Menu
Log in
Forgot password
Become a Member  Get Involved
Search
Log in

News

  • BMB Article Highlight: Dionn Hargreaves et al. (2024)

    12 Sep 2024 10:20 AM | Publications Team (Administrator)

    Relaxation and Noise-Driven Oscillations in a Model of Mitotic Spindle Dynamics

    by Dionn Hargreaves, Sarah Woolner, and Oliver E. Jensen

    Read the paper

    Cell division orientation is controlled by the mitotic spindle, which dynamically positions itself to segregate chromosomes. Often, spindle positioning shows noisy, non-linear oscillations, observed here in dividing embryonic epithelial cells. These oscillations are thought to result from molecular motors that randomly attach, walk along, and detach from spindle microtubules. Prior models predict 1D spindle oscillations, but the effects of noise and nonlinearity remain underexplored. We demonstrate that relaxation oscillations emerge when pulling dominates restoring forces provided by flexible microtubules. Stochastic simulations and analysis reveal noise-induced oscillations, offering new insights into oscillation mechanisms.


    Force generators (molecular motors) attach, walk along, and detach from microtubules to dynamically position the spindle pole, to give rise to noise-induced oscillations.

  • Summer 2024 Newsletter (Part 2)

    05 Sep 2024 10:11 AM | Publications Team (Administrator)

    Sara Loo (Johns Hopkins University), Burcu Gürbüz (Johannes Gutenberg-University Mainz), Thomas Woolley (Cardiff University), and Olivia Chu (Bryn Mawr College).

    1. News - updates from: 

    2. People - Interview with new editor Olivia Chu.

    3. Editorial - After a productive summer - About the SMB and ECMTB Conferences

    4. Featured Figures - SMB Poster prize winners

    To see the articles in this issue, click the links at the above items.

    Contributing content

    Issues of the newsletter are released four times per year in Spring, Summer, Autumn, and Winter. The newsletter serves the SMB community with news and updates, so please share it with your colleagues and contribute content to future issues.

    We welcome your submissions to expand the content of the newsletter.  The next issue will be released in late October, so if you would like to contribute, please send an email to the editors by the start of October 2023 to discuss how your content can be included. This could include summaries of relevant conferences that you have attended, suggestions for interviews, professional development opportunities etc. Please note that job advertisements should be sent to the SMB digest rather than to the newsletter.

    If you have any suggestions on how to improve the newsletter and would like to become more involved and/or contribute, please contact us at any time. We appreciate and welcome feedback and ideas from the community. The editors can be reached at newsletter@smb.org.

    We hope you enjoy this issue of the newsletter!

    Sara, Burcu, Thomas and Olivia

    Editors, SMB Newsletter

    Featured Figures

    By Olivia Chu

    In this issue, we feature the work of Luke Heirene, a graduate student at the University of Oxford, and Yuan Yin, a graduate student at the University of Oxford, who were both poster prize winners at this year’s SMB Annual Meeting. 

    We asked Luke to tell us a bit more about his work here:

    Immunotherapies have seen success in a variety of diseases, including cancer. An important class of immunotherapy are monoclonal antibodies (mAbs). Mabs can induce their anti-tumour effects in a variety of ways. For example, they can inhibit a tumour cell’s ability to downregulate the immune response against it as well as target and stimulate immune effector cells to kill the tumour cell. Regardless of a mAbs mechanism of action, core to their effect are their interactions with target antigens. Processes that alter the ability of a mAb to bind its target antigen, such as differences in binding affinity or antigen expression, will directly impact the resulting therapeutic effect.

    In our work, we use an ODE model of bivalent antibody-antigen binding to establish the key parameters that drive mAb potency and efficacy. We utilise a global parameter sensitivity analysis to establish the parameters that most affect antigen occupancy and bound antibody number, key drivers of mAb potency and efficacy, finding that the most important parameters change with antibody dose. Another key mAb-antigen interaction is the observed increase in binding affinity due to a mAb binding multiple antigens, termed the avidity effect. We use our model to predict antibody binding affinities and antigen expression numbers which result in a large avidity effect. Our results can be used to identify key parameters and interactions that can assist in the preclinical development of mAb therapeutics.


    Figure caption:

    (A) Schematic of model for bivalent mAb-antigen binding (Created with https://www.biorender.com)

    (B) Total order Sobol sensitivity analysis for antigen occupancy as antibody concentration varies on the x-axis.

    (C) Heatmaps displaying the avidity effect as measured by a change in the EC50 between a monovalent and bivalent antibody for different receptor expressions (r_tot) and binding affinities (K_D). The EC50 was calculated as the concentration at which half of the maximum bound antibody number was achieved.

    We asked Yuan to tell us a bit more about her work here:

    ‘Accurate stochastic simulation algorithm for multiscale models of infectious diseases’ by Yuan Yin (University of Oxford), Jennifer A. Flegg (University of Melbourne), Mark B. Flegg (Monash University)

    In the infectious disease literature, significant effort has been devoted to studying dynamics at a single scale. For example, compartmental models describing population-level dynamics are often formulated using differential equations. In cases where small numbers or noise play a crucial role, these differential equations are replaced with memoryless Markovian models, where discrete individuals can be members of a compartment and transition stochastically. Classic stochastic simulation algorithms, such as Gillespie's algorithm and the next reaction method, can be employed to simulate from these Markovian models exactly. The intricate coupling between models at different scales underscores the importance of multiscale modelling in infectious diseases.

    However, several computational challenges arise when the multiscale model becomes non-Markovian. In this study, we address these challenges by developing a novel exact stochastic simulation algorithm. We apply it to a showcase multiscale system where all individuals share the same deterministic within-host model while the population-level dynamics are governed by a stochastic formulation. We demonstrate that as long as the within-host information is simulated at a reasonable resolution, the novel algorithm we develop will always be accurate. Moreover, the novel algorithm we develop is general and can be easily applied to other multiscale models in (or outside) the realm of infectious diseases.

    Figure Caption:

    (a). Sample numerical solution of the within-host CC*V (target cell-limited) model. (b). Viral dynamics for 5 individuals with different calendar infection dates. (c). Propensity of infection per susceptible. (d). Population-level dynamics. Our algorithm (Algo. 2) is compared with an approximate time-driven algorithm (Algo. 1) and a golden-standard exact algorithm (GS). (e). Accuracy comparison between Algo. 1 and Algo. 2 given different population sizes. The markers denote the maximum time resolution where the relative errors are below 5%.


  • Summer 2024 Newsletter (Part 1)

    05 Sep 2024 9:59 AM | Publications Team (Administrator)

    Sara Loo (Johns Hopkins University), Burcu Gürbüz (Johannes Gutenberg-University Mainz), Thomas Woolley (Cardiff University), and Olivia Chu (Bryn Mawr College).
    1. News - updates from: 
    2. People - Interview with new editor Olivia Chu.
    3. Editorial - After a productive summer - About the SMB and ECMTB Conferences
    4. Featured Figures - SMB Poster prize winners

    To see the articles in this issue, click the links at the above items.

    Contributing content

    Issues of the newsletter are released four times per year in Spring, Summer, Autumn, and Winter. The newsletter serves the SMB community with news and updates, so please share it with your colleagues and contribute content to future issues.

    We welcome your submissions to expand the content of the newsletter.  The next issue will be released in late October, so if you would like to contribute, please send an email to the editors by the start of October 2023 to discuss how your content can be included. This could include summaries of relevant conferences that you have attended, suggestions for interviews, professional development opportunities etc. Please note that job advertisements should be sent to the SMB digest rather than to the newsletter.

    If you have any suggestions on how to improve the newsletter and would like to become more involved and/or contribute, please contact us at any time. We appreciate and welcome feedback and ideas from the community. The editors can be reached at newsletter@smb.org.

    We hope you enjoy this issue of the newsletter!

    Sara, Burcu, Thomas and Olivia
    Editors, SMB Newsletter

    News Section

    By Sara Loo 

    In this issue of the News section, we highlight the updates from the SMB Subgroups and Royal Society Publishing. Read on below.

    SMB Subgroups Update

    Mathematical Neuroscience Subgroup

    The SMB Mathematical Neuroscience subgroup was actively engaged at the 2024 SMB annual meeting held at Konkuk University in Seoul, Republic of Korea. The event featured posters, contributed talk sessions, and mini-symposiums covering a diverse range of topics in mathematical neuroscience, including multi-scale networks, neurodegenerative diseases, neural oscillations, and coding. The research presentations were dynamic and well-attended, fostering insightful questions and discussions. 

    The subgroup remained vibrant despite a modest representation, holding a social gathering on Tuesday evening (July 2) at a local Korean Restaurant.  Approximately 15 members attended, enjoying the opportunity to reconnect with old friends and make new connections. 

    Immunobiology and Infection Subgroup

    Immunobiology and Infection Subgroup dinner at KSMB-SMB 2024 in Seoul, South Korea

    The Immunobiology and Infection Subgroup hosted a dinner attended by 30 of its members on the Tuesday of the KSMB-SMB2024 conference. Yongdam Jeong helped coordinate a booking for a local Korean BBQ restaurant called HANAM PIG restaurant. The food was delicious and cooked by the staff on BBQs at every table. There was lots of networking and the overarching feedback from the event was that it was really wonderful to spend time as a group. A huge thank you to Yongdam Jeong and Adrianne Jenner who organized and hosted the event. Looking forward to getting together at SMB 2025!  

    The subgroup’s annual business meeting will be held on September 13, 2024.

    Royal Society Publishing

    The Royal Society's journals Proceedings A and Interface welcome submissions of research and review articles in Mathematical Biology. They offer a range of services including rapid publication, rigorous peer review, international recognition and the option of open access publication. All Royal Society journals are compliant with funder mandates (such as Plan S). Royal Society Publishing is committed to high quality, open and ethical publishing and, as a not-for-profit society publisher, the income they generate goes back into supporting and progressing the global scientific community by funding the activities of the Society. 

    Browse recent content from Interface and Proceedings A including GIS-ODE: linking dynamic population models with GIS to predict pathogen vector abundance across a country under climate change scenarios A J Worton, R A Norman, L Gilbert and R B Porter FREELY available!

    Browse recent theme issues from Philosophical Transactions A including The effectiveness of non-pharmaceutical interventions on the COVID-19 pandemic: the evidence compiled and edited by Professor Sir Mark Walport and the articles are also FREE to access.

    People Section

    By Thomas Woolley

    Interview with Olivia Chu (Bryn Mawr College), one of our new newsletter editors. 

    Editorial

    After a productive summer - About the SMB and ECMTB Conferences

    Reflection on ECMTB

    By Burcu Gürbüz 

    This summer was enriched by two important mathematical biology conferences. First, the joint annual meeting of the Korean Society for Mathematical Biology and the Society for Mathematical Biology (KSMB-SMB 2024 Seoul) was held from June 30 to July 5 at the Konkuk University, Seoul, Republic of Korea. Second, the 13th European Conference on Mathematical and Theoretical Biology (ECMTB'24 Toledo) was held between July 22 - 26 at the University of Castilla La Mancha, Toledo Campus, Spain. 

    ECMTB'24 was successfully organized by Víctor Manuel Pérez García and his team. The biennial conference brought together leading researchers and academics in Mathematical Biology to discuss current and interdisciplinary topics in applied mathematics, theoretical biology, and also to facilitate the development of new techniques and methodologies for modeling complex biological systems. The conference was attended by more than 5000 participants from all over the world. ECMTB'24 had a rich scientific program with mini-symposium and contributed talks, with poster sessions and also with plenary talks with the following details: Evrim Acar Ataman (SIMULA), Christina Cobbold (University of Glasgow), Patricia Reynaud-Bouret (Université Côte d'Azur), Ivana Bozic (University of Washington), Ganna Rozhnova (University Medical Center Utrecht), Mustafa Khammash (ETH Zurich), Anna Marciniak-Czochra (Heidelberg University). As in previous editions, ECMTB'24 provided a platform for sharing research, fostering collaboration, and sparking new ideas for the esteemed researchers, scholars, and enthusiasts who joined the event in this intellectual endeavor. Alan D. Rendall and I had the privilege of organizing a mini-symposium on mathematical analysis, dynamical systems, mathematical modeling, and numerical perspectives. I was amazed by the hospitality and thoughtful organization of the conference team in the fairytale city of Toledo. In my personal experience, I really enjoyed ECMTB'24 - Toledo as it was great to meet old and new friends and distinguished researchers in the field at this prestigious conference. During the event, the annual meeting of the ESTMB was held and Benoit Perthame gave an informative presentation on the activities of the society. For the motivation of young researchers, poster awards were presented.

    In addition to the scientifically rich program, the conference also featured a very thoughtful social program that included a guided tour of the city of Toledo, a cocktail party at the Patio de Covarrubias and a conference dinner at El Cigarral on the Tagus River with a magnificent view of the historic city of Toledo.
    Group picture of the ECMTB’24, Patio de Covarrubias, Toledo, Spain

     Group picture of the ECMTB’24, Patio de Covarrubias, Toledo, Spain


    Reflection on KSMB-SMB 2024

    By Ryan Murphy, University of Melbourne

    The recent KSMB-SMB 2024 conference at Konkuk University, Seoul, Republic of Korea brought together leading and emerging researchers from across the world. The week comprised of a host of fantastic plenaries, mini-symposia presentations, contributed talks and posters, and workshops on the latest advances in mathematical biology across all SMB subgroup areas. It was great to hear the stimulating discussions continue long into the breaks and beyond. 

    There are too many scientific highlights that it would be unfair to name only a few. Alongside the fantastic science and discussion, the conference will long be remembered for the conference dinner with traditional dancing, Taekwondo/K-POP hybrid followed by a performance of Gangnam Style, the organised excursions, and thoughtful touches. I would also like to thank the conference co-chairs Prof. Yangjin Kim and Prof. Ilhyo Jung, all members of the organising committee and scientific committee, and all helpers for making the event such a brilliant success and for setting such a high bar for future editions. 

    On a more personal note, as this was my first in-person SMB conference it was fantastic to put faces to names and be welcomed into the community with friendly and engaging discussions. I would also like to thank the SMB for their support in facilitating my participation through the Landahl Travel Grant. 

    I look forward to seeing you all at SMB 2025!


  • BMB Article Highlight: Albert C. Soewongsono & Michael J. Landis. (2024)

    04 Sep 2024 11:54 AM | Publications Team (Administrator)

    A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics

    by Albert C. Soewongsono & Michael J. Landis

    Read the paper

    Although diffusion approximations are widely used in population genetics, they remain underused for modelling phylogenetic diversification dynamics. We bridge this gap by establishing a general diffusion-based framework to study a wide and highly influential class of phylogenetics birth-death models, known as cladogenetic state-dependent-speciation-extinction (ClaSSE) models. We validate our diffusion-based framework is reliable under a variety of diversification scenarios. We also derive relationships between model rates and their stationary state frequencies. In summary, our work helps to formalize relationships between evolutionary state patterns, process rates, and mixing times for ClaSSE-type models.


    (Upper panel) Relationships between different evolutionary scenarios with species richness at present; (Lower panel) Illustration of an event-based phylogenetic tree viewed as a diffusion-based frequency simulation.


  • BMB Article Highlight: Chenghang Li, et al. (2024)

    28 Aug 2024 11:03 AM | Publications Team (Administrator)

    Mathematical modeling of tumor immune interactions: the role of anti-FGFR and anti-PD-1 in the combination therapy

    by Chenghang Li, Zonghang Ren, Guiyu Yang, Jinzhi Lei

    Read the paper

    Bladder cancer is a malignant tumors of the urinary system known for its high incidence and recurrence rates. Recent studies suggest that combination therapy could improve survival outcomes for bladder cancer patients with high FGFR and PD-L1 expression. This study introduces a mathematical model that integrates the inter-regulatory network of the tumor microenvironment and the competition mechanism between the drug and the ligand-binding receptor. This model describes tumor proliferation dynamics under various treatment strategies and visualizes these process through an agent-based model. The study analyzes the tumor microenvironment dynamics, combination therapy efficacy, treatment sequencing, disease progression, and patient survival.


    The protocol of data-driven mathematical model development and application.


  • BMB Article Highlight: Brock D. Sherlock et al. (2024)

    21 Aug 2024 11:29 AM | Publications Team (Administrator)

    The Distance Between: An Algorithmic Approach to Comparing Stochastic Models to Time-Series Data

    by Brock D. Sherlock, Marko A.A. Boon, Maria Vlasiou, Adelle C.F. Coster

    Read the paper

    Experimental data is often in the form of time-series data with multiple measurements taken at a number of time points. In biological datasets the number of measurements at each time point is often small. So, it can be useful to consider data from multiple experimental protocols to constrain model parameters. In this study, we identify distance metrics for the comparison of stochastic model outputs and time-evolving stochastic measurements of a system. Our distance is across three scales: that of the data at each time point of each type of experiment; a combined distance across the time course of each experiment; and a combined distance across all the experiments. The distances identified offer a means to fit a wide range of models to data.


    The algorithm to produce a hierarchical distance measure over three scales: individual time points, across a time course of a single experiment, and a combined distance over all experiments. This combined distance can then be used for parameter inference, model or other comparisons.


  • BMB Article Highlight: A. Baabdulla and T. Hillen. (2024)

    14 Aug 2024 5:56 AM | Publications Team (Administrator)

    Oscillations in a Spatial Oncolytic Virus Model

    by A. Baabdulla and T. Hillen

    Read the paper

    A viral infection of the tumor has two effects, the virus infects cells which subsequently lyse to release more virus particles, and, the virus marks cancer cells as infected and the immune system comes in to eradicate them. Both processes have to work in balance as to efficiently clear the entire tumor. The basic model for oncolytic viruses is an SIV predator-prey model, which has a Hopf bifurcation and periodic solutions. An interesting question is the spatial coupling of these oscillators as many different types of spatio-temporal patterns are possible (see Figure). The key question for clinical applications is how to manipulate the virus such that the system is in the oscillatory state. We discuss several of these approaches.


    Simulation of an oncolytic virus model using Andrew Krause’s VisualPDE. C shows the cancer cells (brown is low, black is high), I the infected cancer cells (blue is low and white is high), and V the virus (blue is low and red is high).


  • BMB Article Highlight: Mahasa et al. (2024)

    07 Aug 2024 1:58 AM | Publications Team (Administrator)

    A Role of Effector CD8+ T Cells Against Circulating Tumor Cells Cloaked with Platelets: Insights from a Mathematical Model

    by Khaphetsi Joseph Mahasa, Rachid Ouifki, Lisette de Pillis, Amina Eladdadi

    Read the paper

    Circulation of tumor cells, shed from the primary tumor into the blood stream or lymphatic circulation, posits a great threat for patients having metastatic cancers. In this study, we developed a simple mathematical model describing how the primary tumor, CTCs arrested within the circulation, activated platelets and effector CD8+ T cells all shape metastatic framework. Our simulations reveal that high number of activated platelets on CTCs exacerbate CTC’s evasion from immune surveillance. Our model suggests that the efficacy of immunotherapy, based on CD8+ T cells, can be improved by increasing the proliferation rate of CD8+ T cells, although this resolution should be weighted against the CD8+ T cell toxicity in the circulation.


    A schematic diagram of the cellular interactions at the primary site, within the circulation and the secondary site.


  • BMB Article Highlight: Soloviova et al. (2024)

    31 Jul 2024 2:59 AM | Publications Team (Administrator)

    A mathematical model for fibrous dysplasia: The role of the flow of mutant cells

    by Mariia Soloviova, Juan C. Beltrán-Vargas, Luis Fernandez de Castro, Juan Belmonte-Beitia, Víctor M. Pérez-García, Magdalena Caballero

    Read the paper

    Fibrous dysplasia (FD) is a rare mosaic, non-inheritable genetic disorder that affects the skeleton, where normal bone is replaced by weaker, fibrous tissue. This disorder is characterized by expansible lesions prone to fracture, deformity, and pain, and currently has no cure. We have developed a simple mathematical model to better understand the behavior of bone cells in FD. Our model includes the basic biological processes known to occur in FD and tracks the changes in different populations of bone cells over time. We conducted a detailed analysis of the model, examining its properties, the existence and stability of steady states, and the sensitivity of various parameters.


    Representation of the bone-cell populations and interactions between them.


  • BMB Article Highlight: Surasinghe et al. (2024)

    23 Jul 2024 2:10 AM | Publications Team (Administrator)

    Evolutionary invasion analysis of modern epidemics highlights the context-dependence of virulence evolution

    by Sudam Surasinghe, Ketty Kabengele, Paul E. Turner, C. Brandon Ogbunugafor

    Read the paper

    Why do some pathogens evolve to make their hosts more sick, and others less?  This characteristic is embodied in the concept of “virulence,” a central idea in infectious diseases that describes the harm that a pathogen inflicts upon a host. Examining how virulence evolves constitutes a subfield of evolutionary theory, that attempts to make concrete predictions for how we should expect infectious diseases to evolve. In this study, we construct models of various epidemics, and apply a set of mathematical methods based on game theory that identify characteristics of mutant pathogens that render them uninvadable (that is, they cannot be invaded and replaced by a different strain of pathogen).  We demonstrate that pathogens that are spread via different routes—“directly” (as in SARS-CoV-2) or “indirectly” as in diseases like hepatitis C virus in a population of persons who inject drugs—have profoundly different expectations for how. Our findings have implications for how we analyze and prevent modern epidemics. We learn that how virulence will evolve is context-dependent. Consequently, our predictive models of the evolution of virulence should be tailor made to fit the particulars of certain infectious diseases.


    A diagram of an infectious disease model with multiple evolved strains of a pathogen.



© 2023 - Society for Mathematical Biology | Site by HighlandCreative.com.au
Powered by Wild Apricot Membership Software