Biology subjects

Diamanti, E.

Publications and source records attributed to Diamanti, E..

6 recordsLinked to original sources

bioRxiv2025

Working memory expands shared task representations in cortex

Cognition is thought to emerge from the flexible organization of neural activity, yet how this organization reconfigures across behaviors varying in cognitive load remains unclear. We investigated how the structure of working-memory representations in the cortex compares to task representations that do not involve working memory. We used a task-switching paradigm in virtual reality, where mice alternated between a navigation-based working-memory task and a simpler task with matched sensorimotor demands. During behavior, we simultaneously imaged three cortical areas: higher visual area AM, and two association areas--premotor (M2) and retrosplenial cortex. At the single-neuron level, trial-averaged activity appeared similar across tasks. However, pairwise correlations decreased during the working-memory task, particularly in association areas. In addition, the corresponding linear task subspace explained the variance of both tasks equally well, whereas the simpler task subspace failed to do so, suggesting an asymmetric relationship between them. Nonlinear dimensionality reduction revealed a shared low-dimensional structure across tasks. Yet, the organization of neuronal firing fields along this shared structure accounted for the difference in pairwise correlations: in the working-memory task, firing fields were more disjoint, especially among neurons in association areas that formed sequences along the memory dimension. Moreover, the degree of overlap between these firing fields predicted the mices behavioral reliance on working memory. We conclude that behaviors varying in cognitive demands are supported by a single low-dimensional neural structure, which can expand or contract depending on cognitive load. We thus provide a framework for how task representations across the cortex reconfigure to support cognitive processes.

neuroscience↗

bioRxiv2024

IspE Kinase as an Anti-infective Target: Role of a Hydrophobic Pocket in Inhibitor Binding

Enzymes of the methylerythritol phosphate (MEP) pathway are potential targets for antimicrobial drug discovery. Here we focus on 4-diphosphocytidyl-2-C-methyl-D-erythritol (IspE) kinase from the MEP pathway. We use biochemical and structural biology methods to investigate homologs from the pathogenic microorganisms; Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii. We determined the X-ray structures of IspE-inhibitor complexes and studied selected inhibitors binding modes targeting the substrate pocket. The experimental results indicate the need for distinct inhibitor strategies due to structural differences among IspE homologs, particularly for A. baumannii IspE, which displays unique inhibitory profile due to a tighter hydrophobic subpocket in the substrate binding site. This study enhances our understanding of the MEP enzymes and sets the stage for structure-based drug design of selective inhibitors to combat pathogenic microorganisms.

biophysics↗

bioRxiv2023

The Nucleosome Remodelling and Deacetylation complex coordinates the transcriptional response to lineage commitment in pluripotent cells

As cells exit the pluripotent state and begin to commit to a specific lineage they must activate genes appropriate for that lineage while silencing genes associated with pluripotency and preventing activation of lineage-inappropriate genes. The Nucleosome Remodelling and Deacetylation (NuRD) complex is essential for pluripotent cells to successfully undergo lineage commitment. NuRD controls nucleosome density at regulatory sequences to facilitate transcriptional responses, and also has been shown to prevent unscheduled transcription (transcriptional noise) in undifferentiated pluripotent cells. How these activities combine to ensure cells engage a gene expression program suitable for successful lineage commitment has not been determined. Here we show that while NuRD is not required to silence all genes, its activity is important to restrict expression of genes primed for activation upon exit from the pluripotent state, and that NuRD activity facilitates their subsequent transcriptional activation. We further show that NuRD coordinates gene expression changes, which acts to maintain a barrier between different stable states. Thus NuRD-mediated chromatin remodelling serves multiple functions, including reducing transcriptional noise, priming genes for activation and coordinating the transcriptional response to facilitate lineage commitment.

developmental biology↗

bioRxiv2022

Adaptation to ex vivo culture drives human haematopoietic stem cell loss of repopulation capacity in a cell cycle independent manner

Loss of long-term haematopoietic stem cell function (LT-HSC) hampers the success of ex vivo HSC gene therapy and expansion procedures, but the kinetics and the mechanisms by which this occurs remain incompletely characterized. Here through time-resolved scRNA-Seq, matched in vivo functional analysis and the use of a reversible in vitro system of early G1 arrest, we define the sequence of transcriptional and functional events occurring during the first ex vivo division of human LT-HSCs. We demonstrate that contrary to current assumptions, loss of long-term repopulation capacity during culture is independent of cell cycle progression. Instead it is a rapid event that follows an early period of adaptation to culture, characterised by transient gene expression dynamics and constrained global variability in gene expression. Cell cycle progression however contributes to the establishment of differentiation programmes in culture. Our data have important implications for improving HSC gene therapy and expansion protocols.

cell biology↗

bioRxiv2021

Endothelial-specific Gata3 expression is required for haematopoietic stem cell generation

To generate sufficient numbers of transplantable haematopoietic stem cells (HSCs) in vitro, a detailed understanding of how this process takes place in vivo is essential. The endothelial-to-haematopoietic transition (EHT), which culminates in the production of the first HSCs, is a highly complex process during which key regulators are switched on and off at precise moments and which is embedded into a myriad of microenvironmental signals from surrounding cells and tissues. We have previously demonstrated an HSC-supportive function for Gata3 within the sympathetic nervous system and the sub-aortic mesenchyme, but show here that it also plays a cell-intrinsic role during the EHT. It is expressed in haemogenic endothelial cells and early HSC precursors, where its expression correlates with a more quiescent state. Importantly, endothelial-specific deletion of Gata3 shows that it is functionally required for these cells to mature into HSCs, placing Gata3 at the core of the EHT regulatory network.

developmental biology↗

bioRxiv2019

Single-cell molecular profiling provides a high-resolution map of basophil and mast cell differentiation

Differentiation of hematopoietic stem and progenitor cells ensure a continuous supply of mature blood cells. Recent models of differentiation are represented as a landscape, in which individual progenitors traverse a continuum of multipotent cell states before reaching an entry point that marks lineage commitment. Basophils and mast cells have received little attention in these models and their differentiation trajectories are yet to be explored. Here, we have performed multicolor flow cytometry and high-coverage single-cell RNA sequencing analyses to chart the differentiation of hematopoietic progenitors into basophils and mast cells in mouse. Analysis of flow cytometry data reconstructed a detailed map of the differentiation, including a bifurcation of progenitors into two specific trajectories. Molecular profiling and pseudotime ordering of the single cells revealed gene expression changes during differentiation, with temporally separated regulation of mast cell protease genes. We validate that basophil and mast cell signature genes increased along the trajectories into their respective lineage, and we demonstrate how genes critical for each respective lineage are upregulated during the formation of the mature cells. Cell fate assays showed that multicolor flow cytometry and transcriptional profiling successfully predict the bipotent phenotype of a previously uncharacterized population of basophil-mast cell progenitor-like cells in mouse peritoneum. Taken together, we provide a detailed roadmap of basophil and mast cell development through a combination of molecular and functional profiling.

immunology↗