Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms

Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover

Muco-ciliary clearance: A review of modelling techniques.

The airways of the human respiratory system are covered by a protective layer, which is known as airway surface liquid (ASL). This layer consists of two relatively distinct sub-layers; a mucus layer (ML), and a periciliary liquid layer (PCL). In addition, the airways are lined with a dense mat of hair-like structures, called cilia, which beat back and forth in a co-ordinated manner and mainly propel the mucus layer. Such interaction between the cilia and mucus is called 'muco-ciliary clearance' (MCC) which is essential to clear the respiratory airways from the inhaled toxic particles deposited on the mucus. The complex nature of lung clearance mechanisms limit the ability to conduct experiments to investigate micro-scale physiological phenomena. As such, modelling techniques are commonly implemented to investigate the effects of biological parameters on the lung muco-ciliary clearance. In the present work, modelling techniques of cilia-ASL interactions - including continuum cilia modelling and discrete cilia modelling - are reviewed and the numerical procedures and level of complexity related to each technique are explained. This is followed by a detailed analysis of the airway surface liquid modelling approaches. In addition, findings of numerical investigations related to the effects of various parameters such as ciliary beat frequency (CBF), mucus rheology, metachronal waves of cilia, surface tension at the PCL-mucus interface, ciliary length, ciliary density, and airway surface liquid depth on the bronchial and tracheal ASL transport are reviewed. This review also explains how these biological parameters can alter the internal power required to perform ciliary beating. Lastly, the main limitations of current numerical works are discussed and significant research directions are brought forward that may be considered in future models to better understand this complex human biological system and its vital clearance mechanism