Biology subjects

Ribas, L.

Publications and source records attributed to Ribas, L..

9 recordsLinked to original sources

bioRxiv2026

Synergistic effects of hypergravity and immune challenge on the zebrafish larval transcriptome

The transcriptomic interaction between altered gravity and innate immunity remains largely unexplored. In this study, we established a novel dual-stress model combining 3g hypergravity with lipopolysaccharide (LPS) immune challenge in 5 days post-fertilization (dpf) zebrafish (Danio rerio) larvae. RNA sequencing revealed that exposure to hypergravity alone induced no differentially expressed genes (DEGs), indicating a remarkable transcriptional resilience. In contrast, the addition of an immune challenge under hypergravity conditions triggered a substantial transcriptomic response involving 2,706 DEGs. Functional enrichment analyses identified significant alterations in pathways related to immune function, development, and circadian regulation. Targeted qPCR analyses further validated the expression patterns of selected genes. These findings suggest that while zebrafish larvae can effectively tolerate hypergravity alone, the combination of gravitational and immune stressors elicits profound molecular responses. This study provides new insights into the interplay between altered gravity and innate immunity using an animal model, contributing to future strategies aimed at safeguarding astronaut health and supporting space-based aquaculture systems.

genomics↗

bioRxiv2026

Developmental growth rates adapt to enable self-correction of organ morphology after injury.

Proportional organ growth requires tissue-level control of cell behavior. Yet the cues that adapt growth rates, especially after organ injury, remain unclear. Here, we uncover that developing organs are robust to extensive damage, triggering injury-specific mechanisms sufficient to override genetically-encoded size defects. Using precision microsurgery in developing zebrafish pectoral fins, we find that injury drives growth asynchronously across tissues and fin axes, by increasing proliferation and extracellular spacing. Growth compensation scales with the amount of tissue lost, restoring size and structure without compromising developmental timing. A feedback-control model captures these dynamics, suggesting that growth rates are regulated toward an organ-specific target area. At the molecular scale, injury signals bypass developmentally-regulated BMP gradient scaling. Injury instead activates de novo BMP signaling, which supports growth adaptation and rescues wildtype fin size in developmentally small mutants. Our findings identify an injury-dependent compensatory growth mechanism that resets developmental organ size, ensuring functional organ recovery.

developmental biology↗

bioRxiv2026

Lungfish comparative genomics reveals ancient gene networks co-opted for life on land

The transition from water to land was a defining event in vertebrate evolution, requiring major changes in physiology and gene regulation. Lungfish, the closest extant relatives of tetrapods, offer a unique window into this process through their capacity for estivation, a physiological state that mirrors key demands of terrestrial life. Here, we constructed and compared gene co-expression networks across five vertebrate species using multi-tissue transcriptomic data. Focusing on estivating lungfish tissues, we identified conserved modules enriched in core functions, including metabolic regulation, RNA processing, and protein turnover. We further show that a subset of retained ohnologs from the vertebrate 2R-WGD act as network hubs under directional selection in key phylogenetic branches. These genes, involved in membrane trafficking, cytoskeletal regulation, water balance, and stress response, illustrate how duplicated, dosage-sensitive genes were co-opted to meet the physiological demands of terrestrial adaptation. Together, our findings support a model in which ancient whole-genome duplications supplied raw material later shaped by selection and network rewiring to enable extreme physiological adaptations such as estivation. TeaserAncient duplicated gene networks in lungfish estivation reveal how vertebrates repurposed genomic toolkits to adapt to land.

evolutionary biology↗

bioRxiv2024

Identification of sex-biased miRNA markers informative of heat-past events

Elevated temperatures during early developmental stages play a pivotal role in the fate of the final sexual phenotype of fish populations, particularly towards male-skewed sex ratios. This is the case with European sea bass (Dicentrarchus labrax), one of the most important European species in the aquaculture industry. To unveil informative markers of the past thermal events, we investigated changes in the miRNome within the gonads of this species. Consequently, we exposed European sea bass to elevated temperatures during early development and conducted miRNA-sequencing analysis in the ovaries and testes one year post-heat treatment. The examination of miRNA expression levels identified three and twelve miRNAs in ovaries and testes, respectively, reflecting past thermal events. To assess the evolutionary conservation of these identified miRNAs in gonads, we cross-referenced our data with miRNome public information from ovaries and testes in nine additional fish species. This analysis uncovered 43 potential sex-biased markers present in at least five studied species along the evolutionary timeline. For instance, miR-155, miR-429, and miR-140 were female-skewed while miR-184, miR-499, and miR-135 were male-skewed. In addition, among these markers, eight conserved sex-skewed miRNAs proved informative regarding past thermal events in both the ovaries (e.g., miR-192-5p and miR-143-3p) and testes (miR-129-5p, miR-2187a-3p, miR-724-5p, miR-143-3p, miR-194a-5p and miR-223-3p). Notably, miR-223-3p and miR-194a-5p were conserved female-skewed, but showed upregulation in males exposed to high temperature. These miRNAs could serve as markers of heat-induced masculinization of genetic female-prone fish. The current research broadens the inventory of sex-specific miRNAs along evolution in fish and, elucidates thermosensitive miRNAs in the gonads. These findings hold promise as potential tools for predicting historical environmental events associated with masculinization due to high-temperature treatments in cultured species but also perhaps for natural populations exposed to a climate change scenario.

molecular biology↗

bioRxiv2023

Epigenetic and physiological alterations in zebrafish subjected to hypergravity

Gravity is one of the most constant environmental factors across Earths evolution and all organisms are adapted to it. Consequently, spatial exploration has captured the interest in studying the biological changes that physiological alterations are caused by gravity. In the last two decades, epigenetics has explained how the environmental cues are able to altered gene functions in the organisms. Although many studies addressed gravity, the underlying biological and molecular mechanisms that are occurred in altered gravity for those epigenetics-related mechanisms, are mostly inexistent. The present study addressed the effects of hypergravity on development, behavior, gene expression, and most importantly, on the epigenetic changes in a world-wide animal model, the zebrafish (Danio rerio). To perform hypergravity experiments, a custom-centrifuge simulating the large diameter centrifuge (100 rpm [~] 3 g) were designed and zebrafish embryos were exposed during 5 days post fertilization (dpf). Results showed a significant decrease of survival at 2 dpf but not significance in the hatching rate. Physiological and morphological alterations including fish position, movement frequency and swimming behavior showed significant changes due to hypergravity. Epigenetic studies showed a significant hypermethylation of the genome of the zebrafish larvae subjected to 5 days of hypergravity. A downregulation of the gene expression of three epigenetic-related genes (dnmt1, dnmt3, and tet1), although not significant, were further observed. Taken altogether, gravity alterations affected biological responses including epigenetics in fish, providing a valuable roadmap of the putative hazards of living beyond Earth.

cell biology↗

bioRxiv2023

Downstream effects of dre-miR-210-5p in zebrafish primary ovarian cell culture

MicroRNAs (miRNAs) are small, non-coding RNAs that are involved in post-transcriptional gene regulation in many cellular functions and are highly conserved throughout evolution. In teleost fish species, miRNAs are believed to play a role in the reproductive system, but more research is needed to better understand the functions of miRNAs in fish gonads. Furthermore, miR-210 has previously been described to be involved in many processes, such as hypoxia response, angiogenesis, cell proliferation and male infertility. The aim of this study was, first, to develop an in vitro model in fish to study the functions of miRNAs and second, to identify target genes of dre-miR-210-5p by establishing a primary ovarian cell culture in zebrafish (Danio rerio). The cell culture was performed by isolating ovaries from adult female fish (n=4) which were incubated with dre-miR-210-5p mimic or scramble miRNA mimic. Cell survival was studied by flow cytometry analysis and fluorescent microscopy. Following, the effect of dre-miR-210-5p on ovarian cells was uncovered by RNA-sequencing, identifying [~]6,000 targeted-genes differentially expressed (DEGs), of which [~]2,600 downregulated and [~]3,400 upregulated. GO term and KEGG pathway analyses showed downregulated genes involved in cell cycle processes and reproduction-related pathways while, in contrast, immune-related pathways were upregulated after miR-210 mimic treatment in the ovarian cells. To provide the molecular mechanisms triggered by miRNA-210, seed regions of targeted genes were identified and in silico analysis classified DEGs as potential biomarkers in reproduction or immune cell types. These results support the crosstalk between the reproductive and immune system in which dre-miR-210-5p plays a key role in the transcriptomic alteration in the fish ovaries. Take home messagemiR-210 promotes the immune response and suppresses oocyte meiosis in the ovarian cells in zebrafish

molecular biology↗

bioRxiv2022

Peripheral blood mononuclear cells exhibit increased mitochondrial respiration after adjuvant chemo- and radiotherapy for early breast cancer

BackgroundAdjuvant chemo- and radiotherapy cause cellular damage not only to cancerous but also to healthy dividing cells. Antineoplastic treatments have been shown to cause mitochondrial respiratory dysfunction in non-tumorous tissues, but the effects on circulating human peripheral blood mononuclear cells (PBMCs) remain unknown. AimWe aimed to identify changes in mitochondrial respiration of PBMCs after adjuvant chemo- and radiotherapy in postmenopausal early breast cancer (EBC) patients and relate these to metabolic parameters of the patients. MethodsTwenty-three postmenopausal women diagnosed with EBC were examined before and shortly after chemotherapy treatment often administered in combination with radiotherapy (n=18). Respiration (O2 flux per million PBMCs) was assessed by high-resolution respirometry of intact and permeabilized PBMCs. Clinical metabolic characteristics were furthermore assessed. ResultsRespiration of intact and permeabilized PBMCs from EBC patients was significantly increased after adjuvant chemo- and radiotherapy (p=6x10-5 and p=1x10-7, respectively). The oxygen flux attributed to specific mitochondrial complexes and respiratory states increased by 17-43% compared to before therapy commencement. Leukocyte counts (p=1x10-4), hemoglobin levels (p=0.0003), and HDL cholesterol (p=0.003) decreased while triglyceride (p=0.01) and LDL levels (p=0.02) increased after treatment suggesting a worsened metabolic state. None of the metabolic parameters correlated significantly with PBMC respiration. ConclusionThis study shows that mitochondrial respiration in circulating PBMCs is significantly increased after adjuvant chemo- and radiotherapy in postmenopausal EBC patients. The increase might be explained by a shift in PBMC subpopulation proportions towards cells relying on oxidative phosphorylation rather than glycolysis or a generally increased mitochondrial content in PBMCs. Both parameters might be influenced by therapy-induced changes to the bone marrow or vascular microenvironment wherein PBMCs differentiate and reside.

cell biology↗

bioRxiv2021

Deciphering sex-specific miRNAs as heat-recorders in zebrafish

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression in a wide variety of physiological processes, including those related to the reproductive system. Although in the last decade a plethora of miRNAs has been reported, the miRNA alterations occurred by environmental cues and their biological functions have not yet been elucidated. With the aim to identify epigenetic regulations mediated by miRNAs in the gonads in a climate change scenario, zebrafish (Danio rerio) were subjected to high temperatures during sex differentiation (18-32 days post fertilization, dpf), a treatment that results in male-skewed sex ratios. Once the fish reached adulthood (90 dpf), ovaries and testes were sequenced by high-throughput technologies. About 101 million high-quality reads were obtained from gonadal samples. Analyses of the expression levels of the miRNAs identified a total of 23 and 1 differentially expressed (DE) miRNAs in ovaries and testes, respectively, two months after the heat treatment. Most of the identified miRNAs were involved in human sex-related cancer. After retrieving 3 UTR regions, ~400 predicted targets of the 24 DE miRNAs were obtained, some with reproduction-related functions. Their synteny in the zebrafish genome was, for more than half of them, in the chromosomes 7, 2, 4, 3 and 11 in the ovaries, chromosome 4 being the place where the predicted sex-associated-region (sar) is localized in wild zebrafish. Further, spatial localization in the gonads of two selected miRNAs (miR-122-5p and miR-146-5p) showed exclusive expression in the ovarian germ cells. The present study expands the catalog of sex-specific miRNAs and deciphers, for the first time, thermosensitive miRNAs in the zebrafish gonads that might be used as potential epimarkers to predict environmental past events.

genomics↗

bioRxiv2019

Immune genes, IL1β and Casp9, show sexual dimorphic methylation patterns in the zebrafish gonads

There is a crosstalk between the immune and the reproductive systems in which sexual dimorphism is a common pattern in vertebrates. In the last years, epigenetics has emerged as a way to study the molecular mechanisms involved during gonadal development, which are responsible to integrate environmental information that contributes to assign a specific sexual phenotype (either an ovary or a testis). In the fish gonads, it is known of the existence of the reproduction-immune system interactions although the epigenetic mechanisms involved are far to be elucidated. Here, we used the zebrafish (Danio rerio) as a model to study the DNA methylation patterns of two well-known innate immune genes: IL1{beta} and Casp9. DNA methylation levels were studied by a candidate gene approach at single nucleotide resolution and further, gene expression analysis were carried out. Results showed that there was clear sexual dimorphism in the DNA methylation levels of the two immune studied genes, being significantly higher in the testes when compared to the ovaries. In summary, and although much research is needed, here we present two potential candidates as epimarkers with forthcoming applications in the livestock and fish farming production, for example, in immune fish diseases or sexual control programs.

immunology↗