Cellular automaton modelling of platelet aggregation

Platelet aggregation plays an important role in hemostasis, as it prevents blood loss upon vessel wall disruption. Computational modelling is one of the useful approaches to study this system.  The use of a cellular automaton as a model makes it possible both to study the dynamics of individual aggregates and to investigate the behaviour of the system as a whole. The aim of this research is to study platelet aggregation using a model based on a cellular automaton. As a result, a model of platelet aggregation in the basic approximation and with flow condition was constructed. It was shown that under flow conditions, the most number of the aggregates are dimers and trimers, whereas aggregates of large sizes are much less presented.

#platelet aggregation#mathematical modeling#cellular automaton

Annexin V: the membrane-binding protein with diverse functions

Annexin V is an eukaryotic protein from the annexin family which is able to reversibly bind to phospholipid membranes in a Ca2+-dependent manner. It possesses a complex mechanism of the membrane binding which includes the two-dimensional lattice formation from annexin V trimers and significant variation of the membrane structure. The precise functions of annexin V are largely unknown, however, its participation in the blood coagulation, membrane repair process and the Ca2+ channel activity is suggested. The usage of annexin V as a marker of phosphatidylserine-positive cells in in vitro and in vivo studies makes the understanding of the protein role in cellular processes critically important.

The current review is focused on the structure of annexin V and the mechanism and kinetics of its membrane binding. The lipid specificity and the multimerization process will be described. Finally, some of the proposed annexin V functions including inhibition of the blood coagulation and the Ca2+ transport activity will be discussed.

The annexin V structure. A. The view from the convex side. Magenta, N-terminal tail; blue, domain I; yellow, domain II; green, domain III; red, domain IV; orange, Ca2+ ions. In the center of annexin V the charged residues Asp280, Arg276, Asp92, Arg117, Glu112, Arg271 are represented. B. The view from the domain II. The convex and the concave sides are marked by black arrows. Ca2+-binding sites are located on the convex surface, N-terminal tail is on the concave side. Figures were created in VMD for the current review using the structure 1ANX [29] from PDB Data Bank. C. Annexin V from human (ANXA5_HUMAN) and from rat (ANXA5_RAT) sequences alignment. Residues that form the Ca2+-binding sites are highlighted in green and yellow for human and rat annexin V respectively. The alignment was done using the UniProt Align tool.
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#annexin A5#membrane interactions#calcium channel#inhibition of coagulation

Approaches to visualize microtubule dynamics in vitro

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#microtubules#light microscopy#atomic force microscopy#dynamic instability#tubulin#associated proteins

Mechanisms of Human Erythrocytes Volume Stabilization

Functional completeness of erythrocytes depends on high deformability of these cells, that allows them to pass through narrow tissue capillaries. The erythrocytes high deformability is provided due to maintenance of discoid shape with an optimal cell surface area to volume ratio. In its turn this ratio is maintained due to cell volume stabilization at a given cell surface area. In this work, using mathematical simulation, we studied role of Na/K-ATPase, calcium activated potassium channels and adenylate metabolism in human erythrocyte volume stabilization at increase in cell membrane permeability to cations. The simulation took into account a contribution of glycolytic metabolites and adenylates to cytoplasm osmotic pressure. It was shown that the presence in the cell of Na/K-ATPase and two opposite transmembrane gradients of Na+ and K+ ions provide a significantly improved cell volume stabilization at the increase in cell membrane permeability, compared with hypothetical cells, in which the osmotic balance between cell and extracellular compartment is provided due to a gradient of only one ion (Na+). In this case the erythrocyte volume deviates from the optimal value by less than 10% at change in cell membrane permeability from 50 to 200% of its normal value. In this case, however, the intracellular ion concentrations may change significantly (by several times). The adenylate metabolism system can provide an additional regulation of transport ATPases due to regulation of intracellular ATP levels. Under these conditions stabilization of steady-state values of intracellular ion concentrations (ion homeostasis) and of cell volume in the range of cell membrane permeability changes from 50 to 1500% of the normal value. In this case, however, the cell volume and intracellular ion concentrations may significantly deviate from the stabilized values during transitional processes. Simultaneous function of both, ion transport systems and adenylate metabolism allows to provide ion homeostasis and efficient erythrocyte volume stabilization (within 5% deviation from the optimal value) both in steady-state conditions and during transitional processes at increase in cell membrane permeability up to 10-15 times compared with the normal value.

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#red blood cells#metabolism#ion channel

Systems Biology and Physiology Reports in 2021: a yearly report

Dear All,

I am happy to greet all readers, editors, reviewers, staff members and publishers of SBPR on the eve of year 2022. I thank all of you for your efforts in creating this journal and making it work despite all the challenges faced by a new independent journal in the age dominated by huge publishers, research societies and citation systems. Please accept my best wishes for the year 2022 in your professional and personal undertakings!

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First year of open-access scientific journal publishing: our mishaps, our expectations, our plans for the bright future

In silico methods have become a versatile and effective tool for the studies of the natural phenomenon at multiple levels. However, unlike such fields as economics and physics, biology and physiology have always been slightly reluctant in acceptance of the novel systemic approaches. Since scientific articles are among the key metrics for the modern scientific society, the number of scientific journals, devoted to some topic, can be a good marker to evaluate the impact of this topic for the society. Indeed, there are esteemed journals, such as PLOS Computational Biology or Journal of Theoretical Biology, but they focus mainly on a common biological phenomenon, while questions of physiology and pathophysiology are often overlooked. On the other hand, the amount of work on computational biology is steadily growing with ~12000 works published in 2010 and ~28000 in 2020 with the keyword “computational model”, according to PubMed. With all this being said and our great experience in the different aspects of the field of computational physiology, our team has decided that it would be a mistake to lose an opportunity to cover this niche. Likewise, we, as a group of fellow scientists, at the end of 2019 decided to create our own venture and to launch our own scientific journal – Systems Biology and Physiology Reports (SBPReports) [1]. This publisher's would be an attempt to underline our first hectic year of the open access scientific publishing.

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On calcium fluorophore’s impact in platelet signaling studies

Observation of calcium signaling in platelets - blood cells designed to be involved in stopping bleeding and forming blood clots - is an important part of fundamental research in hemostasis. However, such a study is possible only with the use of calcium fluorophores - small molecules that penetrate the platelet membrane due to their hydrophobic -AM part, which is then hydrolyzed by cytosol esterases. In this work, we consider the phenomenon of inhomogeneous loading of calcium fluorophores into platelets.

We used platelets from healthy adult donors loaded with various fluorescent probes (CalBryte590, DiOC6 (3), Fura Red, Fluo-4 and CellTracker Violet BMQC) and immobilized on antibodies to CD31 in parallel plane flow chambers. Total internal reflection fluorescence (TIRF) microscopy was used for observations.

We demonstrated that all studied probes are loaded heterogeneously, with 30% platelets being loaded with a probe 2-6 times higher than the population median value. Using the CalBryte590 probe as an example, we have shown that a decrease in the incubation temperature, the addition of Pluronic 127 to the incubation medium, or membrane cholesterol depletion significantly reduces the heterogeneity of the probe distribution in the population. By looking at platelet activation from the surface, we have shown that the probability of experiencing strong activation, as measured by the intensity of calcium oscillations, correlates with the amount of probe in the platelet.

Thus, we conclude that the type of fluorophore used and the conditions of its loading into platelets can significantly affect the results of experiments on the observation of calcium signaling in platelets.

Overall scheme of the assay. First, whole pre-processed blood is perfused through the flow chamber for 2.5 minutes. Then Tyrode's buffer is perfused through the chamber for 5 minutes to wash away unattached cells. Then, depending on the protocol, the microscopy video is recorded for 5-10 minutes.
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#platelets#calcium fluorophores#membrane#fluorescent probes#intracellular signaling

Immune thrombocytopenia: what can the systems biology and systems physiology offer?

Immune thrombocytopenia (ITP) is an acquired bleeding disorder of autoimmune pathophysiology. The causes of ITP could be related to other pathology (viral, bacterial, or systemic), or ITP could develop without any apparent reason. While the immune system dysregulation mechanisms in ITP were described, its etiology remains unclear. Moreover, all existing treatment approaches are not specific for ITP, and its action is highly patient- specific. Here we describe recent findings in the origins and development of ITP and discuss novel experimental and theoretical approaches to diagnosing ITP and predicting therapy effects.

Schematic of immune thrombocytopenia mechanisms. The thrombocytopenia in patients could be caused by both T-cells cytotoxicity (CTLs are more active because T-regulatory cells and T-helpers provide dysregulated stimuli) and B-cells antibody production (plasma cells are producing antiplatelet antibodies of IgG and IgM classes; B-regulatory cells provide more activating signals to B-cells to produce antibodies). CTLs specifically attack platelets and induce their apoptosis. Antibodies from plasma cells opsonize platelets. Consecutively, opsonized platelets are eliminated through the spleen. CTLs – cytotoxic T-lymphocytes; Treg – T-regulatory cell; Th – T-helper; Breg – B-regulatory cell; BAFF – B-cell activating factor.
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#autoimmunity#ITP#platelets#acute/chronic ITP#computational modeling#murine models

Hubs and Webs in Platelet Intracellular Signalling

In this issue of Systems Biology and Physiology Reports A.A. Martyanov and M.A. Panteleev suggested a review on platelet intracellular signalling network, which is a second part in the discussion on the molecular relationships between platelet activation and responses [1]. The review contains seven thousands words and two hundred references and yet it is not complete, as there are still unclear parts in platelet signalling, especially in its inhibition [2-4]. In an effort to comprehend the platelet activation pattern, I drew a signalling scheme based on the review and data from other authors [2, 3].

Scheme of platelet intracellular signalling with focus on cytosolic calcium as a “Hub”. Cytosolic calcium concentration is given in the shades of red. Almost all types of platelet receptor agonists lead to activation of phospholipase C (PLC), followed by calcium release from intracellular stores (DTS). Calcium concentration is rapidly reduced by calcium-dependent ATPases (SERCA and PMCA). Also, it could be reduced by binding with some buffering proteins, including its effector-proteins (indicated with red dots). Platelet mitochondria also can function as a calcium buffer and, simultaneously, be regulated by calcium concentration. Direct activation is shown by solid green arrows, direct inhibition - by solid red arrows. Indirect interactions are shown by dashed lines. Abbreviations. AC – adenylate cyclase, α2AAR - α2A-adrenergic receptor, CDGEF - CalDAGGEFI, COX – cyclooxygenase, DAG - diacylglycerol, DTS - dense tubular system, Fbg – fibrinogen, IP3R - receptor for inositol-1,4,5-trisphosphate (IP3), Mit - a mitochondrion, mPTP - mitochondrial permeability transition pore, NCLX - mitochondrial sodium/calcium exchanger, OCS - open canalicular system, P2Y - purinergic receptor, PAR - protease-activated receptor, PIP2 - phosphoinositol-4,5-bisphosphate, PIP3 - phosphoinositol-3,4,5-trisphosphate, PI(P)n – phosphoinositides, PKA – protein kinase A, PKG – protein kinase G, PKC – protein kinase C, PL – phospholipid, PLA2 – phospholipase A2, PMCA - plasma membrane calcium ATPase, PR - PGI2 receptor, P-Tyr – phosphorylated tyrosine residue, SERCA - sarcoplasmic/endoplasmic reticulum calcium ATPase, sGC – soluble guanylate cyclase, TR - thromboxane A2 (TxA2) receptor, TRPC - transient receptor potential channel, UNI - mitochondrial uniporter, vWF – von Willebrand Factor, Y-Pase – tyrosine phosphatase.
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Platelet functional responses and signalling: the molecular relationship. Part 2: receptors.

Small, non-nuclear cells, platelets, are primarily designed to form aggregates when blood vessels are damaged, stopping bleeding. To perform this function, platelets can implement several functional responses induced by various agonists and coordinated by a complex network of intracellular signaling triggered by a dozen of different receptors. This review, the second in a series, describes the known intracellular signaling pathways induced by platelet receptors in response to canonical and rare agonists. Particular focus will be on interaction points and “synergy” of platelet activation pathways and intermediate or “secondary” activation mediators that transmit a signal to functional manifestations.

Different degrees of the platelet activation in hemostasis. Upon weak stimulation, platelets pass into a weakly activated state, in which there is no clustering of platelet integrins and no significant change in the shape of platelets. This weak activation is reversible, and it corresponds to the state of platelets in the outer layers ("coat") of the thrombus. Upon stronger activation, platelet shape significantly changes. Platelets become irreversibly activated and aggregate. The secretion of platelet granules also occurs. At the maximum degree of activation, platelet mitochondria collapse, and platelets pass into a procoagulant state, exposing phosphatidylserine, which significantly accelerates blood plasma coagulation.
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#platelets#intracellular signaling#physiology