To grow, bacteria convert nutrients into biomass via the process of transcription-translation. To initiate transcription, RNA polymerase (RNAP) reversibly binds a sigma factor that directs RNAP to a specific subset of genes. In response to changing environmental conditions, bacteria activate alternative sigma factors, changing the global pattern of expressed genes.  Since RNAPs are finite in the cells, sigma factors compete for binding them.

Marine phytoplankton is composed of unicellular algae and their associated bacteria. These algal communities are highly variable in species composition, but their patterns tend to recur seasonally. To clarify the role of the bacterial community in the phytoplankton, we monitored the growth dynamics of several bacterial species and microalgae in community. Supported by Lotka-Volterra models, we found that interactions between bacteria and algae are highly species-specific and depend on algal fitness, bacterial metabolism, and community composition (D2022). 

A poster and a presentation, a talk (INI Cambridge) and a talk (ICTP Trieste) on this topic

Plant leaves host diverse microbial communities comprising both commensals and opportunistic pathogens. In some plants, defense metabolites are toxic to most bacteria, but certain pathogens, can detoxify the environment acting as common good for the whole bacterial community. We built, tested, and modelled a synthetic bacterial community in this scenario and studied the trade-offs between detoxification, nutrient availability, and growth finding best conditions in which the plants by using the toxin can reduce the pathogen, and this latter by detoxifying rescues the bacterial community.

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The cytoplasmic bacterial membrane has a remarkably intricate temporal and spatial organization that is critical for the maintenance of fundamental biological processes. We focused on the theoretical study of the diffusion of single proteins on a curved bacterial membrane, pointing out that the vast majority of membrane proteins assemble in clusters and follow, unexpectedly, Brownian dynamics (L2018).

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In bacteria, the peptidoglycan (PG) layer maintains cell shape by counteracting turgor pressure. During growth, new material is incorporated into the existing layer through the interaction of several enzymes. We theoretically study the dynamics of incorporation of a new material into the PG layer via a coarse-grained mechanical (biophysical) model to assess its stability and understand the evolution of antimicrobial resistance (AMR).

The spherical bacterium Staphylococcus aureus divides by creating a septum between the two hemispherical daughters. Here, we create a mechanistic model describing how the cell coordinates septum formation with cell scission. As the septum develops, mechanical stress in the cell wall near the division site decreases, which could activate autolysins responsible for cell separation. This “mechanical trigger” model explains the variability in division outcomes observed under mutations or antibiotic treatments and suggests for the first time a general coupling between cell geometry, mechanical stress, and antibiotic resistance.

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In E. coli, the NhaA antiporters anchored in the lipid bilayer membrane are responsible for creating a pH gradient by exchanging sodium for protons. Theoretically, this gradient can be exploited to create a difference of potential between the opposite sides of the membrane, which can serves as a biopile. We created synthetic micelles with NhaAs to study such proton flow, which we described by a mathematical model. In this way, we established a rational design for biopile based on antiporters, useful for medical applications (patent) (presentation).