Biology subjects

Ribeiro, F.

Publications and source records attributed to Ribeiro, F..

11 recordsLinked to original sources

bioRxiv2026

Small-molecule targeting MuRF1 enhances functional exercise capacity in rats: an exploratory study

Maintenance of skeletal muscle function is essential for functional independence, quality of life and healthspan. Muscle RING-finger protein-1 (MuRF1) negatively regulates muscle function and mass through ubiquitination and degradation of muscle proteins. Accordingly, genetic and pharmacological inhibition of MuRF1 attenuates muscle wasting and weakness under catabolic stress. To explore the potential of MuRF1 inhibitors (e.g., MyoMed-205) to improve muscle health, we investigated here the long-term effects of MyoMed-205 on functional capacity and muscle physiology in rats under basal conditions. Wistar rats were randomized to control or MyoMed-205 groups and were followed for 4 or 8 weeks. Body weight, food and water intake, and exercise capacity were monitored weekly. At each endpoint, the soleus muscle was collected for histological analyses. MyoMed-205-treated rats showed normal basic survival-related behaviors and body growth. After 8 weeks, MyoMed-205-treated animals exhibited enhanced exercise capacity (speed (m/min): +45%, p = 0.01; endurance (min): +47%, p = 0.03; and distance covered (m): +87%, p = 0.04) compared with baseline performance. Conversely, no differences were found in soleus fiber type distribution, cross-sectional area, or lipid and collagen content. Our findings indicate that MyoMed-205 enhances functional exercise capacity independently of changes in soleus muscle structure in rats under basal conditions.

physiology↗

bioRxiv2025

Small-molecule inhibition of MuRF1 protects against disuse-induced diaphragmatic dysfunction: Underlying molecular mechanisms

BackgroundMechanical inactivity rapidly induces diaphragm muscle fibers contractile dysfunction and atrophy. Diaphragm weakness can impair respiratory function, quality of life, and increase risks of morbidity and mortality. Muscle RING-finger protein-1 (MuRF1) expression is upregulated during denervation and muscle inactivity, and is known to target key muscle proteins for degradation. We previously reported that the small-molecule targeting MuRF1 (MyoMed-205) protects against diaphragm contractile dysfunction and atrophy after 12 hours of unilateral diaphragm denervation (UDD) in rats. In this study, we investigated the mechanisms by which MyoMed-205 protects the diaphragm structure and function during early UDD in rats. MethodsMale Wistar rats were subjected to unilateral diaphragm denervation (UDD) for 12 hours. Immediately after UDD, rats received either a placebo (vehicle) or small-molecule targeting MuRF1 (MyoMed-205, 50 mg/kg bw), and outcomes were compared with Sham-operated controls. Diaphragm was used for histological, morphometric, transcriptomic (RNA-seq), and protein content (Western Blot) analysis. ResultsUDD induced diaphragm slow-(type I: p = 0.03) and fast-twitch (type IIa: p = 0.04; type IIb/x: p = 0.02) fibers atrophy after 12 hours, which was prevented by MyoMed-205 (p < 0.05). Mechanistically, UDD perturbed mechanisms involved with myofiber ultrastructure and contractility, mitochondrial function, proteolysis, and tissue remodeling in the diaphragm. MyoMed-205 enhanced the activation of mechanisms required for sarcomere integrity, calcium handling, antioxidant defense, chaperone-mediated unfolded protein response, and muscle growth. MyoMed-205 also mitigated intramuscular fat deposition and pro-fibrotic responses triggered by UDD. ConclusionSmall-molecule targeting MuRF1 (MyoMed-205) protects against diaphragm muscle contractile dysfunction and atrophy after 12 hours of UDD. Herein, we demonstrate that this protective effect involved augmented activation of signaling pathways controlling muscle structure and function, chaperone-mediated unfolded protein, and muscle growth, while mitigating intramuscular fat deposition and pro-fibrotic responses triggered by UDD at the transcriptional and/or protein level.

physiology↗

bioRxiv2025

Selective breeding and production strategies to support snapper farming in the warming waters of New Zealand's South Island

Diversifying aquaculture species is essential for building resilience in the face of climate change, particularly as warming oceans challenge existing production systems. In New Zealands Marlborough Sounds, rising sea temperatures are making salmon farming increasingly difficult, highlighting the need for climate-adapted alternatives. This study evaluated the aquaculture performance of selectively bred F4 versus unselected F1 Australasian snapper (Chrysophrys auratus) across two rearing environments: sea pens in the Marlborough Sounds and a land-based system in Nelson. Approximately 1,000 F4 and 1,000 F1 snapper were reared from 4 to 30 months of age in each system. At 30 months, selectively bred snapper showed improved growth-body length increased by 1.7% (land-based) and 4.8% (ocean-based), and body weight by 9.8% and 14.2%, respectively compared with F1 snapper. Survival was also significantly higher, with selected snapper outperforming controls by 84.2% in the land-based and 60.8% in the ocean-based system. Mortality peaked in the first winter across both systems, with size-selective patterns in sea pens informing minimum stocking sizes. These findings offer important insights for refining husbandry and selective breeding practices. They are not only relevant for New Zealand but also for global aquaculture sectors seeking robust species suited to changing marine environments.

zoology↗

bioRxiv2025

Democratizing Organ-on-Chip Technologies with a Modular, Reusable, and Perfusion-Ready Microphysiological System

Organ-on-chip (OOC) technologies, also called microphysi-ological systems (MPS), offer dynamic microenvironments that improve upon static culture systems, yet widespread adoption has been hindered by fabrication complexity, reliance on poly-dimethylsiloxane (PDMS), and limited modularity. Here, we present a modular MPS platform designed for ease of use, re-producibility, and broad applicability. The system comprises layered elastomeric inserts for dual monolayer cell culture, which is clamped within a reusable acrylic cassette for perfusion studies. This enables researchers to decouple model establishment from flow experiments and streamline their work-flows. We validated the system using dual epithelial and en-dothelial cell co-culture under static and perfused conditions, including shear-induced alignment of HUVECs. Material testing confirmed biocompatibility, while vinyl cutting reproducibility demonstrated high manufacturing fidelity. The platform reliably supported long-term culture (up to 14 days), and the open insert format facilitated uniform seeding and imaging access. This approach enables parallelized experimentation, minimizes pump usage, and is well-suited for labs without microfabrication infrastructure. By combining fabrication flexibility with biological robustness, this work establishes a generalizable platform for modular tissue-chip development adapted to diverse organ systems and serves as a foundational framework for democratizing advanced in vitro model systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/651503v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1e5fed3org.highwire.dtl.DTLVardef@bcf27eorg.highwire.dtl.DTLVardef@d46f33org.highwire.dtl.DTLVardef@d0912f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: differences in efficiency and resolution coupled to habitat and ecology

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, implementation of eDNA as a standard protocol in long-term monitoring programs, that have traditionally relied on capture-based methods, poses challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For most species or species-groups analyzed individually (13 out of 17), there was a significant correspondence between electrofishing and eDNA metabarcoding detections. The correspondence was weaker when comparing the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

ecology↗

bioRxiv2024

The plant pioneer factor LFY uses trans-kingdom chromatin remodeling mechanisms in vertebrates

Multicellular complexity is thought to have evolved independently in animals and plants, but the molecular constraints driving this complexity are poorly understood. Genetic networks activated during animal and plant development both involve the regulation of nucleosome occupancy by chromatin remodelers. Pioneer factors, often specific to plants or animals, bind to nucleosome-occupied DNA in a sequence-specific manner, recruiting chromatin remodelers to control lineage-specific genetic networks. In this study, a plant-specific pioneer factor, LFY, when expressed in zebrafish cells, recruits the vertebrate chromatin remodeler Smarca4a to make DNA accessible at LFY binding sites. This allows a plant LFY-controlled promoter, introduced into the zebrafish genome, to become transcriptionally active in a Smarca4a-dependent manner. Our findings suggest that the protein-protein interaction between pioneer factors and chromatin remodelers is a trans-kingdom mechanism likely reflecting ancient eukaryotic events that became a key evolutionary constraint in the path to biological complexity.

evolutionary biology↗

bioRxiv2024

Improving whole biodiversity monitoring and discovery with environmental DNA metagenomics

Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SEQIDIST, a framework that combines multilocus BLAST matches against several reference databases followed by analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SEQIDIST on an eDNA metagenomic dataset from a riverine site and compare the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterizing the biological community ([~] 2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SEQIDIST opens the discussion of the archival potential of eDNA metagenomics and its implementation in biodiversity monitoring actions at large planetary and temporal scales.

ecology↗

bioRxiv2023

Reproductive traits of the European catfish (Silurus glanis) during the early stages of invasion in the Lower Tagus River

Freshwater ecosystems face severe challenges from biological invasions, leading to biodiversity loss, disruption of ecosystem services, and economic impacts. Human-mediated activities, such as aquarium trade and sport angling, contribute to species introductions, with potential negative consequences for native ecosystems. The European catfish (Silurus glanis) is one of the worlds largest freshwater fish and has been intentionally introduced into diverse regions, impacting native ecosystems. However, limited research exists on its reproductive traits outside its native range. This study addresses this gap by examining the reproductive characteristics of non-native European catfish populations in the Lower Tagus River in Portugal, focusing on size at maturity, spawning period, and fecundity. The observed balanced sex ratio aligns with studies of native populations. Variations in size at first maturity (TL50) among populations highlight the influence of habitat conditions, temperature, food availability, growth rate, and geographical location on this trait. The extended spawning season (March to June) in the Tagus River is consistent with native populations, but variations may occur based on environmental conditions and water temperature. Absolute fecundity ranged from 8,961 to 335,500 oocytes, showing positive relationships with body size and emphasizing the reproductive potential of European catfish in Portugal. Egg size variations, along with asynchronous egg development, contribute to the species reproductive strategy, favoring its invasive success. Management efforts should include monitoring, regulations on introductions, removal programs, and public awareness to mitigate their impact. Future research should focus on understanding how non-native European catfish populations adapt in various regions and continue to impact ecosystems.

ecology↗

bioRxiv2023

Westwards expansion of the European catfish Silurus glanis in the Douro River (Portugal)

The current study reports the first occurrence and the spread of the European catfish Silurus glanis (Family: Siluridae) in the Portuguese section of the Douro River, suggesting a potential expansion of its distribution in Portugal either via westward dispersal across international rivers and/or human-assisted introductions into new reservoirs and drainages. European catfish has unique features (e.g., opportunistic predator, hunting, and aggregation behaviour) that make it highly suitable for establishing self-sustaining populations in new areas and likely contribute to its invasion success. The species may severely affect native prey communities and modify food web structure and ecosystem functioning. Efficient and sustainable management actions are needed to prevent further introductions in the future.

ecology↗

bioRxiv2022

Specialized Tfh cell subsets driving type-1 and type-2 humoral responses in lymphoid tissue

Effective antibody responses are essential to generate protective humoral immunity. Different inflammatory signals polarize T cells towards an appropriate effector phenotype during an infection or immunization. Th1 and Th2 cells have been associated with the polarization of humoral responses for several decades. However, it is now established that T follicular helper cells (Tfh) have a unique ability to access the B cell follicle and support the Germinal Centre (GCs) responses by providing help to B cells. We investigated the specialization of Tfh cells induced under type-1 and type-2 conditions. We first studied homogenous Tfh cell populations generated by adoptively transferred TCR-transgenic T cells in mice immunized with type-1 and type-2 adjuvants. Using a machine learning approach, we established a gene expression signature that discriminates Tfh cells polarized towards type-1 and type-2 response, defined as Tfh1 and Tfh2 cells. The Tfh1 and Tfh2 distinct signature was validated against datasets of Tfh cells induced following LCMV or helminth infection. Using single-cell transcriptomics, we also dissected the heterogeneity of Tfh cells from the two immunizing conditions. Our results show that Tfh cells acquire a specialized function under distinct types of immune responses, but with the coexistence of a small population of Tfh cells of the alternative type. Furthermore, the specific molecular hallmarks of Tfh1 and Tfh2 cells identified herein offer putative new targets for tuning humoral responses.

immunology↗

bioRxiv2022

Widespread hybridization between invasive bleak (Alburnus alburnus) and native Iberian chubs (Squalius spp.): a neglected threat

Hybridization between native and exotic species is a major conservation issue. In Iberian rivers, which are simultaneously among the most invaded and diverse ecosystems, harboring a high proportion of endemic fishes, this issue is becoming highly concerning. To date, hybridization has been reported to occur between the invasive bleak Alburnus alburnus and the endemic chubs Squalius alburnoides and S. pyrenaicus, in some scattered locations. However, the bleak is increasingly spreading in the region, potentially increasing the risks of hybridization with these and other Squalius species. To gather a more comprehensive picture on the current extension of hybridization, we compiled and mapped records on hybrids between bleak and chubs collected by multiple research teams in different ongoing projects in the Portuguese territory, and genetically assessed the hybrid identity of specimens in an area of sympatry between bleak and S. carolitertii, using nuclear and mitochondrial markers. We found that hybridization with bleak is widespread in several Portuguese river basins and involves at least three endemic chubs, S. alburnoides, S. pyrenaicus and S. carolitertii. This may have serious consequences, including not only waste of reproductive effort and damage of genetic integrity, but also putative shifts on the reproductive dynamics of the Squalius system, which includes endemic hybrids, reproducing sexually and nonsexually. Hybridization should be recognized as a significant impact of biological invasions, and we recommend that future studies should characterize the fitness of hybrids and their ecological and genetic interactions with parental Iberian fish, to elucidate effective conservation measures.

zoology↗