Experimental observation of near-wall effects during the puncture of soft solids.

Performing conventional mechanical characterization techniques on soft materials can be challenging due to issues such as limited sample volumes and clamping difficulties. Deep indentation and puncture is a promising alternative as it is an information-rich measurement with the potential to be performed in a high-throughput manner. Despite its promise, the method lacks standardized protocols, and open questions remain about its possible limitations. Addressing these shortcomings is vital to ensure consistent methodology, measurements, and interpretation across samples and labs. To fill this gap, we examine the role of finite sample dimensions (and by extension, volume) on measured forces to determine the sample geometry needed to perform and unambiguously interpret puncture tests. Through measurements of puncture on a well-characterized elastomer using systematically varied sample dimensions, we show that the apparent mechanical response of a material is in fact sensitive to near-wall effects, and that additional properties, such as the sliding friction coefficient, can only be extracted in the larger dimension case where such effects are negligible.

Genome sequence of Microbacterium foliorum phage CandC.

We report the discovery and genome sequence of CandC, a lytic bacteriophage with siphovirus morphology. CandC was isolated from a soil sample from Plattsburgh, NY, USA (Fall 2021). It has a genome size of 62,344 bp with 106 predicted protein-encoding genes, 30 of which are assigned putative functions.

Mechanical resilience of the sessile tunicate Botryllus schlosseri.

We demonstrate that the sessile tunicate Botryllus schlosseri is remarkably resilient to applied loads by attaching the animals to an extensile substrate subjected to quasistatic equiradial loads. Animals can withstand radial extension of the substrate to strain values as high as 20% before they spontaneously detach. In the small to moderate strain regime, we found no relationship between the dynamic size of the external vascular bed and the magnitude of applied stretch, despite known force sensitivities of the vascular tissue at the cellular level. We attribute this resilience to the presence and mechanical properties of the tunic, the cellulose-enriched gel-like substance that encases the animal bodies and surrounding vasculature.

Molecular-scale substrate anisotropy, crowding and division drive collective behaviours in cell monolayers.

The ability of cells to reorganize in response to external stimuli is important in areas ranging from morphogenesis to tissue engineering. While nematic order is common in biological tissues, it typically only extends to small regions of cells interacting via steric repulsion. On isotropic substrates, elongated cells can co-align due to steric effects, forming ordered but randomly oriented finite-size domains. However, we have discovered that flat substrates with nematic order can induce global nematic alignment of dense, spindle-like cells, thereby influencing cell organization and collective motion and driving alignment on the scale of the entire tissue. Remarkably, single cells are not sensitive to the substrate's anisotropy. Rather, the emergence of global nematic order is a collective phenomenon that requires both steric effects and molecular-scale anisotropy of the substrate. To quantify the rich set of behaviours afforded by this system, we analyse velocity, positional and orientational correlations for several thousand cells over days. The establishment of global order is facilitated by enhanced cell division along the substrate's nematic axis, and associated extensile stresses that restructure the cells' actomyosin networks. Our work provides a new understanding of the dynamics of cellular remodelling and organization among weakly interacting cells.

Modular Synthesis and Patterning of High-Stiffness Networks by Postpolymerization Functionalization with Iron-Catechol Complexes.

Bioinspired iron-catechol cross-links have shown remarkable success in increasing the mechanical properties of polymer networks, in part due to clustering of Fe3+-catechol domains which act as secondary network reinforcing sites. We report a versatile synthetic procedure to prepare modular PEG-acrylate networks with independently tunable covalent bis(acrylate) and supramolecular Fe3+-catechol cross-linking. Initial control of network structure is achieved through radical polymerization and cross-linking, followed by postpolymerization incorporation of catechol units via quantitative active ester chemistry and subsequent complexation with iron salts. By tuning the ratio of each building block, dual cross-linked networks reinforced by clustered iron-catechol domains are prepared and exhibit a wide range of properties (Young's moduli up to ∼245 MPa), well beyond the values achieved through purely covalent cross-linking. This stepwise approach to mixed covalent and metal-ligand cross-linked networks also permits local patterning of PEG-based films through masking techniques forming distinct hard, soft, and gradient regions.

Methods for Paramecium tetraurelia ciliary membrane protein identification and function.

In this chapter we provide some tools to study the ciliary proteins that make it possible for Paramecium cells to swim by beating their cilia. These proteins include many ion channels, accessory proteins, peripheral proteins, structural proteins, rootlets of cilia, and enzymes. Some of these proteins are also found in the soma membrane, but their distinct and critical functions are in the cilia. Paramecium has 4000 or more cilia per cell, giving it an advantage for biochemical studies over cells that have one primarily cilium per cell. Nonetheless, a challenge for studies of many ciliary proteins in Paramecium is their low abundance. We discuss here several strategies to overcome this challenge and other challenges such as working with very large channel proteins. We also include for completeness other techniques that are critical to the study of swimming behavior, such as genetic crosses, recording of swimming patterns, electrical recordings, expression of very large channel proteins, RNA Interference, among others.

Design of Surface-Aligned Main-Chain Liquid-Crystal Networks Prepared under Ambient, Light-Free Conditions Using the Diels-Alder Cycloaddition.

Surface-aligned liquid-crystal networks (LCNs) offer a solution for developing functional materials capable of performing a range of tasks, including actuation, shape memory, and surfaces patterning. Here we show that Diels-Alder cycloaddition can be used to prepare the backbone of planar aligned LCNs under mild ambient conditions without the addition of additives or UV irradiation. The mechanical properties of the networks have robust viscoelastic modulus and stiffness with a reversible local free volume change upon physical aging. This study shows new opportunities to design surface-aligned LCNs based on additive free step-growth Diels-Alder polymerization and enables the potential to incorporate a wider range of photochromic materials into LCNs.

A compact rotary magnetic tweezers device for dynamic material analysis.

Here we present a new, compact magnetic tweezers design that enables precise application of a wide range of dynamic forces to soft materials without the need to raise or lower the magnet height above the sample. This is achieved through the controlled rotation of the permanent magnet array with respect to the fixed symmetry axis defined by a custom-built iron yoke. These design improvements increase the portability of the device and can be implemented within existing microscope setups without the need for extensive modification of the sample holders or light path. This device is particularly well-suited to active microrheology measurements using either creep analysis, in which a step force is applied to a micron-sized magnetic particle that is embedded in a complex fluid, or oscillatory microrheology, in which the particle is driven with a periodic waveform of controlled amplitude and frequency. In both cases, the motions of the particle are measured and analyzed to determine the local dynamic mechanical properties of the material.

Strength of fluid-filled soft composites across the elastofracture length.

Materials that utilize heterogeneous microstructures to control macroscopic mechanical response are ubiquitous in nature. Yet, translating nature's lessons to create synthetic soft solids has remained challenging. This is largely due to the limited synthetic routes available for creating soft composites, particularly with submicron features, as well as uncertainty surrounding the role of such a microstructured secondary phase in determining material behavior. This work leverages recent advances in the development of photocrosslinkable thermogelling nanoemulsions to produce composite hydrogels with a secondary phase assembled at well controlled length scales ranging from tens of nm to tens of µm. Through analysis of the mechanical response of these fluid-filled composite hydrogels, it is found that the size scale of the secondary phase has a profound impact on the strength when at or above the elastofracture length. Moreover, this work shows that mechanical integrity of fluid-filled soft solids can be sensitive to the size scale of the secondary phase.

Rational mechanochemical design of Diels-Alder crosslinked biocompatible hydrogels with enhanced properties.

An important but often overlooked feature of Diels-Alder (DA) cycloadditions is the ability for DA adducts to undergo mechanically induced cycloreversion when placed under force. Herein, we demonstrate that the commonly employed DA cycloaddition between furan and maleimide to crosslink hydrogels results in slow gelation kinetics and "mechanolabile" crosslinks that relate to reduced material strength. Through rational computational design, "mechanoresistant" DA adducts were identified by constrained geometries simulate external force models and employed to enhance failure strength of crosslinked hydrogels. Additionally, utilization of a cyclopentadiene derivative, spiro[2.4]hepta-4,6-diene, provided mechanoresistant DA adducts and rapid gelation in minutes at room temperature. This study illustrates that strategic molecular-level design of DA crosslinks can provide biocompatible materials with improved processing, mechanical durability, lifetime, and utility.

Biofilm disruption enhances growth rate and carbohydrate-active enzyme production in anaerobic fungi.

Anaerobic gut fungi (AGF) are lignocellulose degraders that naturally form biofilms in the rumen of large herbivores and in standard culture techniques. While biofilm formation enhances biomass degradation and carbohydrate-active enzyme (CAZyme) production in some bacteria and aerobic fungi, gene expression and metabolism in AGF biofilms have not been compared to non-biofilm cultures. Here, using the tunable morphology of the non-rhizoidal AGF, Caecomyces churrovis, the impacts of biofilm formation on AGF gene expression, metabolic flux, growth rate, and xylan degradation rate are quantified to inform future industrial scale-up efforts. Contrary to previous findings, C. churrovis upregulated catabolic CAZymes in stirred culture relative to biofilm culture. Using a de novo transcriptome, 197 new transcripts with predicted CAZyme function were identified. Stirred cultures grew and degraded xylan significantly faster than biofilm-forming cultures with negligible differences in primary metabolic flux, offering a way to accelerate AGF biomass valorization without altering the fermentation product profile. The rhizoidal AGF, Neocallimastix lanati, also grew faster with stirring on a solid plant substrate, suggesting that the advantages of stirred C. churrovis cultures may apply broadly to other AGF.

The living interface between synthetic biology and biomaterial design.

Recent far-reaching advances in synthetic biology have yielded exciting tools for the creation of new materials. Conversely, advances in the fundamental understanding of soft-condensed matter, polymers and biomaterials offer new avenues to extend the reach of synthetic biology. The broad and exciting range of possible applications have substantial implications to address grand challenges in health, biotechnology and sustainability. Despite the potentially transformative impact that lies at the interface of synthetic biology and biomaterials, the two fields have, so far, progressed mostly separately. This Perspective provides a review of recent key advances in these two fields, and a roadmap for collaboration at the interface between the two communities. We highlight the near-term applications of this interface to the development of hierarchically structured biomaterials, from bioinspired building blocks to 'living' materials that sense and respond based on the reciprocal interactions between materials and embedded cells.

High-throughput microscopy to determine morphology, microrheology, and phase boundaries applied to phase separating coacervates.

Evolution of composition, rheology, and morphology during phase separation in complex fluids is highly coupled to rheological and mass transport processes within the emerging phases, and understanding this coupling is critical for materials design of multiphase complex fluids. Characterizing these dependencies typically requires careful measurement of a large number of equilibrium and transport properties that are difficult to measure in situ as phase separation proceeds. Here, we propose and demonstrate a high-throughput microscopy platform to achieve simultaneous, in situ mapping of time-evolving morphology and microrheology in phase separating complex fluids over a large compositional space. The method was applied to a canonical example of polyelectrolyte complex coacervation, whereby mixing of oppositely charged species leads to liquid-liquid phase separation into distinct solute-dense and dilute phases. Morphology and rheology were measured simultaneously and kinetically after mixing to track the progression of phase separation. Once equilibrated, the dense phase viscosity was determined to high compositional accuracy using passive probe microrheology, and the results were used to derive empirical relationships between the composition and viscosity. These relationships were inverted to reconstruct the dense phase boundary itself, and further extended to other mixture compositions. The resulting predictions were validated by independent equilibrium compositional measurements. This platform paves the way for rapid screening and formulation of complex fluids and (bio)macromolecular materials, and serves as a critical link between formulation and rheology for multi-phase material discovery.

Ion channels of cilia: Paramecium as a model.

Holotrichous ciliates, like Paramecium, swim through their aqueous environment by beating their many cilia. They can alter swimming speed and direction, which seems to have mesmerized early microscopists of the 1600s. We know from extensive and elegant physiological studies and generation of mutants that these cells can be considered little swimming neurons because their ciliary beating is under bioelectric control of ion channels in the cilia. This chapter will focus on the ionic control of swimming behavior by ciliary ion channels, primarily in the holotrichous ciliate Paramecium. Voltage-gated and calcium-activated channels for calcium, magnesium, sodium, and potassium are regulated in a closely orchestrated manner that allows cilia to bend and propel the cell forward or backward. Sensory input that generates receptor potentials feeds into the control of this channel activity and allows the cell to turn or speed up. This in turn helps the cell to avoid predators or toxic conditions. While the focus is on P. tetraurelia and P. caudatum, the principles of ciliary ion channel activity and control are easily extendable to other ciliates and protists. The high conservation of channel and ion pump structures also extends the lessons from Paramecium to higher organisms.

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture.

BACKGROUND: Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate species or measure species-specific attributes in most multi-species systems. Anaerobic gut fungi (AGF) (Neocallimastigomycetes) are native to the rumen of large herbivores, where they exist as minority members among a wealth of prokaryotes. AGF have significant biotechnological potential owing to their diverse repertoire of potent lignocellulose-degrading carbohydrate-active enzymes (CAZymes), which indirectly bolsters activity of other rumen microbes through metabolic exchange. While decades of literature suggest that polysaccharide degradation and AGF growth are accelerated in co-culture with prokaryotes, particularly methanogens, methods have not been available to measure concentrations of individual species in co-culture. New methods to disentangle the contributions of AGF and rumen prokaryotes are sorely needed to calculate AGF growth rates and metabolic fluxes to prove this hypothesis and understand its causality for predictable co-culture design. RESULTS: We present a simple, microplate-based method to measure AGF and methanogen concentrations in co-culture based on fluorescence and absorbance spectroscopies. Using samples of < 2% of the co-culture volume, we demonstrate significant increases in AGF growth rate and xylan and glucose degradation rates in co-culture with methanogens relative to mono-culture. Further, we calculate significant differences in AGF metabolic fluxes in co-culture relative to mono-culture, namely increased flux through the energy-generating hydrogenosome organelle. While calculated fluxes highlight uncertainties in AGF primary metabolism that preclude definitive explanations for this shift, our method will enable steady-state fluxomic experiments to probe AGF metabolism in greater detail. CONCLUSIONS: The method we present to measure AGF and methanogen concentrations enables direct growth measurements and calculation of metabolic fluxes in co-culture. These metrics are critical to develop a quantitative understanding of interwoven rumen metabolism, as well as the impact of co-culture on polysaccharide degradation and metabolite production. The framework presented here can inspire new methods to probe systems beyond AGF and methanogens. Simple modifications to the method will likely extend its utility to co-cultures with more than two organisms or those grown on solid substrates to facilitate the design and deployment of microbial communities for bioproduction and beyond.

On-Demand Manufacturing Capabilities of Mussels Enable Robust Adhesion to Geometrically Complex Surfaces.

Marine mussels have the remarkable ability to adhere to a variety of natural and artificial surfaces under hostile environmental conditions. Although the molecular composition of mussel adhesives has been well studied, a mechanistic understanding of the physical origins of mussels' impressive adhesive strength remains elusive. Here, we investigated the role of substrate geometry in the adhesive performance of mussels. Experimentally, we created substrates with differing surface properties using 3D printing and laser drilling and introduced these to mussels, which in turn adhered to the engineered surfaces via plaque-thread byssal structures. Tensile testing with in situ imaging was conducted to quantify the adhesion strength of the mussel plaques, and the microstructures of the mechanically deformed plaques were characterized using scanning electron microscopy. Our results reveal that the geometry of the surfaces has no significant impact on the detachment force and the strain, whereas the change in adhesion area leads to a different adhesion stress. Ultrastructural analysis confirms the expected presence of an open-cell foamy network coated with the cuticle. The observed detachment dynamics and failure mechanisms do vary depending on the substrate properties, suggesting the presence of substrate-dependent nonuniform stress distributions at the interface. Together, these results show mussels' remarkable ability to adapt to differing physical conditions and demonstrate the importance of the on-demand and in situ manufacturing of the stiff cuticle and relatively compliant adhesive interlayer. The resultant composite structure avoids the formation of prestress during the formation of the adhesive joint, provides conformability to the surface, and helps compensate for local bending interactions to maintain adhesive strength. Our findings suggest forward design strategies to improve adhesive performance on complex surfaces.

Using Paramecium as a Model for Ciliopathies.

Paramecium has served as a model organism for the studies of many aspects of genetics and cell biology: non-Mendelian inheritance, genome duplication, genome rearrangements, and exocytosis, to name a few. However, the large number and patterning of cilia that cover its surface have inspired extraordinary ultrastructural work. Its swimming patterns inspired exquisite electrophysiological studies that led to a description of the bioelectric control of ciliary motion. A genetic dissection of swimming behavior moved the field toward the genes and gene products underlying ciliary function. With the advent of molecular technologies, it became clear that there was not only great conservation of ciliary structure but also of the genes coding for ciliary structure and function. It is this conservation and the legacy of past research that allow us to use Paramecium as a model for cilia and ciliary diseases called ciliopathies. However, there would be no compelling reason to study Paramecium as this model if there were no new insights into cilia and ciliopathies to be gained. In this review, we present studies that we believe will do this. For example, while the literature continues to state that immotile cilia are sensory and motile cilia are not, we will provide evidence that Paramecium cilia are clearly sensory. Other examples show that while a Paramecium protein is highly conserved it takes a different interacting partner or conducts a different ion than expected. Perhaps these exceptions will provoke new ideas about mammalian systems.

Uncertainty quantification and estimation in differential dynamic microscopy.

Differential dynamic microscopy (DDM) is a form of video image analysis that combines the sensitivity of scattering and the direct visualization benefits of microscopy. DDM is broadly useful in determining dynamical properties including the intermediate scattering function for many spatiotemporally correlated systems. Despite its straightforward analysis, DDM has not been fully adopted as a routine characterization tool, largely due to computational cost and lack of algorithmic robustness. We present statistical analysis that quantifies the noise, reduces the computational order, and enhances the robustness of DDM analysis. We propagate the image noise through the Fourier analysis, which allows us to comprehensively study the bias in different estimators of model parameters, and we derive a different way to detect whether the bias is negligible. Furthermore, through use of Gaussian process regression (GPR), we find that predictive samples of the image structure function require only around 0.5%-5% of the Fourier transforms of the observed quantities. This vastly reduces computational cost, while preserving information of the quantities of interest, such as quantiles of the image scattering function, for subsequent analysis. The approach, which we call DDM with uncertainty quantification (DDM-UQ), is validated using both simulations and experiments with respect to accuracy and computational efficiency, as compared with conventional DDM and multiple particle tracking. Overall, we propose that DDM-UQ lays the foundation for important new applications of DDM, as well as to high-throughput characterization.

Influence of Polarity Change and Photophysical Effects on Photosurfactant-Driven Wetting.

Photosurfactants have shown considerable promise for enabling stimuli-responsive control of the properties and motion of fluid interfaces. Recently, a number of photoswitch chemistries have emerged to tailor the photoresponsive properties of photosurfactants. However, systematic studies investigating how photoresponsive surfactant behavior depends on the photochemical and photophysical properties of the switch remain scarce. In this work, we develop synthetic schemes and surfactant designs to produce a well-controlled library of photosurfactants to comparatively assess the behavior of photoswitch chemistry on interfacial behavior. We employ photoinduced spreading of droplets at fluid interfaces as a model for such studies. We show that although photosurfactant response is largely guided by expected trends with changes in polarity of the photoswitch, interfacial behavior also depends nontrivially and sometimes counter-intuitively on the kinetics and mechanisms of photoswitching, particularly at the interface of two solvents, as well as on complex interactions with other surfactants. Understanding these complexities enables the design of new photosurfactant systems and their optimization toward responsive functions including triggered spreading, dewetting, and destabilization of droplets on solid and fluid surfaces.

Tuning the response of fluid filled hydrogel core-shell structures.

Hydrogels are hydrophilic polymer networks that swell upon submersion in water. Thanks to their bio-compatibility, compliance, and ability to undergo large deformations, hydrogels can be used in a wide variety of applications such as in situ sensors for measuring cell-generated forces and drug delivery vehicles. In this work we investigate the equilibrium mechanical responses that can be achieved with hydrogel-based shells filled with a liquid core. Two types of gel shell geometries are considered - a cylinder and a spherical shell. Each shell is filled with either water or oil and subjected to compressive loading. We illustrate the influence of the shell geometry and the core composition on the mechanical response of the structure. We find that all core-shell structures stiffen under increasing compressive loading due to the load-induced expulsion of water molecules from the hydrogel shell. Furthermore, we show that cylindrical core-shell configurations are stiffer then their spherical equivalents. Interestingly, we demonstrate that the compression of a core-shell structure with an aqueous core leads to the transportation of water molecules from the core into the hydrogel. These results will guide the design of novel core-shell structures with tunable properties and mechanical responses.