Biological Fluid Mechanics Under the Microscope: A Tribute to John Blake

John Blake (1947--2016) was a leader in fluid mechanics, his two principal areas of expertise being biological fluid mechanics on microscopic scales and bubble dynamics. He produced leading research and mentored others in both Australia, his home country, and the UK, his adopted home. This article reviews John Blake's contributions in biological fluid mechanics, as well as giving the author's personal viewpoint as one of the many graduate students and researchers who benefitted from his supervision, guidance and inspiration. The key topics from biological mechanics discussed are: `squirmer' models of protozoa, the method of images in Stokes flow and the `blakelet' solution, discrete cilia modelling via slender body theory, physiological flows in respiration and reproduction, blinking stokeslets in microorganism feeding, human sperm motility, and embryonic nodal cilia.Comment: 23 pages, 11 figures. Submitted versio

Realizing the physics of motile cilia synchronization with driven colloids

Cilia and flagella in biological systems often show large scale cooperative behaviors such as the synchronization of their beats in "metachronal waves". These are beautiful examples of emergent dynamics in biology, and are essential for life, allowing diverse processes from the motility of eukaryotic microorganisms, to nutrient transport and clearance of pathogens from mammalian airways. How these collective states arise is not fully understood, but it is clear that individual cilia interact mechanically,and that a strong and long ranged component of the coupling is mediated by the viscous fluid. We review here the work by ourselves and others aimed at understanding the behavior of hydrodynamically coupled systems, and particularly a set of results that have been obtained both experimentally and theoretically by studying actively driven colloidal systems. In these controlled scenarios, it is possible to selectively test aspects of the living motile cilia, such as the geometrical arrangement, the effects of the driving profile and the distance to no-slip boundaries. We outline and give examples of how it is possible to link model systems to observations on living systems, which can be made on microorganisms, on cell cultures or on tissue sections. This area of research has clear clinical application in the long term, as severe pathologies are associated with compromised cilia function in humans.Comment: 31 pages, to appear in Annual Review of Condensed Matter Physic

Characterization of an in vitro 3D Human Small Airway Epithelia model for the application of integrated strategies in inhaled drug development

Drug Inhalation is one of the most effective administration routes; in fact, first pass metabolism is bypassed, rapid action onset is enabled and drug doses can be kept relatively low compared to other administration routes. The most recent 3D in vitro models allow to mimic some of the pulmonary tissue functionalities. These models reproduce the air-liquid interface, with beating cilia and mucus production, since different types of cells are present. Therefore, these models could be possibly applied to multi-disciplinary investigations following liquid, dry powder or aerosol treatment. In this thesis, an integrated strategy is proposed, with the aim to increase the rate of success in the drug candidate selection phase. Ideally, safety data should be integrated with early pharmacokinetics (PK) and efficacy indications in order to increase chances to select the candidate with the highest safety margins. With this ambitious objective in mind, a human-based 3D model were evaluated as model for the toxicity assessment and drug permeability evaluation. In particular, a commercially available 3D respiratory model SmallAir\u2122 has been qualified for: a) sensibility and specificity in the evaluation of lung toxicity potential of new compounds; b) permeability to test drug transport through tissues for formulation screening purposes; c) quantitative cytokine secretion on cell supernatant; d) cilia beating and muco-ciliary clearance evaluation by image analysis. These tests performed on a human tissue could provide more reliable results also because all tests were performed in the same model and this could be helpful in data integration. This approach could allow to fill gaps in drug discovery for human-relevant screening of new chemical entities (NCEs), best formulation selection, including physiochemical equivalence evaluation generic drug development. In vitro and in silico data can be helpful in predicting PK and toxicity profiles prior to preclinical and clinical studies. This allows to respect the 3Rs principle of replacement, reduction and refinement of in vivo studies. The proposed integrated testing strategy (ITS) has the potential to reduce the attrition in drug development, to optimize the inhaled formulation, to screen compounds for candidate selection and to reduce in vivo studies.For the toxicity tests, well-known respiratory toxic compound were tested both in the SmallAir\u2122 model and in the A549 cell line model. On the basis of results, the SmallAir\u2122 model seemed to be less sensitive than A549, probably due to the 3D structure physiological features. Cilia beating and mucus production can indeed protect the cells from the toxic effect miming the in vivo response. For the permeability study, well-known inhalation compounds with very different permeability values were evaluated both in SmallAir\u2122 model and in the standard Caco2 cell model. For low and high permeable compounds results obtained were comparable in the two test considered systems. The most evident difference was observed with medium permeable compounds, suggesting that the SmallAir\u2122 model should express different efflux pumps on their surface form the standard Caco2 cell model. The SmallAir\u2122 model was also evaluated as in vitro model for the inflammatory mediators assessment. The treatment with TGF-\u3b2 allowed to confirm the activation of the signalling via Smad2 while, inconclusive results were obtained with regards to cytokines and ROS release following Bleomycin treatment. The SmallAir\u2122 model was finally evaluated as in vitro model for the assessment of the Muco-ciliary Clearance (MCC). Results obtained in this project, showed that the SmallAir\u2122 can be a promising model to assess the MCC in vitro after treatment with compound acting on ATP release and Cystic fibrosis transmembrane conductance Inhibitor-172 (CFTR172inh). More test considering different compound, study design and end points has to be conducted, in order to identify a human relevant in vitro lung model to be applied in many fields of analysis

A viscoelastic traction layer model of mucociliary flow

A new mathematical model of the transport of mucus and periciliary liquid (PCL) in the airways by cilia is presented. Mucus is represented by a linearly viscoelastic fluid, the mat of cilia is modelled as an ‘active porous medium.’ The propulsive effect of the cilia is modelled by a time-dependent force acting in a shear-thinned ‘traction layer’ between the mucus and the PCL. The effects of surface and interface tension are modelled by constraining the mucus free surface and mucus–PCL interface to be flat. It is assumed that the epithelium is impermeable to fluid. Using Fourier series, the system is converted into ODEs and solved numerically. We calculate values for mean mucus speed close to those observed by Matsui et~al. [{J. Clin. Invest.}, 102(6):1125’1131, 1998], (~40 μms−1). We obtain more detail regarding the dynamics of the flow and the nonlinear relationships between physical parameters in healthy and diseased states than in previously published models. Pressure gradients in the PCL caused by interface and surface tension are vital to ensuring efficient transport of mucus, and the role of the mucus–PCL interface appears to be to support such pressure gradients, ensuring efficient transport. Mean transport of PCL is found to be very small, consistent with previous analyses, providing insight into theories regarding the normal tonicity of PCL

Nasal drug delivery devices: characteristics and performance in a clinical perspective—a review

Nasal delivery is the logical choice for topical treatment of local diseases in the nose and paranasal sinuses such as allergic and non-allergic rhinitis and sinusitis. The nose is also considered an attractive route for needle-free vaccination and for systemic drug delivery, especially when rapid absorption and effect are desired. In addition, nasal delivery may help address issues related to poor bioavailability, slow absorption, drug degradation, and adverse events in the gastrointestinal tract and avoids the first-pass metabolism in the liver. However, when considering nasal delivery devices and mechanisms, it is important to keep in mind that the prime purpose of the nasal airway is to protect the delicate lungs from hazardous exposures, not to serve as a delivery route for drugs and vaccines. The narrow nasal valve and the complex convoluted nasal geometry with its dynamic cyclic physiological changes provide efficient filtration and conditioning of the inspired air, enhance olfaction, and optimize gas exchange and fluid retention during exhalation. However, the potential hurdles these functional features impose on efficient nasal drug delivery are often ignored. With this background, the advantages and limitations of existing and emerging nasal delivery devices and dispersion technologies are reviewed with focus on their clinical performance. The role and limitations of the in vitro testing in the FDA guidance for nasal spray pumps and pressurized aerosols (pressurized metered-dose inhalers) with local action are discussed. Moreover, the predictive value and clinical utility of nasal cast studies and computer simulations of nasal airflow and deposition with computer fluid dynamics software are briefly discussed. New and emerging delivery technologies and devices with emphasis on Bi-Directional™ delivery, a novel concept for nasal delivery that can be adapted to a variety of dispersion technologies, are described in more depth

A boundary element regularised Stokeslet method applied to cilia and flagella-driven flow

A boundary element implementation of the regularised Stokeslet method of Cortez is applied to cilia and flagella-driven flows in biology. Previously-published approaches implicitly combine the force discretisation and the numerical quadrature used to evaluate boundary integrals. By contrast, a boundary element method can be implemented by discretising the force using basis functions, and calculating integrals using accurate numerical or analytic integration. This substantially weakens the coupling of the mesh size for the force and the regularisation parameter, and greatly reduces the number of degrees of freedom required. When modelling a cilium or flagellum as a one-dimensional filament, the regularisation parameter can be considered a proxy for the body radius, as opposed to being a parameter used to minimise numerical errors. Modelling a patch of cilia, it is found that: (1) For a fixed number of cilia, reducing cilia spacing reduces transport. (2) For fixed patch dimension, increasing cilia number increases the transport, up to a plateau at $9\times 9$ cilia. Modelling a choanoflagellate cell it is found that the presence of a lorica structure significantly affects transport and flow outside the lorica, but does not significantly alter the force experienced by the flagellum.Comment: 20 pages, 7 figures, postprin

A physiologically-motivated compartment-based model of the effect of inhaled hypertonic saline on mucociliary clearance and liquid transport in cystic fibrosis

Background: Cystic Fibrosis (CF) lung disease is characterized by liquid hyperabsorption, airway surface dehydration, and impaired mucociliary clearance (MCC). Herein, we present a compartment-based mathematical model of the airway that extends the resolution of functional imaging data. Methods: Using functional imaging data to inform our model, we developed a system of mechanism-motivated ordinary differential equations to describe the mucociliary clearance and absorption of aerosolized radiolabeled particle and small molecules probes from human subjects with and without CF. We also utilized a novel imaging metric in vitro to gauge the fraction of airway epithelial cells that have functional ciliary activity. Results: This model, and its incorporated kinetic rate parameters, captures the MCC and liquid dynamics of the hyperabsorptive state in CF airways and the mitigation of that state by hypertonic saline treatment. Conclusions: We postulate, based on the model structure and its ability to capture clinical patient data, that patients with CF have regions of airway with diminished MCC function that can be recruited with hypertonic saline treatment. In so doing, this model structure not only makes a case for durable osmotic agents used in lung-region specific treatments, but also may provide a possible clinical endpoint, the fraction of functional ciliated airway

Computational projection of virion transmission rates to the lower airway from the initial sars-cov-2 infection at the nasopharynx

https://www.rhinologyonline.org/Rhinology_online_issues/manuscript_240.pdfAccepted manuscrip

Synthesis of pH responsive carriers for pulmonary drug delivery of anti-tuberculosis therapeutics: mesoporous silica nanoparticles and gelatin nanoparticles

Pulmonary drug delivery has historically been used as a route for delivery of therapeutics for respiratory disease management. However, while there are many advantages, there are also some serious limitations, arising mostly from the physical aspects of the inhaler devices. This is more profound when the devices are the driving force for controlling particle size generation, which results in non-uniform particles that end up being swallowed/wasted/expelled. One promising solution to overcome this limitation is to pre-formulate nano/microscale particles with a high degree of manufacturing control. Nanomedicine has advanced such that there are already several nanoparticle formulations commercially available. In the case of tuberculosis treatment, there is an opportunity not only to examine the use of nanoparticles for inhalation therapy, but to take advantage of the fact that the physiochemical environment of diseased tissue is significantly different to health lung tissue (lower pH and increased enzyme concentrations). We formulated two series of nanoparticles, whose design included moieties that could respond to pH and enzymes. To address variability, a Box-Behnken statistical approach was followed to construct mesoporous silica nanoparticles. These “hard nanoparticles” can entrap both lipophilic and hydrophilic drugs and were coated with a pH-sensitive hydrazone linker. It was observed that pH, calcination temperature and ratio of water to silica source played the greatest role, not only in controlling the physicochemical properties of the nanoparticles but also the drug release rate. A second series of nanoparticles were synthesized based on gelatin. This was done partly to add support the comparison of hard (inorganic silica) versus soft, organic particles, but also to enable enzymatic degradation and drug release. Again, diseased lung tissue expresses increased concentrations of gelatinase enzymes that could be used to stimulate drug release at the site of the disease. In addition, it was observed that the non-ionic surfactant C12E10 could interact with the protein via hydrophobic interactions thus affecting the gelatin folding. The folding states affected crosslinking with the pH responsive linker, which in turn affected the rate of drug release. To support the synthetic work, we sought to develop a unique 3D lung model directly from MRI data of tuberculosis infected lungs. This would not only permit the evaluation of our nanoparticles but could be used as a proxy for in-vivo studies in future to predict lung deposition in diseased lung. Thus, this study shows that it is possible to synthesize pH and enzyme sensitive nanoparticles for pulmonary drug delivery in the treatment and management of pulmonary tuberculosis. These particles could be loaded with either hydrophobic or hydrophilic drugs and their distribution in the airway modelled using an in-silico 3D model based on real data. Further development and verification of these results should improve treatment for pulmonary diseases and conditions such as tuberculosis. This is especially urgent in the face of multi-drug resistance and poor side effects profiles for current treatment