from the parent vessels in response to stimulation by exogenous cues. We have constructed an agent-based model of sprouting angiogenesis to evaluate endothelial cell sprout initiation frequency and location, and we have experimentally validated it using high-resolution time-lapse confocal microscopy. ABM simulations were then compared to a Monte Carlo model, revealing that purely stochastic simulations could not generate sprout locations as accurately as the rule-informed agent-based model. These findings support the use of rule-based approaches for modeling the complex mechanisms underlying sprouting angiogenesis over purely stochastic methods.
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Affiliation(s)
- J Walpole
- Department of Biomedical Engineering, University of Virginia, Virginia, USA.
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Abstract
The vascular network carries blood throughout the body, delivering oxygen to tissues and providing a pathway for communication between distant organs. The network is hierarchical and structured, but also dynamic, especially at the smaller scales. Remodeling of the microvasculature occurs in response to local changes in oxygen, gene expression, cell-cell communication, and chemical and mechanical stimuli from the microenvironment. These local changes occur as a result of physiological processes such as growth and exercise, as well as acute and chronic diseases including stroke, cancer, and diabetes, and pharmacological intervention. While the vasculature is an important therapeutic target in many diseases, drugs designed to inhibit vascular growth have achieved only limited success, and no drug has yet been approved to promote therapeutic vascular remodeling. This highlights the challenges involved in identifying appropriate therapeutic targets in a system as complex as the vasculature. Systems biology approaches provide a means to bridge current understanding of the vascular system, from detailed signaling dynamics measured in vitro and pre-clinical animal models of vascular disease, to a more complete picture of vascular regulation in vivo. This will translate to an improved ability to identify multi-component biomarkers for diagnosis, prognosis, and monitoring of therapy that are easy to measure in vivo, as well as better drug targets for specific disease states. In this review, we summarize systems biology approaches that have advanced our understanding of vascular function and dysfunction in vivo, with a focus on computational modeling.
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Affiliation(s)
- Lindsay E Clegg
- Institute for Computational Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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7
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Mehdizadeh H, Somo SI, Bayrak ES, Brey EM, Cinar A. Design of Polymer Scaffolds for Tissue Engineering Applications. Ind Eng Chem Res 2015. [DOI: 10.1021/ie503133e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hamidreza Mehdizadeh
- Illinois Institute of Technology, 3300 S Federal Street, Chicago, Illinois 60616, United States
| | - Sami I. Somo
- Illinois Institute of Technology, 3300 S Federal Street, Chicago, Illinois 60616, United States
| | - Elif S. Bayrak
- Illinois Institute of Technology, 3300 S Federal Street, Chicago, Illinois 60616, United States
| | - Eric M. Brey
- Illinois Institute of Technology, 3300 S Federal Street, Chicago, Illinois 60616, United States
| | - Ali Cinar
- Illinois Institute of Technology, 3300 S Federal Street, Chicago, Illinois 60616, United States
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8
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BDNF and its TrkB receptor in human fracture healing. Ann Anat 2014; 196:286-95. [DOI: 10.1016/j.aanat.2014.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 12/31/2022]
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9
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Lin CY, Hung SY, Chen HT, Tsou HK, Fong YC, Wang SW, Tang CH. Brain-derived neurotrophic factor increases vascular endothelial growth factor expression and enhances angiogenesis in human chondrosarcoma cells. Biochem Pharmacol 2014; 91:522-33. [PMID: 25150213 DOI: 10.1016/j.bcp.2014.08.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 08/11/2014] [Accepted: 08/11/2014] [Indexed: 01/07/2023]
Abstract
Chondrosarcomas are a type of primary malignant bone cancer, with a potent capacity for local invasion and distant metastasis. Brain-derived neurotrophic factor (BDNF) is commonly upregulated during neurogenesis. The aim of the present study was to examine the mechanism involved in BDNF-mediated vascular endothelial growth factor (VEGF) expression and angiogenesis in human chondrosarcoma cells. Here, we knocked down BDNF expression in chondrosarcoma cells and assessed their capacity to control VEGF expression and angiogenesis in vitro and in vivo. We found knockdown of BDNF decreased VEGF expression and abolished chondrosarcoma conditional medium-mediated angiogenesis in vitro as well as angiogenesis effects in vivo in the chick chorioallantoic membrane and Matrigel plug nude mouse models. In addition, in the xenograft tumor angiogenesis model, the knockdown of BDNF significantly reduced tumor growth and tumor-associated angiogenesis. BDNF increased VEGF expression and angiogenesis through the TrkB receptor, PLCγ, PKCα, and the HIF-1α signaling pathway. Finally, we analyzed samples from chondrosarcoma patients by immunohistochemical staining. The expression of BDNF and VEGF protein in 56 chondrosarcoma patients was significantly higher than in normal cartilage. In addition, the high level of BDNF expression correlated strongly with VEGF expression and tumor stage. Taken together, our results indicate that BDNF increases VEGF expression and enhances angiogenesis through a signal transduction pathway that involves the TrkB receptor, PLCγ, PKCα, and the HIF-1α. Therefore, BDNF may represent a novel target for anti-angiogenic therapy for human chondrosarcoma.
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Affiliation(s)
- Chih-Yang Lin
- Graduate Institute of Basic Medical Science, China Medical University, No. 91, Hsueh-Shih Road, Taichung, Taiwan
| | - Shih-Ya Hung
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Hsien-Te Chen
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Orthopedic Surgery, China Medical University Hospital, Taichung, Taiwan; Department of Materials Science and Engineering, Feng Chia University, Taichung, Taiwan
| | - Hsi-Kai Tsou
- Department of Materials Science and Engineering, Feng Chia University, Taichung, Taiwan; Department of Neurosurgery, Taichung Veterans General Hospital, Taichung, Taiwan; Department of Early Childhood Care and Education, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli County, Taiwan
| | - Yi-Chin Fong
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Orthopedic Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Shih-Wei Wang
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Chih-Hsin Tang
- Graduate Institute of Basic Medical Science, China Medical University, No. 91, Hsueh-Shih Road, Taichung, Taiwan; Department of Pharmacology, School of Medicine, China Medical University, Taichung, Taiwan; Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan.
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Abstract
Endothelial cells (ECs) exhibit dramatic plasticity of form at the single- and collective-cell level during new vessel growth, adult vascular homeostasis, and pathology. Understanding how, when, and why individual ECs coordinate decisions to change shape, in relation to the myriad of dynamic environmental signals, is key to understanding normal and pathological blood vessel behavior. However, this is a complex spatial and temporal problem. In this review we show that the multidisciplinary field of Adaptive Systems offers a refreshing perspective, common biological language, and straightforward toolkit that cell biologists can use to untangle the complexity of dynamic, morphogenetic systems.
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Affiliation(s)
- Katie Bentley
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Andrew Philippides
- Centre for Computational Neuroscience and Robotics, Department of Informatics, University of Sussex, Brighton BN1 9QJ, UK
| | - Erzsébet Ravasz Regan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Deindl E. Mechanistic insights into the functional role of vascular endothelial growth factor and its signalling partner brain-derived neurotrophic factor in angiogenic tube formation. Acta Physiol (Oxf) 2014; 211:268-70. [PMID: 24720532 DOI: 10.1111/apha.12299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- E. Deindl
- Walter-Brendel-Centre of Experimental Medicine; Ludwig-Maximilians-Universität; Munich Germany
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Logsdon EA, Finley SD, Popel AS, Mac Gabhann F. A systems biology view of blood vessel growth and remodelling. J Cell Mol Med 2013; 18:1491-508. [PMID: 24237862 PMCID: PMC4190897 DOI: 10.1111/jcmm.12164] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022] Open
Abstract
Blood travels throughout the body in an extensive network of vessels – arteries, veins and capillaries. This vascular network is not static, but instead dynamically remodels in response to stimuli from cells in the nearby tissue. In particular, the smallest vessels – arterioles, venules and capillaries – can be extended, expanded or pruned, in response to exercise, ischaemic events, pharmacological interventions, or other physiological and pathophysiological events. In this review, we describe the multi-step morphogenic process of angiogenesis – the sprouting of new blood vessels – and the stability of vascular networks in vivo. In particular, we review the known interactions between endothelial cells and the various blood cells and plasma components they convey. We describe progress that has been made in applying computational modelling, quantitative biology and high-throughput experimentation to the angiogenesis process.
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Affiliation(s)
- Elizabeth A Logsdon
- Institute for Computational Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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13
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Abstract
Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines--or agents--to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex.
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Rekhi R, Qutub AA. Systems approaches for synthetic biology: a pathway toward mammalian design. Front Physiol 2013; 4:285. [PMID: 24130532 PMCID: PMC3793170 DOI: 10.3389/fphys.2013.00285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/19/2013] [Indexed: 01/08/2023] Open
Abstract
We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches—stochasticity, complexity, and scale—with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility toward synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications.
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Affiliation(s)
- Rahul Rekhi
- Department of Bioengineering, Rice University Houston, TX, USA
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