Past Mathematical Biology and Ecology Seminar

25 October 2019
14:00
Abstract

We aim to establish and experimentally test mathematical models of embryogenesis. While the foundation of this research is based on models of isolated developmental events, the ultimate challenge is to formulate and understand dynamical systems encompassing multiple stages of development and multiple levels of regulation. These range from specific chemical reactions in single cells to coordinated dynamics of multiple cells during morphogenesis. Examples of our dynamical systems models of embryogenesis – from the events in the Drosophila egg to the early stages of gastrulation – will be presented. Each of these will demonstrate what had been learned from model analysis and model-driven experiments, and what further research directions are guided by these models.

  • Mathematical Biology and Ecology Seminar
18 October 2019
14:00
Abstract

In this talk I shall describe recent work inspired by problems in cell biology, namely how the dynamics of small G-proteins underlies polarity formation. Their dynamics is such that their active membrane bound form diffuses more slowly. Hence you might expect Turing patterns. Yet how do cells form backs and fronts or single isolated patches. In understanding these questions we shall show that the key is to identify the parameter region where Turing bifurcations are sub-critical. What emerges is a unified 2-parameter bifurcation diagram containing pinned fronts, localised spots, localised patterns. This diagram appears in many canonical models such as Schnakenberg and Brusselator, as well as biologically more realistic systems. A link is also found between theories of semi-string interaction asymptotics and so-called homoclinic snaking. I will close with some remarks about relevance to root hair formation and to the importance of subcriticality in biology. 

  • Mathematical Biology and Ecology Seminar
21 June 2019
14:00
Abstract

Mitral regurgitation is one of the most common valve diseases in the UK and contributes to 50% of the transcatheter mitral valve replacement (TMVR) procedures with bioprosthetic valves. TMVR is generally performed in frailer, older patients unlikely to tolerate open-heart surgery or further interventions. One of the side effects of implanting a bioprosthetic valve is a condition known as left ventricular outflow obstruction, whereby the implanted device can partially obstruct the outflow of blood from the left ventricle causing high flow resistance. The ventricle has then to pump more vigorously to provide adequate blood supply to the circulatory system and becomes hypertrophic. This ultimately results in poor contractility and heart failure.
We developed personalised image-based models to characterise the complex relationship between anatomy, blood flow, and ventricular function both before and after TMVR. The model prediction provides key information to match individual patient and device size, such as postoperative changes in intraventricular pressure gradients and blood residence time. Our pilot data from a cohort of 7 TMVR patients identified a correlation between the degree of outflow obstruction and the deterioration of ventricular function: when approximately one third of the outflow was obstructed as a result of the device implantation, significant increases in the flow resistance and the average time spent by the blood inside the ventricle were observed, which are in turn associated with hypertrophic ventricular remodelling and blood stagnation, respectively. Currently, preprocedural planning for TMVR relies largely on anecdotal experience and standard anatomical evaluations. The haemodynamic knowledge derived from the models has the potential to enhance significantly pre procedural planning and, in the long term, help develop a personalised risk scoring system specifically designed for TMVR patients.
 

  • Mathematical Biology and Ecology Seminar
14 June 2019
14:00
Abstract


Cellular migration can be affected by short-range interactions between cells such as volume exclusion, long-range forces such as chemotaxis, or reactions such as phenotypic switching. In this talk I will discuss how to incorporate these processes into a discrete or continuum modelling frameworks. In particular, we consider a system with two types of diffusing hard spheres that can react (switch type) upon colliding. We use the method of matched asymptotic expansions to obtain a systematic model reduction, consisting of a nonlinear reaction-diffusion system of equations. Finally, we demonstrate how this approach can be used to study the effects of excluded volume on cellular chemotaxis. This is joint work with Dan Wilson and Helen Byrne.
 

  • Mathematical Biology and Ecology Seminar
7 June 2019
14:00
Abstract

Mechanobiology is a field of science that aims to understand how mechanics regulate biology. It focuses on how mechanical forces and alterations in mechanical properties of cell or tissues regulate biological processes in development, physiology and disease. In fact, all these processes occur in our body, which presents a clear structural and hierarchical organization that goes from the organism to the cellular level. To advance in the understanding of all these processes at different scales requires the use of simplified representations of our body, which is normally known as modelling or equivalently the creation of a model. Different types of models can be found in the literature: in-vitro, in-vivo and in-silico models.

Here, I will present our modelling strategy in which we integrate different mathematical models and experiments in order to tackle relevant mechanical-based mechanisms in wound healing and cancer metastasis progression [1,2]. In fact, we have focused our research on individual [3] and collective cell migration [4], because it is a crucial event in all these mechanisms. Therefore, unravelling the intrinsic mechanisms that cells use to define their migration is an essential element for advancing the development of new technologies in regenerative medicine and cancer.

Due to the complexity of all these mechanisms, mathematical modelling is a relevant tool for providing deeper insight and quantitative predictions of the mechanical interplay between cells and extracellular matrix during cell migration. To assess the predictive capacity of these models, we will compare our numerical results with microfluidic-based experiments [2], which provide experimental information to test and refine the main assumptions of our models.

Actually, we design and fabricate multi-channel 3D microfluidics cell culture chips, which allow recreating the physiology and disease of one organ or any biological process with a precise control of the micro environmental factors [5]. Therefore, this kind of organ-on-a-chip experiments constitutes a novel modelling strategy of in vitro multicellular human systems that in combination with mathematical simulations provide a relevant tool for research in mechanobiology.

References

Escribano J, Chen M, Moeendarbary E, Cao X, Shenoy V, Garcia-Aznar JM, Kamm RD, Spill F.  Balance of Mechanical Forces Drives Endothelial Gap Formation and May Facilitate Cancer and Immune-Cell Extravasation. PLOS Computational Biology, in press.

  • Mathematical Biology and Ecology Seminar
31 May 2019
14:00
Abstract

Cardiac fibrosis plays a significant role in the disruption of healthy electrical signalling in the heart, creating structural heterogeneities that induce and stabilise arrhythmia.  However, a proper understanding of the consequences of cardiac fibrosis must take into account the complex and highly variable patterns of its spatial localisation in the heart, which significantly affects the extent and manner of its impacts on cardiac wave propagation. In this work we present a methodology for the algorithmic generation of fibrotic patterns via Perlin noise, a technique for computationally efficient generation of textures in computer graphics.

Our approach works directly from image data to create populations of pattern realisations that all resemble the target image under a set of metrics. Our technique thus serves as a type of data enrichment, enabling analysis of how variability in the precise placement of fibrotic structures modulates their electrophysiological impact. We demonstrate our method, and the types of analysis it can enable, using a widely referenced histological image of four different types of microfibrotic structure. Our generator and Bayesian tuning method prove flexible enough to successfully capture each of these very distinct patterns.

We demonstrate the importance of this tool, by presenting 2D simulations overlayed on the generated images that highlight the effects of microscopic variability on the electrophysiological impact of fibrosis. Finally, we discuss the application of our methodology to the increasingly available imaging data of fibrotic patterning on a more macroscopic scale, and indeed to other areas of science underpinned by image based modelling and simulation.    

  • Mathematical Biology and Ecology Seminar
17 May 2019
14:00
Abstract

Competition between peptides for binding and presentation by MHC class I molecules decides the immune response to foreign or tumor antigens. Many previous studies have attempted to classify the immunogenicity of a peptide using machine learning algorithms to predict the affinity, or half-life, of the peptide binding to MHC. However immunopeptidome analyses have shown a poor correlation between sequence based predictions and the abundance on the cell surface of the experimentally identified peptides. Such metrics are, for instance, only comparable when the abundance of competing peptides can be accurately quantified. We have developed a model for predicting the relative presentation of competing peptides that takes into account off-rate, source protein abundance and turnover and cofactor-assisted MHC assembly with peptides. This model is mechanism based so that it can accommodate complex biology phenomena such as inflammation, up or downregulation of peptide loading complex chaperones, appearance of a mutanome. We have used aspects of the model to drive an investigation of the precise molecular mechanism of peptide selection by MHC I and its associated intracellular cofactors.

  • Mathematical Biology and Ecology Seminar
10 May 2019
(All day)
PLEASE NOTE THAT THIS SEMINAR IS CANCELLED DUE TO UNFORESEEN CIRCUMSTANCES
Abstract

PLEASE NOTE THAT THIS SEMINAR IS CANCELLED DUE TO UNFORSEEN CIRCUMSTANCES.

  • Mathematical Biology and Ecology Seminar

Pages