Global transcriptional response to salt shock of the plant microsymbiont Mesorhizobium loti MAFF303099

Soil salinity affects rhizobia both as free-living bacteria and in symbiosis with the host. The aim of this study was to examine the transcriptional response of the Lotus microsymbiont Mesorhizobium loti MAFF303099 to salt shock. Changes in the transcriptome of bacterial cells subjected to a salt shock of 10% NaCl for 30 min were analyzed. From a total of 7231 protein-coding genes, 385 were found to be differentially expressed upon salt shock, among which 272 were overexpressed. Although a large number of overexpressed genes encode hypothetical proteins, the two most frequently represented COG categories are "defense mechanisms" and "nucleotide transport and metabolism". A significant number of transcriptional regulators and ABC transporters genes were upregulated. Chemotaxis and motility genes were not differentially expressed. Moreover, most genes previously reported to be involved in salt tolerance were not differentially expressed. The transcriptional response to salt shock of a rhizobium with low ability to grow under salinity conditions, but enduring a salinity shock, may enlighten us concerning salinity stress response mechanisms.

Molecular mechanisms controlling physiological plasticity in marine mussels under the influence of natural and anthropogenic stress factors

Marine mussels are exceptionally well-adapted to live in transitional habitats where they are exposed to fluctuating environmental parameters and elevated levels of natural and anthropogenic stressors throughout their lifecycle. However, there is a dearth of information about the molecular mechanisms that assist in dealing with environmental changes. This project aims to investigate the molecular mechanisms governing acclimatory and stress responses of the Mediterranean mussel (Mytilus galloprovincialis) by addressing relevant life stages and environmental stressors of emerging concern. The experimental approach consisted of two phases to explore (i) the physiological processes at early life history and the consequences of plastic pollution and (ii) the adult physiology processes under natural habitats. As the first phase, I employed a plastic leachate (styrene monomer), and polystyrene microplastics to understand the modulation of cytoprotective mechanisms during the early embryo stages. Results revealed the onset of transcriptional impairments of genes involved in MXR-related transporters and other physiological processes induced by styrene and PS-MPs. In the second phase, as a preliminary analysis, microbiota profile of adult mussels at the tissue scale and its surrounding water was explored to understand microbiota structures that may reflect peculiar adaptations to the respective tissue functions. The broader experiment has been implemented to understand the variability of transcriptional profiles in the mussel digestive glands in the natural setting. All the genes employed in this study have shown possibilities to use as molecular biomarker responses throughout the year for monitoring the physiology of mussels living in a particular environment and, in turn, more properly detecting changes in the environment. As a whole, my studies provide insights into the interactions between environmental parameters, and intrinsic characters, and physiology of marine bivalves, and it could help to interpretation of responses correctly under stress conditions and climate change scenarios.

Exploiting molecular simulations as an atomic-level microscope to elucidate clinically relevant cation chloride cotransporters

The cation chloride cotransporters (CCCs) represent a vital family of ion transporters, with several members implicated in significant neurological disorders. Specifically, conditions such as cerebrospinal fluid accumulation, epilepsy, Down’s syndrome, Asperger’s syndrome, and certain cancers have been attributed to various CCCs. This thesis delves into these pharmacological targets using advanced computational methodologies. I primarily employed GPU-accelerated all-atom molecular dynamics simulations, deep learning-based collective variables, enhanced sampling methods, and custom Python scripts for comprehensive simulation analyses. Our research predominantly centered on KCC1 and NKCC1 transporters. For KCC1, I examined its equilibrium dynamics in the presence/absence of an inhibitor and assessed the functional implications of different ion loading states. In contrast, our work on NKCC1 revealed its unique alternating access mechanism, termed the rocking-bundle mechanism. I identified a previously unobserved occluded state and demonstrated the transporter's potential for water permeability under specific conditions. Furthermore, I confirmed the actual water flow through its permeable states. In essence, this thesis leverages cutting-edge computational techniques to deepen our understanding of the CCCs, a family of ion transporters with profound clinical significance.