Biology subjects

Esposito, M.

Publications and source records attributed to Esposito, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A behaviourally normed database of 1,377 natural sounds for auditory cognition and neuroscience

Natural-sound research requires stimulus sets that combine acoustic standardization with detailed behavioural characterization. We present 1,377 two-second sounds representing 240 expert-defined source--action classes. We call this database "MaMa Sounds", as it resulted from the collaborative effort of two academic teams in Maastricht and Marseille. The sounds were manually curated, segmented, sampled at 16 kHz, and labelled with a noun identifying the source and a verb identifying the action. We release deidentified trial-level identification and familiarity data together with multiple per-sound norms (e.g., identification accuracy, confidence and agreement; familiarity), along with overall norms derived with principal component analysis. Noun, verb, and joint noun--verb norms are provided as direct means and medians with the number of contributing observations. This battery preserves process-specific information, while two principal-component scores provide compact overall behavioural-identifiability measures derived from response ease, semantic correspondence, agreement, and familiarity. The repository also contains deterministic response-cleaning code, participant and reference Word2Vec representations, and code reproducing the public sound-level tables. The resource supports stimulus selection, matching, and continuous modelling in auditory cognition and neuroscience.

neuroscience↗

bioRxiv2026

Multiscale Temporal Processing Supports Sound Recognition under Causal Constraints

The auditory system operates under a fundamental computational constraint: at any moment, it has access only to past and present acoustic information. At the same time, it processes sounds across multiple temporal scales, although the computational advantage of this organization remains unclear. Despite both being defining characteristics of biological auditory processing, causal processing and multiscale temporal processing are rarely considered together in computational models. Here, we introduce the Multiscale Convolutional Recurrent Neural Network (MSCRNN) architecture, a brain-inspired model designed to test whether processing sounds across multiple temporal contexts improves recognition under causal constraints. Multiscale processing substantially improved recognition under causal constraints, enabling performance comparable to non-causal architectures after an initial evidence-accumulation period while providing only limited benefit when future acoustic information was available. Analyses of the networks internal representations revealed a progressive transformation from stream-specific acoustic representations to increasingly integrated category-level representations across recurrent processing stages. Together, these findings provide a computational rationale for why biological auditory systems may benefit from multiscale temporal processing under causal constraints and establish the MSCRNN as an interpretable framework for generating and testing hypotheses about the temporal dynamics of auditory processing using electrophysiological and neuroimaging data.

neuroscience↗

bioRxiv2026

An imaging framework for nuclei-based three-dimensional cell quantification in intact tissue using phase-contrast X-ray CT

Objective. Quantitative analysis of cellular morphology and spatial organisation within intact tissue remains challenging, particularly when three-dimensional information must be preserved. This study investigates whether laboratory propagation-based phase-contrast X-ray computed tomography (CT) can support nuclei-based quantitative analysis in unstained tissue while retaining the surrounding tissue architecture. Approach. We propose a nuclei-based quantitative imaging workflow that combines laboratory propagation-based phase-contrast X-ray CT with volumetric segmentation. Intact unstained liver tissue was imaged at cellular resolution, then nuclei were segmented throughout the reconstructed volume and quantitative metrics describing the nuclear morphology and spatial organisation were extracted. The resulting measurements were evaluated in two non-overlapping volumes of interest and compared with histological reference data using thickness-matched virtual CT slices. Main results. The proposed workflow enabled visualisation and segmentation of individual nuclei throughout intact unstained liver tissue. Comparable nuclear morphology and spatial organisation metrics were obtained from two non-overlapping volumes of interest, indicating stable segmentation performance within the analysed specimen. Comparison with H&E histology demonstrated broad agreement in nuclear morphology. Significance. This work demonstrates the feasibility of nuclei-based quantitative analysis using laboratory phase-contrast X-ray CT in intact unstained tissue. The approach provides volumetric cellular information while preserving tissue architecture and may complement conventional histological assessment in applications requiring three- dimensional analysis. These findings highlight the potential of laboratory phase-contrast CT for quantitative tissue characterisation and spatial cellular analysis

bioengineering↗

bioRxiv2026

Comparative analysis of BCG vaccination routes in mice reveals preferential reprogramming of pulmonary macrophages upon mucosal administration.

Bacille Calmette-Guerin (BCG) is the only licensed vaccine against tuberculosis (TB) but provides inconsistent protection against disease. Studies in non-human primates show that intravenous BCG confers superior protection compared to intradermal vaccination, yet how different vaccination routes reprogram lung immunity in mice - the primary model for mechanistic studies - remains incompletely defined at single cell or spatial resolution. Moreover, while lung macrophages are key effectors during Mycobacterium tuberculosis infection, most studies have focused on alveolar macrophages, leaving interstitial macrophage responses to vaccination largely unexplored. Here, we define the cellular and spatial immune landscape shaped by three BCG vaccination routes in mice using flow cytometry, single-cell RNA sequencing, and spatial transcriptomics. Comparing intratracheal (IT), intravenous (IV), and subcutaneous (SC) vaccination, we demonstrate that mucosal IT delivery uniquely reprograms interstitial macrophages, establishes spatially organized immune hubs with CD4 T cells, and provides superior protection against infectious challenge. These findings identify IM as key mediators of mucosal vaccine-induced protection and provide a framework for the rational optimization of vaccines against respiratory pathogens.

immunology↗

bioRxiv2025

Access to germinal center IL-4 microniches drives tissue-divergence of IgE memoryresponses

Immunoglobulin E (IgE) drives allergic disease, yet how memory B cells (MBCs) reactivate to produce IgE, and how tissue localization shapes recall responses, remains unclear. Using mouse models of airborne exposure to house dust mites and Alternaria, we found that allergen sensitization generates lymphoid- and lung-resident MBCs. Upon allergen re-exposure, these populations followed distinct differentiation trajectories: lymph node MBCs engaged a germinal center (GC)-dependent pathway that generated both IgG1 and IgE plasma cells (PCs), whereas lung MBCs followed a GC-independent route producing mainly IgG1 PCs. GC re-entry granted MBCs access to an IL-4-rich microniche formed by Tfh cells, which was essential for IgE production. Disrupting GC re-entry, IL-4 signaling, or Tfh-derived IL-4 during recall markedly reduced allergen-specific IgE titers. These findings reveal a spatially and cytokine-restricted mechanism that confines IgE memory to lymphoid organs, positioning GC IL-4 microniches as anatomical safeguards against IgE production at barrier sites frequently exposed to environmental antigens.

immunology↗

bioRxiv2025

STAMPS: Signal-peptide Transformer for Augmenting Mammalian Protein Secretion

While secretion plays a key role in the diverse applications of cell engineering, to date only a handful of mammalian signal peptides have been characterised in depth and systematic efforts to build novel variants remain sporadic. We present STAMPS (Signal-peptide Transformer for Augmenting Mammalian Protein Secretion), a generative, autoregressive transformer fine-tuned on [~]6,000 mammalian signal peptides to design de novo sequences that modulate and enhance secretion across proteins and hosts. We show that STAMPS can be used to identify candidate signal peptides that outperform the widely used IgG {kappa} light-chain leader (IgKL) when used to secrete EGFP in HEK293T and CHO cells, and hEPO in HEK293T cells. When incorporated in an industrial cell line development framework, STAMPS leads to the generation of signal peptides that yield [~]2.3-fold gain in secretion of a VHH-Fc compared to the internal industrial benchmark in CHO G22 cells, with the same candidates ranking highly in both CHO and HEK293T hosts. Sequence-to-function analysis highlights a longer, strongly hydrophobic core and a tightly positioned cleavage site as drivers of this strong performance. Together, these results establish data-driven, generative design of mammalian signal peptides as a practical route to tune and improve secretion for bioproduction and cell engineering applications.

synthetic biology↗

bioRxiv2025

Role of Klhl14 in senescence and epithelial-to-mesenchymal transition via TGF- modulation

KLHL14, a component of an E3-ubiquitin ligase complex, has emerged as a context-dependent oncogene or tumor suppressor, particularly important for thyroid development. Yet its role in thyroid biology remains largely unexplored. In this study, we uncover a central function for KLHL14 in maintaining thyroid epithelial identity and regulating tissue homeostasis. Using a thyroid organoid model, we show that KLHL14 is essential for the proper growth and maturation of thyroid cells. Reduction of KLHL14 expression disrupts organoid development and triggers a dual cellular response involving features of both senescence and epithelial-to-mesenchymal transition. These phenotypic changes are accompanied by increased cellular plasticity and migratory capacity. Mechanistically, we identify TGF-{beta} signaling as a key pathway activated upon KLHL14 depletion, contributing to the observed cellular reprogramming. Inhibiting TGF-{beta} restores growth and reduces markers of senescence and EMT, positioning KLHL14 as an upstream modulator of this signaling axis. These findings reveal a previously unrecognized role for KLHL14, suggesting that its dysfunction may contribute to disease progression in aggressive thyroid cancers. This work broadens our understanding of thyroid epithelial biology and provides molecular insights extendable to other tissues, highlighting KLHL14 as a potential target for therapeutic interventions in malignancies displaying the herein explored features.

cell biology↗

bioRxiv2025

HIF-1α+ CD4 T cells coordinate a tissue resident immune cell network in the lung

A deeper understanding of how tissue localized immune cells arise and function is critical for developing mucosal vaccines. Currently, there are no murine models that specifically target tissue T cells while leaving their lymphoid counterparts untouched. Here we leverage the observation that during influenza infection, HIF-1 regulatory activity is higher in the lung compared to lymph node CD4 T cells. Inducible deletion of Hif1a in CD4 T cells, at the onset of its activity in the lung, reduces the tissue resident T cell compartment with minimal impact on peripheral immunity. HIF-1-active CD4 T cells occupy the border of tertiary lymphoid structures, where they coordinate an IL-21-dependent network of spatially co-localized immune cells including macrophages, NK cells and IgA+ B cells. A similar HIF-1-dependent network is engaged in a lung adenocarcinoma model, highlighting a broader role for HIF-1+ CD4 T cells in integrating protective immunity during infection and cancer.

immunology↗

bioRxiv2024

Partitioning the genomic journey to becoming Homo sapiens

What makes us human? Homo sapiens diverged from its ancestors in fundamental ways, as reflected in recent genomic acquisitions, such as the PAR2-Y chromosome translocation. Here we show that despite morphological and cultural differences between modern and archaic humans, these human groups share these recent acquisitions. Our modern lineage shows recent functional variants in only 56 genes, of which 24 are linked to brain functions and skull morphology. Nevertheless, these acquisitions failed to introgress into Neanderthals when archaic and modern populations admixed after 350 kya, suggesting their exclusive link to the modern human niche or that Neanderthals small population size hindered their spread. Taken together, our results point to a scenario where Modern and Archaic should be regarded as populations of an otherwise common human species, which independently accumulated mutations and cultural innovations.

evolutionary biology↗

bioRxiv2024

Egocentric anchoring-and-adjustment of social knowledge in the hippocampal formation

Recent work suggests the hippocampal formation(HF) assimilates relational social knowledge similar to how it transforms egocentric spatial cues into map-like representations. Yet whether hippocampal map-like representations of social knowledge still represent lingering egocentric biases is unclear. We test if a prominent egocentric bias involving an implicit reliance on self-knowledge when rating others, anchoring-and-adjustment, is present when the relative attributes of different social entities are assimilated by the HF. Participants provided likelihood ratings of partaking in everyday activities for themselves, fictitious individuals, and familiar social groups. Adapting a functional neuroimaging task from Kaplan and Friston, participants then learned a strangers preference for an activity relative to one of the fictitious individuals and inferred how the strangers preference related to the groups preferences. Egocentric anchoring-and-adjustment was present when participants rated the other entities. Isolating the neural representation of egocentric anchoring-and-adjustment when flexibly comparing different social entities, the HF and dorsomedial prefrontal cortex(dmPFC) represented group-self rating discrepancy. Furthermore, the HF also reflected how well group preferences were remembered, where memory for group preferences correlates with task performance. We found the HF selectively represented group identity over other learned entities, confirming that the HF was primarily engaged by social comparisons in a more ample frame of reference. Taken together, these results imply that self-knowledge influences how the HF assimilates map-like knowledge about others.

neuroscience↗

bioRxiv2024

Flexible hippocampal representation of abstract boundaries supports memory-guided choice.

Hippocampal cognitive maps encode the relative locations of spatial cues in an environment and adapt their representation when boundaries geometrically change. Hippocampal cognitive maps can represent abstract knowledge, yet its unclear whether the hippocampus is sensitive to changes to the extreme coordinates, boundaries, of abstract spaces. We created a memory-guided choice task to test whether the human hippocampus and medial prefrontal cortex(mPFC) flexibly learn abstract boundary representations in distinct two-dimensional(2D) knowledge spaces. Participants built up a 2D map-like representation of abstract boundaries, where the hippocampus and mPFC represented a decision cues Euclidean distance to the closest boundary. Notably, mPFC distance representations selectively reflected individual performance improvements during the task. Testing for neural sensitivity to boundary-defined contextual changes, only the hippocampus flexibly represented abstract boundaries, which related to choice behavior. These findings suggest that abstract knowledge retrieval within dynamically changing contexts is facilitated by generalized mPFC and flexible hippocampal boundary representations.

neuroscience↗

bioRxiv2024

Bridging Auditory Perception and Natural Language Processing with Semantically informed Deep Neural Networks

Sound recognition is effortless for humans but poses a significant chal-lenge for artificial hearing systems. Deep neural networks (DNNs), especially convolutional neural networks (CNNs), have recently sur-passed traditional machine learning in sound classification. However, current DNNs map sounds to labels using binary categorical variables, neglecting the semantic relations between labels. Cognitive neuroscience research suggests that human listeners exploit such semantic informa-tion besides acoustic cues. Hence, our hypothesis is that incorporating semantic information improves DNNs sound recognition performance, emulating human behavior. In our approach, sound recognition is framed as a regression problem, with CNNs trained to map spec-trograms to continuous semantic representations from NLP models (Word2Vec, BERT, and CLAP text encoder). Two DNN types were trained: semDNN with continuous embeddings and catDNN with cat-egorical labels, both with a dataset extracted from a collection of 388,211 sounds enriched with semantic descriptions. Evaluations across four external datasets, confirmed the superiority of semantic labeling from semDNN compared to catDNN, preserving higher-level relations. Importantly, an analysis of human similarity ratings for natural sounds, showed that semDNN approximated human listener behavior better than catDNN, other DNNs, and NLP models. Our work contributes to understanding the role of semantics in sound recognition, bridging the gap between artificial systems and human auditory perception.

neuroscience↗

bioRxiv2023

Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase

BackgroundAntibiotic resistance, which is mediated by environmental reservoirs, poses a threat to human and animal health. Aquatic biofilms impacted by treated wastewater (WW) are known environmental reservoirs for antibiotic resistance, however the specific influence of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited as to whether genes with low sequence similarity to reference ARGs actually encode for functional ARGs, particularly within complex aquatic microbial communities. ResultsTo disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or nonultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in metagenomic abundances in biofilms grown with increasing percentages of nonultrafiltered WW. In contrast, sulfonamide and BEL family beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to nonultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs which exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing low sequence identity with known ARGs. ConclusionsThis discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted metagenomic analysis on the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms.

microbiology↗

bioRxiv2023

Vitamin B12 status and folic acid supplementation influence mitochondrial heteroplasmy levels in mice as they age.

One-carbon metabolism is a complex network of metabolic reactions that are essential for cellular function including DNA synthesis. Vitamin B12 and folate are micronutrients that are utilized in this pathway and their deficiency can result in the perturbation of one-carbon metabolism and subsequent perturbations in DNA replication and repair. This effect has been well characterized in nuclear DNA but to date, mitochondrial DNA (mtDNA) has not been investigated extensively. Mitochondrial variants have been associated with several inherited and age-related disease states; therefore, the study of factors that impact heteroplasmy are important for advancing our understanding of the mitochondrial genomes impact on human health. Heteroplasmy studies require robust and efficient mitochondrial DNA enrichment to carry out in-depth mtDNA sequencing. Many of the current methods for mtDNA enrichment can introduce biases and false positive results. Here we use a method that overcomes these limitations and have applied it to assess mitochondrial heteroplasmy in mouse models of altered one-carbon metabolism. Vitamin B12 deficiency was found to cause increased levels of mitochondrial DNA heteroplasmy across all tissues that were investigated. Folic acid supplementation also contributed to elevated mitochondrial DNA heteroplasmy across all mouse tissues investigated. Heteroplasmy analysis of human data from the Framingham Heart Study suggested a potential sex-specific effect of folate and vitamin B12 status on mitochondrial heteroplasmy. This is a novel relationship that may have broader consequences for our understanding of one-carbon metabolism, mitochondrial related disease and the influence of nutrients on DNA mutation rates. Significance StatementUsing a sensitive method for mitochondrial heteroplasmy analysis, we show that both vitamin B12 and folic acid can impact mitochondrial DNA mutation. This effect requires further investigation of the potential impact on humans.

molecular biology↗

bioRxiv2022

Mito-SiPE: A sequence-independent, PCR-free mitochondrial DNA enrichment method for ultra-deep sequencing that minimises amplification and alignment artifacts.

BackgroundDeep sequencing is often used to measure somatic variation in the mitochondrial genome. Selective enrichment methods, such as PCR amplification or probe hybridization/capture are commonly used. These methods can introduce bias and are prone to contamination by nuclear-mitochondrial sequences (NUMTs); elements that can introduce artefacts into analyses such as an assessment of mitochondrial heteroplasmy. ResultsHere, we demonstrate a method to obtain ultra-deep (>80,000X) sequencing coverage of the mitochondrial genome by selectively purifying the intact organelle itself using differential centrifugation and alkaline lysis. We applied this approach to seven different mouse tissues. Isolation of mitochondria yields a preparation of highly enriched mtDNA. We compared this method to the commonly used PCR-based method. Mito-SiPE avoids false-heteroplasmy calls that occur when long-range PCR amplification is used for mtDNA enrichment. DiscussionWe have described a modified version of a long-established protocol for purifying mtDNA and have quantified the increased level of mitochondrial DNA post-enrichment in 7 different mouse tissues. This method will enable researchers to identify changes in low-frequency heteroplasmy without introducing PCR biases or NUMT contamination that are falsely identified as heteroplasmy when long-range PCR is used.

genomics↗

bioRxiv2022

Foxg1 regulates translation of neocortical neuronal genes, including the main NMDA receptor subunit gene, Grin1.

Mainly known as a transcription factor patterning the rostral brain and governing its histogenesis, Foxg1 has been also detected outside the nucleus, however biological meaning of that has been only partially clarified. Here, moving from Foxg1 expression in cytoplasm of neocortical neurons, we investigated its implication in translational control. We documented an impact of Foxg1 on ribosomal recruitment of Grin1-mRNA, encoding for the main subunit of NMDA receptor. Next, we showed that Foxg1 increases Grin1 protein level by enhancing translation of its mRNA, while not increasing its stability. Such enhancement was associated to augmented translational initiation and, possibly, polypeptide elongation. Molecular mechanisms at the basis of this activity included Foxg1 interaction with Eif4e and Eef1d as well as with Grin1-mRNA. Besides, we found that, within murine neocortical cultures, Grin1 de novo synthesis undergoes a prominent and reversible, homeostatic regulation and Foxg1 is instrumental to that. Finally, through TRAP-seq, we discovered that Foxg1 is implicated in the translation of hundreds of neuronal genes at the level of ribosome engagement and progression. All that points to Foxg1 as a key effector, crucial to multi-scale temporal tuning of neocortical pyramid activity, an issue with profound physiological and neuropathological implications.

molecular biology↗

bioRxiv2021

An epigenetic switch regulates the ontogeny of AXL positive/EGFR-TKI resistant cells by modulating miR-335 expression

Lung cancer remains the leading cause of cancer-related mortality worldwide, despite current advancements in research and therapeutics. Many patients diagnosed with lung cancer will develop resistance to chemotherapeutic agents. In the context of non-small cell lung cancers (NSCLC) harboring EGFR oncogenic mutations, augmented levels of AXL and GAS6 have been found to drive Erlotinib resistance in certain tumors with mesenchymal-like features. By studying the ontogeny of AXL-positive cells, we have identified a novel non-genetic mechanism of drug resistance based on cell-state transition. We demonstrate that AXL-positive cells are already present as a sub-population of cancer cells in Erlotinib-naive tumors and tumor-derived cell lines, and that the expression of AXL is regulated through a stochastic mechanism centered on the epigenetic regulation of miR-335. The existence of a cell-intrinsic program through which AXL-positive/Erlotinib-resistant cells emerge infers the need of treating tumors harboring EGFR-oncogenic mutations upfront with combinatorial treatments targeting both AXL-negative and AXL-positive cancer cells.

cancer biology↗

bioRxiv2020

Arousal levels explain inter-subject variability of neuromodulation effects

Over the past two decades, the postulated modulatory effects of transcranial direct current stimulation (tDCS) on the human brain have been extensively investigated, with attractive real-world applications. However, recent concerns on reliability of tDCS effects have been raised, principally due to reduced replicability and to the great interindividual variability in response to tDCS. These inconsistencies are likely due to the interplay between the level of induced cortical excitability and unaccounted individual state-dependent factors. On these grounds, we aimed to verify whether the behavioural effects induced by a common prefrontal tDCS montage were dependent on the participants arousal levels. Pupillary dynamics were recorded during an auditory oddball task while applying either a sham or real tDCS. The tDCS effects on reaction times and pupil dilation were evaluated as a function of subjective and physiological arousal predictors. Both predictors significantly explained performance during real tDCS, namely reaction times improved only with moderate arousal levels; likewise, pupil dilation was affected according to the ongoing levels of arousal. These findings highlight the critical role of arousal in shaping the neuromodulatory outcome, and thus encourage a more careful interpretation of null or negative results.

neuroscience↗