Biology subjects

Rossi, R.

Publications and source records attributed to Rossi, R..

17 recordsLinked to original sources

bioRxiv2026

A Modular Bio-Hybrid Skin Model for Optical Testing Applications

Synthetic optical skin models offer reproducible, tunable optical properties but lack biological responsiveness, while tissue engineered skin models provide cellular authenticity but suffer from optical variability and limited controllability. The growing demand for alternatives to animal models in the development and validation of optical biomedical technologies highlights the need for a new class of test system that combines the strengths of both approaches while addressing their respective limitations. Here, we introduce the concept of a modular biohybrid skin model, a new testing concept that integrates an optically defined artificial epidermal layer, incorporating polydopamine nanoparticles for changes in skin tone, with living human keratinocytes in two and three-dimensional configurations. In the Optical Protection Model, UV-B-induced apoptosis in primary keratinocytes is quantitatively modulated by model pigmentation level, demonstrating a relationship between optical attenuation and caspase 3/7 activity across three artificial skin tone conditions. In a Structured Dermal Model, keratinocytes seeded onto a hydrogel scaffold localize within follicle-like microcavities, as confirmed by live/dead staining and confocal z-stack imaging. Together, these experiments lead to a new category of test system in the space between inert optical models and variable tissue models that may contribute to reducing the reliance on animal models in biomedical optics.

bioengineering↗

bioRxiv2026

Seven mutations unlock strict synthetic methylotrophy in engineered Pseudomonas putida

Methanol is a reduced, soluble one-carbon (C1) feedstock for sustainable bioproduction, but converting this potential into robust microbial growth remains difficult. Several synthetic C1 assimilation routes depend on autocatalytic cycles, whose operation requires coordinated control of redox balance, toxic intermediates, substrate regeneration, and host regulation. Here, we implemented the serine-threonine cycle (STC) in the soil bacterium Pseudomonas putida and used growth-coupled selection with adaptive laboratory evolution (ALE) to transition from mixotrophic C1 incorporation to strict methylotrophy. The evolved strain grew with methanol as the sole carbon and energy source under atmospheric CO2 with a doubling time of ca. 40 h. Whole-genome sequencing, reverse genetics, biosensors, isotope labelling, and comparative RNA sequencing showed that evolution repeatedly targeted native pyrroloquinoline quinone (PQQ)-dependent methanol oxidation, membrane-bound transhydrogenase activity, glycine regeneration, STC enzyme balance, and global regulatory nodes. Additional ALE under glycine-methanol co-feeding increased growth rates and exposed further targets for improving cycle flux. These results establish P. putida as a chassis for strict synthetic methylotrophy and define actionable engineering routes toward C1 biomanufacturing. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/739708v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1642d2dorg.highwire.dtl.DTLVardef@1d203d1org.highwire.dtl.DTLVardef@f8a5d7org.highwire.dtl.DTLVardef@4fe272_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

Antidepressants interact with sex steroid receptors and their intracellular signaling components

There is growing interest in understanding how hormonal signaling pathways contribute to the pathophysiology of mood disorders, based on the premise that fluctuations in sex hormones influence mood, a relationship particularly evident in conditions such as premenstrual dysphoric disorder, prenatal depression, postpartum depression, and perimenopausal depression. Estrogen receptor alpha (ER) is predominantly localized in the nucleus, but can also be associated with the cell membrane, thus mediating a broad range of genomic and non-genomic effects through distinct intracellular pathways. By employing a combination of computational simulations and in vitro biochemical and cell-based assays, we systematically evaluated the potential binding and functional interactions of antidepressant compounds with ER. Our results provide compelling evidence that antidepressants may not only affect classical monoaminergic targets but also modulate hormone receptor activity, particularly that of ER. These findings are consistent with the hypothesis that ER plays an important role in mood regulation and highlight it as a potential therapeutic target. Moreover, this work raises the possibility that the clinical efficacy of certain antidepressants may, at least in part, derive from their capacity to influence estrogen receptor-mediated signaling. Significance statementClinical observations suggest a link between female sex hormones and mood, highlighted by the higher prevalence of depression in women and increased vulnerability to depression during hormonal fluctuations. Here, we report that structurally diverse conventional and rapid-acting antidepressants directly interact with estrogen receptor alpha (ER). This interaction is associated with rapid intracellular signaling in cellular models. These findings indicate that, alongside their conventional targets, antidepressants may also engage sex steroid receptor components and signaling. This work broadens our basic understanding of antidepressant pharmacology at the cellular level, offering an additional perspective that may inform future research into the biological mechanisms of mood disorders and suggest a framework for developing targeted therapies for hormone-associated depressive disorders.

pharmacology and toxicology↗

bioRxiv2026

Cortical plasticity of the tactile mirror system in borderline personality disorder

Individuals with borderline personality disorder (BPD) show alterations in empathic abilities, potentially involving automatic simulation processes supported by mirror-like mechanisms in the somatosensory domain. Within the tactile mirror system (TaMS), observing touch on another persons body activates cortical regions involved in tactile perception, including the primary somatosensory cortex (S1). Although mirror-like alterations have been suggested in BPD, the underlying mechanisms of plasticity remain underexplored. Here, we used a cross-modal paired associative stimulation (cm-PAS) protocol to investigate the plasticity mechanisms of TaMS functioning in BPD. Twenty-four individuals with BPD and 24 healthy controls (HCs) were included. Empathic abilities were assessed using self-report questionnaires. Participants performed tactile acuity and visuo-tactile spatial congruity (VTSC) tasks before and after a cm-PAS protocol. During cm-PAS, images of a hand being touched were paired with transcranial magnetic stimulation over the S1. The effects of cm-PAS were assessed on tactile acuity, as an index of S1 activity, and VTSC performance, as an index of TaMS functioning. Preregistered analyses revealed that patients with BPD tended to have lower cognitive empathy than HCs, with no significant cm-PAS effects on tactile acuity or VTSC performance in HCs, precluding between-group comparisons of plasticity effects. Exploratory analyses were conducted to further investigate potential sources of variability in the effects of cm-PAS, as well as the relationship between cognitive empathy and visuo-tactile processing as measure of TaMS functioning. Preregistered Stage 1 protocol: https://osf.io/sqnwd (date of in-principle acceptance: 25/06/2023).

neuroscience↗

bioRxiv2025

Extracellular vesicles from morphine-exposed prefrontal cortex carry transcriptomic and proteomic signatures of synaptic dysfunction

Extracellular vesicles (EVs) released by neurons and glial cells mediate intercellular communication in the brain and regulate synaptic function, neuronal survival, and neuropathological processes. Although chronic opioid exposure induces widespread neuroadaptations, the contribution of brain-derived EVs (BDEVs) to these processes remains largely unknown. Here, we isolated BDEVs from the prefrontal cortex of rats chronically exposed to morphine and performed integrative transcriptomic and proteomic analyses of their molecular cargo. Total RNA sequencing combined with unbiased proteomics revealed that morphine profoundly reprograms the BDEV transcriptome and proteome, enriching pathways related to synaptic plasticity, endoplasmic reticulum (ER) stress, mitochondrial dysfunction, and neurodegeneration. Among the most prominent alterations, the synaptic regulator ARC was consistently modulated at the mRNA level, while the ER stress marker HSPA5 was altered at both mRNA and protein levels. Functional assays further demonstrated that BDEVs derived from morphine-treated rats were sufficient to reconfigure transcriptional programs in naive cortical neurons, affecting genes associated with synaptic remodeling and excitability. Collectively, these findings provide the first evidence that chronic opioid exposure reprograms BDEV cargo in a brain region critical for addiction and that these vesicles can propagate transcriptional reorganization to recipient neurons. BDEVs thus emerge as active mediators of morphine-induced neuroadaptations and as potential targets for biomarker discovery and therapeutic intervention in opioid use disorder.

neuroscience↗

bioRxiv2025

First Comprehensive Examination of the Molecular Phylogenetics of Saki Monkeys, Genus Pithecia Desmarest, 1804, Reveals an Unexpectedly Low Taxonomic Diversity

Saki monkeys (Pithecia) are found exclusively in the Amazon, ranging from the Guiana Shield in the east to the Andean foothills in the west. The taxonomy of this genus is complex due to indeterminate type localities, numerous synonyms, sexual dichromatism and considerable geographical diversity in coat colour patterns. Previous assessments have indicated two to four species and a variable few subspecies based on morphological analyses of museum specimens. Just two species have been consistently recognised--Pithecia pithecia and Pithecia monachus. This study presents the first comprehensive molecular phylogeny of the genus, using mitochondrial cytochrome b sequences from 137 individuals across their range and a ddRADseq genomic analysis on 34 individuals. The phylogenetic results revealed three main clades: (1) Guiana Shield sakis, (2) Sedimentary Basin and Brazilian Shield sakis, and (3) a basal P. albicans south of the Rio Solimoes. The ddRADseq data further clarified species boundaries and relationships, identifying six distinct species: P. chrysocephala and P. pithecia sensu Hershkovitz (1987) on the Guiana Shield; P. albicans in central Amazonia south of the Rio Solimoes; P. monachus in western Amazonia; P. irrorata between the rios Purus, Tapajos, and Juruena; and P. vanzolinii in a limited area east of the Rio Jurua.

zoology↗

bioRxiv2025

Meteorin resolves nociceptive hypersensitivity by reducing connexin-mediated coupling in satellite glial cells

Neuropathic pain, a persistent condition arising from injury to the nervous system, involves complex interactions between neurons and non-neuronal cells, including satellite glial cells (SGCs) in the dorsal root ganglia (DRG). In this study, we examined the glial-targeting effects of meteorin, a neurotrophic protein with gliogenic properties, using mouse models of neuropathic and inflammatory pain. Systemic meteorin administration reversed mechanical hypersensitivity across diverse neuropathic and inflammatory pain models, with therapeutic effects persisting beyond the treatment period. We identified SGCs as the principal site of meteorin expression and action in the DRG, where it selectively activated SGCs and altered their functional state. Proteomic profiling revealed meteorin-mediated downregulation of gap junction proteins in SGCs, particularly connexin 43, which was corroborated by immunohistochemical analyses. Functional assessments demonstrated that meteorin treatment normalized injury-induced increases in intercellular coupling between SGCs, establishing a mechanistic link between glial network modulation and pain resolution. These findings identify meteorin as a regulator of SGC communication through connexin-dependent mechanisms. The sustained therapeutic effects and multi-model efficacy highlight meteorin as a potential intervention for neuropathic pain while advancing our understanding of SGC plasticity in sensory processing.

neuroscience↗

bioRxiv2025

Mapping satellite glial cell heterogeneity reveals distinct spatial organization and signifies functional diversity in the dorsal root ganglion

Satellite glial cells (SGCs) envelop the somata, axon hillock, and initial axon segment of sensory neurons in the dorsal root ganglia (DRG), playing a critical role in regulating the neuronal microenvironment. While DRG neurons have been extensively studied and classified based on size, molecular markers, and functional characteristics, very little is still known about SGC heterogeneity and its potential implications on sensory processing in the DRG. Single cell transcriptional analyses have proposed the existence of SGC subtypes, yet in situ validation, spatial distribution, and potential functional implications of such subtypes are still largely unexplored. Here, we present the first comprehensive in situ characterization of SGC heterogeneity within the mouse DRG. By integrating single-cell RNA sequencing with immunohistochemistry, in situ hybridization, and advanced imaging techniques, distinct SGC subclusters were identified, validated, and spatially mapped within their native anatomical context. We visually identify four distinct subpopulations: 1) a predominant population of perisomatic SGC sheaths defined by the expression of marker proteins traditionally used to characterize the entire SGC population, including FABP7, KIR4.1, GS, and CX43. 2) OCT6+ SGCs occasionally being found in mosaic perisomatic sheaths, and consistently associated with axonal glomeruli, primarily ensheathing initial segment axon. 3) SCN7A+ SGCs, exhibiting no/low expression of traditional SGC markers and forming specialized homogenous sheaths around non-peptidergic neuron subtypes, implicating their potential role in pruritic (itch-related) conditions. 4) Interferon response gene-expressing SGCs, responding to Herpes Simplex Virus infection, suggesting potential involvement in antiviral protection. Finally, we investigate human DRG and find an inner perisomatic SGC layer surrounded by an outer SGC layer, with traditional and novel markers distinctively distributed between the two layers. Our results provide novel insight into SGC heterogeneity in the DRG and suggests distinct functional properties for such subtypes of relevance for the neuronal microenvironment.

neuroscience↗

bioRxiv2025

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

BackgroundMost populations of spider monkeys (Ateles) and muriquis (Brachyteles), two Neotropical primate genera, are under severe anthropogenic threats. Yet, taxon-wide population-level studies leveraging their degree of endangerment linked to their genetic diversity patterns and demographic history are lacking. To properly address this, there is a need to expand from morphological and genetic marker-based studies. ResultsWe generated high-coverage genome sequencing for 58 individuals sampled across 8 Atelidae species, in the first population-wide study of all extant spider monkey species, in the wild and captivity, alongside northern muriquis (Brachyteles hypoxanthus). Additionally, we present a high-contiguity reference genome for Ateles hybridus. Here, we observe the overall levels of genetic diversity and genetic load of the analyzed populations do not align to their IUCN endangerment category. Moreover, we show that in the wild, genetic load is overall higher compared to the captive populations analyzed. Then, we depict two main trans and cis-Andean sister clades in Ateles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions between Ateles and B. hypoxanthus are involved in central nervous system development and photorreception. ConclusionsOur study shows i) the lack of concordance between the genetic diversity levels and extinction risk of these populations, suggestive of recent and strong external drivers; ii) increased genetic load in the wild in contrast to effective captive management, indicating mostly past demographic events; iii) structure and dynamics in spider monkeys that agrees with common biogeographical patterns and iv) genetic divergence between Ateles and Brachyteles potentially linked to distinct environmental light levels.

genomics↗

bioRxiv2024

Investigating visuo-tactile mirror properties in Borderline Personality Disorder: a TMS-EEG study

Patients with Borderline Personality Disorder (pw-BPD) are characterized by lower levels of cognitive empathy compared to healthy controls (HCs), indicating difficulties in understanding others perspective. A candidate neural mechanism subtending empathic abilities is represented by the Tactile Mirror System (TaMS), which refers to mirror-like mechanisms in the somatosensory cortices. However, little is known about TaMS alterations in BPD, specifically in terms of brain connectivity within this network. Here, we aimed at providing novel insights on TaMS as neurophysiological candidate for BPD empathic deficits, with a special focus on TaMS connectivity by means of the combined use of transcranial magnetic stimulation and electroencephalography (TMS-EEG). Twenty pw-BPD and 20 HCs underwent a thorough investigation: we collected measures of empathic abilities obtained from self-report questionnaires, behavioral performance in a visuo-tactile spatial congruency task, and TMS-evoked potentials (TEPs) as effective connectivity indexes. In the TMS-EEG session, TMS was delivered over the right primary somatosensory cortex (S1) following the presentation of real touches and visual touches, while 74-channel EEG was continuously recorded. In the visuo-tactile spatial congruency task and the TMS-EEG recording, control conditions with visual touches on objects instead of body parts enabled to disentangle the involvement of TaMS from non-specific effects. The study is the first one employing TMS-EEG in pw-BPD and it has been preregistered before data collection. Consistent with previous findings, results show that pw-BPD reported significantly lower levels of cognitive empathy. Moreover, pw-BPD made significantly more errors than controls in the visuo-tactile spatial congruency task during visual touches on human body parts and not on objects. Finally, pw-BPD displayed a different connectivity pattern from S1-TEPs that was not specific for TaMS: they showed a lower P60 component during touch observation, as well as reduced amplitude of later TEPs responses (after [~]100 ms) during real touches. Overall, the present study shows behavioral evidence of TaMS impairment and a more general alteration in the connectivity pattern of the somatosensory network in pw-BPD.

neuroscience↗

bioRxiv2023

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats these species are facing. Here, we present high coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human-specific. This study will open a wide range of research avenues for future primate genomic research. One-Sentence SummaryThe whole genome sequences of 233 primate species provide insight into the determinants of genetic diversity, phylogenomics, and human uniqueness.

genomics↗

bioRxiv2022

Prospective isolation according to melanin pigment content of melanoma cells with heterogeneous potentials for disease propagation

Functional variation between cancer cells (intra-tumoral heterogeneity) poses a major challenge to treating and managing cancer patients. Melanomas are typically composed of cancer cells with heterogeneous content of melanin pigment. Pigment production is a hallmark of normal melanocytic differentiation, however the functional consequences of melanin production in melanoma cells remains poorly understood owing to a lack of experimental approaches for detection of pigment in unfixed cells. Here, we describe a novel flow cytometric method for high purity separation of viable melanoma cells based on their content of melanin pigment, exploiting the infrared light scattering properties of melanin. By fluorescence-activated cell sorting, we show that melanoma cells with low-pigment content (LPCs) in culture and in patient tumors are far more abundant than high-pigment cells (HPCs), and have substantially increased potentials for colony formation in vitro and for tumor formation in vivo. RNAseq analysis revealed activation of P53 in HPCs associated with perturbed cell cycling, whereas LPCs displayed upregulation of MYC-associated transcription and activated ribosome biogenesis. The latter was reduced by topoisomerase 2 beta targeting with CX-5461, which also induced senescent HPC phenotypes and irreversible loss of clonogenic activity. These data illuminate an inverted pyramid hierarchical model of melanoma cell propagation wherein abundant LPCs frequently renew their own malignant potential to propagate disease, but also rarely generate HPCs that lose this ability in a manner that may be promoted as an anti-melanoma strategy.

cancer biology↗

bioRxiv2022

Multi-environment genome-wide association mapping of culm morphology traits in barley

In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image-analysis based protocol to accurately phenotype culm diameter and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in 7 different environments revealed genetic control as supported by high heritability values, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. In addition, culm traits showed strong negative correlations with lodging but weak correlations with plant height across row-types, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 QTLs for the studied traits, including subpopulation-specific QTLs and several main effect loci for culm traits showing negative effects on lodging without impacting plant height. Providing first insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments. One-sentence summaryGenetic analysis of a diverse collection of European barleys reveals genomic regions underpinning stem morphological features associated with lodging resistance.

plant biology↗

bioRxiv2021

Phenological segregation suggests speciation by time in the planktonic diatom Pseudo-nitzschia allochrona sp. nov.

The emergence of new species is poorly understood in marine plankton, where the lack of physical barriers and homogeneous environmental conditions limit spatial and ecological segregation. Here we combine molecular and ecological information from a long term time series and propose Pseudo-nitzschia allochrona, a new cryptic diatom, as a possible case of speciation by temporal segregation. The new species differs in several genetic markers (18S, LSU and ITS rDNA fragments and rbcL) and is reproductively isolated from its closest relative, which is morphologically identical. Data from a long term plankton time series show Pseudo-nitzschia allochrona invariably occurring in summer-autumn in the Gulf of Naples, where its sister species are instead found in winter-spring. Temperature and nutrients are the main factors associated with the occurrence of P. allochrona, which could have evolved in sympatry by switching its phenology and occupying a new ecological niche. This case of possible speciation by time shows the relevance of combining ecological time series with molecular information to shed light on the eco-evolutionary dynamics of marine microorganisms.

evolutionary biology↗

bioRxiv2020

Long-read isoform sequencing reveals survival-associated splicing in breast cancer

Tumors display widespread transcriptome alterations, but the full repertoire of isoform-level alternative splicing in cancer is not known. We developed a long-read RNA sequencing and analytical platform that identifies and annotates full-length isoforms, and infers tumor-specific splicing events. Application of this platform to breast cancer samples vastly expands the known isoform landscape of breast cancer, identifying thousands of previously unannotated isoforms of which ~30% impact protein coding exons and are predicted to alter protein localization and function, including of the breast cancer-associated genes ESR1 and ERBB2. We performed extensive cross-validation with -omics data sets to support transcription and translation of novel isoforms. We identified 3,059 breast tumor-specific splicing events, including 35 that are significantly associated with patient survival. Together, our results demonstrate the complexity, cancer subtype-specificity, and clinical relevance of novel isoforms in breast cancer that are only annotatable by LR-seq, and provide a rich resource of immuno-oncology therapeutic targets.

genomics↗

bioRxiv2020

Limited window for donation of convalescent plasma with high live-virus neutralizing antibodies for COVID-19 immunotherapy

The optimal timeframe for donating convalescent plasma to be used for COVID-19 immunotherapy is unknown. To address this important knowledge deficit, we determined in vitro live-virus neutralizing capacity and persistence of IgM and IgG antibody responses against the receptor-binding domain and S1 ectodomain of the SARS-CoV-2 spike glycoprotein in 540 convalescent plasma samples obtained from 175 COVID-19 plasma donors for up to 142 days post-symptom onset. Robust IgM, IgG, and viral neutralization responses to SARS-CoV-2 persist, in the aggregate, for at least 100 days post-symptom onset. However, a notable acceleration in decline in virus neutralization titers [≥]160, a value suitable for convalescent plasma therapy, was observed starting 60 days after first symptom onset. Together, these findings better define the optimal window for donating convalescent plasma useful for immunotherapy of COVID-19 patients and reveal important predictors of an ideal plasma donor, including age and COVID-19 disease severity score. One Sentence SummaryEvaluation of SARS-CoV-2 anti-spike protein IgM, IgG, and live-virus neutralizing titer profiles reveals that the optimal window for donating convalescent plasma for use in immunotherapy is within the first 60 days of symptom onset.

immunology↗

bioRxiv2018

A seleno-hormetine protects bone marrow hematopoietic cells against ionizing radiation-induced toxicity

2,2-diselenyldibenzoic acid (DSBA) is a mild thiol peroxidase agent presently in preclinical development. This study reports that the drug has novel seleno-hormetic properties in both murine bone marrow and human liver cells. According with previous in vitro findings, mechanistic aspects of such properties were confirmed to include the activation of Nrf2 transcription factor and an increased expression of downstream stress response genes in the liver and in hematopoietic stem and progenitor cells of the myeloid lineage. These genes include glutathione S-transferase that is reported to represent a major player in the metabolism and pharmacological function of seleno-organic compounds. As a practical application, DSBA administration prevented bone marrow toxicities following acute exposure to sub-lethal doses of ionizing radiation in C57 BL/6 mice.\n\nIn conclusion, this study demonstrates for the first time the pharmacological properties of DSBA in vivo. The findings suggest applications for this selenohormetine in radioprotection and prevention protocols.

cancer biology↗