Biology subjects

Fontana, F.

Publications and source records attributed to Fontana, F..

8 recordsLinked to original sources

bioRxiv2026

Folding-Driven Control of the Functional PP1 Complex via Multiscale Modeling

Understanding how conformational dynamics regulate protein complex assembly remains a central challenge in molecular systems biology. Here, we develop a multiscale modeling framework that integrates all-atom molecular dynamics (MD) simulations with rule-based kinetic modeling to investigate the formation of the PP1-GADD34-eIF2 complex, a critical regulator of the integrated stress response. Using umbrella sampling, we compute the potential of mean force (PMF) for key interactions, revealing strong thermodynamic driving forces for eIF2 binding ({Delta}G = -89.5 kJ/mol, KD {approx} 0.07 fM) and moderate affinity for PP1-GADD34 association ({Delta}G = -40.7 kJ/mol, KD {approx} 0.138 M). These energetics inform a PySB-based model that incorporates GADD34's folding state as a continuous variable ({varphi}), linking conformational transitions to holoenzyme assembly and activity. Simulations show that catalytic efficiency is maximized when GADD34 folding free energy is 20 kJ/mol and {varphi} = 0.9, reflecting a highly ordered state stabilized by actin and PP1 binding. Comparative analysis of energy-constrained and optimized parameter regimes reveals that folding-dependent assembly enhances both eIF2 dephosphorylation and information transmission, with channel capacities increasing from <0.002 bits to >5.5 bits. These results demonstrate how conformational regulation encodes system-level function and underscore the utility of multiscale models in bridging molecular energetics with dynamic biochemical control.

biophysics↗

bioRxiv2026

Integrated CHARGE syndrome models reveal epigenetic modulators of reproductive phenotypes

Loss-of-function variants in CHD7 cause CHARGE syndrome (CS), a rare developmental disorder showing multisystem malformations, including reproductive defects linked to gonadotropin-releasing hormone (GnRH) neuron dysfunction. CHD7 encodes a chromatin remodeler essential for early transcriptional regulation across various tissues. Currently, no pharmacological treatments exist, and approaches aimed at identifying tissue-specific CHD7 targets are also lacking, making CS treatment an unmet clinical need. To explore mechanisms relevant to CS-associated reproductive defects, we established a dual screening platform combining CRISPR-engineered Chd7-depleted mouse GnRH neurons with a Caenorhabditis elegans chd-7 mutant showing reproductive abnormalities. Transcriptomic and functional analyses of Chd7-deficient cells revealed impaired cellular processes along with dysregulation of semaphorin (Sema) genes, key regulators of GnRH neuron development. A screen of 234 epigenetic modulators in C. elegans identified compounds modifying aberrant mutant phenotype, two of which also rescued cellular defects and Sema expression in vitro. Altogether, these findings indicate that CHD7 deficiency reshapes neuroendocrine-relevant pathways and that selected compounds modulate CS-associated phenotypes across species, with SEMA signalling emerging as candidate druggable downstream pathway in CS requiring further mechanistic validation.

developmental biology↗

bioRxiv2026

Mapping the thymus in the viscoelastic landscape of biological tissues

The thymus plays a pivotal role in the generation of immunocompetent T cells. Although its function is dependent on its complex extracellular matrix, its 3D architecture and mechanical properties remain poorly characterised This knowledge gap limits efforts to model and engineer the organ, which is a critical step towards the development of strategies for the treatment of many haematological and autoimmune diseases. Here, we provide the first comprehensive multiscale dataset of bovine thymic extracellular matrix architecture and viscoelastic behaviour, including quantitiative descriptors such as relaxation times, instantaneous and equilibrium elastic moduli, storage and loss moduli, and spatial mechanical heterogeneity. Taken together, our data define the thymus as a compliant, highly dissipative viscoelastic organ with a fibrillar architecture. They also represent a unique database, which, for the first time, paves the way for quantitative thymus tissue engineering.

bioengineering↗

bioRxiv2025

On-site microbial community analysis in rivers: integrating autonomous sampling with a portable sequencing workflow

Studies focused on bacterial diversity in rivers often face significant limitations. Traditional sampling approaches frequently overlook spatial and temporal variability at the reach scale. Molecular techniques, such as metabarcoding and metagenomics, can partially address this issue by providing deeper insights. However, this approach usually involves highly specialized laboratories and high costs, making large-scale and long-term monitoring of river networks unfeasible in most cases. Thus, we developed a methodology based on remote-controlled boats, allowing the collection of integrated samples in freshwater ecosystems. Combined with a portable laboratory, this approach enabled the development of new surface water monitoring strategies. Here, we describe the operational application of this system for in situ monitoring of bacterioplankton communities across 8 sections of the Ter River (Catalonia, Spain). [To explore its potential, we applied both 16S rRNA gene sequencing using Nanopore technology (MinION) in the field, and shotgun metagenomics using Illumina technology in the laboratory, acknowledging the intrinsic differences between sequencing targets, platforms, and analysis pipelinesMinIONMinION sequencing enabled microbiome characterization and identification of the main bacterial taxa just 72 h after sampling, offering significantly lower costs and reduced manpower requirements. Furthermore, amplification facilitated the full characterization of bacterioplankton diversity along the river, preventing the exclusion of uncommon taxa. While shotgun metagenomics is still necessary for understanding the functional activity of these organisms, our approach provides a cost-effective framework for developing efficient follow-up sampling methodologies.

microbiology↗

bioRxiv2024

Evolvoid: A genetic algorithm for shaping optimal cellular constructs

We describe an in-silico pipeline, Evolvoid, based on Genetic Algorithms (GAs) for identifying the optimal morphologies of cell-laden constructs. Driven by an ad hoc selection rule (i.e., the so-called fitness function (FF)), Evolvoid iteratively identifies the characteristics (i.e., the genome) of the survival of the fittest individual of a given population throughout generations. The FF is based on universally observed biophysical laws, representing the optimal trade-off between i) high cell viability and robustness to changes in environmental oxygen and ii) a low surface energy. The Shannon entropy is used to evaluate genome complexity, with the most complex fittest individuals showing quantitative and qualitative biological resemblance to in vitro constructs. Evolvoid paves the way for the development of "lab on a laptop": high-fidelity and cost-effective digital twins of cellular constructs which could augment or even substitute costly in vitro models.

bioengineering↗

bioRxiv2024

Connexin43 in mesenchymal lineage cells regulates body adiposity and energy metabolism in mice

Connexin43 (Cx43) is the most abundant gap junction protein present in the mesenchymal lineage. In mature adipocytes, Cx43 mediates white adipose tissue (WAT) "beiging" in response to cold exposure and maintains the mitochondrial integrity of brown adipose tissue (BAT). We found that genetic deletion of Gja1 (Cx43 gene) in cells that give rise to chondro-osteogenic and adipogenic precursors driven by the Dermo1/Twist2 promoter leads to lower body adiposity and partial protection against the weight gain and metabolic syndrome induced by a high fat diet (HFD) in both sexes. These protective effects from obesogenic diet are related to increased locomotion, fuel utilization, energy expenditure, non-shivering thermogenesis, and better glucose tolerance in conditionally Gja1 ablated mice. Accordingly, Gja1 mutant mice exhibit reduced adipocyte hypertrophy, partially preserved insulin sensitivity, increased BAT lipolysis and decreased whitening under HFD. This metabolic phenotype is not reproduced with more restricted Gja1 ablation in differentiated adipocytes, suggesting that Cx43 has a hitherto unknown function in adipocyte progenitors or other targeted cells, resulting in restrained energy expenditures and fat accumulation. These results disclose an hitherto unknown action of Cx43 in adiposity, and offer a promising new pharmacologic target for improving metabolic balance in diabetes and obesity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=157 HEIGHT=200 SRC="FIGDIR/small/574415v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@1ade7d3org.highwire.dtl.DTLVardef@4edbd7org.highwire.dtl.DTLVardef@1431c1borg.highwire.dtl.DTLVardef@ea6bbb_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis

Subclinical mastitis is one of the most widespread diseases affecting dairy herds with detrimental effects on animal health as well as on milk productivity and quality. Despite the multi-factorial nature of this intramammary infection, the presence of pathogenic bacteria is regarded one of the main drivers of subclinical mastitis, leading to a disruption of the homeostasis of the bovine milk microbial community. However, the bovine milk microbiota alterations associated with subclinical mastitis still represents a largely unexplored research area. In this context, the species-level milk microbiota of a total of 75 milk samples, collected from both healthy and subclinical mastitis-affected cows from two different stables, was deeply profiled through an ITS, rather than a traditional, and less informative, 16S rRNA gene microbial profiling-based sequencing. Surprisingly, the obtained data of the present pilot study, not only revealed that subclinical mastitis is characterized by a reduced number of species in the bovine milk microbiota, but also that this disease does not induce standard alterations of the milk microbial community across stables. In addition, a flow cytometry-based total bacterial cell enumeration highlighted that subclinical mastitis is accompanied by a significant increment in the number of milk microbial cells. Furthermore, the combination of the metagenomic approach and total bacterial cell enumeration allowed to identify different potential microbial marker strictly correlated with subclinical mastitis across stables.

microbiology↗

bioRxiv2020

Early Alpine human occupation backdates westward human migration in Late Glacial Europe

The end of the Last Glacial Maximum (LGM) in Europe (~16.5 ka ago) set in motion major changes in human culture and population structure1. In Southern Europe, Early Epigravettian material culture was replaced by Late Epigravettian art and technology about 18-17 ka ago at the beginning of southern Alpine deglaciation, although available genetic evidence from individuals who lived ~14 ka ago2-5 opened up questions on the impact of migrations on this cultural transition only after that date. Here we generate new genomic data from a human mandible uncovered at the Late Epigravettian site of Riparo Tagliente (Veneto, Italy), that we directly dated to 16,980-16,510 cal BP (2{sigma}). This individual, affected by a low-prevalence dental pathology named focal osseous dysplasia, attests that the very emergence of Late Epigravettian material culture in Italy was already associated with migration and genetic replacement of the Gravettian-related ancestry. In doing so, we push back by at least 3,000 years the date of the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bolling/Allerod warming event (~14 ka ago4,6). Our results suggest that demic diffusion from a genetically diverse population may have substantially contributed to cultural changes in LGM and post-LGM Southern Europe, independently from abrupt shifts to warmer and more favourable conditions.

genomics↗