Biology subjects

Mancini, L.

Publications and source records attributed to Mancini, L..

17 recordsLinked to original sources

bioRxiv2026

Evolution of moss leaf-like organs through variations in deeply conserved developmental principles

Leaves and leaf-like organs with laminar structures and determinate growth arose multiple times independently in land plants. The cellular basis of leaf development is well characterized in flowering plants, and molecular studies have shown that the plant hormone auxin plays a central role in this process, orchestrating cellular growth and differentiation. Auxin is also crucial for the formation of phyllids, the leaf-like organs of bryophytes, yet its precise role in morphogenesis remains unclear. More broadly, whether similar developmental principles are shared across distantly related evolutionary lineages is unknown. Here, we combine live-imaging, genetics, pharmacological treatments, and modeling to investigate the cellular and molecular basis of phyllid development in the model moss Physcomitrium patens. By tracking phyllid morphogenesis from a single initial cell to full maturity, we uncover the cellular growth dynamics underlying organ development. We demonstrate that auxin spatially inhibits cell divisions and promotes cellular elongation and differentiation. However, unlike in vascular plants, moss PIN transporters do not participate in polar auxin transport during phyllid development but mainly reduce intracellular auxin concentration. These findings indicate that while auxins role in organogenesis is conserved, its transport mechanisms have diverged across land plants. Overall, our study reveals shared principles of planar organ morphogenesis, highlighting how the repeated deployment of similar developmental strategies, with lineage-specific variations, drove the convergent evolution of leaves and leaf-like organs. One-Sentence SummaryAuxin modulates a conserved developmental program in moss leaf-like organs by spatiotemporally controlling cell division and growth.

plant biology↗

bioRxiv2025

Ionic environment and nutrients affect the cysB-dependent conditional susceptibility of E. coli to mecillinam

Antibiotic efficacy is influenced by environmental context. Urinary E. coli isolates lacking a functional cysB gene have been shown to be resistant to the {beta}-lactam antibiotic mecillinam under high-osmolarity conditions, suggesting that increased fluid intake might synergize with drug treatment. In this study, we further explore E. coli susceptibility to mecillinam across growth conditions. We show that while osmolarity has a mild protective effect on cysB knockout and reference strain, it is the presence of certain salts that leads to the resistant phenotype in the mutant. Such conditional resistance is specific to mecillinam and rapidly wanes when salts are removed. In agreement with our previous work showing that slow growing cells escape mecillinam-induced bursting by maintaining a small size, for both strains we observe low susceptibility to mecillinam in scarcely nutritious pooled human urine. As we supplement urine with nutrients, we observe a sharp transition to susceptibility when growth rate surpasses 0.6 h-1. Growth in the presence of salt or uncharged osmolites decreases cell size of both reference strain and cysB knockout offering a potential explanation to the observed mild protective effects of osmolarity. Our findings give insights into the mechanism of cysB dependent susceptibility to mecillinam and, due to the dual impact of nutrients and osmolites on treatment, allow us to reformulate ideas on potential diet recommendations. While increased fluid intake will decrease urine osmolarity, it will also reduce nutrient content, limiting mecillinam efficacy. We suggest instead that reducing sodium intake during mecillinam treatment might avoid this trade-off.

microbiology↗

bioRxiv2025

Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community within alveoli-like geometries

The bodies of macroorganisms host microbes living in multi-species communities. Sequencing approaches have revealed that different organs host different microbiota and tend to be infected by different pathogens, drawing correlations between environmental parameters at the organ level and microbial composition. However, less is known about the microscale dimension of microbial ecology, particularly during infection. In this study, we focus on the role of microscale spatial structure, studying its influence on the ecology of a polymicrobial infection of P. aeruginosa, S. aureus and C. albicans. Although these pathogens are commonly found together in the lungs of chronically ill patients, it is unclear whether they coexist or compete and segregate in different niches. We find that, while P. aeruginosa quickly outcompetes C. albicans and S. aureus on large surfaces, robust spatial organization and coexistence emerges in microfluidic microchambers that mimic the spatial characteristics of alveoli. In these microenvironments, slowly growing C. albicans is able to leverage fast eccentric hyphal growth to conquer boundary spaces, where it establishes itself excluding the other pathogens. We show that the emerging spatial patterning is robust to changes in the virulence of the community, enabling coexistence and potentially determining infection severity and outcomes. Our findings reveal a previously unrecognized role of mechanical forces in shaping infection dynamics, suggesting that microenvironmental structure is a critical determinant of pathogen coexistence, virulence, and treatment outcomes. Because adaptations, such as changes in morphology, are widespread among microbes, these results are generalizable to other ecologies and environments.

microbiology↗

bioRxiv2024

Antibiotics change the growth rate heterogeneity and morphology of bacteria

A better understanding of the system-level effects of antibiotics is necessary to fight the rise of antibiotic resistance. Utilising the Multipad Agarose Plate (MAP), we monitor the growth rate and cell morphology of three clinically relevant species (E.coli, S.aureus and P.aeruginosa) after exposure to 11 different concentrations of 13 antibiotics (for a total of 24 microbe-antibiotic combinations). As the drug dose approaches the MIC and regardless of the mode of action, our results show a consistent increase in growth rate heterogeneity. Remarkably, drugs that affect protein synthesis consistently show the opposite trend, reducing heterogeneity. We hypothesize that growth rate heterogeneity under antibiotic treatment might therefore depend on the functional distance of the target from ribosomal activity, which is key in determining growth rate. Low heterogeneity is desirable from a clinical perspective, as the opposite is often associated to persistence and antibiotic survival. For all of the antibiotics and species tested, we also find a striking and non-trivial correlation between morphological alterations and growth inhibition. This observation allows us to introduce a new morphological parameter, MOR50, that enables the estimation of minimum inhibitory concentration (MIC) for antibiotic susceptibility testing (AST) with a single snapshot after 2.5 hours of incubation. In addition to introducing a novel, resource-efficient, rapid AST method, our findings shed new light on the effects of antibiotic perturbations on bacteria at the system level that might inform treatment design.

microbiology↗

bioRxiv2024

Surface versus volume synthesis governs growth-dependent efficacy of a β-lactam antibiotic

The efficacy of {beta}-lactam antibiotics depends strongly on bacterial growth rate. This can lead to poor correlation between in vivo action and in vitro assays, hindering effective prescribing - yet the mechanisms underlying growth-rate dependent {beta}-lactam action remain unclear. Here, we investigate growth-rate dependent action of mecillinam, a {beta}-lactam that targets the elongation-mediating PBP2 peptidoglycan transpeptidase enzyme, on Escherichia coli cells. We show that mecillinam alters the balance between the rates of cell surface area and volume synthesis in a growth-rate dependent manner. Under mecillinam treatment, cell volume increases exponentially at a rate [fi]xed by the growth medium, but the cells ability to produce new surface area is compromised by the antibiotic. On rich medium, this imbalance leads to lysis, but on poor medium, slow-growing cells reach a new balance between surface area and volume synthesis, allowing sustained growth even at concentrations of mecillinam far above the EUCAST MIC value. A mathematical model based on surface area vs volume synthesis can quantitatively explain growth-medium dependent differences in mecillinam killing, as well as rescue from killing when cell morphology is perturbed in a microfluidic device. {beta}-lactam antibiotic action is mechanistically complex, yet our work suggests that simple conceptual principles can help understand the interplay between molecular mechanism and cell physiology, potentially contributing to more effective use of these drugs.

microbiology↗

bioRxiv2024

Multipad Agarose Plate (MAP): A Rapid and High-Throughput Approach for Antibiotic Susceptibility Testing

We describe a phenotypic antibiotic susceptibility testing (AST) method that can provide an eightfold speedup in turnaround time compared to the current clinical standard by leveraging advances in microscopy and single-cell imaging. A newly developed growth plate containing 96 agarose pads, termed the Multipad Agarose Plate (MAP), can be assembled at low costs. Pads can be prepared with dilution series of antibiotics. Bacteria are seeded on the pads and automatically imaged using brightfield microscopy, with a fully automated segmentation pipeline quantifying microcolony formation and growth rate. Using a test set of nine antibiotics with very different targets, we demonstrate that accurate minimum inhibitory concentration (MIC) measurements can be performed based on the growth rate of microcolonies within three hours of incubation with the antibiotic. Faster, reliable and high throughput methods for AST, such as MAP, could improve patient care by expediting treatment initiation and alleviating the burden of antimicrobial resistance.

microbiology↗

bioRxiv2023

Prosaposin maintains adult neural stem cells in a state associated with deep quiescence

In most vertebrates, adult neural stem cells (NSCs) continuously give rise to neurons in discrete brain regions. A critical process for maintaining NSC pools over long periods of time in the adult brain is NSC quiescence, a reversible and tightly regulated state of cell cycle arrest. Recently, lysosomes were identified to regulate the NSC quiescence-proliferation balance. However, it remains controversial whether lysosomal activity promotes NSC proliferation or quiescence, and a finer influence of lysosomal activity on NSC quiescence duration or depth remains unexplored. Using RNA-sequencing and pharmacological manipulations, we show that lysosomes are necessary for NSC quiescence maintenance. Additionally, we reveal that expression of psap, encoding the lysosomal regulator Prosaposin, is enriched in quiescent NSCs (qNSCs) that reside upstream in the NSC lineage and display a deep/long quiescence phase in the adult zebrafish telencephalon. We show that shRNA-mediated psap knock-down increases the proportion of activated NSCs (aNSCs) as well as NSCs that reside in shallower quiescence states (signed by ascl1a and deltaA expression). Collectively, our results identify the lysosomal protein Psap as a (direct or indirect) quiescence regulator and unfold the interplay between lysosomal function and NSC quiescence heterogeneities.

neuroscience↗

bioRxiv2023

A synthetic signalling network imitating the action of immune cells in response to bacterial metabolism

State-of-the-art bottom-up synthetic biology allows us to replicate many basic biological functions in artificial cell-like devices. To mimic more complex behaviours, however, artificial cells would need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here we considered a sophisticated biological response, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. We designed a consortium consisting of two synthetic agents - responsive DNA-based particles and antibiotic-loaded lipid vesicles - whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilisation and exposure to antibiotics. Our results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.

synthetic biology↗

bioRxiv2022

Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression

The maintenance of neural stem cells (NSCs) in the adult brain depends on their activation frequency and division mode. We use long-term intravital imaging of NSCs in the zebrafish adult telencephalon to link activation and division mode with predictive cellular and molecular parameters. We reveal that apical surface area and expression of the Notch ligand DeltaA predict NSC activation frequency, while deltaA expression marks NSC commitment to neurogenesis. We also find that deltaA-negative NSCs constitute the bona fide self-renewing NSC pool and systematically engage in asymmetric divisions generating a self-renewing deltaAneg and a neurogenic deltaApos NSC. Finally, modulation of Notch signaling during imaging indicates that the prediction of activation frequency by apical size, and the asymmetric divisions of deltaAneg NSCs, are functionally independent of Notch. These results provide dynamic qualitative and quantitative readouts of NSC lineage progression in vivo and support a hierarchical organization of NSCs in differently fated sub-populations.

neuroscience↗

bioRxiv2021

Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions

To swim and navigate, motile bacteria synthesize a complex motility machinery involving flagella, motors, and a sensory system. A myriad of studies has elucidated the molecular processes involved, but less is known about the coordination of motility expression with cellular physiology: In Escherichia coli, motility genes are strongly upregulated in nutrient-poor conditions compared to nutrient-replete conditions; yet a quantitative link to cellular motility has not been developed. Here, we systematically investigate gene expression, swimming behavior, and cell growth across a broad spectrum of exponential growth condition. We establish that E. coli up-regulates the expression of motility genes at slow growth to compensate for reduction in cell size, such that the number of flagella per cell is maintained across conditions. The observed 4-5 flagella per cell is the minimum number needed to keep the majority of cells motile. This simple regulatory objective allows E. coli cells to remain motile across a broad range of growth conditions while keeping the biosynthetic and energetic demands to establish and drive the motility machinery at the minimum needed. Given the strong reduction in flagella synthesis resulting from cell size increases at fast growth, our findings also provide a novel physiological perspective on bacterial cell size control: A larger cell-size at fast growth is an efficient strategy to increase the allocation of cellular resources to the synthesis of those proteins required for fast growth, while maintaining processes such as motility which are only needed on a per-cell basis.

microbiology↗

bioRxiv2021

DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.

BO_SCPLOWACKGROUNDC_SCPLOWQuantitative imaging of epithelial tissues prompts for bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common pre-processing step consists in projecting the acquired 3D volume on a 2D plane mapping the tissue surface. Indeed, while segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in Developmental and Cell Biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement. RO_SCPLOWESULTSC_SCPLOWHere we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes, and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a user-friendly and configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools. CO_SCPLOWONCLUSIONSC_SCPLOWWe find that LocalZProjector performs well even in situations where the volume to project also contains un-wanted signal in other layers. We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs.

bioinformatics↗

bioRxiv2020

In vitro selection of a microbial consortium predictive of synergistic functioning along multiple ecosystem scales

Soil microbes form complex interactive networks throughout the soil and plant rhizosphere. These interactions can result in emergent properties for consortia that are not predictable from the phenotypes of constituents in isolation. We used a four-species consortium to assess the capacity of individual microbial species versus different consortia permutations of the four species to contribute to increased P-solubilization using soil incubations and plant growth experiments. We found that as different combinations of bacterial species were assembled into differing consortia, they demonstrated differing abilities to stimulate soil P cycling and plant growth. The combination of all four microbes in the consortia were much more effective at solubilizing P and stimulating plant growth than any of the individual bacterial species alone. This suggests that in vivo functionally synergistic soil microbial consortia can be adept at performing specific ecosystem functions in situ. Improving our understanding of the mechanisms that facilitate synergistic functioning examined in this study is important for maximizing future food production and agroecosystem sustainability.

ecology↗

bioRxiv2020

Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human whole-brain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process.

neuroscience↗

bioRxiv2020

Dynamic spatiotemporal coordination of neural stem cell fate decisions through local feedback in the adult vertebrate brain

Neural stem cell (NSC) populations persist in the adult vertebrate brain over a life time, and their homeostasis is controlled at the population level. The nature and properties of these coordination mechanisms remain unknown. Here we combine dynamic imaging of entire NSC populations in their in vivo niche over weeks, pharmacological manipulations, mathematical modeling and spatial statistics, and demonstrate that NSCs use spatiotemporally resolved local feedbacks to coordinate their decision to divide. These involve a Notch-mediated inhibition from transient neural progenitors, and a dispersion effect from dividing NSCs themselves, exerted with a delay of 9-12 days. Simulations from a stochastic NSC lattice model capturing these interactions demonstrate that they are linked by lineage progression and control the spatiotemporal distribution of output neurons. These results highlight how local and temporally delayed interactions occurring between brain germinal cells generate self-propagating dynamics that maintain NSC population homeostasis with specific spatiotemporal correlations.

neuroscience↗

bioRxiv2020

Environmental conditions define theenergetics of bacterial dormancy and itsantibiotic susceptibility

Bacterial cells that stop growing but maintain viability and the capacity to regrow are termed dormant and have been shown to transiently tolerate high concentrations of antimicrobials. The proposed mechanism behind the enhanced survival capabilities of these cells is the reduced energy supply. However, not all reported results are in agreement, and the exact role of energetics remains unsolved. Because dormancy merely indicates growth arrest, which can be induced by various stimuli, we hypothesise that dormant cells may exist in a range of energetic states that depend on the environment. We first establish conditions that are capable of inducing dormancy, and subsequently measure the energy profiles they elicit in single dormant cells. Our simultaneous measurements of proton motive force (PMF), cytoplasmic pH and ATP concentrations confirm that dormant cells exhibit characteristic energetic profiles that can vary in level and dynamics, depending on the stimulus leading to growth arrest. We test whether the energetic makeup is associated with survival to antibiotics of different classes and find that, while growth arrest remains the dominant mechanism enabling survival, some correlations with cellular energetics exist. Our results pave the way to a classification of dormant states based on energy profiles, support a novel relationship between environment and drug susceptibility of dormant cells and suggest that knowledge of the conditions present at the infection site is necessary to design appropriate treatments.

microbiology↗

bioRxiv2019

Escherichia coli’s physiology can turn membrane voltage dyes into actuators

The electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes, and Vm also plays a role in signal transduction. Therefore, measuring it is of great interest, and over the years a variety of techniques has been developed for the purpose. In bacteria, given their small size, Nernstian membrane voltage probes are arguably the favourite strategy, and their cytoplasmic accumulation depends on Vm according to the Nernst equation. However, a careful calibration of Nernstian probes that takes into account the trade-offs between the ease with which the signal from the dye is observed, and the dyes interactions with cellular physiology, is rarely performed. Here we use a mathematical model to understand such trade-offs and, based on the knowledge gained, propose a general work-flow for the characterization of Nernstian dye candidates. We demonstrate the work-flow on the Thioflavin T dye in Escherichia coli, and identify conditions in which the dye turns from a Vm probe into an actuator.\n\nSIGNIFICANCE STATEMENT\n\nThe phospholipid bilayer of a biological membrane is virtually impermeable to charged molecules. Much like in a rechargeable battery, cells harness this property to store an electrical potential that fuels life reactions but also transduces signals. Measuring this electrical potential, also referred to as membrane voltage, is therefore of great interest and a variety of techniques have been employed for the purpose, starting as early as the 1930s. For the case of bacteria, which are smaller in size and possess a stiffer cell wall, arguably the most popular approach to measuring membrane voltage are Nernstian probes that accumulate across the bacterial membrane according to the Nernst potential. The present study characterizes the undesired effects Nernstian probes can have on cell physiology, which can be crucial for the accurate interpretation of experimental results. Using mathematical modelling and experiments, the study provides a general, simple workflow to characterise and minimise these effects.

biophysics↗

bioRxiv2016

Uncovering the underlying mechanisms and whole-brain dynamics of therapeutic deep brain stimulation for Parkinson’s disease

Deep brain stimulation (DBS) for Parkinsons disease is a highly effective treatment in controlling otherwise debilitating symptoms yet the underlying brain mechanisms are currently not well understood. We used whole-brain computational modeling to disclose the effects of DBS ON and OFF during collection of resting state fMRI in ten Parkinsons Disease patients. Specifically, we explored the local and global impact of DBS in creating asynchronous, stable or critical oscillatory conditions using a supercritical bifurcation model. We found that DBS shifts the global brain dynamics of patients nearer to that of healthy people by significantly changing the bifurcation parameters in brain regions implicated in Parkinsons Disease. We also found higher communicability and coherence brain measures during DBS ON compared to DBS OFF. Finally, by modeling stimulation we identified possible novel DBS targets. These results offer important insights into the underlying effects of DBS, which may in time offer a route to more efficacious treatments.

neuroscience↗