Biology subjects

Brambilla, E.

Publications and source records attributed to Brambilla, E..

7 recordsLinked to original sources

bioRxiv2025

Context-Dependent Adaptation in Structured Environments

Adaptive evolution often leads to niche specialization, but successful colonization of a new niche can depend as much on ecological context as on genetic change. This is especially true in spatially structured environments, where the physical construction of habitat and the order of arrival of mutants can shape evolutionary outcomes. In static broth cultures, the air-liquid interface (ALI) provides a high-oxygen niche typically colonized by mat-forming mutants. In Pseudomonas fluorescens, a range of single mutations that upregulate cellulose production give rise to "wrinkly spreader" (WS) types--canonical niche specialists that out-compete ancestral types at the ALI. Yet we discover that this is a half-truth: WS mutants frequently fail to establish when introduced alone at low density, but co-culture with ancestral types rescues colonization. Microscopy and model simulations show that ancestors physically scaffold the ALI, enabling stable attachment and facilitating the in situ emergence of an array of genetically diverse WS mutants. Ancestors later disperse, vacate the niche allowing WS mutant expansion. This transient asymmetric interaction reveals that even strongly adaptive mutations may require ecological facilitation to succeed. More broadly, our findings challenge simple narratives of adaptive replacement and underscore how transient ecological dependencies can shape the trajectory of evolutionary change.

evolutionary biology↗

bioRxiv2024

Glia-enriched stem-cell 3D model of the human brain mimics the glial-immune neurodegenerative phenotypes of multiple sclerosis

The role of central nervous system (CNS) glia in sustaining self-autonomous inflammation and driving clinical progression in multiple sclerosis (MS) is gaining scientific interest. We applied a single transcription factor (SOX10)-based protocol to accelerate oligodendrocyte differentiation from hiPSC-derived neural precursor cells, generating self-organizing forebrain organoids. These organoids include neurons, astrocytes, oligodendroglia, and hiPSC-derived microglia to achieve immunocompetence. Over 8 weeks, organoids reproducibly generated mature CNS cell types, exhibiting single-cell transcriptional profiles similar to the adult human brain. Exposed to inflamed cerebrospinal fluid (CSF) from MS patients, organoids properly mimic macroglia-microglia neuro-degenerative phenotypes and intercellular communication seen in chronic active MS. Oligodendrocyte vulnerability emerged by day 6 post-MS-CSF exposure, with nearly 50% reduction. Temporally-resolved organoid data support and expand on the role of soluble CSF mediators in sustaining downstream events leading to oligodendrocyte death and inflammatory neurodegeneration. Such findings support implementing this organoid model for drug screening to halt inflammatory neurodegeneration.

neuroscience↗

bioRxiv2024

Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome.

Gene expression in bacterial cells is dependent on a genes position along the genome, mainly because of the effects of neighbouring genes expression, but also because of the local activity of nucleoid proteins, differing levels of DNA supercoiling and changes in gene copy number with growth rate and growth phase. This genome position dependence can be a source of specific regulation, however, in some cases it is necessary to have gene expression insulated from these local effects. Escherichia coli cells express ribosomal RNA from multiple operons found at different sites along the genome. The number of ribosomal operons varies in different strains and correlates with the maximal growth rate. rRNA promoters are under the regulation of Fis, H-NS, DNA supercoiling and ppGpp. These factors are known to result in growth phase and growth rate dependent regulation of gene expression. Here we show that the combined action of Fis and H-NS also provides insulation from the activity of both local and global regulatory factors. Furthermore, our results indicate that the presence of a divergently expressed gene can also act as an insulator revealing a DNA supercoiling gradient from the origin to the terminus. The organisation of ribosomal promoters therefore has been selected to allow for gene duplication independently of the influence of local genome organisation and neighbouring genes activity.

cell biology↗

bioRxiv2021

Heparin protects human neural progenitor cells from Zika Virus-induced cell death and preserves their differentiation into mature neural-glia cells

Zika virus (ZIKV) is an arbovirus member of the Flaviviridae family that causes severe congenital brain anomalies in infected fetuses. Human neural progenitor cells (hNPCs) are highly permissive to ZIKV infection, causing inhibition of cell proliferation concomitant with an induction of cell death. We previously demonstrated that pharmaceutical-grade heparin inhibited virus-induced cell death with minor effects on in vitro virus replication in ZIKV-infected hNPCs. Here we show that heparin prevented ZIKV-induced intracellular vacuoles, a signature characteristic of paraptosis, but also inhibited necrosis and apoptosis of hNPCs when grown as neurospheres (NS). Furthermore, heparin preserved the differentiation of both ZIKV-infected human-induced pluripotent stem cells (hiPSC) derived-NPCs and fetus-derived NPCs into neural-glial cells. Collectively, these results highlight the potential neuroprotective effect of heparin that could be re-purposed and exploited to drive the development of novel agents for preventing ZIKV damage.

microbiology↗

bioRxiv2020

Neural precursor cells contribute to decision-making by tuning striatal connectivity via secretion of IGFBPL-1

The adult brain retains endogenous neural stem/precursors cells (eNPCs) in two major neurogenic niches, the subgranular zone (SGZ) in the hippocampus and the subventricular zone (SVZ). While in humans and rodents the SGZ contributes to memory functions by generating new neurons that integrate into hippocampal circuitry, the role of eNPCs of the SVZ is less clear. SVZ-eNPCs contribute to the generation of new neurons fated to the olfactory bulb (OB) in rodents but not in humans where they are thought to contribute to striatal neurogenesis as a result of tissue damage. Here, we show in mice and humans a novel non-neurogenic physiological role of adult SVZ-eNPCs in supporting cognitive functions by regulating striatal neuronal activity. We first provide evidence that GABAergic transmission between parvalbumin-expressing fast-spiking interneurons (FSIs) and medium spiny neurons (MSNs) is tuned by SVZ-eNPCs via secretion of Insulin-Like Growth Factor Binding Protein Like 1 (IGFBPL-1) that, in turn, regulates the Insulin-Like Growth Factor (IGF-1) signalling cascade. Consistently, selective ablation of SVZ-eNPCs and in vivo disruption of the IGF-signalling determine the impairment of intrastriatal coherence. A finding associated with a higher failure rate of GABAergic transmission mediated by FSIs and with striatum-related behavioural dysfunctions impairing decision making. Human validation studies revealed IGFBPL-1 expression in the SVZ and in foetal and induced-pluripotent stem cell-derived NPCs as well as a strong correlation in neurological patients between SVZ pathological damage, reduction of striatum volume and impairment of information processing speed. All in all, our results highlight a novel non-neurogenic homeostatic role exerted by SVZ-eNPCs on striatal GABAergic neurons that might contribute to cognitive processes involving decisions-making tasks.

neuroscience↗

bioRxiv2019

Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data

The emergence of Next-Generation Sequencing (NGS) has revolutionized the way of reaching a genome sequence, with the promise of potentially providing a comprehensive characterization of DNA variations. Nevertheless, detecting somatic mutations is still a difficult problem, in particular when trying to identify low abundance mutations such as subclonal mutations, tumour-derived alterations in body fluids or somatic mutations from histological normal tissue. The main challenge is to precisely distinguish between sequencing artefacts and true mutations, particularly when the latter are so rare they reach similar abundance levels as artefacts. Here, we present needlestack, a highly sensitive variant caller, which directly learns from the data the level of systematic sequencing errors to accurately call mutations. Needlestack is based on the idea that the sequencing error rate can be dynamically estimated from analyzing multiple samples together. We show that the sequencing error rate varies across alterations, illustrating the need to precisely estimate it. We evaluate the performance of needlestack for various types of variations, and we show that needlestack is robust among positions and outperforms existing state-of-the-art method for low abundance mutations. Needlestack, along with its source code is freely available on the GitHub plateform: https://github.com/IARCbioinfo/needlestack.

bioinformatics↗

bioRxiv2019

A decrease in transcription capacity limits growth rate upon translation inhibition

AbstractIn bacterial cells, inhibition of ribosomes by sublethal concentrations of antibiotics leads to a decrease in growth rate despite an increase in ribosome content. The limitation of ribosomal activity results in an increase in the level of expression from ribosomal promoters; this can deplete the pool of RNA polymerase (RNAP) that is available for the expression of non-ribosomal genes. However, the magnitude of this effect remains to be quantified. Here, we use the change in the activity of constitutive promoters with different affinities for RNAP to quantify the change in the concentration of free RNAP. The data are consistent with a significant decrease in the amount of RNAP available for transcription of both ribosomal and non ribosomal genes. Results obtained with different reporter genes reveal an mRNA length dependence on the amount of full-length translated protein, consistent with the decrease in ribosome processivity affecting more strongly the translation of longer genes. The genes coding for the {beta} and {beta} subunits of RNAP are amongst the longest genes in the E. coli genome, while the genes coding for ribosomal proteins are among the shortest genes. This can explain the observed decrease in transcription capacity that favors the expression of genes whose promoters have a high affinity for RNAP, such as ribosomal promoters.\n\nImportanceExposure of bacteria to sublethal concentrations of antibiotics can lead to bacterial adaptation and survival at higher doses of inhibitors, which in turn can lead to the emergence of antibiotic resistance. The presence of sublethal concentrations of antibiotics targeting translation results in an increase in the amount of ribosomes per cell and a decrease in the cells growth rate. In this work, we have found that inhibition of ribosome activity can result in a decrease in the amount of free RNA polymerase available for transcription, thus limiting the protein expression rate via a different pathway than what was expected. This result can be explained by our observation that long genes, such as those coding for RNA polymerase subunits, have a higher probability of premature translation termination in the presence of ribosome inhibitors, while expression of short ribosomal genes is affected less, consistent with their increased concentration.

microbiology↗