Electron microscopy of fine fibrin clots and fine and coarse fibrin films: Observations of fibers in cross-section and in deformed states

Fine fibrin clots and coarse and fine fibrin films (both ligated and unligated), formed by shrinkage of clots in one dimension, were examined by electron microscopy. Specimens of clots were prepared by critical point drying and by embedding and sectioning; specimens of films were prepared by embedding and sectioning only. In the fine clots, network junctions appeared to be formed by fiber segments in which two or more protofibrils were gently twisted around each other for distances of the order of 200 nm and then diverged to give trifunctional branch points. This topology appeared to be preserved in the fine films. It is proposed that the strength of the junctions is primarily provided by the twisting topology, though reinforced by non-covalent bonding involving the B sites uncovered by thrombin. In coarse films, bundles of protofibrils, lying primarily in the film plane, had diameters of 40 to 200 nm and were gently twisted around each other to form thicker cables. Uniaxial stretching, up to 100%, of either fine or coarse film before fixing caused suprisingly extensive orientation of the protofibrils or bundles. However, random orientation was recovered if a stretched ligated film was allowed to retract to its original dimensions before fixing. In a stretched coarse film sectioned perpendicular to the stretch direction, fiber bundles could be seen in cross-section; these were roughly circular with scalloped edges. The changes with stretching and recovery are discussed in relation to possible mechanisms of deformation and elastic energy storage.     

Stress relaxation in fine fibrin films: Comparison of films prepared with thrombin and ancrod

Measurements of stress relaxation in uniaxial extension have been made on fibrin film prepared from fine bovine fibrin clots (i.e., clots in which there is minimal lateral aggregation of protofibrils), both ligated and unligated, and polymerized with both thrombin and ancrod, plasticized with either aqueous buffer or glycerol. The stress 100 s after imposition of strain was approximately proportional to In λ, where λ is the stretch ratio. Ligated thrombin films showed comparatively little relaxation over a period of one day and almost complete recovery after release of stress. In unligated thrombin films, there was substantial relaxation in two stages, as previously observed for coarse films, and substantial irrecoverable deformation. The extent of relaxation and the proportion of strain that was irrecoverable increased with the magnitude of the strain. In ancrod films (unligated), there was much more relaxation (stress decaying by as much as a factor of 10) and much more irrecoverable deformation (about 70% of the initial deformation); these results did not depend on the magnitude of the strain. When an ancrod film was released after relaxation and submitted to a second stretch, the extent of the second relaxation was much less. These observations are discussed in relation to the structure of fine films and possible mechanisms for relaxation and irrecoverable deformation.     

Fibrin and plasminogen structures essential to stimulation of plasmin formation by tissue-type plasminogen activator

Plasminogen activation catalysed by tissue-type plasminogen activator (t-PA) has been examined in the course of concomitant fibrin formation and degradation. Plasmin generation has been measured by the spectrophotometric method of Petersen et al. (Biochem. J. 225 (1985) 149-158), modified so as to allow for light scattering caused by polymerized fibrin. Glu1-, Lys77- and Val442-plasminogen are activated in the presence of fibrinogen, des A- and des AB-fibrin and the rate of plasmin formation is found to be greatly enhanced by both des A- and des AB-fibrin polymer. Plasmin formation from Glu1- and Lys77-plasminogen yields a sigmoidal curve, whereas a linear increase is obtained with Val442-plasminogen. The rate of plasmin formation from Glu1- and Lys77-plasminogen declines in parallel with decreasing turbidity of the fibrin polymer effector. In order to study the effect of polymerization, this has been inhibited by the synthetic polymerization site analogue Gly-Pro-Arg-Pro, by fibrinogen fragment D1 or by prior methylene blue-dependent photooxidation of the fibrinogen used. Inhibition of polymerization by Gly-Pro-Arg-Pro reduces plasmin generation to the low rate observed in the presence of fibrinogen. Antipolymerization with fragment D1 or photooxidation has the same effect on Glu1-plasminogen activation, but only partially reduces and delays the stimulatory effect on Lys77- and Val442-plasminogen activation. The results suggest that protofibril formation (and probably also gelation) of fibrin following fibrinopeptide release is essential to its stimulatory effect. The gradual increase and subsequent decline in the rate of plasmin formation from Glu1- or Lys77-plasminogen during fibrinolysis may be explained by sequential exposure, modification and destruction of different t-PA and plasminogen binding sites in fibrin polymer.     

Rheology of fibrin clots. I. Dynamic viscoelastic properties and fluid permeation

The storage and loss shear moduli (G', G″) of human fibrin clots have been measured in small oscillating deformations over a frequency range of 0.01 to 160 Hz with the modified Birnboim transducer apparatus. Most clots were prepared by the action of thrombin on purified fibrinogen, under various conditions of pH and ionic strength to produce networks ranging from coarse to fine structure; some were liaated by fibrinoligase. The fine, unligated clot showed very little mechanical loss or frequency dependence of G' over the experimental frequency range, though loss mechanisms evidently appear at higher frequencies; G' was proportional to the 1.5 power of fibrin concentration. The coarse, unligated clot showed a slight increase of G' with frequency, reflecting some relaxation mechanisms with time constants whose reciprocals lie in the experimental frequency range. Ligation did not greatly affect the magnitude of G'. However, clots prepared by dilution of solutions of fibrin monomer in 1 M sodium bromide had smaller moduli by a factor of ten than corresponding clots prepared by the action of thrombin of fibrinogen. Oscillatory measurements in the Birnboim apparatus with closed-end (annular pumping) geometry revealed a low-frequency anomaly which was shown to be due to permeation of fluid through the clot structure, and from these measurements the Darcy constants for coarse clots were calculated. From the Darcy constants, the average thicknesses of the fibrous elements of the structures were estimated to be from 300 to 700 A.     

Studies of fibrin film. I. Stress relaxation and birefringence

Measurements of stress relaxation in uniaxial extension and associated time-dependent birefringence have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 13–22% fibrin plasticized with either aqueous buffer or glycerol. Both unligated and ligated (i.e., with α-α and γ-γ ligation by fibrinoligase, factor XIIIa) films were studied. Both types showed two stages of stress relaxation, with time scales of approximately 10 and 10³–10⁴ s, respectively, with a plateau region between. In the plateau, the nominal (engineering) stress for ligated glycerol-plasticized film is proportional to In λ, where λ is the stretch ratio, up to λ ? 2, and it decreases with increasing temperature. For unligated glycerol-plasticized film, the stresses are smaller by a factor of one-half to one-third. For ligated film, the second stage of relaxation is relatively slight, and recovery after release of stress is often nearly complete. For unligated film, the second stage involves a substantial drop in stress, and after recovery there is a significant permanent set. A second relaxation for ligated film reproduces the first, but for unligated film it reproduces the first only if the initial relaxation is terminated before the second stage; otherwise, the second relaxation shows a weaker structure. The behavior of water-plasticized film is similar to that of glycerol-plasticized except that the second stage of relaxation occurs at shorter times. During the first stage of stress relaxation, up to about 100 s, the birefringence and the stress-optical coefficient increase; during the plateau zone of stress relaxation, the birefringence of ligated films is approximately constant and is proportional to 2λ²/(λ² + 1) ? 1, where λ is the stretch ratio. This dependence is predicted by a two-dimensional model in which rodlike elements in the plane of the film are oriented with independent alignment. During the final stage of stress relaxation, the birefringence of ligated films decreases slightly; that of unligated films decreases substantially, but less rapidly than the stress, corresponding to a further increase in the stress-optical coefficient. With additional information from small-angle x-ray scattering reported in an accompanying paper, the first stage of relaxation is attributed to partial release of bending forces in the fibers by orientation, accompanied by increased birefringence. The second stage is attributed, for ligated films, to an internal transition in the fibrin units accompanied by elongation of some of the fibers; and in the unligated films, to a combination of the latter transition with slippage of protofibrils lengthwise within the fiber bundles that causes some loss of orientation, which diminishes the birefringence.     

Gel formation by fibrin oligomers without addition of monomers

Soluble fibrin oligomers were formed by reacting fibrinogen with thrombin under fine clotting conditions where the action of thrombin is the rate-determining step for polymerization, and by inhibiting the reaction shortly before gelation. Oligomeric fibrin was separated from unreacted fibrinogen and small oligomers by gel permeation chromatography. Electron microscopy revealed that the largest soluble fibrin oligomers resemble the protofibrils present in fine clots, but are somewhat shorter and entirely lack the twisted, trifunctional junctions that contribute to the elastic properties of fine clots. When thrombin was added to the soluble fibrin oligomers, polymerization resumed and clots were formed at a more rapid rate than from fibrinogen at the same concentration and resulted in a less-opaque clot under coarse clotting conditions. The results confirm a prediction of a theory for the polymerization of fibrin and provide additional evidence that the final state of a coarse fibrin clot depends on the mobility of protofibrils during its formation.     

Analysis of fibrous network fluid permeation data using the theory of ultracentrifugation: application to fibrin gels

A new and alternative method for calculating the strand diameter of fibrous gel networks from fluid permeation data is developed and used to analyze and compare previous Darcy constant measurements of fibrin gels. The calculated diameters from the various sets of experimental data using this method gives for a coarse fibrin clot a strand diameter of approximately 1000 A and for a fine fibrin clot a strand diameter of 170 A.     

Rheology of fibrin clots: III. Shear creep and creep recovery of fine ligated and coarse unligated clots

Creep and creep recovery of human fibrin clots in small shearing deformations have been investigated over a time scale from 24 to 10⁴ s. Coarse, unligated dots and fine dots ligated by fibrinoligase in the presence of calcium ions were studied to suppllement previous data on coarse ligated and fine unligated clots. Stress was found to be proportional to strain up to at least a maximum shear strain (in torsion geometry) of 2.6%. The initial modulus (25 s after imposition of stress) is proportional to approximately the 1.5 power of concentration for fine ligated and coarse unligated clots. For fine unligated clots, there is comparatively little creep subsequent to the initial deformation; ligation (in this case involving mostly the γ chains) reduces the creep to nearly zero. For coarse unligated dots, there is substantially more creep under constant stress, and creep recovery is not complete. legation (in this casa involving both γ and α chains) largely suppresses the creep and causes the recovery to be complete. If the structure is fully formed before creep begins, tests of creep recovery by the Boltzmann superposition principle show adherence to linear viscoelastic behavior for all four clot types. Otherwise, the Boltzmann test fails and the recovery is much less than calculated. For fine ligated clots, the observed recovery agrees well with that calculated on the basis of a dual structure model in which an additional independent structure is built up in the deformed state, so that the state of ease after removal of stress is a balance between two structures deformed in opposite senses, it is postulated that the coherence and elastic modulus of the fine ligated dot are largely due to steric blocking of long protofibrils with a high flexural stiffness. In the coarse clot, it is proposed that the structure involves extensive branching of thick bundles of protofibrils, which become permanently secured by the ligation of the α chains of the fibrin.     

Cross-linking of cold-insoluble globulin by fibrin-stabilizing factor.

Cold-insoluble globulin (CI globulin) was purified from human plasma and identified on the basis of its sedimentation coefficient, electrophoretic mobility, and concentration in normal plasma. CI globulin was distinguished from antihemophilic factor (AHF) by amino acid analysis, position of elution from 4% agarose, and electrophoretic migration in polyacrylamide gels in the presence of sodium dodecyl sulfate without prior reduction. CI globulin and AHF could not be distinguished by polyacrylamide gel electrophoresis in sodium dodecyl sulfate after reduction and probably have very similar subunit molecular weights. CI globulin apparently consists of two polypeptide chains, each of molecular weight 2.0 x 10(5), held together by disulfide bonds. CI globulin was a substrate for activated fibrin-stabilizing factor (FSF, blood coagulation factor XIII). FSF catalyzed the incorporation of a fluorescent primary amine, N-(5-aminopentyl)-5-dimethylaminonaphthalene-1-sulfonamide, into CI globulin and also catalyzed the cross-linking of CI globulin into multimers, as judged by polyacrylamide gel electrophoresis in sodium dodecyl sulfate after reduction. In the presence of fibrin, cross-linking of CI globulin by FSF occurred without the formation of CI globulin multimers. Instead, polypeptides with apparent molecular weights of 2.6 x 10(5) and 3.0 x 10(5) were seen. The formation of these polypeptides coincided with the loss of the alpha chain of fibrin and CI globulin. The polypeptides were not seen when fibrin alone was cross-linked. The formation of the polypeptides was greater in fine clots than in coarse clots, and greater in clots incubated at 0 degrees than in clots incubated at 37 degrees. In clots made from purified fibrinogen, CI globulin, and FSF, the concentration of CI globulin in the clot liquor was greater if either FSF or calcium ion was omitted and cross-linking did not take place. These observations suggest that CI globulin is enzymically cross-linked to one of the chains of fibrin, most likely the alpha chain, and is thus covalently incorporated into the fibrin clot. CI globulin is very similar to a protein in the plasma membrane of fibroblasts. The cross-linking of CI globulin to itself and to fibrin may typify reactions also involving the fibroblast membrane protein.     

Altered structure and function of fibrinogen after cleavage by Factor VII Activating Protease (FSAP)

Factor VII Activating Protease (FSAP) is a plasma protease affecting both coagulation and fibrinolysis. Although a role in hemostasis is still unclear, the identification of additional physiologic substrates will help to elucidate its role in this context. FSAP has been reported to cleave fibrinogen, but the functional consequences of this are not known. We have therefore undertaken this study to determine the implications of this cleavage for fibrin-clot formation and its lysis. Treatment of human fibrinogen with FSAP released an N-terminal peptide from the Bβ chain (Bβ1-53) and subsequently the fibrinopeptide B; within the Aα chain a partial truncation of the αC-region by multiple cleavages was seen. The truncated fibrinogen showed a delayed thrombin-catalyzed polymerization and formed fibrin clots of reduced turbidity, indicative of thinner fibrin fibers. Confocal laser scanning and scanning electron microscopy of these clots revealed a less coarse fibrin network with thinner fibers and a smaller pore size. A lower pore size was also seen in permeability studies. Unexpectedly, FSAP-treated fibrinogen or plasma exhibited a significantly faster tPA-driven lysis, which correlated exclusively with cleavage of fibrinogen and not with activation of plasminogen activators. Similar observations were also made in plasma after activation of endogenous zymogen FSAP, but not in plasma of carrier of the rare Marburg I single nucleotide polymorphism. In conclusion, altering fibrin clot properties by fibrinogenolysis is a novel function of FSAP in the vasculature, which facilitates clot lysis and may in vivo contribute to reduced fibrin deposition during thrombosis.     

Crystallization of macromolecular heparin

X-ray fibre-diffraction photographs were obtained from oriented films of the sodium salt of macromolecular heparin (molecular weight approx. 10(6)) prepared from rat skin. Two distinct molecular chain conformations corresponding to two different crystal lattices were observed as a function of relative humidity. The first conformation, obtained at 78% relative humidity, has a layer-line spacing of 1.73nm, which can be interpreted as an approximate twofold helix. On increasing the relative humidity to 84% a second phase with a layer-line repeat of 1.65nm is obtained with the reflexions indexing on a triclinic unit cell similar to that obtained previously (Nieduszynski & Atkins, 1973) for pig mucosal heparin.     

Partial purification, from Xenopus laevis oocytes, of an ATP-dependent activity required for nucleosome spacing in vitro.

A critical feature of chromatin with regard to structure and function is the regular spacing of nucleosomes. In vivo, spacing of nucleosomes occurs in at least two steps, but the mechanism is not understood. In this report, we have mimicked the two-step process in vitro. A novel spacing activity has been partially purified from Xenopus laevis ovaries. When this activity is added, either at the beginning or at the end of a nucleosomal assembly reaction, it can convert a DNA template consisting of irregularly spaced nucleosomes into a chromatin structure made up of regularly spaced nucleosomes with a repeat length of about 165 base pairs. The reaction requires ATP. Histone H1 is able to increase the nucleosomal repeat from 165 to 190 base pairs. This two-step increase in nucleosomal repeat length suggests that both the spacing activity and histone H1 contribute to generating repeat lengths of greater than 165 base pairs and that their contributions may be additive. Alternatively, the critical step in the spacing reaction may not be the formation of the 165-base pair repeat but may be the sliding of nucleosomes or the reorganization of the octamer structure induced by the spacing activity.     

Ligation of fibrinogen by factor XIIIa with dithiothreitol: mechanical properties of ligated fibrinogen gels

Human fibrinogen (concentration 8.4 mg/mL) was ligated (cross-linked) with factor XIIIa and dithiothreitol (DTT) at pH 8.5, ionic strength 0.45. With 7.5 μg/mL of factor XIIIa alone, there was almost no γ-γ ligation, but with 2 mM DTT added, oligomers appeared, and γ-γ and Aα-Aα ligation was nearly complete after 3 days. At 38 μg/mL of factor XIIIa, some γ-γ and Aα-Aα ligation occurred even without DTT. For fibrinogen concentrations of 4.0 and 8.4 mg/mL, 38 μ/mL factor XIIIa, 2.0 mM DTT, clot-like gels formed and the shear modulus of elasticity increased slowly over several days to a constant value. The final modulus was similar in magnitude to those of ligated clots of α-fibrin (clotted by thrombin) and α-fibrin (clotted by batroxobin) under the same conditions. However, the opacity was somewhat higher; whereas in fine fibrin clots there is minimal lateral association of the protofibrils, in fibrinogen gels at the same pH and ionic strength the protofibrils (which are presumably single chains of fibrinogen monomers joined end to end at their D domains) are evidently associated in bundles (although not to the degree seen in coarse fibrin clots). Creep and creep recovery measurements showed almost perfect elastic behavior, with essentially no creep under stress and complete recovery after removal of stress. The modulus was scarcely affected by introduction of lithium bromide by diffusion to a concentration of 0.6M, which in unligated fibrin clots causes substantial softening. Whereas in fine fibrin clots (both αβ-fibrin and α-fibrin) factor XIIIa causes only γ-γ ligation, addition of 2 mM DTT produced some α-α ligation in these also.     

Lateral packing of protofibrils in fibrin fibers and fibrinogen polymers

The distinctive transverse banding pattern of fibrin fibers clearly indicates ordering of molecules in the longitudinal direction. In this study we examined the fibers of fibrin clots, as well as two types of fibrinogen polymers, by thin-section electron microscopy. The fibrinogen polymers have a transverse banding pattern identical to that of fibrin fibers—clearly indicating a regular longitudinal repeat—but they are larger in diameter, and show little or no branching. We therefore expected their overall ordering to be better than that of fibrin fibers. Several different fixation protocols were used. We readily observed the typical transverse banding seen previously by negative stain and metal replication techniques. However, only very rarely was any regular lateral lattice seen in any of the samples. X-ray diffraction was used to examine unfixed specimens of the two fibrinogen polymers and, once again, although a longitudinal repeat was evident, only rarely was evidence for lateral crystallinity seen. The electron-microscope and x-ray results showed that the needles and pellet fibers of fibrinogen have essentially the same internal architecture as thick fibrin fibers, and that all three types of polymer, although clearly transversely banded, have almost no crystallinity in their lateral protofibril packing.     

Identification of fibrin oligomers in sonicated fibrin clots

Clots of bovine fibrin, with both coarse and fine structure, and ligated to different extents by fibrinoligase, have been broken up by ultrasonic agitation and the sonicates have been examined by ultracentrifugal sedimentation. Sonication is followed by gross aggregation of the fragments unless guanidine hydrochloride is introduced (order of 1 M). In that case, sonicates of gamma-ligated fine clots contain two species whose sedimentation coefficients correspond to fibrin monomer and an oligomer with twice the monomer cross-section area and at least 20 monomer units, presumably with the structure of lateral dimerization with staggered overlapping. If the gamma ligation is incomplete, shorter oligomers are identified. The monomer and oligomer with degree of polymerization greater than 20 appear also in sonicates of coarse clots, but in smaller amounts, the principal product consisting of larger aggregates. The implications of these results with respect to metastability of the fine clot and the pattern of polymerization are discussed.     

Biomass and production of fine and coarse roots during regrowth of a disturbed subtropical humid forest in north-east India

Seasonal variation and depthwise distribution of dry matter in roots of different diameter classes and their annual production were studied using sequential core sampling. The investigations were carried out in three stands of a subtropical humid forest of north-east India representing different stages of regrowth after tree cutting. The mean annual standing crop of fine (<2 mm in diameter) and coarse (2–15 mm diameter) roots increased gradually from 5.4 Mg ha^-1 and 0.7 Mg ha^-1 in 7-yr old regrowth to 9.4 Mg ha^-1 and 2.8 Mg ha^-1 in 16-yr old regrowth, respectively. The contribution of fine roots to the total root mass declined from 88% in 7-yr old regrowth to 77% in both 13 and 16-yr old regrowths, while that of coarse roots increased from 12 to 23%. A major portion of fine roots (59–62%) was present in 0–10 cm soil layer, but the coarse roots were concentrated in 10–20 cm soil depth (38–48%). In all the three stands, biomass of both fine and coarse roots followed a unimodal growth curve by showing a gradual increase from spring/pre-rainy season to autumn/post-rainy season. Biomass to necromass ratio increased from 2.5 in the 7-yr old to 3.2 in the 16-yr old stand. The annual fine root production increased from 5.9 Mg ha^-1 to 7.7 Mg ha^-1 and total root production from 7.6 Mg ha^-1 to 14.7 Mg ha^-1 from 7-yr to 16-yr old regrowth.     

Crystallization of macromolecular heparin (Short Communication)

X-ray fibre-diffraction photographs were obtained from oriented films of the sodium salt of macromolecular heparin (molecular weight approx. 10⁶) prepared from rat skin. Two distinct molecular chain conformations corresponding to two different crystal lattices were observed as a function of relative humidity. The first conformation, obtained at 78% relative humidity, has a layer-line spacing of 1.73nm, which can be interpreted as an approximate twofold helix. On increasing the relative humidity to 84% a second phase with a layer-line repeat of 1.65nm is obtained with the reflexions indexing on a triclinic unit cell similar to that obtained previously (Nieduszynski & Atkins, 1973) for pig mucosal heparin.     

Rheology of fibrin clots. IV. Darcy constants and fiber thickness.

Measurements of small oscillatory deformations of a fibrin clot by axial motion of a rod in a closed tube reveal an anomalous mechanical loss due to permeation of fluid through the clot structure. The Darcy constant for permeation can be calculated from data at the frequency where the apparent storage and loss shear moduli are equal, without the necessity of measurements at much lower frequencies as previously employed. From the Darcy constant, the average number of fibrin monomer units (v) per cross-section of a fibrous element of the clot can be calculated; it ranges from 4 to several hundred. In the range of fibrin concentration(c) from 3 to 14 milligrams, v is approximately proportional to c-2 for clots of coarse structure and to c-0.5 for clots of fine structure.     

Identification of a site in fibrin(ogen) which is involved in the acceleration of plasminogen activation by tissue-type plasminogen activator

The rate of activation of plasminogen by tissue-type plasminogen activator is greatly increased by fibrin, but not by fibrinogen. A possible explanation for this phenomenon could be that conformational changes take place during the transformation of fibrinogen to fibrin which lead to exposure of sites involved in the accelerated plasmin formation. This is also supported by our recent observation that some enzymatically prepared fragments of fibrinogen and fibrin (D EGTA, D-dimer, Y) and also CNBr fragment 2 from fibrinogen have this property. CNBr fragment 2 consists of amino acid residues A alpha (148-207), B beta (191-224) + (225-242) + (243-305) and gamma 95-265, kept together by disulphide bonds. In order to study the localization of a stimulating site within this structure we purified the chain remnants of CNBr fragment 2 after reduction and carboxymethylation, and found that only A alpha 148-207 was stimulating. This was further confirmed by digesting pure A alpha-chains with CNBr and purifying the resulting A alpha-chain fragments. CNBr digests of B beta- and gamma-chains were not stimulatory. The A alpha-chain remnant (residues 111-197) in D EGTA and D-dimer also comprise the major part (residues A alpha 148-197) of the CNBr A alpha-chain fragment. We conclude that a site capable of accelerating the plasminogen activation by tissue-type plasminogen activator preexists in fibrinogen, that this site becomes exposed upon fibrin formation or disruption of fibrinogen by plasmin or CNBr and that this site is within the stretch A alpha 148-197, which is retained in the A alpha-chain remnants of fibrinogen degradation products.