Biology subjects

Magnani, M.

Publications and source records attributed to Magnani, M..

4 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

A bioprinted silk marrow niche reveals mechanical regulation of human megakaryopoiesis under genotoxic stress

Hematopoietic stem and progenitor cells (HSPCs) reside in a mechanically distinct bone marrow niche, yet how niche biomechanics shape genome stability and stress responses has been difficult to test because conventional two-dimensional (2D) culture lacks marrow viscoelasticity and uses surfaces that activate platelets, confounding hematopoietic readouts. Here, we show that this methodological gap has masked a basic principle: the marrow niche actively constrains genotoxic stress signaling in HSPCs, and 2D culture systematically overstates DNA damage and impairs differentiation in vitro. We engineered silk fibroin, a biologically inert biomaterial that does not activate platelets and recapitulates marrow viscoelasticity, into SilkInk, a 3D-bioprintable bioink, and used it to reconstruct a biomimetic marrow microenvironment. HSPCs encapsulated in SilkInk preserved clonogenic potential and multilineage differentiation, whereas 2D-cultured HSPCs activated cytoskeletal-tension and genome-surveillance programs characteristic of chronic stress, including pathways related to replication stress, DNA damage response, and redox stress. Cell phenotyping and single-cell RNA sequencing during megakaryopoiesis revealed that SilkInk supported coordinated endomitotic progression and terminal maturation, with progression from CD34+CD61-CD41-CD42b- progenitors to CD34-CD61+CD41+CD42b+ megakaryocytes, including increased 8N and >16N populations, whereas 2D culture and conventional 3D hydrogels sustained DNA damage signaling and impaired thrombopoiesis. The same hierarchy held under cytotoxic challenge, as 5-fluorouracil amplified DNA damage and crippled platelet output in 2D, whereas SilkInk-encapsulated HSPCs maintained differentiation, mirroring native marrow resilience. These findings reposition niche mechanics as an active determinant of hematopoietic genome stability and establish SilkInk as a physiologically faithful platform for studying hematopoiesis and predicting marrow responses to chemotherapy.

Cell Biology↗

bioRxiv2025

Functional and compositional diversity display a maximum at intermediate levels of fire frequency when modeling the plant-fire feedback

Fires are generally considered to promote biodiversity, although the exact relationship is unclear, because it can be affected by several factors, including fire regime and ecosystem type. Given the ongoing global change, a better understanding of this connection is needed to assess the extent to which projected increases in fire frequency may affect current biodiversity trends. A major challenge lies in vegetation-fire feedback, which often mediates changes in fire regimes. To shed light on the role of fires in promoting or limiting biodiversity, we studied the compositional and functional diversity of simulated plant communities along a gradient of fire frequencies. We extended an existing model to include a large number of species. The model reproduces plant successional dynamics and is parameterized to represent Boreal and Mediterranean communi-ties. Fire events are stochastic, with frequencies that depend on community flammability, and plants have different fire responses, thus creating a vegetation-fire feedback. For both ecosys-tems, we found that fires generally had a positive effect on both compositional and functional diversity. Furthermore, in most cases, both peaked at intermediate fire frequencies. Interestingly, compositional and functional diversity were correlated but did not reach their maximum values in the same communities. This seemingly underlines that a certain degree of functional similarity may be necessary to achieve maximum species richness. These results stem from the vegetation-fire feedback, highlighting its importance for predicting ecosystem responses to global change, including biodiversity losses and wildfire regime shifts.

ecology↗

bioRxiv2024

Engineered Oxalate decarboxylase boosts activity and stability for biological applications

Oxalate decarboxylase (OxDC) from Bacillus subtilis is a Mn-dependent hexameric enzyme which converts oxalate to carbon dioxide and formate. Recently, OxDC has attracted the interest of the scientific community, due to its biotechnological and medical applications for the treatment of hyperoxalurias, a group of pathologic conditions associated with excessive oxalate urinary excretion due to either increased endogenous production or increased exogenous absorption. The fact that OxDC displays optimum pH in the acidic range, represents a big limitation for most biotechnological applications involving processes occurring at neutral pH, where the activity and stability of the enzyme are remarkably reduced. Here, through bioinformatics-guided protein engineering, followed by combinatorial mutagenesis and analyses of activity and thermodynamic stability, we identified a double mutant of OxDC endowed with enhanced catalytic efficiency and stability under physiological conditions. The obtained engineered form of OxDC offers a potential tool for improved intestinal oxalate degradation in hyperoxaluria patients.

biochemistry↗