Fibrin polymerization in blood coagulation-a statistical model

Computational Biomechanical Modeling of Fibrin Networks and Platelet-Fiber Network Interactions

Fibrin deformation and interaction of fibrin with other blood components play critical roles in hemostasis and thrombosis. In this review, computational and mathematical biomechanical models of fibrin network deformation and contraction at different spatio-temporal scales as well as challenges in developing and calibrating multiscale models are discussed. There are long standing challenges. For instance, applicability of models to identify and test potential mechanisms of the biomechanical processes mediating interactions between platelets and fiber networks in blood clot stretching and contraction needs to be examined carefully. How the structural and mechanical properties of major blood clot components influences biomechanical responses of the entire clot subjected to external forces, such as blood flow or vessel wall deformations needs to be investigated thoroughly.

Development of a mesoscopic framework spanning nanoscale protofibril dynamics to macro-scale fibrin clot formation

Thrombi form a micro-scale fibrin network consisting of an interlinked structure of nanoscale protofibrils, resulting in haemostasis. It is theorized that the mechanical effect of the fibrin clot is caused by the polymeric protofibrils between crosslinks, or to their dynamics on a nanoscale order. Despite a number of studies, however, it is still unknown, how the nanoscale protofibril dynamics affect the formation of the macro-scale fibrin clot and thus its mechanical properties. A mesoscopic framework would be useful to tackle this multi-scale problem, but it has not yet been established. We thus propose a minimal mesoscopic model for protofibrils based on Brownian dynamics, and performed numerical simulations of protofibril aggregation. We also performed stretch tests of polymeric protofibrils to quantify the elasticity of fibrin clots. Our model results successfully captured the conformational properties of aggregated protofibrils, e.g., strain-hardening response. Furthermore, the results suggest that the bending stiffness of individual protofibrils increases to resist extension.

Toward Understanding the Genetic Basis of Yak Ovary Reproduction: A Characterization and Comparative Analyses of Estrus Ovary Transcriptiome in Yak and Cattle

Background

Yaks (Bos grunniens) are endemic species that can adapt well to thin air, cold temperatures, and high altitude. These species can survive in harsh plateau environments and are major source of animal production for local residents, being an important breed in the Qinghai–Tibet Plateau. However, compared with ordinary cattle that live in the plains, yaks generally have lower fertility. Investigating the basic physiological molecular features of yak ovary and identifying the biological events underlying the differences between the ovaries of yak and plain cattle is necessary to understand the specificity of yak reproduction. Therefore, RNA-seq technology was applied to analyze transcriptome data comparatively between the yak and plain cattle estrous ovaries.

Results

After deep sequencing, 3,653,032 clean reads with a total of 4,828,772,880 base pairs were obtained from yak ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome, among which, 12,731 and 14,631 genes were assigned to Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, comparison of yak and cattle ovary transcriptome data revealed that 1307 genes were significantly and differentially expressed between the two libraries, wherein 661 genes were upregulated and 646 genes were downregulated in yak ovary. Functional analysis showed that the differentially expressed genes were involved in various Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. GO annotations indicated that the genes related to “cell adhesion,” “hormonal” biological processes, and “calcium ion binding,” “cation transmembrane transport” molecular events were significantly active. KEGG pathway analysis showed that the “complement and coagulation cascade” pathway was the most enriched in yak ovary transcriptome data, followed by the “cytochrome P450” related and “ECM–receptor interaction” pathways. Moreover, several novel pathways, such as “circadian rhythm,” were significantly enriched despite having no evident associations with the reproductive function.

Conclusion

Our findings provide a molecular resource for further investigation of the general molecular mechanism of yak ovary and offer new insights to understand comprehensively the specificity of yak reproduction.

Numerical validation of a synthetic cell-based model of blood coagulation

In Fasano et al. (2012) a new reduced mathematical model for blood coagulation was proposed, incorporating biochemical and mechanical actions of blood flow and including platelets activity. The model was characterized by a considerable simplification of the differential system associated to the biochemical network and it incorporated the role of blood slip at the vessel wall as an extra source of activated platelets. The purpose of this work is to check the validity of the reduced mathematical model, using as a benchmark the model presented in Anand et al. (2008), and to investigate the importance of the blood slip velocity in the blood coagulation process.

A constitutive model for a maturing fibrin network

Blood clot formation is crucial to maintain normal physiological conditions but at the same time involved in many diseases. The mechanical properties of the blood clot are important for its functioning but complicated due to the many processes involved. The main structural component of the blood clot is fibrin, a fibrous network that forms within the blood clot, thereby increasing its mechanical rigidity. A constitutive model for the maturing fibrin network is developed that captures the evolving mechanical properties. The model describes the fibrin network as a network of fibers that become thicker in time. Model parameters are related to the structural properties of the network, being the fiber length, bending stiffness, and mass-length ratio. Results are compared with rheometry experiments in which the network maturation is followed in time for various loading frequencies and fibrinogen concentrations. Three parameters are used to capture the mechanical behavior including the mass-length ratio. This parameter agrees with values determined using turbidimetry experiments and is subsequently used to derive the number of protofibrils and fiber radius. The strength of the model is that it describes the mechanical properties of the maturing fibrin network based on it structural quantities. At the same time the model is relatively simple, which makes it suitable for advanced numerical simulations of blood clot formation during flow in blood vessels.

Modelling the influence of endothelial heterogeneity on the progression of arterial disease: application to abdominal aortic aneurysm evolution

We sophisticate a fluid-solid growth computational framework for modelling aneurysm evolution. A realistic structural model of the arterial wall is integrated into a patient-specific geometry of the vasculature. This enables physiologically representative distributions of haemodynamic stimuli, obtained from a rigid-wall computational fluid dynamics analysis, to be linked to growth and remodelling algorithms. Additionally, a quasistatic structural analysis quantifies the cyclic deformation of the arterial wall so that collagen growth and remodelling can be explicitly linked to the cyclic deformation of vascular cells. To simulate aneurysm evolution, degradation of elastin is driven by reductions in wall shear stress (WSS) below homeostatic thresholds. Given that the endothelium exhibits spatial and temporal heterogeneity, we propose a novel approach to define the homeostatic WSS thresholds: We allow them to be spatially and temporally heterogeneous. We illustrate the application of this novel fluid-solid growth framework to model abdominal aortic aneurysm (AAA) evolution and to examine how the influence of the definition of the WSS homeostatic threshold influences AAA progression. We conclude that improved understanding and modelling of the endothelial heterogeneity is important for modelling aneurysm evolution and, more generally, other vascular diseases where haemodynamic stimuli play an important role.