Advancing Open Science

Background. Dystroglycanopathies (DGPs) constitute a set of recessive, neuromuscular congenital dystrophies that result from impaired glycosylation of dystroglycan (DG). These disorders typically course with CNS alterations, which, alongside gradual muscular dystrophy, may include brain malformations, intellectual disability and a panoply of ocular defects. In this process, the protein products of 22 genes, collectively dubbed DGP-associated genes, directly or indirectly participate sequentially along a complex, branched biosynthetic pathway. POMGNT2 and POMGNT1 are two enzymes whose catalytic activity consists of transferring the same substrate, a molecule of N-acetylglucosamine (GlcNAc) to a common substrate, the O-mannosylated α subunit of DG. Despite their presumptive role in retinal homeostasis, there are currently no reports describing their expression pattern or function in this tissue. Purpose. This work focuses on POMGNT2 and POMGNT1 expression in the mammalian retina, and on the characterization of their distribution across retinal layers, and in the 661W photoreceptor cell line. Methods. The expression of POMGNT2 protein in different mammalian species’ retinas, including those of mice, rats, cows and monkeys, was assessed by immunoblotting. Additionally, POMGNT2 and POMGNT1 distribution profiles were analyzed using immunofluorescence confocal microscopy in retinal sections of monkeys and mice, and in 661W cultured cells. Results. Expression of POMGNT2 was detected in the neural retina of all species studied, being present in both cytoplasmic and nuclear fractions of the monkey and mouse, and in 661W cells. In the cytoplasm, POMGNT2 was concentrated in the endoplasmic reticulum (ER) and/or Golgi complex, depending on the species and cell type, whereas POMGNT1 accumulated only in the Golgi complex in both monkey and mouse retinas. Additionally, both proteins were present in the nucleus of the 661W cells, concentrating in the euchromatin and heterochromatin, as well as in nuclear PML and Cajal bodies, and nuclear speckles. Conclusions. Our results are indicative that POMGNT2 and POMGNT1 participate in the synthesis of O-mannosyl glycans added to α-dystroglycan in the ER and/or Golgi complex in the cytoplasm of mammalian retinal cells. Also, they could play a role in the modulation of gene expression at the mRNA level, which remains to be established, in a number of nuclear compartments in transformed retinal neurons.

Background. Hypophosphatasia (HPP) is a rare genetic disorder caused by impaired tissue non-specific alkaline phosphatase (ALPL/TNSALP) activity that impacts the musculoskeletal and neurological systems. It is extremely variable, with up to six forms of increasing severity. The large phenotypic variability and the still remaining high number of variants of uncertain significance (VUS) in the ALPL gene represent a conundrum for clinicians dealing with people suspected to be suffering from HPP. Methods. We applied a multi-faceted bench-based and high-throughput bioinformatics analysis to investigate the effect of 21 ALPL variants (18 deleterious—pathogenic or likely pathogenic—and 3 VUS) on the structure and function of the mutated encoded protein. The results were compared with available clinical and biochemical data. Results. Most variants were downregulated or not expressed by Western blot analysis. Impairment of the enzymatic activity was confirmed in vitro for all variants by a specific colorimetric enzymatic assay. In silico prediction was in line with functional data and allowed for preliminary categorization of variants based on their impact on both the overall stability of the protein complex and local structural alterations. Coherence among bioinformatics, experimental and clinical data was documented for more than 70% of the variants. Conclusions. Functional and in silico characterizations of ALPL variants in people with a suspicion of HPP offer integrative strategies to genotyping in assisting clinicians for diagnosis confirmation in doubtful cases.

Branching structures such as vascular networks are representative morphological patterns in living systems, and they often arise from collective cell migration. Angiogenesis, the sprouting of new blood vessels from pre-existing ones, is a fundamental process in development. Experimental and theoretical studies have demonstrated that sprout formation depends on the collective movements and shapes of endothelial cells, as well as the remodelling of the extracellular matrix. Many discrete models have been proposed to describe cell dynamics, successfully reproducing vascular patterns and collective behaviours. In this study, we present a two-dimensional mathematical model that represents each endothelial cell as an ellipse and incorporates the effects of the extracellular matrix. We performed computer simulations under two scenarios: invasion from a pre-formed sprout and collective advancement into an extracellular matrix region. The results show that the extracellular matrix helps maintain linear sprout extension and suppresses the formation of dispersed or curved branches, while elongated cell shapes promote sprouting more effectively than round cells. The model also reproduces experimentally observed behaviours such as tip-cell replacement and the mixing of cells within sprouts. These findings highlight the importance of integrating cell shape and extracellular matrix remodelling to understand early blood vessel formation.

This study looks at the impact of geopolitical risk on the volatility of wheat futures returns over the period 2012–2023, while controlling for inventories, shipping rates, and speculative activity. Using the volatility of CBOT first nearby futures returns, we apply a quantile regression approach to assess the impact of the variables on different parts of the volatility distribution. More specifically, we adopt the Quantile Autoregressive Distributed Lag (QARDL) model, which allows for examining the dynamic short- and long-run effects. We find that geopolitical risk has a non-linear, large positive effect on the top quartile of the distribution of wheat futures returns. We also show that the response of the volatility of wheat futures to shocks in the control variables is mostly non-linear across the conditional quantiles, significant in the tails and not around the median.

This study aims to investigate the ecological role of sponges as habitat formers on soft-bottom habitats of the mesophotic zone. As habitat formers, sponges significantly enhance benthic habitat complexity and establish associations with a plethora of organisms consequently augmenting local biodiversity. This role becomes particularly critical in areas subjected to intensive bottom trawling, where sponges often comprise a substantial portion of the discarded material. The examination of 114 massive sponge specimens, belonging to 10 sponge species, which were collected as bycatch from bottom trawls in the Aegean and Ionian ecoregions, revealed a total of over 4600 associated individuals of 78 invertebrate taxa, with crustaceans, mollusks, and polychaetes being the dominant groups. The composition of sponge-associated communities showed strong similarities to previously reported cases from shallow water hard substrates of the eastern Mediterranean, while displaying host-specific differences likely influenced by sponge morphology. Although depth did not significantly affect species richness, Shannon diversity, or evenness, a decrease in abundance of associated invertebrates was observed in deeper samples, suggesting a depth-related pattern that deserves further investigation. By forming stable substrate “islands” in otherwise unstable soft substrate environments, sponges play a vital role in structuring benthic communities. Their removal through bottom trawling not only results in the loss of the sponges themselves, but also disrupts the diverse communities they support. We suggest that sponge-associated fauna should be recognized as part of the discarded bycatch and emphasize the need for broader assessments of sponge-mediated biodiversity across similar Mediterranean habitats to support effective management and conservation strategies.

Rapid urbanization and limited land resources have intensified parking shortages in China’s core and old urban districts, highlighting the tension between parking supply and public space. This study investigates the staged impacts of shared autonomous vehicles (SAVs) on private car ownership and parking demand within the context of urban renewal. Using a case study of Qintai Community in Wuhan, we combined resident surveys (135 valid samples), on-site parking facility assessments, and demand forecasting models to evaluate changes in parking requirements across different timeframes. Results indicate that SAVs can substantially reduce private car ownership and reshape parking demand structures, with short-term transitional pressures followed by long-term demand contractions. Furthermore, SAV adoption offers opportunities to reallocate parking land for multifunctional urban uses, alleviating land-use conflicts in high-density neighborhoods. The findings contribute to a dynamic framework for staged parking optimization, integrating technological innovation with community-level urban renewal strategies. This study underscores the importance of linking residents’ behavioral shifts with infrastructure adaptation, providing evidence-based guidance for sustainable urban transport and space management.

Understory vegetation plays a pivotal role in enhancing forest biodiversity, and its restoration is crucial for sustainable forest development, energy flow, and nutrient cycling. However, the dynamics of the biomass, diversity, and species composition of understory vegetation in plantations in south China, along with their key drivers, remain poorly understood. This study investigated four mature plantation types (Pinus massoniana, Pinus caribaea, Cunninghamia lanceolata, and mixed Chinese fir–broadleaf forests) in south China through plot surveys, environmental factor measurements, and structural equation modeling (SEM) to explore the diversity, biomass allocation patterns, and driving mechanisms of understory vegetation. The results demonstrated the following. (1) The introduced Caribbean pine forests exhibited higher shrub biomass than native Masson pine forests, which was driven by their high canopy openness favoring light-demanding species (e.g., Melicope pteleifolia, IV = 33.93%), but their low mingling degree limited herb diversity. (2) Masson pine forests showed superior shrub diversity due to their random spatial distribution and higher soil total potassium (TK) content. (3) Mixed Chinese fir–broadleaf forests achieved 24.50–66.06% higher herb biomass compared to coniferous monocultures, supported by high mingling degree, random spatial configuration, and phosphorus-potassium-enriched soil, with concurrently improved herb diversity. SEM revealed that stand structure (DBH, density, mingling degree) directly drove shrub diversity by regulating light availability, while herb biomass was primarily governed by soil total phosphorus (TP) and pH. Canopy-induced light suppression negatively affected herb diversity. We recommend optimizing stand density and canopy structure through thinning and pruning to enhance light heterogeneity alongside supplementing slow-release P fertilizers in P-deficient stands. This study provides theoretical support for the multi-objective management of south China plantations, emphasizing the synergistic necessity of stand structure optimization and soil amendment.

A new version of the L-CADEL elbow joint assisting device is presented as version v5. The design is revised based on the experience of previous versions and on the requirements that consider the application for physical exercise for the elderly people at home. A laboratory prototype has been created with lightweight, portable and easy-to-use functionality that is confirmed by lab test results. A web interface was developed to manage the device as well as to acquire and elaborate data. Results of lab tests are discussed to validate the design feasibility and to characterize the operation performance for future clinical assessments.