Importance of the biofilm matrix for the erosion stability of Bacillus subtilis NCIB 3610 biofilms.

Production and secretion of biomolecules can provide new emergent functionalities to the synthesizing organism. In particular, the secretion of extracellular polymeric substances (EPS) by biofilm forming bacteria creates a biofilm matrix that protects the individual bacteria within the biofilm from external stressors such as antibiotics, chemicals and shear flow. Although the main matrix components of biofilms formed by Bacillus subtilis are known, it remains unclear how these matrix components contribute to the erosion stability of B. subtilis biofilms. Here, we combine different biophysical techniques to assess this relation. In particular, we quantify the importance of specific biofilm matrix components on the erosion behavior of biofilms formed by the well-studied Bacillus subtilis NCIB 3610. We find that the absence of biofilm matrix components decreases the erosion stability of NCIB 3610 biofilms in water, largely by abolishing the hydrophobic surface properties of the biofilm and by reducing the biofilm stiffness. However, the erosion resistance of NCIB 3610 biofilms is strongly increased in the presence of metal ions or the antibiotic ciprofloxacin. In the first case, unspecific ionic cross-linking of biofilm components or individual bacteria seems to be responsible for the observed effect, and in the second case there seems to be an unspecific interaction between the antibiotic and the biofilm matrix. Taken together, our results emphasize the importance of the biofilm matrix to reduce biofilm erosion and give insights into how the specific biomolecules interact with certain chemicals to fulfill this task.

Controlled nanoparticle release from a hydrogel by DNA-mediated particle disaggregation.

For many pharmaceutical applications, it is important that different drugs are present in the human body at distinct time points. Typically, this is achieved by a sequential administration of different therapeutic agents. A much easier alternative would be to develop a drug delivery system containing a whole set of medically active compounds which are liberated in an orchestrated and controlled manner. Yet, such a controlled, sequential release of drugs from a carrier system that can be used in a physiological situation is difficult to achieve. Here, we combine two molecular mechanisms, i.e. a build-up of osmotic pressure by the depletion of a control molecule and triggered disaggregation of nanoparticle clusters by synthetic DNA sequences. With this approach, we gain spatio-temporal control over the release of molecules and nanoparticles from a gel environment. The strategy presented here has strong implications for developing complex drug delivery systems for wound healing applications or for the sustained release of pharmaceuticals from a drug-loaded gel and will lower the need for multiple drug administrations.

The structure and mechanical properties of articular cartilage are highly resilient towards transient dehydration.

Articular cartilage is a mechanically highly challenged material with very limited regenerative ability. In contrast to elastic cartilage, articular cartilage is exposed to recurring partial dehydration owing to ongoing compression but maintains its functionality over decades. To extend our current understanding of the material properties of articular cartilage, specifically the interaction between the fluid and solid phase, we here analyze the reversibility of tissue dehydration. We perform an artificial dehydration that extends beyond naturally occurring levels and quantify material recovery as a function of the ionic strength of the rehydration buffer. Mechanical (indentation, compression, shear, and friction) measurements are used to evaluate the influence of de- and rehydration on the viscoelastic properties of cartilage. The structure and composition of native and de/rehydrated cartilage are analyzed using histology, scanning electron microscopy, and atomic force microscopy along with a 1,9-dimethylmethylene blue (DMMB) assay. A broad range of mechanical and structural properties of cartilage can be restored after de- and rehydration provided that a physiological salt solution is used for rehydration. We detect only minor alterations in the microarchitecture of rehydrated cartilage in the superficial zone and find that these alterations do not interfere with the viscoelastic and tribological properties of the tissue. STATEMENT OF SIGNIFICANCE: We here demonstrate the sturdiness of articular cartilage towards changes in fluid content and show that articular cartilage recovers a broad range of its material properties after dehydration. We analyze the reversibility of tissue dehydration to extend our current understanding of how the material properties of cartilage are established, focusing on the interaction between the fluid and solid phase. Our findings suggest that the high resilience of the tissue minimizes the risk of irreversible material failure and thus compensates, at least in part, its poor regenerative abilities. Tissue engineering approaches should thus not only reproduce the correct tissue mechanics but also its pronounced sturdiness to guarantee a similar longevity.

A single charge in the actin binding domain of fascin can independently tune the linear and non-linear response of an actin bundle network.

Actin binding proteins (ABPs) not only set the structure of actin filament assemblies but also mediate the frequency-dependent viscoelastic moduli of cross-linked and bundled actin networks. Point mutations in the actin binding domain of those ABPs can tune the association and dissociation dynamics of the actin/ABP bond and thus modulate the network mechanics both in the linear and non-linear response regime. We here demonstrate how the exchange of a single charged amino acid in the actin binding domain of the ABP fascin triggers such a modulation of the network rheology. Whereas the overall structure of the bundle networks is conserved, the transition point from strain-hardening to strain-weakening sensitively depends on the cross-linker off-rate and the applied shear rate. Our experimental results are consistent both with numerical simulations of a cross-linked bundle network and a theoretical description of the bundle network mechanics which is based on non-affine bending deformations and force-dependent cross-link dynamics.

Draft Genome Sequence of the Biofilm-Producing Bacillus subtilis Strain B-1, Isolated from an Oil Field.

We report here the draft genome sequence of the Bacillus subtilis strain B-1, a strain known to form biofilms. The biofilm matrix mainly consists of the biopolymer γ-polyglutamate (γ-PGA). The sequence of the genome of this strain allows the study of specific genes involved in biofilm formation.

Adapting a commercial shear rheometer for applications in cartilage research.

Cartilage research typically requires a broad range of experimental characterization techniques and thus various testing setups. Here, we describe how several of those tests can be performed with a single experimental platform, i.e. a commercial shear rheometer. Although primarily designed for shear experiments, such a rheometer can be equipped with different adapters to perform indentation and creep measurements, quantify alterations in the sample thickness, and conduct friction measurements in addition to shear rheology. Beyond combining four distinct experimental methods into one setup, the modified rheometer allows for performing material characterizations over a broad range of time scales, frequencies, and normal loads.

Carbohydrate coating reduces adhesion of biofilm-forming Bacillus subtilis to gold surfaces.

The growth of bacterial biofilms in pipes and food tanks causes severe problems in industry. Biofilms growing on medical implants or catheters are of great concern, as they can cause serious infections and decrease the functionality of the medical device. The prevention of bacterial adhesion--the first step in colonization and biofilm formation--is therefore very important. Current research comprises alterations in surface properties, the prevention of adhesin biosynthesis, inhibition with receptor analogs, or the development of anti-adhesive vaccines. We present a new approach that allows us to study bacterial adhesion with high sensitivity in real-time while testing several different surfaces in parallel. Using the cantilever-array technique we demonstrate that coating of gold surfaces with mono- or disaccharides results in a reduction of the bacterial adhesion of the biofilm-forming bacterium Bacillus subtilis NCIB 3610 to these gold surfaces. This reduction in bacterial adhesion is independent of the studied carbohydrate. Using several mutant strains, we investigate the underlying molecular interactions, and our results suggest that adhesion to gold surfaces is mediated by thiol groups present in proteins of the bacterial cell membrane or biofilm matrix proteins expressed at low levels by the wild-type strain. Furthermore, our data indicate that the adhesion of B. subtilis NCIB 3610 to carbohydrate-coated gold surfaces is facilitated by interactions between carbohydrates installed on the cantilever gold surface and an exopolysaccharide expressed by this strain. Understanding general and specific contributions of molecular interactions mediating bacterial adhesion will enable its prevention in the future.

Selected metal ions protect Bacillus subtilis biofilms from erosion.

Many problems caused by bacterial biofilms can be traced back to their high resilience towards chemical perturbations and their extraordinary sturdiness towards mechanical forces. However, the molecular mechanisms that link the mechanical properties of a biofilm with the ability of bacteria to survive in different chemical environments remain enigmatic. Here, we study the erosion stability of Bacillus subtilis (B. subtilis) biofilms in the presence of different chemical environments. We find that these biofilms can utilize the absorption of certain metal ions such as Cu(2+), Zn(2+), Fe(2+), Fe(3+) and Al(3+) into the biofilm matrix to avoid erosion by shear forces. Interestingly, many of these metal ions are toxic for planktonic B. subtilis bacteria. However, their toxic activity is suppressed when the ions are absorbed into the biofilm matrix. Our experiments clearly demonstrate that the biofilm matrix has to fulfill a dual function, i.e. regulating both the mechanical properties of the biofilm and providing a selective barrier towards toxic chemicals.

An adsorption chromatography assay to probe bulk particle transport through hydrogels.

Biopolymer-based hydrogels such as mucus and the basal lamina play a key role in biology, where they control the exchange of material between different compartments. They also pose a barrier that needs to be overcome for successful drug delivery. Characterizing the permeability properties of such hydrogels is mandatory for the development of suitable drug delivery vectors and pharmaceutics. Here, we present an experimental method to measure bulk particle transport through hydrogels. We validate our assay by applying it to mucin hydrogels and show that the permeability properties of these mucin hydrogels can be modulated by polymer density and pH, in agreement with previous results obtained from single particle tracking. The method we present here is easy to handle, inexpensive, and high-throughput compatible. It is also a suitable platform for the design and screening of drugs that aim at modifying the barrier properties of hydrogels. This system can also aid in the characterization and development of synthetic gels for a range of biomedical applications.

Slow dynamics and internal stress relaxation in bundled cytoskeletal networks.

Crosslinked and bundled actin filaments form networks that are essential for the mechanical properties of living cells. Reconstituted actin networks have been extensively studied not only as a model system for the cytoskeleton, but also to understand the interplay between microscopic structure and macroscopic viscoelastic properties of network-forming soft materials. These constitute a broad class of materials with countless applications in science and industry. So far, it has been widely assumed that reconstituted actin networks represent equilibrium structures. Here, we show that fully polymerized actin/fascin bundle networks exhibit surprising age-dependent changes in their viscoelastic properties and spontaneous dynamics, a feature strongly reminiscent of out-of-equilibrium, or glassy, soft materials. Using a combination of rheology, confocal microscopy and space-resolved dynamic light scattering, we demonstrate that actin networks build up stress during their formation and then slowly relax towards equilibrium owing to the unbinding dynamics of the crosslinking molecules.

Structural and viscoelastic properties of actin/filamin networks: cross-linked versus bundled networks.

The high diversity of cytoskeletal actin structures is accomplished by myriads of actin binding proteins (ABPs). Depending on its concentration, even a single type of ABP can induce different actin microstructures. Thus, for an overall understanding of the cytoskeleton, a detailed characterization of the cross-linker's effect on structural and mechanical properties of actin networks is required for each ABP. Using confocal microscopy and macrorheology, we investigate both cross-linked and bundled actin/filamin networks and compare their microstructures as well as their viscoelastic properties in the linear and the nonlinear regime.

Cytoskeletal polymer networks: viscoelastic properties are determined by the microscopic interaction potential of cross-links.

Although the structure of cross-linking molecules mainly determines the structural organization of actin filaments and with that the static elastic properties of the cytoskeleton, it is largely unknown how the biochemical characteristics of transiently cross-linking proteins (actin-binding proteins (ABPs)) affect the viscoelasticity of actin networks. In this study, we show that the macroscopic network response of reconstituted actin networks can be traced back to the microscopic interaction potential of an individual actin/ABP bond. The viscoelastic response of cross-linked actin networks is set by the cross-linker off-rate, the binding energy, and the characteristic bond length of individual actin/ABP interactions.

Transient binding and dissipation in cross-linked actin networks.

In contrast with entangled actin solutions, transiently cross-linked actin networks can provide highly elastic properties while still allowing for local rearrangements in the microstructure-on biological relevant time scales. Here, we show that thermal unbinding of transient cross-links entails local stress relaxation and energy dissipation in an intermediate elasticity dominated frequency regime. We quantify the viscoelastic response of an isotropically cross-linked actin network by experimentally tuning the off rate of the transiently cross-linking molecules, their density, and the solvent viscosity. We reproduce the measured frequency response by a semiphenomenological model that is predicated on microscopic unbinding events.

Cross-linking molecules modify composite actin networks independently.

While cells make use of many actin binding proteins (ABPs) simultaneously to tailor the mechanical properties of the cytoskeleton, the detailed interplay of different ABPs is not understood. By a combination of macrorheological measurements and confocal microscopy, we show that the ABPs fascin and filamin modify the structural and viscoelastic properties of composite in vitro actin networks independently. The outnumbering ABP dictates the local network structure and therefore also dominates the macromechanical network response.

Cross-linker unbinding and self-similarity in bundled cytoskeletal networks.

The macromechanical properties of purely bundled in vitro actin networks are not only determined by the micromechanical properties of individual bundles but also by molecular unbinding events of the actin-binding protein (ABP) fascin. Under high mechanical load the network elasticity depends on the forced unbinding of individual ABPs in a rate dependent manner. Cross-linker unbinding in combination with the structural self-similarity of the network enables the introduction of a concentration-time superposition principle--broadening the mechanically accessible frequency range over 8 orders of magnitude.

Mechanics of bundled semiflexible polymer networks.

While actin bundles are used by living cells for structural fortification, the microscopic origin of the elasticity of bundled networks is not understood. Here, we show that above a critical concentration of the actin binding protein fascin, a solution of actin filaments organizes into a pure network of bundles. While the elasticity of weakly cross-linked networks is dominated by the affine deformation of tubes, the network of bundles can be fully understood in terms of nonaffine bending undulations.