Biology subjects

Ricci, A.

Publications and source records attributed to Ricci, A..

12 recordsLinked to original sources

bioRxiv2026

Integrated metabolic and proteostatic profiling reveals remodeling of proteolytic pathways associated with redox-bioenergetic dysfunction in a PAHenu2 mouse model of phenylketonuria

Phenylketonuria (PKU) is a genetic metabolic disorder caused by the lack of functional phenylalanine hydroxylase (PAH). Elevated levels of phenylalanine (Phe) are known to be neurotoxic; however, the molecular mechanisms underlying Phes effects remain elusive. This study investigates the impact of PKU on proteostasis, redox balance, and metabolism in BTBR PAHenu2 mice, a severe disease animal model. Combined proteomics and metabolomics revealed impaired redox homeostasis in the brain and disrupted mitochondrial energy metabolism (ATP and TCA intermediates). The dysregulation was further supported by decreased levels of ATP, reduced glutathione (GSH), cysteine, and reduced catalase activity. Western blot analyses revealed substantial remodeling of protein degradation systems: the 19S regulatory (Rpt1) subunit and 26S proteasome content and activity were significantly increased, and ubiquitinated protein levels were elevated, indicating protein turnover and activation of the ubiquitin-proteasome system. Autophagy was also activated, as evidenced by a reduced LC3-II/LC3-I ratio, decreased p62 levels, unchanged ATG5 levels, and increased HSPA8 protein expression. By contrast, UPR markers remained stable despite an increase in the oxidized-to-reduced PDI ratio, suggesting a localized shift without activation of a full ER stress response. In parallel, systemic alterations were assessed in whole blood. Indeed, GSH, cysteine, ATP and ADP were decreased in PKU, whereas NADPH increased. These changes were accompanied by reduced activities of GSH reductase and GSH peroxidase, thereby confirming metabolic and redox disruption. Collectively, these findings indicate that PKU is associated with activation of protein degradation pathways as an adaptive response to cellular stress combined with redox imbalance and energy dysregulation. Highlights- Proteasome complex levels and activity were upregulated in PAHenu2 mouse brains - Autophagy was also enhanced in PAHenu2 mouse brains - Despite increased PDI oxidation, the Unfolded Protein Response was not activated - Redox and energy metabolism were disrupted in both brain and blood

molecular biology↗

bioRxiv2026

Unraveling the Regenerative Proteomic Signature of Helix aspersa's Slime in Human Dermal Fibroblasts by Data-driven Proteomics Approach

Proteins orchestrate essential cellular processes, including metabolism, communication, survival, and regeneration, making proteomic profiling a powerful strategy to elucidate complex biological responses. Snail slime (SnS) has emerged as a bioactive material with documented pro-healing, antioxidant, and anti-inflammatory properties; however, its effects at the proteome level in normal human dermal fibroblasts (NHDFs) remain unexplored. In this study, an LC-MS-based proteomic approach (Data are available via ProteomeXchange with identifier PXD075292) combined with network and Gene Ontology enrichment analyses was employed to investigate SnS-induced molecular reprogramming in NHDFs, followed by functional assays. Results show that SnS is well tolerated for up to 72 h, confirming its cytocompatibility, followed by proteomic analysis revealing enrichment of biological processes related to apoptosis regulation, oxidative stress response, wound healing, cell migration, and anti-aging. Network analysis identified AKT, PI3K, SRC, and KRAS family members as key hub proteins, indicating convergence on central signaling pathways controlling survival, redox balance, and migratory activity. Functional assays demonstrated a time-dependent, controlled modulation of apoptosis consistent with cellular turnover, alongside a hormetic redox response characterized by transient ROS signaling followed by enhanced antioxidant capacity. Importantly, SnS significantly accelerated fibroblast migration, achieving complete wound closure within 24 h. Collectively, these findings demonstrate that SnS induces coordinated proteomic and functional reprogramming that integrates redox modulation, controlled apoptosis, and enhanced migration, providing a mechanistic basis for its pro-healing and anti-aging effects and supporting its potential as a regenerative biomaterial.

cell biology↗

bioRxiv2025

LipiGo: A Versatile DNA-Lipid Nanoparticle Hybrid for Precision Drug Delivery

Lipid nanoparticles (LNPs) are established carriers for nucleic acid delivery, however, achieving efficient delivery to non-hepatic tissues remains a major challenge. Here, we present LipiGo, a nanocarrier platform engineered by integrating short single stranded DNA molecules into the lipid nanoparticle structure. Using whole body tissue clearing, advanced imaging and AI-based analysis, we show that LipiGo redirects functional mRNA delivery to lymphoid organs, particularly the spleen. Immune cell profiling further reveals enhanced uptake within key immune populations, including antigen-presenting cells, compared to standard LNPs. Beyond passive redistribution, LipiGo leverages DNA hybridization to enable modular attachment of targeting ligands for active targeting as demonstrated by cell-specific delivery to white adipocytes. Overall, the dual-purpose design principle of LipiGo demonstrates high modularity and efficiency, enabling tissue and cell specific delivery beyond hepatic applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/676334v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@9b69eorg.highwire.dtl.DTLVardef@1b45bd0org.highwire.dtl.DTLVardef@1f7b79dorg.highwire.dtl.DTLVardef@37a673_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

The Characteristic Timescales of the Arabidopsis thaliana Metabolism and the Phenotypic Effects of Forcing Them

Response mechanisms preserve steady states in complex systems (including living systems). These mechanisms respond with characteristic timescales. Therefore, they can be identified and probed with oscillatory forcing. This approach is rarely used in plant biology. Sub-circadian intermittent illumination (i.e., square waves of light/dark periods of equal duration) of Arabidopsis thaliana plants cause remarkable phenotypical effects. We show these effects are highly dependent on the duration of the light-dark cycle, identifying characteristic timescales in three distinct windows (10.5-42 s, 168-336 s, and 1350-5400 s). Among these effects is an extension of the life cycle by 60%, a 2-fold increase in flower setting, and a near complete elimination of lateral root development. This oscillatory light forcing is compatible with vertical farming where it could reduce energy and chemical inputs and highlights the methodological value of temporal-forcing of environmental parameters on sub-circadian timescales in plant systems.

biophysics↗

bioRxiv2024

Dynamic modulation of auditory hair cell stereocilia membrane mechanics by the scrambling mechanotransduction complex

Inner ear sensory hair cells convert mechanical deflection of their hair bundle into an electrical signal by gating novel mechanoelectrical transduction (MET) channels. Transmembrane channel-like proteins (TMCs) are a component of the MET machinery and part of a superfamily of molecules whose members are ion channels or lipid scramblases. As the stereocilia membrane modulates MET channels properties and the stereocilia membrane has different properties than the soma, we investigated the potential scramblase activity of the MET machinery using a novel viscosity sensor BODIPY 1c. Developmental, genetic, electrophysiological and pharmacological data demonstrate that both TMC1 and TMC2 are mechanosensitive scramblases as activity depends on MET channel being open. Blockage of scramblase activity unmasks a second process that increases effective membrane viscosity independent of MET machinery. Together our data reveal a dynamic regulation of stereocilia membrane that may underlie the speed and sensitivity of the MET process.

cell biology↗

bioRxiv2024

Development of a highly active engineered PETase enzyme for polyester degradation

Polyethylene terephthalate (PET) accounts for {approx}6% of global plastic production, contributing considerably to the global solid waste stream and environmental plastic pollution. Since the discovery of PET-depolymerizing enzymes, enzymatic PET recycling has been regarded as a promising method for plastic disposal, particularly in the context of a circular economy strategy. However, as the PET degrading enzymes developed so far suffer from relatively limited thermostability, low catalytic efficiency, as well as degradation intermediate-induced inhibition, their large scale industrial applications are still largely hampered. To overcome these limitations, we used in silico protein design methods to develop an engineered Leaf-branch Compost Cutinase (LCC), named DRK3, that features enhanced thermal stability and PETase activity relative to the current gold standard LCC enzyme (LCC-ICCG). DRK3 features a 4.1{degrees}C increase in melting temperature relative to the LCC-ICCG enzyme. Under optimal reaction conditions (68{degrees}C), the DRK3 enzyme hydrolyzes amorphous PET material into TPA with a 2-fold higher efficiency compared to LCC-ICCG. Owing to its enhanced properties, DRK3 may be a promising candidate for future applications in industrial PET recycling processes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/602061v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@125688eorg.highwire.dtl.DTLVardef@f360f8org.highwire.dtl.DTLVardef@634486org.highwire.dtl.DTLVardef@127f622_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Inhibitory fear memory engram in the mouse central lateral amygdala

Engrams are cellular substrates of memory traces that have been identified in various brain areas, including the amygdala. Most engrams identified so far are formed by excitatory, glutamatergic neurons. However, little attention has been paid to defining GABAergic inhibitory engrams. Here, we report an inhibitory engram in the central lateral amygdala (CeL), a crucial area for Pavlovian fear conditioning. This engram is primarily composed of GABAergic somatostatin-expressing (SST+) and to a lesser extent of protein kinase C-{delta}-expressing [PKC-{delta}(+)] neurons. Fear memory is accompanied by a preferential enhancement of mIPSC frequency onto PKC-{delta}(+) neurons as well as a general increment of amplitude. Moreover, non-engram cells exhibit higher mIPSC frequency than engram cells. The inhibition of the CeL GABAergic engram disinhibits the activity of engram-targeted areas and increases selectively the encoded fear expression. Our data defines the behavioral function of an engram formed exclusively by GABAergic inhibitory neurons in the mammalian CNS.

neuroscience↗

bioRxiv2023

Into the deep: The subthalamic and para-subthalamic nuclei in behavioral avoidance

The subthalamic nucleus (STN) is a key component of the brain network for movement control. However, the STN is strikingly heterogeneous and also intricately engaged in limbic and cognitive functions. The STN shows aberrant firing activity in several neurological and neuropsychiatric disorders, including Parkinso[n]s disease (PD). Deep brain stimulation (DBS) in the STN alleviates motor impairment in PD, but patients have reported altered mood as adverse side-effect. Recent observations suggest that optogenetic STN activation in mice induces flight behavior. We hypothesized that STN activation stand at risk of causing an aversive response with behavioral avoidance as consequence. The STN is directly adjoined with the para-STN (pSTN), a hypothalamic area correlated with appetitive and aversive behavior. STN-DBS aiming to correct STN might thereby also modulate pSTN. To dissociate the impact of STN and pSTN, we took advantage of selective promoters in mice, identified in our recent RNA- sequencing of the subthalamic area, to selectively direct optogenetic excitation. Acute photostimulation resulted in aversion via both the STN and pSTN, but only STN- stimulation-paired cues resulted in conditioned avoidance. Viral-genetic tracing coupled with electrophysiological recordings identified a polysynaptic pathway from the STN to the lateral habenula, a critical hub for aversion and associated with clinical depression. This study demonstrates that STN activation is directly correlated with aversion, and thereby contributes neurobiological underpinnings to emotional affect upon STN manipulation with implications for STN-targeted treatment outcome.

neuroscience↗

bioRxiv2023

GIPC3 couples to MYO6 and PDZ domain proteins and shapes the hair cell apical region

GIPC3 has been implicated in auditory function. Initially localized to the cytoplasm of inner and outer hair cells of the cochlea, GIPC3 increasingly concentrated in cuticular plates and at cell junctions during postnatal development. Early postnatal Gipc3KO/KO mice had mostly normal mechanotransduction currents, but had no auditory brainstem response at one month of age. Cuticular plates of Gipc3KO/KO hair cells did not flatten during development as did those of controls; moreover, hair bundles were squeezed along the cochlear axis in mutant hair cells. Junctions between inner hair cells and adjacent inner phalangeal cells were also severely disrupted in Gipc3KO/KO cochleas. GIPC3 bound directly to MYO6, and the loss of MYO6 led to altered distribution of GIPC3. Immunoaffinity purification of GIPC3 from chicken inner ear extracts identified co-precipitating proteins associated with adherens junctions, intermediate filament networks, and the cuticular plate. Several of immunoprecipitated proteins contained GIPC-family consensus PDZ binding motifs (PBMs), including MYO18A, which binds directly to the PDZ domain of GIPC3. We propose that GIPC3 and MYO6 couple to PBMs of cytoskeletal and cell-junction proteins to shape the cuticular plate. Summary statementThe PDZ-domain protein GIPC3 couples the molecular motors MYO6 and MYO18A to actin cytoskeleton structures in hair cells. GIPC3 is necessary for shaping the hair cells cuticular plate and hence the arrangement of the stereocilia in the hair bundle.

cell biology↗

bioRxiv2020

Abdominal pain assessment in rabbits: using the CANCRS to recognize pain and testing its internal validity over time

A composite scale for pain assessment in rabbits has been previously designed and tested (CANCRS). The present study describes the refinement of the scale and the evaluation of its ability to detect pain variations over time. Furthermore, a comparison between the CANCRS and the Visual Analogue Scale (VAS) has been performed, to underline the differences between an objective (CANCRS) and a subjective (VAS) assessment of abdominal pain. In the first part of the study, 86 rabbits (n=47 heathy patients and n=39 patients with gastrointestinal stasis syndrome) underwent pain assessments with the VAS and the CANCRS. Thirty-two patients with gastrointestinal stasis syndrome participated to the second part of the study. These patients underwent four pain assessments with the CANCRS. The first assessment took place before meloxicam administration and the others after 30, 60 and 90 minutes. The CANCRS showed differences between healthy and diseased rabbits (P = 0.0001), median scores were 5 (IQR 4 - 6) and 9 (IQR 7 - 11) respectively. The VAS showed differences between healthy and diseased rabbits (P = 0.02), the median scores were 4 (IQR 2 - 5.35) and 5.3 (IQR 2.65 - 6.45) respectively. The cut-off scores for the CANCRS and for the VAS for differentiation between healthy and diseased patients were 7 (Sp 89%, Se 79%) and 4.4 (Sp 59%, Se 69%) respectively. Sensitivity and specificity for each parameter of the CANCRS were calculated, in order to obtain weighting factors. Accordingly, the evaluation of respiratory pattern and vocalizations should be excluded from the CANCRS, since their performances in pain evaluation are poor. Internal validity of the CANCRS was tested assessing pain before and after the analgesic treatment and the results showed significancy at each time point. The CANCRS showed better performances than the VAS and its responsiveness to pain variations has been verified.

zoology↗

bioRxiv2020

Circulating Mitochondrial DNA is an Early Indicator of Severe Illness and Mortality from COVID-19

Mitochondrial DNA (MT-DNA) are intrinsically inflammatory nucleic acids released by damaged solid organs. Whether the appearance of cell-free MT-DNA is linked to poor COVID-19 outcomes remains undetermined. Here, we quantified circulating MT-DNA in prospectively collected, cell-free plasma samples from 97 subjects with COVID-19 at the time of hospital presentation. Circulating MT-DNA were sharply elevated in patients who eventually died, required ICU admission or intubation. Multivariate regression analysis revealed that high circulating MT-DNA levels is an independent risk factor for all of these outcomes after adjusting for age, sex and comorbidities. Additionally, we found that circulating MT-DNA has a similar or superior area-under-the curve when compared to clinically established measures of systemic inflammation, as well as emerging markers currently of interest as investigational targets for COVID-19 therapy. These results show that high circulating MT-DNA levels is a potential indicator for poor COVID-19 outcomes.

immunology↗

bioRxiv2019

Development and validation of a multidimensional composite pain scale for Rabbit (CANCRS) in a clinical environment

The main objective of this study was to develop a multidimensional composite pain scale for assessing and quantifying pain in rabbits (CANCRS); to this purpose, Rabbit Grimace Scale (RbtGS) and a scale including clinical parameters (CPS) were merged; the two scales performances were also evaluated individually, in order to validate RbtGS in a clinical setting and to verify clinical parameters usefulness in detecting pain.\n\nRabbits (n=116) were evaluated by two raters, who could be veterinarians (V) or veterinary medicine students (S). Raters were asked to report the time needed for any evaluation and a total score, in order to define a pain class. Pain classes (No pain, Discomfort, Moderate pain and Severe pain) matched presumptive pain classes and accordingly, the validity of the three scales was measured using Chi-square test.\n\nPatients (n=69) were evaluated by one V and one S, allowing to assess the impact that the experience has on the results. Inter-rater reliability was tested for each scale using intra-class correlation coefficient (ICC) and for each parameter of the CANCRS using Cohens kappa. Validity results show that only CANCRS and RbtGS efficiently reveal pain, but both tend to underestimate it.\n\nInter-rater reliability was very good for both CANCRS and CPS, suggesting that experience has little influence on the results; raters experience has a greater impact using RbtGS.\n\nInter-rater agreement was at least good for each parameter.\n\nIn conclusion, CPS alone is neither effective or reliable in quantifying pain.\n\nThe RbtGS is a useful tool in clinical practice, when coping with many rabbit breeds; however, training is beneficial for a better use of the scale.\n\nThe CANCRS is easy and fast to use and enrich RbtGS with some clinical parameters that should be monitored during any clinical examination, leading to a more exhaustive evaluation of the patient.

animal behavior and cognition↗