Complex rheology in biological systems

Bacterial spreading via motility and growth plays a central role in agriculture, biotechnology, the environment, and medicine. These processes are typically studied in the lab in liquid cultures or on flat surfaces. However, many bacterial habitats, eg soils, sediments, and biological gels/tissues, are more complex and crowded 3D spaces. In this talk, Professor Datta will describe his group's work using tools and approaches from soft matter and rheology, imaging, and biophysical modelling to unravel how life in a complex 3D space influences how bacteria spread. He has developed the ability to (i) directly visualise bacteria from the scale of a single cell to that of an entire population, and (ii) 3D-print precisely structured multi-cellular communities, in crowded 3D media more akin to their natural habitats. His experiments using this platform have revealed previously unknown ways in which living in a complex space fundamentally alters how bacteria move and grow, both at the single cell and population scales. Moreover, our results indicate that bacterial colonies can be modelled as 'active fluids' whose rheology is governed by the coupling between cellular motility, growth, and external chemical signals. This provides new ways to predict and control the organisation of bacteria, and other forms of 'active matter', in complex environments more accurately. These findings could also potentially help provide quantitative guidelines for the control of these dynamics in processes ranging from bioremediation and agriculture to drug delivery.

Mucus is a viscoelastic fluid that participates to the protective barrier of many mammals' epithelia. In the airways, together with cilia beating, mucus rheological properties are crucial for lung mucociliary function, and, when impaired, potentially participate to the onset and progression of chronic pulmonary diseases. Human bronchial epithelium (HBE) cultures are highly reliable models to assess non contaminated mucus.

Hallmarks of shear-thinning and elasticity are obtained at the macroscale whereas at the micro-scale, HBE mucus appears as a heterogeneous medium showing an almost Newtonian behaviour in some extended regions and an elastic behaviour and adhesion forces close to boundaries. Finally, Dr Massiera reports an original method to measure mucus microrheology directly on the tissue culture using optical tweezers, showing that mucus gradually varies in rheological response, from an elastic behaviour close to the epithelium to a viscous one far away. Taken together, all these results collectively support a structure composed of a network of elastic adhesive filaments with a large mesh-size, embedded in a very soft gel.

The gastrointestinal (GI) tract actively transports food along different organs to mix it with secretions and break down food particles, which can then be absorbed by the body while waste is eliminated. This involves a variety of biological, chemical, and physical phenomena. Understanding flow phenomena in the GI tract is important for human health, as it can impact drug delivery, the spatiotemporal organisation of the microbiota, and lead to health problems related to GI motility dysfunction. This presentation demonstrates how the gastrointestinal tract handles complex flow by providing two examples: one at the organ scale and the other at the microscopic scale.

The first example aims to demonstrate how complex fluid dynamics modelling of video defecography can aid in diagnosing defecation disorders. A two-dimensional patient-specific simulation was developed based on standard X-ray video defecographies to quantify velocity, pressure, and stress fields during defecation for patients with normal and pathological defecatory function. The results showed that normal defecation involved a proximal–distal pressure gradient from both the anorectal junction and the anal canal, with the flow dominated by shear-thinning viscous properties. Impaired defecations were also simulated and compared to normal defecation, leading to a discussion of critical factors that could aid in effective medical management.

In the second example, the focus is on how fluid is transported and mixed at small scales using microscopic finger-like structures, the so-called villi. A numerical model was developed to simulate flow and mixing due to the active movement of villi. By using the physiological pattern of contractions, it was shown that villi can either transport fluid in the longitudinal direction of the small intestine and/or induce radial mixing. These phenomena are due to a combination of geometric effects (wave propagation) and inertia at moderate Reynolds number.

Classic polymer physics successfully describes most of the polymeric materials we see every day. Yet, it relies on the assumption that polymers do not change topology (or architecture) in time or that if they do alter their morphology, they do so in equilibrium. This assumption spectacularly fails for DNA in vivo, which is constantly topologically re-arranged by ATP-consuming proteins within the cell. Inspired by this, Dr Michieletto's group studies entangled systems of DNA functionalised by certain proteins which can selectively alter DNA’s topology and architecture in time and may expend energy to do so. Solutions of 'topologically active' DNA are a new class of polymeric systems that display unconventional out-of-equilibrium viscoelastic behaviours and can be conveniently realised in vitro.

In this talk Dr Michieletto will present some of his recent work in this field, from the microrheology of entangled DNA undergoing digestion by restriction enzymes, condensation by T4 ligase and loop extrusion by condensin, to the topological gelation of recombining rings and the thinning of DNA solutions by Nucleoid Associated Proteins. He will discuss his current efforts in exploring this new direction using a combination of theory, simulations and experiments spanning a range of length and time-scales from single molecule to bulk rheology. 

Bacterial biofilms generate their own internal stresses by growth and production of exopolysaccharides (EPS). A central question seems to be how these bacterial colonies reconcile the mechanical strength to protect themselves from the access to nutrients. Professor Vermant focuses on colonies which generate a significant amount of EPS. A first challenge he will address is to measure the rheological properties in situ, either macroscopically or using active microrheological measurement. Second, Professor Vermant will discuss the relevance of the rheological properties and their time evolution in the development and transport phenomena within the biofilm.

Biofilms are aggregates of microorganisms in which cells are embedded in a self-secreted matrix of polymeric substances, which protects the microbial community from chemical and mechanical insults, thus favouring its survival and evolutionary success. As a result, biofilms have a crucial impact in environmental, industrial, and medical settings. Despite this, there is a severe lack of understanding of how the environment shapes biofilms’ physico-chemical properties and, in turn, how their characteristics drive their response to environmental conditions. 

Dr Secchi investigates how environmental conditions drive biofilm assembly and the emergence of distinctive morphological and rheological properties. In particular, she focuses on fluid flow, given its ubiquities in the aquatic habitats where biofilms are found. Flow can influence several stages of biofilm formation, starting from surface colonisation. On curved surfaces, flow can promote the formation of colonisation hotspots, which lately impact biofilm formation. Surface geometry, flow shear, fluid rheology, and bacterial phenotype are the parameters controlling surface colonisation. She will also show that during biofilm maturation in porous systems, the interplay between biological functions, ie growth, and physics mechanisms, ie flow shear stress, controls biofilm morphology, rheology, and ultimately affects the physiological protective function of biofilms. By shedding light on this interplay, we can control biofilm development, showing the prominent role that physics can play in developing novel antifouling strategies. 

Cytoskeleton plays a critical role in the cell shape, locomotion, growth, and division in response to the surrounding environment. Since it may be affected by diseases and drugs, quantification of the rheological cell properties can help understanding their impact. In this study, the breast cancer cell line MCF-7 was treated with different concentrations of microtubule-active drugs. The cell vitality over 90% was possible to obtain in the concentration range far beyond the cytotoxicity level by treating the cells with low concentration of hydroxyurea prior to the drugs treatment. The stiffness of the drug treated cells in a monolayer was measured by a modified narrow-gap rheometer. With a precision for its gap error better than ±0.4μm, it allows detecting in oscillation the viscoelastic response of cells fixed to both rheometer plates at gap widths of micrometer scale down to the linear viscoelastic regime. With known cell coverage, the average cell moduli can be determined from single experimental runs. Studying the impact of bubbles and dust shows that these error sources have no significant impact on our data. Ms Lee found that the gap width has a strong impact on normal force and storage and loss moduli. She observed two regimes depending on the gap width, apparently caused by the cells’ nuclei and cytoskeleton. Yet, no clear impact of the microtubule-active drugs was observed in the linear viscoelastic range.