Cytoplasmic stabilities of 3'UTR-polymorphic prothrombin mRNAs

Spatiotemporal control of micromechanics and microstructure in acoustically-responsive scaffolds using acoustic droplet vaporization

Acoustically-responsive scaffolds (ARSs), which are composite fibrin hydrogels, have been used to deliver regenerative molecules. ARSs respond to ultrasound in an on-demand, spatiotemporally-controlled manner via a mechanism termed acoustic droplet vaporization (ADV). Here, we study the ADV-induced, time-dependent micromechanical and microstructural changes to the fibrin matrix in ARSs using confocal fluorescence microscopy as well as atomic force microscopy. ARSs, containing phase-shift double emulsion (PSDE, mean diameter: 6.3 μm), were exposed to focused ultrasound to generate ADV - the phase transitioning of the PSDE into gas bubbles. As a result of ADV-induced mechanical strain, localized restructuring of fibrin occurred at the bubble-fibrin interface, leading to formation of locally denser regions. ADV-generated bubbles significantly reduced fibrin pore size and quantity within the ARS. Two types of ADV-generated bubble responses were observed in ARSs: super-shelled spherical bubbles, with a growth rate of 31 μm per day in diameter, as well as fluid-filled macropores, possibly as a result of acoustically-driven microjetting. Due to the strain stiffening behavior of fibrin, ADV induced a 4-fold increase in stiffness in regions of the ARS proximal to the ADV-generated bubble versus distal regions. These results highlight that the mechanical and structural microenvironment within an ARS can be spatiotemporally modulated using ultrasound, which could be used to control cellular processes and further the understanding of ADV-triggered drug delivery for regenerative applications.

High-performance nanomaterials formed by rigid yet extensible cyclic β-peptide polymers

Organisms have evolved biomaterials with an extraordinary convergence of high mechanical strength, toughness, and elasticity. In contrast, synthetic materials excel in stiffness or extensibility, and a combination of the two is necessary to exceed the performance of natural biomaterials. We bridge this materials property gap through the side-chain-to-side-chain polymerization of cyclic β-peptide rings. Due to their strong dipole moments, the rings self-assemble into rigid nanorods, stabilized by hydrogen bonds. Displayed amines serve as functionalization sites, or, if protonated, force the polymer to adopt an unfolded conformation. This molecular design enhances the processability and extensibility of the biopolymer. Molecular dynamics simulations predict stick-slip deformations dissipate energy at large strains, thereby, yielding toughness values greater than natural silks. Moreover, the synthesis route can be adapted to alter the dimensions and displayed chemistries of nanomaterials with mechanical properties that rival nature.

Synthetic materials tend to excel in either stiffness or extensibility, whereas a combination of the two is necessary to exceed the performance of natural biomaterials. Here the authors present a bioinspired polymer consisting of cyclic β-peptide rings that is capable of transitioning between rigid and unfolded conformations on demand.

Fibrinogen and factor XIII: newly recognized roles in venous thrombus formation and composition

PURPOSE OF REVIEW

In spite of significant morbidity and mortality associated with venous thromboembolism, the underlying pathogenesis remains poorly understood.

RECENT FINDINGS

Clues to operant pathogenic mechanisms are found in the unique morphology and composition of these thrombi, which have substantial red blood cell and fibrin content. Recent studies have revealed biochemical and biophysical mechanisms that dictate fibrin structure in venous thrombi and promote retention of red blood cells within the contracted clots. These mechanisms include newly recognized contributions of fibrin network structure and factor XIII(a)-mediated fibrin crosslinking to venous thrombus composition, size, and stability.

SUMMARY

Continued work to elucidate mechanisms by which fibrin(ogen), factor XIII, and red blood cells contribute to venous thrombus formation, structure, and stability may expose novel molecular targets and strategies for reducing thrombosis and thrombotic complications in certain at-risk patients.

Complex strain induced structural changes observed in fibrin assembled in human plasma

The structure of the core scaffold of blood clots, the interlinked 3-dimensional network of fibrin fibers, is modified by mechanical forces generated by platelet driven clot retraction, wound repair and shear stress through blood flow. Here X-ray diffraction is used to investigate how uniaxial strain, ε (ε = extension/original length), alters fiber structure in highly aligned human plasma clots covalently cross-linked by Factor XIIIa. Three stretch sensitive axially repeating structures are identified. Firstly, the foundation structure with an initial ≈22 nm axial repeat stretches, fades then disappears at ε ≈ 0.40. A second, lengthened transitory structure emerges at the low strains (ε ≈ 0.20) believed to be developed by cells. Finally, a third shortened structure appears after relaxation. Simultaneously as strain progresses an increasing fraction of molecules become axially disordered. Weak off-axis diffraction maxima indicate the presence of lateral ordering up to ε = 0.40 that partially recovers after relaxation. The reappearance of both axial and lateral order on relaxation demonstrates a surprising resilience in structure. In view of the range and importance of fibrin's functions, this structural heterogeneity, triggered in vivo by cell traction or shear stress, is likely to be of clinical significance.

Emerging hydrogel designs for controlled protein delivery

Hydrogels have evolved into indispensable biomaterials in the fields of drug delivery and regenerative medicine. This minireview aims to highlight the recent advances in the hydrogel design for controlled release of bioactive proteins. The latest developments of enzyme-responsive and externally regulated drug delivery systems are summarized. The design strategies and applications of phase-separated hydrogel systems are also described. We expect that these emerging approaches will enable expanded use of hydrogels in biomedicine and healthcare.

AFM-based mechanical characterization of single nanofibres

Nanofibres are found in a broad variety of hierarchical biological systems as fundamental structural units, and nanofibrillar components are playing an increasing role in the development of advanced functional materials. Accurate determination of the mechanical properties of single nanofibres is thus of great interest, yet measurement of these properties is challenging due to the intricate specimen handling and the exceptional force and deformation resolution that is required. The atomic force microscope (AFM) has emerged as an effective, reliable tool in the investigation of nanofibrillar mechanics, with the three most popular approaches-AFM-based tensile testing, three-point deformation testing, and nanoindentation-proving preferable to conventional tensile testing in many (but not all) cases. Here, we review the capabilities and limitations of each of these methods and give a comprehensive overview of the recent advances in this field.

Multi-scale strain-stiffening of semiflexible bundle networks

Bundles of polymer filaments are responsible for the rich and unique mechanical behaviors of many biomaterials, including cells and extracellular matrices. In fibrin biopolymers, whose nonlinear elastic properties are crucial for normal blood clotting, protofibrils self-assemble and bundle to form networks of semiflexible fibers. Here we show that the extraordinary strain-stiffening response of fibrin networks is a direct reflection of the hierarchical architecture of the fibrin fibers. We measure the rheology of networks of unbundled protofibrils and find excellent agreement with an affine model of extensible wormlike polymers. By direct comparison with these data, we show that physiological fibrin networks composed of thick fibers can be modeled as networks of tight protofibril bundles. We demonstrate that the tightness of coupling between protofibrils in the fibers can be tuned by the degree of enzymatic intermolecular crosslinking by the coagulation factor XIII. Furthermore, at high stress, the protofibrils contribute independently to the network elasticity, which may reflect a decoupling of the tight bundle structure. The hierarchical architecture of fibrin fibers can thus account for the nonlinearity and enormous elastic resilience characteristic of blood clots.

Structural determinants of human ζ-globin mRNA stability

Background

The normal accumulation of adult α and β globins in definitive erythrocytes is critically dependent upon processes that ensure that the cognate mRNAs are maintained at high levels in transcriptionally silent, but translationally active progenitor cells. The impact of these post-transcriptional regulatory events on the expression of embryonic ζ globin is not known, as its encoding mRNA is not normally transcribed during adult erythropoiesis. Recently, though, ζ globin has been recognized as a potential therapeutic for α thalassemia and sickle-cell disease, raising practical questions about constitutive post-transcriptional processes that may enhance, or possibly prohibit, the expression of exogenous or derepresssed endogenous ζ-globin genes in definitive erythroid progenitors.

Methods

The present study assesses mRNA half-life in intact cells using a pulse-chase approach; identifies cis-acting determinants of ζ-globin mRNA stability using a saturation mutagenesis strategy; establishes critical 3′UTR secondary structures using an in vitro enzymatic mapping method; and identifies trans-acting effector factors using an affinity chromatographical procedure.

Results

We specify a tetranucleotide 3′UTR motif that is required for the high-level accumulation of ζ-globin transcripts in cultured cells, and formally demonstrate that it prolongs their cytoplasmic half-lives. Surprisingly, the ζ-globin mRNA stability motif does not function autonomously, predicting an activity that is subject to structural constraints that we subsequently specify. Additional studies demonstrate that the ζ-globin mRNA stability motif is targeted by AUF1, a ubiquitous RNA-binding protein that enhances the half-life of adult β-globin mRNA, suggesting commonalities in post-transcriptional processes that regulate globin transcripts at all stages of mammalian development.

Conclusions

These data demonstrate a mechanism for ζ-globin mRNA stability that exists in definitive erythropoiesis and is available for therapeutic manipulation in α thalassemia and sickle-cell disease.

Mechanical clot damage from cavitation during sonothrombolysis

Recent studies have shown that high intensity focused ultrasound (HIFU) accelerates thrombolysis for ischemic stroke. Although the mechanisms are not fully understood, cavitation is thought to play an important role. The goal of this paper is to investigate the potential for cavitation to cause mechanical damage to a blood clot. The amount of damage to the fiber network caused by a single bubble expansion and collapse is estimated by two independent approaches: One based on the stretch of individual fibers and the other based on the energy available to break individual fibers. The two methods yield consistent results. The energy method is extended to the more important scenario of a bubble outside a blood clot that collapses asymmetrically creating an impinging jet. This leads to significantly more damage compared to a bubble embedded within the clot structure. Finally, as an example of how one can apply the theory, a simulation of the propagation of HIFU waves through model calvaria of varying density is explored. The maximum amount of energy available to cause damage to a blood clot increases as the density of the calvaria decreases.

A reverse time-course method for transcriptional chase analyses of mRNA half-lives in cultured cells

Standard methods for assessing mRNA stabilities in intact cells are labor-intensive and can generate half-life (t_1/2) measures that are both imprecise and inaccurate. We describe modifications to a conventional tetracycline-conditional transcriptional chase method for analyzing mRNA stability that significantly simplify its conduct, while generating highly reproducible and accurate t_1/2 values. The revised method–which is conducted as a reverse time course, and which accounts for interval expansion in the number of cultured cells–is validated for the analyses of mRNAs with both short and long half-lives. This approach facilitates accurate assessment of mRNA metabolism, providing a user-friendly tool for detailed investigations into their structures and functions, as well as the processes that contribute to their post-transcriptional regulation.

Fibrinogen unfolding mechanisms are not too much of a stretch

Molecular explanations for the extraordinary elasticity and extensibility of fibrin fibers are still lacking. Now, Zhmurov et al. (2011) use force spectroscopy experiments, and innovative simulations that match the time and force scales of these experiments, to study fibrinogen behavior under an applied force providing deeper insights into this process.

The Mechanical Properties of Dry, Electrospun Fibrinogen Fibers

Due to their low immunogenicity, biodegradability and native cell-binding domains, fibrinogen fibers may be good candidates for tissue engineering scaffolds, drug delivery vehicles and other medical devices. We used a combined atomic force microscope (AFM)/optical microscope technique to study the mechanical properties of individual, electrospun fibrinogen fibers in dry, ambient conditions. The AFM was used to stretch individual fibers suspended over 13.5 µm wide grooves in a transparent substrate. The optical microscope, located below the sample, was used to monitor the stretching process. Electrospun fibrinogen fibers (diameter, 30-200 nm) can stretch to 74 % beyond their original length before rupturing at a stress of 2.1 GPa. They can stretch elastically up to 15 % beyond their original length. Using incremental stress-strain curves the viscoelastic behavior of these fibers was determined. The total stretch modulus was 4.2 GPa while the relaxed elastic modulus was 3.7 GPa. When held at constant strain, fibrinogen fibers display stress relaxation with a fast and slow relaxation time of 1.2 s and 11 s.In comparison to native and electrospun collagen fibers, dry electrospun fibrinogen fibers are significantly more extensible and elastic. In comparison to wet electrospun fibrinogen fibers, dry fibers are about 1000 times stiffer.