Nuno Araujo


Affiliation: FCUL



Title: Modeling biological matter at microscale: from cells to tissues

Abstract: 


Abstract: The modeling of biological matter such as cells and tissue is ambitious. It not only involves processes at length and time scales over several orders of magnitude, but also biochemical processes occurring in the interior of the cell are likely to be relevant. In addition, in complex environments they are able self-propel, grow, divide, change shape, and respond slowly with memory, posing several changes to their theoretical model. In this talk, we will discuss how he have been combining theoretical modeling and advanced computational techniques to develop coarse-grained model that can reach the relevant scales and still describe the desired phenomena. Examples will include the bacteria motility in the presence of static and moving obstacles, the proliferation of cells in granular beds, and the mechanics of cell tissues on substrates.

Maros Pleska

Affiliation: The Rockefeller University

Title: The structure of noise: Non-genetic individuality,changeability and inheritance in microbial behavior

Abstract: Clonal populations ofmicroorganisms thriving in constant and homogeneous environments often displayremarkable phenotypic diversity, often termed as phenotypic “noise”. Severalmolecular processes capable of generating such diversity have been elucidatedin the context of individual genes, but how the signatures of these processespropagate to shape the structure of non-genetic diversity in the context ofcomposite traits remains mostly unclear. I will introduce a generalexperimental and theoretical framework that recently allowed us to quantifybacterial swimming behavior, a highly dynamic and complex aspect of thephenotype, using a small number of orthogonal and interpretable behavioraltraits. I will also discuss how representing the whole-lifetime behavior ofindividuals by trajectories in a low-dimensional trait space allowed us todecompose trait variation into individual sources, thus providing acoarse-grained overview of the population and temporal structure of non-geneticdiversity. Finally, will I briefly outline how the described framework foranalyzing the behavior of microorganisms can be extended to more complexecological settings in order to probe the interplay between non-geneticdiversity, phenotypic plasticity, and ecological dynamics.

Bingkan Xue


Affiliation:University of Florida



Title: Internal cues and memory for population adaptationin varying environments



Abstract: To adapt to varying environments, organisms canrely on external cues to infer and express favorable traits. Such cues arevaluable for the population if they are informative about the environmental condition. We propose an alternative source of information, which comes frominternal states of the organisms, without them having to sense externalsignals. These internal states can become correlated with the externalenvironment through the process of selection, thus being available as internalcues. We argue that these internal states also serve as a form of memory thatallows organisms to exploit temporal structure in the environment to predictfuture conditions. The value of such memory for population adaptation is givenby the amount of information between the past and future environments. We illustrate these theoretical ideas with the example of seed dormancy by considering the dependence of the germination fraction on the seed age.

Saúl Ares

Affiliation: CNB-CSIC

Title: Regulation and Feedback in Biological Systems: From Epidemics to Organ Development

Abstract: In this seminar, I will provide an overview of our current research on diverse topics related to the complexities of biological systems. I will discuss epidemic dynamics and vaccination strategies, organ size precision and feedback control mechanisms in the developing Drosophila eye, the interplay of light and temperature on plant growth, and the genetic regulation and physical constraints in pattern formation in nitrogen-fixing filaments of cyanobacteria. I will highlight key findings and their implications, emphasizing the importance of multidisciplinary approaches, mathematical modeling, and simulations in advancing our understanding of complex biological systems. This blackboard talk intends to encourage discussion, and we can delve into particular details based on feedback and interests from the audience.

Anne-Florence Bitbol 

Affiliation: EPFL

Title: Impact of population spatial structure on mutant fixation, from models on graphs to the gut 

Abstract: Microbial populations often have complex spatial structures, with homogeneous competition holding only at a local scale. Population structure can strongly impact evolution, in particular by affecting the fixation probability of mutants. I will first discuss a general model for describing structured populations on graphs. I will show that by tuning migration asymmetry in the rare migration regime, the star graph transitions from amplifying to suppressing natural selection. I will also discuss the impact of increasing migration rates. The results from our model are universal in the sense that they do not hinge on a modeling choice of microscopic dynamics or update rules. Instead, they depend on migration asymmetry, which can be experimentally tuned and measured. Then I will show that the specific structure of the gut, with hydrodynamics and gradients of food and bacterial concentrations, can increase the fixation probability of neutral mutants. Our results can be rationalized by introducing an active population, which consists of those bacteria that are actively consuming food and dividing. Thus, the specific environment of the gut enhances neutral bacterial diversity.