Mathematical Biology and Ecology Seminar

Please note that the list below only shows forthcoming events, which may not include regular events that have not yet been entered for the forthcoming term. Please see the past events page for a list of all seminar series that the department has on offer.

Past events in this series
Tomorrow
14:00
Dr Leopold Parts
Abstract

Variation in the genome is a powerful instrument for learning about differences between individuals. It avoids the problems of reverse causality, is abundant in natural populations, and can be generated in a targeted manner in the lab. I will talk about our approaches for using different types of genetic variation to understand cellular traits, and the computational models we developed for the purpose. We previously traced the signal from common alleles to RNA abundance and protein levels, as well as cellular growth rate, finding both shared and independent causes of variability. Currently, we employ genome engineering methods to learn about gene essentiality. To undertake experiments at scale, we have developed models to predict the mutational outcome of CRISPR/Cas9 editing, and to efficiently analyse genome-wide screens. I will present the data motivating these models, their formulation, inference, and results.

  • 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
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
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
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
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