Biology subjects

Succurro, A.

Publications and source records attributed to Succurro, A..

3 recordsLinked to original sources

bioRxiv2018

Emergent sub-population behavior uncovered with a community dynamic metabolic model of Escherichia coli diauxic growth

Microbial communities have adapted to greatly variable environments in order to survive both short-term perturbations and permanent changes. The diauxic shift of Escherichia coli, growing first on glucose and, after it is exhausted, on acetate, is still today actively studied. As a fundamental example of metabolic adaptation, we are interested in understanding if diauxie in monocultures of E. coli is a coordinated and uniform metabolic shift, or rather the observable emergent result of individual sub-populations behavior. To do so we first develop a modeling framework that integrates dynamic models (ordinary differential equation systems) with structural models (metabolic networks), providing an open source modeling framework that is suitable to investigate the dynamics of microbial communities. We apply our methods to model E. coli either as having an average, unique metabolic state or as being the combination of two E. coli populations adapted to one of the two carbon sources. Our results are in strong agreement with previously published data and suggest that rather than a coordinated metabolic shift, diauxie could be the emergent pattern resulting from a survival strategy where individual cells differentiate for optimal growth on different substrates in view of environmental fluctuations. This work offers a new perspective on how to use dynamic metabolic modeling to investigate population dynamics, as the proposed approach can be easily transfered to studies on other multi-species communities as well as single cells.\n\nImportanceEscherichia coli diauxie is a fundamental example of metabolic adaptation that has not yet been completely understood, and to this aim approaches integrating experimental and theoretical biology are needed. We present a novel dynamic metabolic modeling approach that captures diauxie as an emergent property of sub-population dynamics rather than a homogeneous metabolic shift in E. coli monocultures. Without fine tuning of the parameters of E. coli core genome-scale model we obtain good agreement with published data. Our results suggest a change of paradigm in using single organism metabolic models, which can only to a certain approximation represent the average population metabolic state. We finally provide an open source modeling framework that can be applied to model multi-organism dynamics in variable environments.

systems biology↗

bioRxiv2016

Dynamical modelling of the heat shock response in Chlamydomonas reinhardtii

Global warming is exposing plants to more frequent heat stress, with consequent crop yield reduction. Organisms exposed to large temperature increases protect themselves typically with a heat shock response (HSR). To study the HSR in photosynthetic organisms we present here a data driven mathematical model describing the dynamics of the HSR in the model organism Chlamydomonas reinhartii. Temperature variations are sensed by the accumulation of unfolded proteins, which activates the synthesis of heat shock proteins (HSP) mediated by the heat shock transcription factor HSF1. Our dynamical model employs a system of ordinary differential equations mostly based on mass-action kinetics to study the time evolution of the involved species. The signalling network is inferred from data in the literature, and the multiple experimental data-sets available are used to calibrate the model, which allows to reproduce their qualitative behaviour. With this model we show the ability of the system to adapt to temperatures higher than usual during heat shocks longer than three hours by shifting to a new steady state. We study how the steady state concentrations depend on the temperature at which the steady state is reached. We systematically investigate how the accumulation of HSPs depends on the combination of temperature and duration of the heat shock. We finally investigate the system response to a smooth variation in temperature simulating a hot day.

plant biology↗

bioRxiv2016

Dynamics of the bacterial community associated with Phaeodactylum tricornutum cultures

The pennate diatom Phaeodactylum tricornutum is a model organism able to synthesise industrially-relevant molecules. Large-scale monocultures are prone to bio-contamination, however, little is known about the identity of the invading organisms. To gain insight into the bacterial community associated with diatoms, we translated the complexity of a natural system into reproducible experiments where we investigated the microbiome of P. tricornutum cultures. The results revealed a dynamic bacterial community that changed over time and in differing media conditions. We propose a network of putative interactions between P. tricornutum and the main bacterial factions, which is translated into a set of ordinary differential equations constituting a computational dynamic model. The proposed mathematical model is able to capture the population dynamics, further supporting the hypothesised interactions. The interdisciplinary approach implemented provides a framework for understanding the dynamics of diatom-associated microbial communities, and provides a foundation for further systematic investigations of host-microbe interactions.

ecology↗