Structure of fibrin gels studied by elastic light scattering techniques: dependence of fractal dimension, gel crossover length, fiber diameter, and fiber density on monomer concentration

Fibrin-Dextran Hydrogels with Tunable Porosity and Mechanical Properties

Hydrogels as scaffolds in tissue engineering have gained increasing attention in recent years. Natural hydrogels, e.g., collagen or fibrin, are limited by their weak mechanical properties and fast degradation, whereas synthetic hydrogels face issues with biocompatibility and biodegradation. Therefore, combining natural and synthetic polymers to design hydrogels with tunable mechanical stability and cell affinity for biomedical applications is of interest. By using fibrin with its excellent cell compatibility and dextran with controllable mechanical properties, a novel bio-based hydrogel can be formed. Here, we synthesized fibrin and dextran-methacrylate (MA)-based hydrogels with tailorable mechanical properties, controllable degradation, variable pore sizes, and ability to support cell proliferation. The hydrogels are formed through in situ gelation of fibrinogen and dextran-MA with thrombin and dithiothreitol. Swelling and nuclear magnetic resonance diffusometry measurements showed that the water uptake and mesh sizes of fabricated hydrogels decrease with increasing dextran-MA concentrations. Cell viability tests confirm that these hydrogels exhibit no cytotoxic effect.

Light Scattering and Turbidimetry Techniques for the Characterization of Nanoparticles and Nanostructured Networks

Light scattering and turbidimetry techniques are classical tools for characterizing the dynamics and structure of single nanoparticles or nanostructured networks. They work by analyzing, as a function of time (Dynamic Light Scattering, DLS) or angles (Static Light Scattering, SLS), the light scattered by a sample, or measuring, as a function of the wavelength, the intensity scattered over the entire solid angle when the sample is illuminated with white light (Multi Wavelength Turbidimetry, MWT). Light scattering methods probe different length scales, in the ranges of ~5−500 nm (DLS), or ~0.1−5 μm (Wide Angle SLS), or ~1−100 μm (Low Angle SLS), and some of them can be operated in a time-resolved mode, with the possibility of characterizing not only stationary, but also aggregating, polymerizing, or self-assembling samples. Thus, the combined use of these techniques represents a powerful approach for studying systems characterized by very different length scales. In this work, we will review some typical applications of these methods, ranging from the field of colloidal fractal aggregation to the polymerization of biologic networks made of randomly entangled nanosized fibers. We will also discuss the opportunity of combining together different scattering techniques, emphasizing the advantages of a global analysis with respect to single-methods data processing.

Intermediate Structural Hierarchy in Biological Networks Modulates the Fractal Dimension and Force Distribution of Percolating Clusters

Globular protein hydrogels are an emerging class of materials with the potential for rational design, and a generalized understanding of how their network properties emerge from the structure and dynamics of the building block is a key challenge. Here we computationally investigate the effect of intermediate (polymeric) nanoscale structure on the formation of protein hydrogels. We show that changes in both the cross-link topology and flexibility of the polymeric building block lead to changes in the force transmission around the system and provide insight into the dynamic network formation processes. The preassembled intermediate structure provides a novel structural coordinate for the hierarchical modulation of macroscopic network properties, as well as furthering our understanding of the general dynamics of network formation.

Molecular packing structure of fibrin fibers resolved by X-ray scattering and molecular modeling

Fibrin is the major extracellular component of blood clots and a proteinaceous hydrogel used as a versatile biomaterial. Fibrin forms branched networks built of laterally associated double-stranded protofibrils. This multiscale hierarchical structure is crucial for the extraordinary mechanical resilience of blood clots, yet the structural basis of clot mechanical properties remains largely unclear due, in part, to the unresolved molecular packing of fibrin fibers. Here the packing structure of fibrin fibers is quantitatively assessed by combining Small Angle X-ray Scattering (SAXS) measurements of fibrin reconstituted under a wide range of conditions with computational molecular modeling of fibrin protofibrils. The number, positions, and intensities of the Bragg peaks observed in the SAXS experiments were reproduced computationally based on the all-atom molecular structure of reconstructed fibrin protofibrils. Specifically, the model correctly predicts the intensities of the reflections of the 22.5 nm axial repeat, corresponding to the half-staggered longitudinal arrangement of fibrin molecules. In addition, the SAXS measurements showed that protofibrils within fibrin fibers have a partially ordered lateral arrangement with a characteristic transverse repeat distance of 13 nm, irrespective of the fiber thickness. These findings provide fundamental insights into the molecular structure of fibrin clots that underlies their biological and physical properties.

Filamentous and step-like behavior of gelling coarse fibrin networks revealed by high-frequency microrheology

By a micro-experimental methodology, we study the ongoing molecular process inside coarse fibrin networks by means of microrheology. We made these networks gelate around a probe microbead, allowing us to observe a temporal evolution compatible with the well-known molecular formation of fibrin networks in four steps: monomer, protofibril, fiber and network. Thanks to the access that optical-trapping interferometry provides to the short-time scale on the bead's Brownian motion, we observe a Kelvin-Voigt mechanical behavior from low to high frequencies, range not available in conventional rheometry. We exploit that mechanical model for obtaining the characteristic lengths of the filamentous structures composing these fibrin networks, whose obtained values are compatible with a non-affine behavior characterized by bending modes. At very long gelation times, a ω^7/8 power-law is observed in the loss modulus, theoretically related with the longitudinal response of the molecular structures.

Revealing the molecular origins of fibrin's elastomeric properties by in situ X-ray scattering

Fibrin is an elastomeric protein forming highly extensible fiber networks that provide the scaffold of blood clots. Here we reveal the molecular mechanisms that explain the large extensibility of fibrin networks by performing in situ small angle X-ray scattering measurements while applying a shear deformation. We simultaneously measure shear-induced alignment of the fibers and changes in their axially ordered molecular packing structure. We show that fibrin networks exhibit distinct structural responses that set in consecutively as the shear strain is increased. They exhibit an entropic response at small strains (<5%), followed by progressive fiber alignment (>25% strain) and finally changes in the fiber packing structure at high strain (>100%). Stretching reduces the fiber packing order and slightly increases the axial periodicity, indicative of molecular unfolding. However, the axial periodicity changes only by 0.7%, much less than the 80% length increase of the fibers, suggesting that fiber elongation mainly stems from uncoiling of the natively disordered αC-peptide linkers that laterally bond the molecules. Upon removal of the load, the network structure returns to the original isotropic state, but the fiber structure becomes more ordered and adopts a smaller packing periodicity compared to the original state. We conclude that the hierarchical packing structure of fibrin fibers, with built-in disorder, makes the fibers extensible and allows for mechanical annealing. Our results provide a basis for interpreting the molecular basis of haemostatic and thrombotic disorders associated with clotting and provide inspiration to design resilient bio-mimicking materials. STATEMENT OF SIGNIFICANCE: Fibrin provides structural integrity to blood clots and is also widely used as a scaffold for tissue engineering. To fulfill their biological functions, fibrin networks have to be simultaneously compliant like skin and resilient against rupture. Here, we unravel the structural origin underlying this remarkable mechanical behaviour. To this end, we performed in situ measurements of fibrin structure across multiple length scales by combining X-ray scattering with shear rheology. Our findings show that fibrin sustains large strains by undergoing a sequence of structural changes on different scales with increasing strain levels. This demonstrates new mechanistic aspects of an important biomaterial's structure and its mechanical function, and serves as an example in the design of biomimicking materials.

Fast and reliable advanced two-step pore-size analysis of biomimetic 3D extracellular matrix scaffolds

The tissue microenvironment is a major contributor to cellular functions, such as cell adhesion, migration and invasion. A critical physical parameter for determining the effect of the microenvironment on cellular functions is the average pore-size of filamentous scaffolds, such as 3D collagen fiber matrices, which are assembled by the polymerization of biopolymers. The scaffolds of these matrices can be analyzed easily by using state-of-the-art laser scanning confocal imaging. However, the generation of a quantitative estimate of the pore-size in a 3D microenvironment is not trivial. In this study, we present a reliable and fast analytical method, which relies on a two-step 3D pore-size analysis utilizing several state-of-the-art image analysis methods, such as total variation (TV) denoising and adaptive local thresholds, and another crucial parameter, such as pore-coverage. We propose an iterative approach of pore-size analysis to determine even the smallest and obscure pores in a collagen scaffold. Additionally, we propose a novel parameter, the pseudo-pore-size, which describes a virtual scaffold porosity. In order to validate the advanced two-step pore-size analysis different types of artificial collagens, such as a rat and bovine mixture with two different collagen concentrations have been utilized. Additionally, we compare a traditional approach with our method using an artificially generated network with predefined pore-size distributions. Indeed, our analytical method provides a precise, fast and parameter-free, user-independent and automatic analysis of 3D pore topology, such as pore-sizes and pore-coverage. Additionally, we are able to determine non-physiological network topologies by taking the pore-coverage as a goodness-of-fit parameter.

Effect of iron oxide nanoparticles on fibrin gel formation and its fractal dimension

In this paper, we studied the influence of nonmagnetic iron oxide nanoparticles on fibrin gel formation and its structure using dynamic light scattering. The surface of nanoparticles produced by a new method in acoustoplasma discharge with cavitation has specific morphology and accelerates the rate of fibrin gel formation, i.e., activates the enzyme thrombin. We studied changes in the form of autocorrelation functions of the scattered light intensity for fibrinogen-thrombin samples with different thrombin concentrations as well as the nanoparticles addition. Appearance of the power-law term in the function was an indicator of gel formation in the sample. Application of Martin's theory allows estimating the exponent φ of power-law function and the contribution of the diffusive mode of protofibrils. We found that an increase in thrombin concentration or its activation with iron oxide nanoparticles leads to decreasing contribution of the diffusive mode, and increasing contribution of the exponent of power-law function. The values of fractal dimension D_f calculated using Muthukumar's theory are 1.61 ± 0.13 and 1.69 ± 1.11 for samples with low and high concentrations of thrombin respectively and 1.77 ± 0.08 for the sample with thrombin activated by nanoparticles. Such an increase in fractal dimension shows an increase in the complexity of the fibrin gel structure (or density).

Fibrinography: A Multiwavelength Light-Scattering Assay of Fibrin Structure

We have previously developed a fibrin structural assay dedicated to purified fibrinogen-thrombin system. Here, we extend the pertinence of this test, called Fibrinography, to tissue factor-triggered plasma coagulation. We show that Fibrinography determines quantitatively the structure of fibrin fibers in plasma with an excellent reproducibility. We compare this assay with the commonly used single wavelength turbidity method, showing that the latter is not a proper structural assay, but determines essentially the fibrinogen content in plasma. In addition, we also show, in model plasmas, that Fibrinography is able to discriminate normal and hypocoagulant plasmas, and even between hypercoagulant plasmas. Therefore, Fibrinography, by measuring the final step of the coagulation cascade, may be used to evaluate patients’ plasma in hypo- or hypercoagulant diseases.

An Investigation Into the Effects of In Vitro Dilution With Different Colloid Resuscitation Fluids on Clot Microstructure Formation

BACKGROUND

Balancing the beneficial effects of resuscitation fluids against their detrimental effect on hemostasis is an important clinical issue. We aim to compare the in vitro effects of 3 different colloid resuscitation fluids (4.5% albumin, hydroxyethyl starch [Voluven 6%], and gelatin [Geloplasma]) on clot microstructure formation using a novel viscoelastic technique, the gel point. This novel hemorheologic technique measures the biophysical properties of the clot and provides an assessment of clot microstructure from its viscoelastic properties. Importantly, in contrast to many assays in routine clinical use, the measurement is performed using unadulterated whole blood in a near-patient setting and provides rapid assessment of coagulation. We hypothesized that different colloids will have a lesser or greater detrimental effect on clot microstructure formation when compared against each other.

METHODS

Healthy volunteers were recruited into the study (n = 104), and a 20-mL sample of whole blood was obtained. Each volunteer was assigned to 1 of the 3 fluids, and the sample was diluted to 1 of 5 different dilutions (baseline, 10%, 20%, 40%, and 60%). The blood was tested using the gel point technique, which measures clot mechanical strength and quantifies clot microstructure (df) at the incipient stages of fibrin formation.

RESULTS

df and clot mechanical strength decrease with progressive dilution for all 3 fluids. A significant reduction in df from baseline was recorded at dilutions of 20% for albumin (P < .0001), 40% for starch (P < .0001), and 60% for gelatin (P < .0001). We also observed significant differences, in terms of df, when comparing the different types of colloid (P < .0001). We found that albumin dilution produced the largest changes in clot microstructure, providing the lowest values of df (= 1.41 ± 0.061 at 60% dilution) compared with starch (1.52 ± 0.081) and gelatin (1.58 ± 0.063).

CONCLUSIONS

We show that dilution with all 3 fluids has a significant effect on coagulation at even relatively low dilution volumes (20% and 40%). Furthermore, we quantify, using a novel viscoelastic technique, how the physiochemical properties of the 3 colloids exert individual changes on clot microstructure.

Buffers Strongly Modulate Fibrin Self-Assembly into Fibrous Networks

Fibrin is a plasma protein with a central role in blood clotting and wound repair. Upon vascular injury, fibrin forms resilient fibrillar networks (clots) via a multistep self-assembly process, from monomers, to double-stranded protofibrils, to a branched network of thick fibers. In vitro, fibrin self-assembly is sensitive to physicochemical conditions like the solution pH and ionic strength, which tune the strength of the noncovalent driving forces. Here we report a surprising finding that the buffer-which is necessary to control the pH and is typically considered to be inert-also significantly influences fibrin self-assembly. We show by confocal microscopy and quantitative light scattering that various common buffering agents have no effect on the initial assembly of fibrin monomers into protofibrils but strongly hamper the subsequent lateral association of protofibrils into thicker fibers. We further find that the structural changes are independent of the molecular structure of the buffering agents as well as of the activation mechanism and even occur in fibrin networks formed from platelet-poor plasma. This buffer-mediated decrease in protofibril bundling results in a marked reduction in the permeability of fibrin networks but only weakly influences the elastic modulus of fibrin networks, providing a useful tuning parameter to independently control the elastic properties and the permeability of fibrin networks. Our work raises the possibility that fibrin assembly in vivo may be regulated by variations in the acute-phase levels of bicarbonate and phosphate, which act as physiological buffering agents of blood pH. Moreover, our findings add a new example of buffer-induced effects on biomolecular self-assembly to recent findings for a range of proteins and lipids.

Photoactivatable fluorescent probes reveal heterogeneous nanoparticle permeation through biological gels at multiple scales

Diffusion through biological gels is crucial for effective drug delivery using nanoparticles. Here, we demonstrate a new method to measure diffusivity over a large range of length scales - from tens of nanometers to tens of micrometers - using photoactivatable fluorescent nanoparticle probes. We have applied this method to investigate the length-scale dependent mobility of nanoparticles in fibrin gels and in sputum from patients with cystic fibrosis (CF). Nanoparticles composed of poly(lactic-co-glycolic acid), with polyethylene glycol coatings to resist bioadhesion, were internally labeled with caged rhodamine to make the particles photoactivatable. We activated particles within a region of sample using brief, targeted exposure to UV light, uncaging the rhodamine and causing the particles in that region to become fluorescent. We imaged the subsequent spatiotemporal evolution in fluorescence intensity and observed the collective particle diffusion over tens of minutes and tens of micrometers. We also performed complementary multiple particle tracking experiments on the same particles, extending significantly the range over which particle motion and its heterogeneity can be observed. In fibrin gels, both methods showed an immobile fraction of particles and a mobile fraction that diffused over all measured length scales. In the CF sputum, particle diffusion was spatially heterogeneous and locally anisotropic but nevertheless typically led to unbounded transport extending tens of micrometers within tens of minutes. These findings provide insight into the mesoscale architecture of these gels and its role in setting their permeability on physiologically relevant length scales, pointing toward strategies for improving nanoparticle drug delivery.

Fibrin Formation, Structure and Properties

Fibrinogen and fibrin are essential for hemostasis and are major factors in thrombosis, wound healing, and several other biological functions and pathological conditions. The X-ray crystallographic structure of major parts of fibrin(ogen), together with computational reconstructions of missing portions and numerous biochemical and biophysical studies, have provided a wealth of data to interpret molecular mechanisms of fibrin formation, its organization, and properties. On cleavage of fibrinopeptides by thrombin, fibrinogen is converted to fibrin monomers, which interact via knobs exposed by fibrinopeptide removal in the central region, with holes always exposed at the ends of the molecules. The resulting half-staggered, double-stranded oligomers lengthen into protofibrils, which aggregate laterally to make fibers, which then branch to yield a three-dimensional network. Much is now known about the structural origins of clot mechanical properties, including changes in fiber orientation, stretching and buckling, and forced unfolding of molecular domains. Studies of congenital fibrinogen variants and post-translational modifications have increased our understanding of the structure and functions of fibrin(ogen). The fibrinolytic system, with the zymogen plasminogen binding to fibrin together with tissue-type plasminogen activator to promote activation to the active proteolytic enzyme, plasmin, results in digestion of fibrin at specific lysine residues. In spite of a great increase in our knowledge of all these interconnected processes, much about the molecular mechanisms of the biological functions of fibrin(ogen) remains unknown, including some basic aspects of clotting, fibrinolysis, and molecular origins of fibrin mechanical properties. Even less is known concerning more complex (patho)physiological implications of fibrinogen and fibrin.

Effects of unidirectional flow shear stresses on the formation, fractal microstructure and rigidity of incipient whole blood clots and fibrin gels

Incipient clot formation in whole blood and fibrin gels was studied by the rheometric techniques of controlled stress parallel superposition (CSPS) and small amplitude oscillatory shear (SAOS). The effects of unidirectional shear stress on incipient clot microstructure, formation kinetics and elasticity are reported in terms of the fractal dimension (d_f) of the fibrin network, the gel network formation time (T_GP) and the shear elastic modulus, respectively. The results of this first haemorheological application of CSPS reveal the marked sensitivity of incipient clot microstructure to physiologically relevant levels of shear stress, these being an order of magnitude lower than have previously been studied by SAOS. CSPS tests revealed that exposure of forming clots to increasing levels of shear stress produces a corresponding elevation in d_f, consistent with the formation of tighter, more compact clot microstructures under unidirectional flow. A corresponding increase in shear elasticity was recorded. The scaling relationship established between shear elasticity and d_f for fibrin clots and whole blood confirms the fibrin network as the dominant microstructural component of the incipient clot in terms of its response to imposed stress. Supplementary studies of fibrin clot formation by rheometry and microscopy revealed the substantial additional network mass required to increase d_f and provide evidence to support the hypothesis that microstructural changes in blood clotted under unidirectional shear may be attributed to flow enhanced thrombin generation and activation. CSPS also identified a threshold value of unidirectional shear stress above which no incipient clot formation could be detected. CSPS was shown to be a valuable haemorheological tool for the study of the effects of physiological and pathological levels of shear on clot properties.

The clinical relevance of altered fibrinogen packaging in the presence of 17β-estradiol and progesterone

BACKGROUND

The effect of endogenous hormone concentrations, specifically 17β-estradiol and progesterone, on fibrin network formation has not been established.

OBJECTIVES

It is essential to understand natural hormone mechanisms since these hormones are still present in circulation while hormonal contraceptives, which are associated with increased risk of venous thromboembolism, are used.

METHODS

Due to the fact that these hormones are known to increase hypercoagulability and the prothrombotic state scanning electron microscopy (SEM), atomic force microscopy (AFM), thromboelastography (TEG) and turbidimetry were employed to investigate the morphology, surface roughness, viscoelastic properties and formation and lysis of fibrin.

RESULTS

17β-estradiol and progesterone showed hypercoagulable viscoelastic properties and decreased the diameter and surface roughness of fibrin while increasing dense matted deposit occurrence. Our results suggest that the additional burden of hormonal load, together with the presence of endogenous estrogen and progesterone, may result in a prothrombotic and hypercoagulable state in females with an inflammatory predisposition.

CONCLUSION

Our results are of clinical importance when considering hormones as either pathological agent or therapeutic intervention as will be assessed in future investigation.

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.

Spatiotemporal characterization of a fibrin clot using quantitative phase imaging

Studying the dynamics of fibrin clot formation and its morphology is an important problem in biology and has significant impact for several scientific and clinical applications. We present a label-free technique based on quantitative phase imaging to address this problem. Using quantitative phase information, we characterized fibrin polymerization in real-time and present a mathematical model describing the transition from liquid to gel state. By exploiting the inherent optical sectioning capability of our instrument, we measured the three-dimensional structure of the fibrin clot. From this data, we evaluated the fractal nature of the fibrin network and extracted the fractal dimension. Our non-invasive and speckle-free approach analyzes the clotting process without the need for external contrast agents.

A comprehensive mechanism of fibrin network formation involving early branching and delayed single- to double-strand transition from coupled time-resolved X-ray/light-scattering detection

The formation of a fibrin network following fibrinogen enzymatic activation is the central event in blood coagulation and has important biomedical and biotechnological implications. A non-covalent polymerization reaction between macromolecular monomers, it consists basically of two complementary processes: elongation/branching generates an interconnected 3D scaffold of relatively thin fibrils, and cooperative lateral aggregation thickens them more than 10-fold. We have studied the early stages up to the gel point by fast fibrinogen:enzyme mixing experiments using simultaneous small-angle X-ray scattering and wide-angle, multi-angle light scattering detection. The coupled evolutions of the average molecular weight, size, and cross section of the solutes during the fibrils growth phase were thus recovered. They reveal that extended structures, thinner than those predicted by the classic half-staggered, double-stranded mechanism, must quickly form. Following extensive modeling, an initial phase is proposed in which single-bonded "Y-ladder" polymers rapidly elongate before undergoing a delayed transition to the double-stranded fibrils. Consistent with the data, this alternative mechanism can intrinsically generate frequent, random branching points in each growing fibril. The model predicts that, as a consequence, some branches in these expanding "lumps" eventually interconnect, forming the pervasive 3D network. While still growing, other branches will then undergo a Ca(2+)/length-dependent cooperative collapse on the resulting network scaffolding filaments, explaining their sudden thickening, low final density, and basic mechanical properties.

Mechanics of biological networks: from the cell cytoskeleton to connective tissue

From the cell cytoskeleton to connective tissues, fibrous networks are ubiquitous in metazoan life as the key promoters of mechanical strength, support and integrity. In recent decades, the application of physics to biological systems has made substantial strides in elucidating the striking mechanical phenomena observed in such networks, explaining strain stiffening, power law rheology and cytoskeletal fluidisation - all key to the biological function of individual cells and tissues. In this review we focus on the current progress in the field, with a primer into the basic physics of individual filaments and the networks they form. This is followed by a discussion of biological networks in the context of a broad spread of recent in vitro and in vivo experiments.

Intrinsically conducting polyaminoanthraquinone nanofibrils: interfacial synthesis, formation mechanism and lead adsorbents

Water-dispersible and self-stabilized conductive polyaminoanthraquinone nanofibirls synthesizedviainterfacial polymerization showed high adsorption capacities toward toxic lead.

Modeling of fibrin gels based on confocal microscopy and light-scattering data

Fibrin gels are biological networks that play a fundamental role in blood coagulation and other patho/physiological processes, such as thrombosis and cancer. Electron and confocal microscopies show a collection of fibers that are relatively monodisperse in diameter, not uniformly distributed, and connected at nodal points with a branching order of ∼3-4. Although in the confocal images the hydrated fibers appear to be quite straight (mass fractal dimension D(m) = 1), for the overall system 1<D(m)<2. Based on the confocal images, we developed a method to generate three-dimensional (3D) in silico gels made of cylindrical sticks of diameter d, density ρ, and average length <L>, joined at randomly distributed nodal points. The resulting 3D network strikingly resembles real fibrin gels and can be sketched as an assembly of densely packed fractal blobs, i.e., regions of size ξ, where the fiber concentration is higher than average. The blobs are placed at a distance ξ0 between their centers of mass so that they are overlapped by a factor η =ξ/ξ0 and have D(m) ∼1.2-1.6. The in silico gels' structure is quantitatively analyzed by its 3D spatial correlation function g(3D)(r) and corresponding power spectrum I(q) = FFT(3D[g3D(r)]), from which ρ, d, D(m), η, and ξ0 can be extracted. In particular, ξ0 provides an excellent estimate of the gel mesh size. The in silico gels' I(q) compares quite well with real gels' elastic light-scattering measurements. We then derived an analytical form factor for accurately fitting the scattering data, which allowed us to directly recover the gels' structural parameters.

Fast two-dimensional bubble analysis of biopolymer filamentous networks pore size from confocal microscopy thin data stacks

The average pore size ξ0 of filamentous networks assembled from biological macromolecules is one of the most important physical parameters affecting their biological functions. Modern optical methods, such as confocal microscopy, can noninvasively image such networks, but extracting a quantitative estimate of ξ0 is a nontrivial task. We present here a fast and simple method based on a two-dimensional bubble approach, which works by analyzing one by one the (thresholded) images of a series of three-dimensional thin data stacks. No skeletonization or reconstruction of the full geometry of the entire network is required. The method was validated by using many isotropic in silico generated networks of different structures, morphologies, and concentrations. For each type of network, the method provides accurate estimates (a few percent) of the average and the standard deviation of the three-dimensional distribution of the pore sizes, defined as the diameters of the largest spheres that can be fit into the pore zones of the entire gel volume. When applied to the analysis of real confocal microscopy images taken on fibrin gels, the method provides an estimate of ξ0 consistent with results from elastic light scattering data.

Mechanisms of fibrin polymerization and clinical implications

Research on all stages of fibrin polymerization, using a variety of approaches including naturally occurring and recombinant variants of fibrinogen, x-ray crystallography, electron and light microscopy, and other biophysical approaches, has revealed aspects of the molecular mechanisms involved. The ordered sequence of fibrinopeptide release is essential for the knob-hole interactions that initiate oligomer formation and the subsequent formation of 2-stranded protofibrils. Calcium ions bound both strongly and weakly to fibrin(ogen) have been localized, and some aspects of their roles are beginning to be discovered. Much less is known about the mechanisms of the lateral aggregation of protofibrils and the subsequent branching to yield a 3-dimensional network, although the αC region and B:b knob-hole binding seem to enhance lateral aggregation. Much information now exists about variations in clot structure and properties because of genetic and acquired molecular variants, environmental factors, effects of various intravascular and extravascular cells, hydrodynamic flow, and some functional consequences. The mechanical and chemical stability of clots and thrombi are affected by both the structure of the fibrin network and cross-linking by plasma transglutaminase. There are important clinical consequences to all of these new findings that are relevant for the pathogenesis of diseases, prophylaxis, diagnosis, and treatment.

Visualization of the dynamics of fibrin clot growth 1 molecule at a time by total internal reflection fluorescence microscopy

Individual fluorescently labeled fibrin(ogen) molecules and their assembly to make a clot were observed by total internal reflection fluorescence microscopy (TIRFM). We used the bleaching of the fluorescent labels to determine the number of active fluorophores attached nonspecifically to each molecule. From the total intensity of bleaching steps, as single-molecule signature events, and the distribution of active labeling, we developed a new single-molecule intensity calibration, which accounts for all molecules, including those “not seen.” Live observation of fibrin polymerization in TIRFM by diffusive mixing of thrombin and plasma revealed the real-time growth kinetics of individual fibrin fibers quantitatively at the molecular level. Some fibers thickened in time to thousands of molecules across, equivalent to hundreds of nanometers in diameter, whereas others reached an early stationary state at smaller diameters. This new approach to determine the molecular dynamics of fiber growth provides information important for understanding clotting mechanisms and the associated clinical implications.

Multiangle static and dynamic light scattering in the intermediate scattering angle range

We describe a light scattering apparatus based on a novel optical scheme covering the scattering angle range 0.5° ≤ θ ≤ 25°, an intermediate regime at the frontier between wide angle and small angle setups that is difficult to access by existing instruments. Our apparatus uses standard, readily available optomechanical components. Thanks to the use of a charge-coupled device detector, both static and dynamic light scattering can be performed simultaneously at several scattering angles. We demonstrate the capabilities of our apparatus by measuring the scattering profile of a variety of samples and the Brownian dynamics of a dilute colloidal suspension.

Nanostructure of the fibrin clot

The nanostructure of the fibrin fibers in fibrin clots is investigated by using spectrometry and small angle x-ray scattering measurements. First, an autocoherent analysis of the visible light spectra transmitted through formed clots is demonstrated to provide robust measurements of both the radius and density of the fibrin fibers. This method is validated via comparison with existing small-angle and dynamic light-scattering data. The complementary use of small angle x-ray scattering spectra and light spectrometry unambiguously shows the disjointed nature of the fibrin fibers. Indeed, under quasiphysiological conditions, the fibers are approximately one-half as dense as their crystalline fiber counterparts. Further, although the fibers are locally crystalline, they appear to possess a lateral fractal structure.

In situ formation, manipulation, and imaging of droplet-encapsulated fibrin networks

The protein fibrin plays a principal role in blood clotting and forms robust three dimensional networks. Here, microfluidic devices have been tailored to strategically generate and study these bionetworks by confinement in nanoliter volumes. The required protein components are initially encapsulated in separate droplets, which are subsequently merged by electrocoalescence. Next, distinct droplet microenvironments are created as the merged droplets experience one of two conditions: either they traverse a microfluidic pathway continuously, or they "park" to fully evolve an isotropic network before experiencing controlled deformations. High resolution fluorescence microscopy is used to image the fibrin networks in the microchannels. Aggregation (i.e."clotting") is significantly affected by the complicated flow fields in moving droplets. In stopped-flow conditions, an isotropic droplet-spanning network forms after a suitable ripening time. Subsequent network deformation, induced by the geometric structure of the microfluidic channel, is found to be elastic at low rates of deformation. A shape transition is identified for droplets experiencing rates of deformation higher than an identified threshold value. In this condition, significant densification of protein within the droplet due to hydrodynamic forces is observed. These results demonstrate that flow fields considerably affect fibrin in different circumstances exquisitely controlled using microfluidic tools.

Cl- and F- anions regulate the architecture of protofibrils in fibrin gel

Ischemic heart disease is the leading cause of serious morbidity and mortality in Western society. One of the therapeutic approaches is based on the use of thrombolitic drugs that promote clot lysis. Even if the mechanisms leading to clot lysis are not completely understood, it is widely accepted that they depend on the complex biochemical reactions that occur among fibrin fibers and fibrinolitic agents, and by their ready diffusion into the fibers. Here we investigate the effects of specific anions on the architecture of protofibrils within fibrin fibers in fibrin gels prepared in a para-physiological solution. The results obtained through small-angle X-ray scattering (SAXS) demonstrate that the characteristic axial and longitudinal repeat distances among protofibrils are strongly affected by the action of Cl(-) and F(-) anions.

Dynamic imaging of fibrin network formation correlated with other measures of polymerization

Using deconvolution microscopy, we visualized in real time fibrin network formation in the hydrated state. Individual mobile fibers were observed before the gel point determined by eye. After gelation, an initial fibrin network was seen, which evolved over time by addition of new fibers and elongation and branching of others. Furthermore, some fibers in the network moved for a time. We quantified network formation by number of branch points, and longitudinal and lateral growth of fibers. Eighty percent of branch points were formed, and 70% of all fibers reached their maximum length at the gel point. In contrast, at the gel point, fiber diameter, measured as fluorescence intensity, was less than 25% and turbidity was less than 15% of the maximum values of the fully formed clot. The cumulative percentage of fibers reaching their final length and the number of branch points attained maximum values at 60% of maximum turbidity. Lateral fiber growth reached a plateau at the same time as turbidity. Measurements of clot mechanical properties revealed that the clots achieved maximum stiffness and minimum plasticity after the structural parameters reached their maxima. These results provide new information on the relative time sequence of events during fibrin network formation.

Rheometry and associated techniques for blood coagulation studies

This review considers various rheometrical approaches that have been adopted to study blood coagulation, with special reference to the rheological assessment of clotting time and studies of the evolution of viscoelasticity during the course of fibrin polymerization and cross-linking. The significance of the Gel Point in blood coagulation studies is discussed as a common feature of many of these studies in that they attempt to detect a liquid-to-solid transition during coagulation. Coagulation studies based on various forms of complex shear modulus measurements are considered, the latter being based principally on controlled stress and controlled strain rheometers. Also considered are the long established technique of thromboelastography and several emerging techniques such as wave propagation measurements, free oscillation rheometry, quartz crystal microbalance measurements and surface plasmon resonance.

Equibiaxial cyclic stretch stimulates fibroblasts to rapidly remodel fibrin

Understanding the effects of the mechanical environment on wound healing is critical for developing more effective treatments to reduce scar formation and contracture. The aim of this study was to investigate the effects of dynamic mechanical stretch on cell-mediated early wound remodeling independent of matrix alignment which obscures more subtle remodeling mechanisms. Cyclic equibiaxial stretch (16% stretch at 0.2 Hz) was applied to fibroblast-populated fibrin gel in vitro wound models for eight days. Compaction, density, tensile strength, and collagen content were quantified as functional measures of remodeling. Stretched samples were approximately ten times stronger, eight-fold more dense, and eight times thinner than statically cultured samples. These changes were accompanied by a 15% increase in net collagen but no significant differences in cell number or viability. When collagen crosslinking was inhibited in stretched samples, the extensibility increased and the strength decreased. The apparent weakening was due to a reduction in compaction rather than a decrease in ability of the tissue to withstand tensile forces. Interestingly, inhibiting collagen crosslinking had no measurable effects on the statically cultured samples. These results indicate that amplified cell-mediated compaction and even a slight addition in collagen content play substantial roles in mechanically induced wound strengthening. These findings increase our understanding of how mechanical forces guide the healing response in skin, and the methods employed in this study may also prove valuable tools for investigating stretch-induced remodeling of other planar connective tissues and for creating mechanically robust engineered tissues.

Fibrinogen and fibrin

Fibrinogen is a large, complex, fibrous glycoprotein with three pairs of polypeptide chains linked together by 29 disulfide bonds. It is 45 nm in length, with globular domains at each end and in the middle connected by alpha-helical coiled-coil rods. Both strongly and weakly bound calcium ions are important for maintenance of fibrinogen's structure and functions. The fibrinopeptides, which are in the central region, are cleaved by thrombin to convert soluble fibrinogen to insoluble fibrin polymer, via intermolecular interactions of the "knobs" exposed by fibrinopeptide removal with "holes" always exposed at the ends of the molecules. Fibrin monomers polymerize via these specific and tightly controlled binding interactions to make half-staggered oligomers that lengthen into protofibrils. The protofibrils aggregate laterally to make fibers, which then branch to yield a three-dimensional network-the fibrin clot-essential for hemostasis. X-ray crystallographic structures of portions of fibrinogen have provided some details on how these interactions occur. Finally, the transglutaminase, Factor XIIIa, covalently binds specific glutamine residues in one fibrin molecule to lysine residues in another via isopeptide bonds, stabilizing the clot against mechanical, chemical, and proteolytic insults. The gene regulation of fibrinogen synthesis and its assembly into multichain complexes proceed via a series of well-defined steps. Alternate splicing of two of the chains yields common variant molecular isoforms. The mechanical properties of clots, which can be quite variable, are essential to fibrin's functions in hemostasis and wound healing. The fibrinolytic system, with the zymogen plasminogen binding to fibrin together with tissue-type plasminogen activator to promote activation to the active enzyme plasmin, results in digestion of fibrin at specific lysine residues. Fibrin(ogen) also specifically binds a variety of other proteins, including fibronectin, albumin, thrombospondin, von Willebrand factor, fibulin, fibroblast growth factor-2, vascular endothelial growth factor, and interleukin-1. Studies of naturally occurring dysfibrinogenemias and variant molecules have increased our understanding of fibrinogen's functions. Fibrinogen binds to activated alphaIIbbeta3 integrin on the platelet surface, forming bridges responsible for platelet aggregation in hemostasis, and also has important adhesive and inflammatory functions through specific interactions with other cells. Fibrinogen-like domains originated early in evolution, and it is likely that their specific and tightly controlled intermolecular interactions are involved in other aspects of cellular function and developmental biology.

Visualization and mechanical manipulations of individual fibrin fibers suggest that fiber cross section has fractal dimension 1.3

We report protocols and techniques to image and mechanically manipulate individual fibrin fibers, which are key structural components of blood clots. Using atomic force microscopy-based lateral force manipulations we determined the rupture force, FR, f fibrin fibers as a function of their diameter, D, in ambient conditions. As expected, the rupture force increases with increasing diameter; however, somewhat unexpectedly, it increases as FR approximately D1.30+/-0.06. Moreover, using a combined atomic force microscopy-fluorescence microscopy instrument, we determined the light intensity, I, of single fibers, that were formed with fluorescently labeled fibrinogen, as a function of their diameter, D. Similar to the force data, we found that the light intensity, and thus the number of molecules per cross section, increases as I approximately D1.25+/-0.11. Based on these findings we propose that fibrin fibers are fractals for which the number of molecules per cross section increases as about D1.3. This implies that the molecule density varies as rhoD approximately D -0.7, i.e., thinner fibers are denser than thicker fibers. Such a model would be consistent with the observation that fibrin fibers consist of 70-80% water and only 20-30% protein, which also suggests that fibrin fibers are very porous.

Kinetics of Fibrinopeptide Release by Thrombin as a Function of CaCl2Concentration: Different Susceptibility of FPA and FPB and Evidence for a Fibrinogen Isoform-Specific Effect at Physiological Ca2+Concentration†

The kinetics of release of fibrinopeptide A (FPA) and B (FPB) by thrombin were investigated on unfractionated fibrinogen samples as a function of CaCl(2) concentration. A 50 mM Tris, 104 mM NaCl, pH 7.4 (TBS) buffer, to which 1 mM EDTA-Na(2) (TBE) or 2.5 (TBC2.5), 14 (TBC14), and 30 mM CaCl(2) (TBC30) was alternatively added, was employed. The % FPA versus time curves were fitted with single stretched-exponential growth functions, where the stretch parameter beta likely reflects substrate polydispersity (beta = 1, monodisperse). For TBE, TBS, TBC14, and TBC30, we found beta approximately 1, with corresponding normalized rate constants (K(a)) of 3.8, 4.2, 2.7, and 1.9 x 10(-5) [(NIHu/L)s](-1). Surprisingly, in TBC2.5 we found beta = 0.69, with an "average" K(a) of 3.5 x 10(-5) [(NIHu/L)s](-1). This effect disappeared [beta = 0.97, K(a) = 2.7 x 10(-5) [(NIHu/L)s](-1)] with an increase in the ionic strength I to that of TBC30 with 186 mM NaCl (TBCaNa buffer). FPB releases were instead consistent with a nonstretched consecutive exponential growth function, except in TBC30 where some FPB appeared to be cleaved independently. Log-log plots of K(a) versus Ca(2+) concentration, Cl(-) concentration, or I showed a strong linear correlation with only the latter two except in TBCaNa, again suggesting specific effects of the physiological Ca(2+) concentration and I on FPA release. The corresponding K(b) plots showed instead that both total depletion and high Ca(2+) hampered FPB release. To further investigate the TBC2.5 beta = 0.69 effect, FG polydispersity was assessed by Western blot analyses. The thrombin-binding gamma'-chain isoform was approximately 4%, resulting in a bound:free thrombin ratio of approximately 25:75. With regard to the C-terminal ends of the Aalpha-chains, approximately 45% were either intact or lightly degraded, while the remaining approximately 55% were more degraded. Fitting the % FPA release data in TBC2.5 with a sum of two exponentials resulted in a faster component and a slower component (K(a1)/K(a2) approximately 6), with a ratio of approximately 48:52. While a role for the gamma'-chain isoform cannot be excluded, this good correlation with the C-terminal degradation of the Aalpha-chains suggests their calcium-dependent involvement in FPA release.