Defining the role of neutrophils in the lung during infection: Implications for tuberculosis disease.

Neutrophils are implicated in the pathogenesis of many diseases involving inflammation. Neutrophils are also critical to host defence and have a key role in the innate immune response to infection. Despite their efficiencies against a wide range of pathogens however, their ability to contain and combat Mycobacterium tuberculosis (Mtb) in the lung remains uncertain and contentious. The host response to Mtb infection is very complex, involving the secretion of various cytokines and chemokines from a wide variety of immune cells, including neutrophils, macrophages, monocytes, T cells, B cells, NK cells and dendritic cells. Considering the contributing role neutrophils play in the advancement of many diseases, understanding how an inflammatory microenvironment affects neutrophils, and how neutrophils interact with other immune cells, particularly in the context of the infected lung, may aid the design of immunomodulatory therapies. In the current review, we provide a brief overview of the mechanisms that underpin pathogen clearance by neutrophils and discuss their role in the context of Mtb and non-Mtb infection. Next, we examine the current evidence demonstrating how neutrophils interact with a range of human and non-human immune cells and how these interactions can differentially prime, activate and alter a repertoire of neutrophil effector functions. Furthermore, we discuss the metabolic pathways employed by neutrophils in modulating their response to activation, pathogen stimulation and infection. To conclude, we highlight knowledge gaps in the field and discuss plausible novel drug treatments that target host neutrophil metabolism and function which could hold therapeutic potential for people suffering from respiratory infections.

Applications of mechanistic modelling to clinical and experimental immunology: an emerging technology to accelerate immunotherapeutic discovery and development.

The application of in-silico modelling is beginning to emerge as a key methodology to advance our understanding of mechanisms of disease pathophysiology and related drug action, and in the design of experimental medicine and clinical studies. From this perspective, we will present a non-technical discussion of a small number of recent and historical applications of mathematical, statistical and computational modelling to clinical and experimental immunology. We focus specifically upon mechanistic questions relating to human viral infection, tumour growth and metastasis and T cell activation. These exemplar applications highlight the potential of this approach to impact upon human immunology informed by ever-expanding experimental, clinical and 'omics' data. Despite the capacity of mechanistic modelling to accelerate therapeutic discovery and development and to de-risk clinical trial design, it is not utilized widely across the field. We outline ongoing challenges facing the integration of mechanistic modelling with experimental and clinical immunology, and suggest how these may be overcome. Advances in key technologies, including multi-scale modelling, machine learning and the wealth of 'omics' data sets, coupled with advancements in computational capacity, are providing the basis for mechanistic modelling to impact on immunotherapeutic discovery and development during the next decade.

Factors that drive the increasing use of FFPE tissue in basic and translational cancer research.

The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.

Basal Tear Osmolarity as a metric to estimate body hydration and dry eye severity.

The osmolarities of various bodily fluids, including tears, saliva and urine, have been used as indices of plasma osmolality, a measure of body hydration, while tear osmolarity is used routinely in dry eye diagnosis, the degree of tear hyperosmolarity providing an index of disease severity. Systemic dehydration, due to inadequate water intake or excessive water loss is common in the elderly population, has a high morbidity and may cause loss of life. Its diagnosis is often overlooked and there is a need to develop a simple, bedside test to detect dehydration in this population. We hypothesize that, in the absence of tear evaporation and with continued secretion, mixing and drainage of tears, tear osmolarity falls to a basal level that is closer to that of the plasma than that of a tear sample taken in open eye conditions. We term this value the Basal Tear Osmolarity (BTO) and propose that it may be measured in tear samples immediately after a period of evaporative suppression. This value will be particular to an individual and since plasma osmolarity is controlled within narrow limits, it is predicted that it will be stable and have a small variance. It is proposed that the BTO, measured immediately after a defined period of eye closure, can provide a new metric in the diagnosis of systemic dehydration and a yardstick against which to gauge the severity of dry eye disease.

Mechanical Cell-Cell Communication in Fibrous Networks: The Importance of Network Geometry.

Cells contracting in extracellular matrix (ECM) can transmit stress over long distances, communicating their position and orientation to cells many tens of micrometres away. Such phenomena are not observed when cells are seeded on substrates with linear elastic properties, such as polyacrylamide (PA) gel. The ability for fibrous substrates to support far reaching stress and strain fields has implications for many physiological processes, while the mechanical properties of ECM are central to several pathological processes, including tumour invasion and fibrosis. Theoretical models have investigated the properties of ECM in a variety of network geometries. However, the effects of network architecture on mechanical cell-cell communication have received little attention. This work investigates the effects of geometry on network mechanics, and thus the ability for cells to communicate mechanically through different networks. Cell-derived displacement fields are quantified for various network geometries while controlling for network topology, cross-link density and micromechanical properties. We find that the heterogeneity of response, fibre alignment, and substrate displacement fields are sensitive to network choice. Further, we show that certain geometries support mechanical communication over longer distances than others. As such, we predict that the choice of network geometry is important in fundamental modelling of cell-cell interactions in fibrous substrates, as well as in experimental settings, where mechanical signalling at the cellular scale plays an important role. This work thus informs the construction of theoretical models for substrate mechanics and experimental explorations of mechanical cell-cell communication.

Modeling Longitudinal Preclinical Tumor Size Data to Identify Transient Dynamics in Tumor Response to Antiangiogenic Drugs.

Experimental evidence suggests that antiangiogenic therapy gives rise to a transient window of vessel normalization, within which the efficacy of radiotherapy and chemotherapy may be enhanced. Preclinical experiments that measure components of vessel normalization are invasive and expensive. We have developed a mathematical model of vascular tumor growth from preclinical time-course data in a breast cancer xenograft model. We used a mixed-effects approach for model parameterization, leveraging tumor size data to identify a period of enhanced tumor growth that could potentially correspond to the transient window of vessel normalization. We estimated the characteristics of the window for mice treated with an anti-VEGF antibody (bevacizumab) or with a bispecific anti-VEGF/anti-angiopoietin-2 antibody (vanucizumab). We show how the mathematical model could theoretically be used to predict how to coordinate antiangiogenic therapy with radiotherapy or chemotherapy to maximize therapeutic effect, reducing the need for preclinical experiments that directly measure vessel normalization parameters.

Vascular phenotype identification and anti-angiogenic treatment recommendation: A pseudo-multiscale mathematical model of angiogenesis.

The development of anti-angiogenic drugs for cancer therapy has yielded some promising candidates, but novel approaches for interventions to angiogenesis have led to disappointing results. In addition, there is a shortage of biomarkers that are predictive of response to anti-angiogenic treatments. Consequently, the complex biochemical and physiological basis for tumour angiogenesis remains incompletely understood. We have adopted a mathematical approach to address these issues, formulating a spatially averaged multiscale model that couples the dynamics of VEGF, Ang1, Ang2 and PDGF, with those of mature and immature endothelial cells and pericyte cells. The model reproduces qualitative experimental results regarding pericyte coverage of vessels after treatment by anti-Ang2, anti-VEGF and combination anti-VEGF/anti-Ang2 antibodies. We used the steady state behaviours of the model to characterise angiogenic and non-angiogenic vascular phenotypes, and used mechanistic perturbations representing hypothetical anti-angiogenic treatments to generate testable hypotheses regarding transitions to non-angiogenic phenotypes that depend on the pre-treatment vascular phenotype. Additionally, we predicted a synergistic effect between anti-VEGF and anti-Ang2 treatments when applied to an immature pre-treatment vascular phenotype, but not when applied to a normalised angiogenic pre-treatment phenotype. Based on these findings, we conclude that changes in vascular phenotype are predicted to be useful as an experimental biomarker of response to treatment. Further, our analysis illustrates the potential value of non-spatial mathematical models for generating tractable predictions regarding the action of anti-angiogenic therapies.

The sensitivity of Turing self-organization to biological feedback delays: 2D models of fish pigmentation.

Turing morphogen models have been extensively explored in the context of large-scale self-organization in multicellular biological systems. However, reconciling the detailed biology of morphogen dynamics, while accounting for time delays associated with gene expression, reveals aberrant behaviours that are not consistent with early developmental self-organization, especially the requirement for exquisite temporal control. Attempts to reconcile the interpretation of Turing's ideas with an increasing understanding of the mechanisms driving zebrafish pigmentation suggests that one should reconsider Turing's model in terms of pigment cells rather than morphogens (Nakamasu et al., 2009, PNAS, 106: , 8429-8434; Yamaguchi et al., 2007, PNAS, 104: , 4790-4793). Here the dynamics of pigment cells is subject to response delays implicit in the cell cycle and apoptosis. Hence we explore simulations of fish skin patterning, focussing on the dynamical influence of gene expression delays in morphogen-based Turing models and response delays for cell-based Turing models. We find that reconciling the mechanisms driving the behaviour of Turing systems with observations of fish skin patterning remains a fundamental challenge.

Investigating the Turing conditions for diffusion-driven instability in the presence of a binding immobile substrate.

Turing's diffusion-driven instability for the standard two species reaction-diffusion system is only achievable under well-known and rather restrictive conditions on both the diffusion rates and the kinetic parameters, which necessitates the pairing of a self-activator with a self-inhibitor. In this study we generalize the standard two-species model by considering the case where the reactants can bind to an immobile substrate, for instance extra-cellular matrix, and investigate the influence of this dynamics on Turing's diffusion-driven instability. Such systems have been previously studied on the grounds that binding of the self-activator to a substrate may effectively reduce its diffusion rate and thus induce a Turing instability for species with equal diffusion coefficients, as originally demonstrated by Lengyel and Epstein (1992) under the assumption that the bound state dynamics occurs on a fast timescale. We, however, analyse the full system without any separation of timescales and demonstrate that the full system also allows a relaxation of the standard constraints on the reaction kinetics for the Turing instability, increasing the type of interactions that could give rise to spatial patterning. In particular, we show that two self-activators can undertake a diffusively driven instability in the presence of a binding immobile substrate, highlighting that the interactions required of a putative biological Turing instability need not be associated with a self-activator-self-inhibitor morphogen pair.

The mechanics of hyperactivation in adhered human sperm.

Hyperactivation is an important phenomenon exhibited by mammalian sperm during the process of acquiring fertilization capacity. The majority of studies have focused on incubation-induced hyperactivation in non-human species, which typically differ in size, shape, and are more homogeneous than human sperm. We develop an alternative approach via drug-induction, using high-speed imaging and analysis of same-cell changes in the flagellar movement of adhered cells. Following stimulation with 4-aminopyridine, approximately two-thirds (21 of 34) of the cells analysed exhibited a waveform with a single characteristic frequency; in all cases, the frequency was lower than before stimulation. The remaining cells (13 of 34) exhibited a more complex motility with multiple-frequency modes. The lowest mode in all cases was lower than the frequency prior to stimulation. Flagellar bending increased in all cells following stimulation and was significantly greater in the multiple-frequency responders. Despite the increased bending, time-averaged hydrodynamic power dissipation decreased significantly when assessed across all cells, the effect being significantly greater in the multiple-frequency responders than single frequency. These results reveal the heterogeneity of responses of human sperm to a hyperactivating stimulus, the methodology being potentially useful for assessing dynamic responses to stimuli in human sperm, and physiological selection of cells for assisted reproduction.

Meniscal tear film fluid dynamics near Marx's line.

Extensive studies have explored the dynamics of the ocular surface fluid, though theoretical investigations are typically limited to the use of the lubrication approximation, which is not guaranteed to be uniformly valid a-priori throughout the tear meniscus. However, resolving tear film behaviour within the meniscus and especially its apices is required to characterise the flow dynamics where the tear film is especially thin, and thus most susceptible to evaporatively induced hyperosmolarity and subsequent epithelial damage. Hence, we have explored the accuracy of the standard lubrication approximation for the tear film by explicit comparisons with the 2D Navier-Stokes model, considering both stationary and moving eyelids. Our results demonstrate that the lubrication model is qualitatively accurate except in the vicinity of the eyelids. In particular, and in contrast to lubrication theory, the solution of the full Navier-Stokes equations predict a distinct absence of fluid flow, and thus convective mixing in the region adjacent to the tear film contact line. These observations not only support emergent hypotheses concerning the formation of Marx's line, a region of epithelial cell staining adjacent to the contact line on the eyelid, but also enhance our understanding of the pathophysiological consequences of the flow profile near the tear film contact line.

Modelling biological invasions: Individual to population scales at interfaces.

Extracting the population level behaviour of biological systems from that of the individual is critical in understanding dynamics across multiple scales and thus has been the subject of numerous investigations. Here, the influence of spatial heterogeneity in such contexts is explored for interfaces with a separation of the length scales characterising the individual and the interface, a situation that can arise in applications involving cellular modelling. As an illustrative example, we consider cell movement between white and grey matter in the brain which may be relevant in considering the invasive dynamics of glioma. We show that while one can safely neglect intrinsic noise, at least when considering glioma cell invasion, profound differences in population behaviours emerge in the presence of interfaces with only subtle alterations in the dynamics at the individual level. Transport driven by local cell sensing generates predictions of cell accumulations along interfaces where cell motility changes. This behaviour is not predicted with the commonly used Fickian diffusion transport model, but can be extracted from preliminary observations of specific cell lines in recent, novel, cryo-imaging. Consequently, these findings suggest a need to consider the impact of individual behaviour, spatial heterogeneity and especially interfaces in experimental and modelling frameworks of cellular dynamics, for instance in the characterisation of glioma cell motility.

Modelling Aedes aegypti mosquito control via transgenic and sterile insect techniques: endemics and emerging outbreaks.

The invasion of pest insects often changes or destroys a native ecosystem, and can result in food shortages and disease endemics. Issues such as the environmental effects of chemical control methods, the economic burden of maintaining control strategies and the risk of pest resistance still remain, and mosquito-borne diseases such as malaria and dengue fever prevail in many countries, infecting over 100 million worldwide in 2010. One environmentally friendly method for mosquito control is the Sterile Insect Technique (SIT). This species-specific method of insect control relies on the mass rearing, sterilization and release of large numbers of sterile insects. An alternative transgenic method is the Release of Insects carrying a Dominant Lethal (RIDL). Our objective is to consider contrasting control strategies for two invasive scenarios via SIT and RIDL: an endemic case and an emerging outbreak. We investigate how the release rate and size of release region influence both the potential for control success and the resources needed to achieve it, under a range of conditions and control strategies, and we discuss advantageous strategies with respect to reducing the release resources and strategy costs (in terms of control mosquito numbers) required to achieve complete eradication of wild-type mosquitoes.

Coupling fluid and solute dynamics within the ocular surface tear film: a modelling study of black line osmolarity.

We present a mathematical model describing the spatial distribution of tear film osmolarity across the ocular surface of a human eye during one blink cycle, incorporating detailed fluid and solute dynamics. Based on the lubrication approximation, our model comprises three coupled equations tracking the depth of the aqueous layer of the tear film, the concentration of the polar lipid, and the concentration of physiological salts contained in the aqueous layer. Diffusive boundary layers in the salt concentration occur at the thinnest regions of the tear film, the black lines. Thus, despite large Peclet numbers, diffusion ameliorates osmolarity around the black lines, but nonetheless is insufficient to eliminate the build-up of solute in these regions. More generally, a heterogeneous distribution of solute concentration is predicted across the ocular surface, indicating that measurements of lower meniscus osmolarity are not globally representative, especially in the presence of dry eye. Vertical saccadic eyelid motion can reduce osmolarity at the lower black line, raising the prospect that select eyeball motions more generally can assist in alleviating tear film hyperosmolarity. Finally, our results indicate that measured evaporative rates will induce excessive hyperosmolarity at the black lines, even for the healthy eye. This suggests that further evaporative retardation at the black lines, for instance due to the cellular glycocalyx at the ocular surface or increasing concentrations of mucus, will be important for controlling hyperosmolarity as the black line thins.

Re-evaluating the use of Voronoi Tessellations in the assessment of oxygen supply from capillaries in muscle.

The ability to characterise capillary supply plays a key role in developing effective therapeutic interventions for numerous pathological conditions, such as capillary loss in skeletal or cardiac muscle. However, quantifying capillary supply is fraught with difficulties. Averaged measures such as capillary density or mean inter-capillary distance cannot account for the local geometry of the underlying capillary distribution, and thus can only highlight a tissue wide, global hypoxia. Detailed tissue geometry, such as muscle fibre size, has been incorporated into indices of capillary supply by considering the distribution of Voronoi tessellations generated from capillary locations in a plane perpendicular to muscle fibre orientation, implicitly assuming that each Voronoi polygon represents the area of supply of its enclosed capillary. Using a modelling framework to assess the capillary supply capacity under maximal sustainable conditions in muscle, we theoretically demonstrate that Voronoi tessellations often provide an accurate representation of the regions supplied by each capillary. However, we highlight that this use of Voronoi tessellations is inappropriate and inaccurate in the presence of extensive capillary rarefaction and pathological variations in oxygen tension of different capillaries. In such cases, oxygen flux trapping regions are developed to provide a more general representation of the capillary supply regions, in particular incorporating the additional influences of heterogeneity that are absent in the consideration of Voronoi tessellations.

Modelling a tethered mammalian sperm cell undergoing hyperactivation.

The beat patterns of mammalian sperm flagella can be categorised into two different types. The first involves symmetric waves propagating down the flagellum with a net linear propulsion of the sperm cell. The second, hyperactive, waveform is classified by vigorous asymmetric waves of higher amplitude, lower wavenumber and frequency propagating down the flagellum resulting in highly curved trajectories. The latter beat pattern is part of the capacitation process whereby sperm prepare for the prospective penetration of the zona pellucida and fusion with the egg. Hyperactivation is often observed to initiate as sperm escape from epithelial and ciliary bindings formed within the isthmic regions of the female oviducts, leading to a conjecture in the literature that this waveform is mechanically important for sperm escape. Hence, we explore the mechanical effects of hyperactivation on a tethered sperm, focussing on a Newtonian fluid. Using a resistive force theory model we demonstrate that hyperactivation can indeed generate forces that pull the sperm away from a tethering point and consequently a hyperactivated sperm cell bound to an epithelial surface need not always be pushed by its flagellum. More generally, directions of the forces generated by tethered flagella are insensitive to reductions in beat frequency and the detailed flagellar responses depend on the nature of the binding at the tethering point. Furthermore, waveform asymmetry and amplitude increases enhance the tendency for a tethered flagellum to start tugging on its binding. The same is generally predicted to be true for reductions in the wavenumber of the flagellum beat, but not universally so, emphasising the dynamical complexity of flagellar force generation. Finally, qualitative observations drawn from experimental data of human sperm bound to excised female reproductive tract are also presented and are found to be consistent with the theoretical predictions.

Predicting the safety and efficacy of buffer therapy to raise tumour pHe: an integrative modelling study.

BACKGROUND: Clinical positron emission tomography imaging has demonstrated the vast majority of human cancers exhibit significantly increased glucose metabolism when compared with adjacent normal tissue, resulting in an acidic tumour microenvironment. Recent studies demonstrated reducing this acidity through systemic buffers significantly inhibits development and growth of metastases in mouse xenografts. METHODS: We apply and extend a previously developed mathematical model of blood and tumour buffering to examine the impact of oral administration of bicarbonate buffer in mice, and the potential impact in humans. We recapitulate the experimentally observed tumour pHe effect of buffer therapy, testing a model prediction in vivo in mice. We parameterise the model to humans to determine the translational safety and efficacy, and predict patient subgroups who could have enhanced treatment response, and the most promising combination or alternative buffer therapies. RESULTS: The model predicts a previously unseen potentially dangerous elevation in blood pHe resulting from bicarbonate therapy in mice, which is confirmed by our in vivo experiments. Simulations predict limited efficacy of bicarbonate, especially in humans with more aggressive cancers. We predict buffer therapy would be most effectual: in elderly patients or individuals with renal impairments; in combination with proton production inhibitors (such as dichloroacetate), renal glomular filtration rate inhibitors (such as non-steroidal anti-inflammatory drugs and angiotensin-converting enzyme inhibitors), or with an alternative buffer reagent possessing an optimal pK of 7.1-7.2. CONCLUSION: Our mathematical model confirms bicarbonate acts as an effective agent to raise tumour pHe, but potentially induces metabolic alkalosis at the high doses necessary for tumour pHe normalisation. We predict use in elderly patients or in combination with proton production inhibitors or buffers with a pK of 7.1-7.2 is most promising.

Comment on the article by J. Elgeti, U. B. Kaupp, and G. Gompper: hydrodynamics of sperm cells near surfaces.

A recent study by Elgeti et al. used multiparticle collision dynamics to simulate a long-standing problem: the approach of sperm to surfaces, and subsequent accumulation. The authors highlight differences in their predictions with those of the earlier Stokes flow simulations of Smith et al. attributing the differences to methodological flaws in the earlier article. In this Comment, we discuss the criticisms leveled in detail, and review some recently published work that shows how species-specific details of cell morphology provides a more likely explanation for the differing predictions of the two studies. We also highlight experimental work that supports the study of Smith et al.

The dynamics of Turing patterns for morphogen-regulated growing domains with cellular response delays.

Since its conception in 1952, the Turing paradigm for pattern formation has been the subject of numerous theoretical investigations. Experimentally, this mechanism was first demonstrated in chemical reactions over 20 years ago and, more recently, several examples of biological self-organisation have also been implicated as Turing systems. One criticism of the Turing model is its lack of robustness, not only with respect to fluctuations in the initial conditions, but also with respect to the inclusion of delays in critical feedback processes such as gene expression. In this work we investigate the possibilities for Turing patterns on growing domains where the morphogens additionally regulate domain growth, incorporating delays in the feedback between signalling and domain growth, as well as gene expression. We present results for the proto-typical Schnakenberg and Gierer-Meinhardt systems: exploring the dynamics of these systems suggests a reconsideration of the basic Turing mechanism for pattern formation on morphogen-regulated growing domains as well as highlighting when feedback delays on domain growth are important for pattern formation.