Spatiotemporal dynamics of insulitis in human Type 1 diabetes

This is the final version of the article. Available from the publisher via the DOI in this record.Type 1 diabetes (T1D) is an auto-immune disease characterised by the selective destruction of the insulin secreting beta cells in the pancreas during an inflammatory phase known as insulitis. Patients with T1D are typically dependent on the administration of externally provided insulin in order to manage blood glucose levels. Whilst technological developments have significantly improved both the life expectancy and quality of life of these patients, an understanding of the mechanisms of the disease remains elusive. Animal models, such as the NOD mouse model, have been widely used to probe the process of insulitis, but there exist very few data from humans studied at disease onset. In this manuscript, we employ data from human pancreases collected close to the onset of type 1 diabetes and propose a spatio-temporal computational model for the progression of insulitis in human T1D, with particular focus on the mechanisms underlying the development of insulitis in pancreatic islets. This framework allows us to investigate how the time-course of insulitis progression is affected by altering key parameters, such as the number of the CD20+ B cells present in the inflammatory infiltrate, which has recently been proposed to influence the aggressiveness of the disease. Through the analysis of repeated simulations of our stochastic model which track the number of beta cells within an islet, we find that increased numbers of B cells in the peri-islet space lead to faster destruction of the beta cells. We also find that the balance between the degradation and repair of the basement membrane surrounding the islet is a critical component in governing the overall destruction rate of the beta cells and their remaining number. Our model provides a framework for continued and improved spatio-temporal modelling of human T1D.This work was generously supported by the Wellcome Trust Institutional Strategic Support Award (WT105618MA). KT gratefully acknowledges the financial support of the EPSRC via grant EP/N014391/1. We are also pleased to acknowledge financial support from the European Unions Seventh Framework Programme PEVNET [FP7/2007-2013] under grant agreement number 261441 to NM. The participants of the PEVNET consortium are described at http://www.uta.fi/med/pevnet/ publications.html. Additional support was from a JDRF Career Development Award (5-CDA-2014-221-A-N) to SR and project grant 15/0005156 from Diabetes UK (to NM and SR)

Entrainment dynamics organised by global manifolds in a circadian pacemaker model

This is the final version. Available on open access from Frontiers Media via the DOI in this recordCircadian rhythms are established by the entrainment of our intrinsic body clock to periodic forcing signals provided by the external environment, primarily variation in light intensity across the day/night cycle. Loss of entrainment can cause a multitude of physiological difficulties associated with misalignment of circadian rhythms, including insomnia, excessive daytime sleepiness, gastrointestinal disturbances, and general malaise. This can occur after travel to different time zones, known as jet lag; when changing shift work patterns; or if the period of an individual’s body clock is too far from the 24-hour period of environmental cycles. We consider the loss of entrainment and the dynamics of re-entrainment in a two-dimensional variant of the Forger-Jewett-Kronauer model of the human circadian pacemaker forced by a 24-hour light/dark cycle. We explore the loss of entrainment by continuing bifurcations of one-to-one entrained orbits under variation of forcing parameters and the intrinsic clock period. We show that the severity of the loss of entrainment is dependent on the type of bifurcation inducing the change of stability of the entrained orbit, which is in turn dependent on the environmental light intensity. We further show that for certain perturbations, the model pblackicts a counter-intuitive rapid re-entrainment if the light intensity is sufficiently high. We explain this phenomenon via computation of invariant manifolds of fixed points of a 24-hour stroboscopic map and show how the manifolds organise re-entrainment times following transitions between day and night shift work.Medical Research Council (MRC)US-UK Fulbright CommissionEngineering and Physical Sciences Research Council (EPSRC)National Science Foundation (NSF

Spatial distribution of heterogeneity as a modulator of collective dynamics in pancreatic beta-cell networks and beyond

This is the final version. Available on open access from Frontiers Media via the DOI in this recordData availability statement: The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://github.com/dgalvis/network_spatialWe study the impact of spatial distribution of heterogeneity on collective dynamics in gap-junction coupled beta-cell networks comprised on cells from two populations that differ in their intrinsic excitability. Initially, these populations are uniformly and randomly distributed throughout the networks. We develop and apply an iterative algorithm for perturbing the arrangement of the network such that cells from the same population are increasingly likely to be adjacent to one another. We find that the global input strength, or network drive, necessary to transition the network from a state of quiescence to a state of synchronised and oscillatory activity decreases as network sortedness increases. Moreover, for weak coupling, we find that regimes of partial synchronisation and wave propagation arise, which depend both on network drive and network sortedness. We then demonstrate the utility of this algorithm for studying the distribution of heterogeneity in general networks, for which we use Watts–Strogatz networks as a case study. This work highlights the importance of heterogeneity in node dynamics in establishing collective rhythms in complex, excitable networks and has implications for a wide range of real-world systems that exhibit such heterogeneity.University of Birmingham Dynamic Investment FundEngineering and Physical Sciences Research Council (EPSRC)Medical Research Council (MRC)Diabetes UKUKRIEuropean Union Horizon 202

Cardiopulmonary responses to maximal aerobic exercise in patients with cystic fibrosis (article)

This is the final version. Available from Public Library of Science via the DOI in this record.The dataset associated with this article is located in ORE at: https://doi.org/10.24378/exe.1105Cystic fibrosis (CF) is a debilitating chronic condition, which requires complex and expensive disease management. Exercise has now been recognised as a critical factor in improving health and quality of life in patients with CF. Hence, cardiopulmonary exercise testing (CPET) is used to determine aerobic fitness of young patients as part of the clinical management of CF. However, at present there is a lack of conclusive evidence for one limiting system of aerobic fitness for CF patients at individual patient level. Here, we perform detailed data analysis that allows us to identify important systems-level factors that affect aerobic fitness. We use patients’ data and principal component analysis to confirm the dependence of CPET performance on variables associated with ventilation and metabolic rates of oxygen consumption. We find that the time at which participants cross the gas exchange threshold (GET) is well correlated with their overall performance. Furthermore, we propose a predictive modelling framework that captures the relationship between ventilatory dynamics, lung capacity and function and performance in CPET within a group of children and adolescents with CF. Specifically, we show that using Gaussian processes (GP) we can predict GET at the individual patient level with reasonable accuracy given the small sample size of the available group of patients. We conclude by presenting an example and future perspectives for improving and extending the proposed framework. The modelling and analysis have the potential to pave the way to designing personalised exercise programmes that are tailored to specific individual needs relative to patient’s treatment therapies.Wellcome TrustEngineering and Physical Sciences Research Counci

Variability in cyanobacteria sensitivity to antibiotics and implications for environmental risk assessment

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record© 2019 Once released into the environment antibiotics can kill or inhibit the growth of bacteria, and in turn potentially have effects on bacterial community structure and ecosystem function. Environmental risk assessment (ERA) seeks to establish protection limits to minimise chemical impacts on the environment, but recent evidence suggests that the current regulatory approaches for ERA for antibiotics may not be adequate for protecting bacteria that have fundamental roles in ecosystem function. In this study we assess the differences in interspecies sensitivity of eight species of cyanobacteria to seven antibiotics (cefazolin, cefotaxime, ampicillin, sufamethazine, sulfadiazine, azithromycin and erythromycin) with three different modes of action. We found that variability in the sensitivity to these antibiotics between species was dependent on the mode of action and varied by up to 70 times for β-lactams. Probabilistic analysis using species sensitivity distributions suggest that the current predicted no effect concentration PNEC for the antibiotics may be either over or under protective of cyanobacteria dependent on the species on which it is based and the mode of action of the antibiotic; the PNECs derived for the macrolide antibiotics were over protective but PNECs for β-lactams were generally under protective. For some geographical locations we identify a significant risk to cyanobacteria populations based upon measured environmental concentrations of selected antibiotics. We conclude that protection limits, as determined according to current regulatory guidance, may not always be protective and might be better derived using SSDs and that including toxicity data for a wider range of (cyano-) bacteria would improve confidence for the ERA of antibiotics.AstraZeneca Global SHE Research ProGrammeMedical Research Council (MRC

Mathematical Modelling of Endocrine Systems

This is the final (in press) version. Available from Elsevier via the DOI in this recordHormone rhythms are ubiquitous and essential to sustain normal physiological functions. Combined mathematical modelling and experimental approaches have shown that these rhythms result from regulatory processes occurring at multiple levels of organisation and require continuous dynamic equilibration, particularly in response to stimuli. We review how such an interdisciplinary approach has been successfully applied to unravel complex regulatory mechanisms in the metabolic, stress, and reproductive axes. We discuss how this strategy is likely to be instrumental for making progress in emerging areas such as chronobiology and network physiology. Ultimately, we envisage that the insight provided by mathematical models could lead to novel experimental tools able to continuously adapt parameters to gradual physiological changes and the design of clinical interventions to restore normal endocrine function.Medical Research Council (MRC)Engineering and Physical Sciences Research Council (EPSRC)Wellcome Trus

Robust spike timing in an excitable cell with delayed feedback

This is the author accepted manuscript. The final version is available from the Royal Society via the DOI in this recordData and materials availability: Data and computer code related to the mathematical model and dynamic clamp experiments can be downloaded from the GitHub repository https://github.com/SlowinskiPiotr/MorrisLecarDDEThe initiation and regeneration of pulsatile activity is a ubiquitous feature observed in excitable systems with delayed feedback. Here, we demonstrate this phenomenon in a real biological cell. We establish a critical role of the delay resulting from the finite propagation speed of electrical impulses on the emergence of persistent multiple-spike patterns. We predict the co-existence of a number of such patterns in a mathematical model and use a biological cell subject to dynamic clamp to confirm our predictions in a living mammalian system. Given the general nature of our mathematical model and experimental system, we believe that our results capture key hallmarks of physiological excitability that are fundamental to information processing.Medical Research Council (MRC)Wellcome TrustEngineering and Physical Sciences Research Council (EPSRC)Technical University of Munich – Institute for Advanced StudyRoyal Societ

Vangl2 promotes the formation of long cytonemes to enable distant Wnt/β-catenin signaling

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: The FCCS data that support the findings of this study are available in Dryad, Dataset https://doi.org/10.5061/dryad.cfxpnvx4p. Additional data that support the findings of this study are available from the corresponding author upon reasonable request. Source data are provided with this paper.Wnt signaling regulates cell proliferation and cell differentiation as well as migration and polarity during development. However, it is still unclear how the Wnt ligand distribution is precisely controlled to fulfil these functions. Here, we show that the planar cell polarity protein Vangl2 regulates the distribution of Wnt by cytonemes. In zebrafish epiblast cells, mouse intestinal telocytes and human gastric cancer cells, Vangl2 activation generates extremely long cytonemes, which branch and deliver Wnt protein to multiple cells. The Vangl2-activated cytonemes increase Wnt/β-catenin signaling in the surrounding cells. Concordantly, Vangl2 inhibition causes fewer and shorter cytonemes to be formed and reduces paracrine Wnt/β-catenin signaling. A mathematical model simulating these Vangl2 functions on cytonemes in zebrafish gastrulation predicts a shift of the signaling gradient, altered tissue patterning, and a loss of tissue domain sharpness. We confirmed these predictions during anteroposterior patterning in the zebrafish neural plate. In summary, we demonstrate that Vangl2 is fundamental to paracrine Wnt/β-catenin signaling by controlling cytoneme behaviour.Biotechnology and Biological Sciences Research Council (BBSRC)Living Systems Institute, University of ExeterMedical Research Council (MRC)National Research Foundation of SingaporeNational Medical Research CouncilWellcome Trus

Investigation of the utility of the 1.1B4 cell as a model human beta cell line for study of persistent enteroviral infection.

This is the final version. Available on open access from Nature Research via the DOI in this record. Data availability: The research data supporting this publication are provided within this paper.The generation of a human pancreatic beta cell line which reproduces the responses seen in primary beta cells, but is amenable to propagation in culture, has long been an important goal in diabetes research. This is particularly true for studies focussing on the role of enteroviral infection as a potential cause of beta-cell autoimmunity in type 1 diabetes. In the present work we made use of a clonal beta cell line (1.1B4) available from the European Collection of Authenticated Cell Cultures, which had been generated by the fusion of primary human beta-cells with a pancreatic ductal carcinoma cell, PANC-1. Our goal was to study the factors allowing the development and persistence of a chronic enteroviral infection in human beta-cells. Since PANC-1 cells have been reported to support persistent enteroviral infection, the hybrid 1.1B4 cells appeared to offer an ideal vehicle for our studies. In support of this, infection of the cells with a Coxsackie virus isolated originally from the pancreas of a child with type 1 diabetes, CVB4.E2, at a low multiplicity of infection, resulted in the development of a state of persistent infection. Investigation of the molecular mechanisms suggested that this response was facilitated by a number of unexpected outcomes including an apparent failure of the cells to up-regulate certain anti-viral response gene products in response to interferons. However, more detailed exploration revealed that this lack of response was restricted to molecular targets that were either activated by, or detected with, human-selective reagents. By contrast, and to our surprise, the cells were much more responsive to rodent-selective reagents. Using multiple approaches, we then established that populations of 1.1B4 cells are not homogeneous but that they contain a mixture of rodent and human cells. This was true both of our own cell stocks and those held by the European Collection of Authenticated Cell Cultures. In view of this unexpected finding, we developed a strategy to harvest, isolate and expand single cell clones from the heterogeneous population, which allowed us to establish colonies of 1.1B4 cells that were uniquely human (h1.1.B4). However, extensive analysis of the gene expression profiles, immunoreactive insulin content, regulated secretory pathways and the electrophysiological properties of these cells demonstrated that they did not retain the principal characteristics expected of human beta cells. Our data suggest that stocks of 1.1B4 cells should be evaluated carefully prior to their use as a model human beta-cell since they may not retain the phenotype expected of human beta-cells.JDRFJDRFMedical Research Council (MRC)Diabetes UKNorman Family TrustEuropean Foundation for the Study of Diabete

Morphogen-directed cell fate boundaries: slow passage through bifurcation and the role of folded saddles

This is the final version. Available on open access from Elsevier via the DOI in this recordOne of the fundamental mechanisms in embryogenesis is the process by which cells differentiate and create tissues and structures important for functioning as a multicellular organism. Morphogenesis involves diffusive process of chemical signalling involving morphogens that pre-pattern the tissue. These morphogens influence cell fate through a highly nonlinear process of transcriptional signalling. In this paper, we consider this multiscale process in an idealised model for a growing domain. We focus on intracellular processes that lead to robust differentiation into two cell lineages through interaction of a single morphogen species with a cell fate variable that undergoes a bifurcation from monostability to bistability. In particular, we investigate conditions that result in successful and robust pattern formation into two well-separated domains, as well as conditions where this fails and produces a pinned boundary wave where only one part of the domain grows. We show that successful and unsuccessful patterning scenarios can be characterised in terms of presence or absence of a folded saddle singularity for a system with two slow variables and one fast variable; this models the interaction of slow morphogen diffusion, slow parameter drift through bifurcation and fast transcription dynamics. We illustrate how this approach can successfully model acquisition of three cell fates to produce three-domain “French flag” patterning, as well as for a more realistic model of the cell fate dynamics in terms of two mutually inhibiting transcription factors.Engineering and Physical Sciences Research Council (EPSRC