Biology subjects

Aguilera, F.

Publications and source records attributed to Aguilera, F..

9 recordsLinked to original sources

bioRxiv2026

Who takes the risk to forage? Testing consistent inter-individual behavioural variation in wild vervet monkeys (Chlorocebus pygerythrus)

Risk-taking behaviour permeates daily decision-making across many taxa and has significant impact on fitness outcomes. Previous research finds that individuals display consistent tendencies in their propensity to take risks, often labelled as a "Boldness-Shyness" personality trait. In this experimental study, we investigated repeatability in risk-taking behaviour in 241 wild vervet monkeys by measuring their responses to capture threat (via human-initiated darting procedure) and predation threat (via two predator models). We further examined the influence of socio-demographic, group identity and hormonal factors on risk-taking behaviour. We found that multiple behavioural responses, including the likelihood of approaching a food source under threat, were consistent across contexts. Risk-taking behaviour was influenced by age, sex, dominance rank, and hormonal profiles: juveniles, males, and higher-ranking individuals were more likely to approach food under (perceived) predation risk. Additionally, we observed significant among-group differences, suggesting that individuals within the same social group exhibit similar risk sensitivities, potentially due to social facilitation or shared environmental effects. The findings contribute to our understanding of animal personality and the ecological and social drivers underlying variation in risk-related behaviours.

animal behavior and cognition↗

bioRxiv2025

Near telomere-to-telomere genome assembly of the Chilean jack mackerel Trachurus murphyi

The Chilean jack mackerel (Trachurus murphyi) is an economically important pelagic fish widely distributed across the South Pacific Ocean. Due to intense fishing pressure and the lack of high-quality genomic resources, the development of sustainable fisheries management strategies has been hindered. Here, we present a near telomere-to-telomere genome assembly of T. murphyi using PacBio and Hi-C sequencing data. The assembled genome spans 818.31 Mb, with a contig N50 length of 24.89 Mb and a scaffold N50 length of 34.34 Mb. The assembly is anchored on 24 pseudo-chromosomes, covering 95.80% of the genome. BUSCO analysis indicates a high level of completeness at 99.0%, and telomeres and centromeres were identified on pseudo-chromosomes. Repetitive sequences account for 24.24% of the total genome, and 47,734 protein-coding genes were annotated, 90.98% of them with assigned function. Comparative genomics analyses reveal strong synteny with its congeneric Trachurus species. This high-quality genome assembly serves as a valuable resource for studying the genetic diversity and population structure of the Chilean jack mackerel and provides a solid foundation for future management and conservation efforts.

genomics↗

bioRxiv2025

Zebrafish armc9 mutant reveals a link between ARM-Type fold domain loss, inflammation, and spinal curvature

The vertebral column (VC) defines the central axis of vertebrates. Among its malformations, adolescent idiopathic scoliosis (AIS) is the most common, characterized by lateral spine curvature without congenital abnormalities. While its etiology remains elusive, genetic studies in zebrafish have linked AIS to skeletogenesis, cilia structure, cerebrospinal fluid flow, and inflammation. In this study, we characterized the zebrafish armc9 mutant, exhibiting AIS-like curvature without vertebral malformations, subcommissural organ, or Reissner fiber structure disruptions. We also detected an inflammatory response at the curvature origin. Structural bioinformatics and molecular docking analyses suggest that the mutant Armc9 protein partially lacks the functional ARM-type fold domain, which is crucial for its interaction with Togaram1, revealing that both proteins are relevant for ciliary signaling and spine curvature. Phylogenetic analyses indicate that the ARMC gene family encompasses 12 members, highlighting that the Armc9 gene has deep evolutionary roots. Our results demonstrate that the zebrafish armc9 mutant accurately represents the AIS phenotype, suggesting that the loss of Armc9s C-terminal ARM-type fold domain could affect the ciliary integrity and contribute to spine curvature by altering the skeletogenic environment. Taken together, this study proposes that the zebrafish armc9 mutant offers a unique opportunity to understand the etiology of AIS and provides new insights into the molecular interaction networks of Armc9 in ciliary signaling.

developmental biology↗

bioRxiv2024

Longitudinal transcriptional changes reveal genes from the natural killer cell-mediated cytotoxicity pathway as critical players underlying COVID-19 progression

Patients present a wide range of clinical severities in response SARS-CoV-2 infection, but the underlying molecular and cellular reasons why clinical outcomes vary so greatly within the population remains unknown. Here, we report that negative clinical outcomes in severely ill patients were associated with divergent RNA transcriptome profiles in peripheral immune cells compared with mild cases during the first weeks after disease onset. Protein-protein interaction analysis indicated that early-responding cytotoxic NK cells were associated with an effective clearance of the virus and a less severe outcome. This innate immune response was associated with the activation of select cytokine-cytokine receptor pathways and robust Th1/Th2 cell differentiation profiles. In contrast, severely ill patients exhibited a dysregulation between innate and adaptive responses affiliated with divergent Th1/Th2 profiles and negative outcomes. This knowledge forms the basis of clinical triage that may be used to preemptively detect high-risk patients before life-threatening outcomes ensue. Highlights- Mild COVID-19 patients displayed an early transcriptional commitment with NK cell function, whereas severe patients do so with neutrophil function. - The identified co-expressed genes give insights into a coordinated transcriptional program of NK cell cytotoxic activity being associated with mild patients. - Key checkpoints of NK cell cytotoxicity that were enriched in mild patients include: KLRD1, CD247, and IFNG. - The early innate immune response related to NK cells connects with the Th1/Th2 adaptive immune responses, supporting their relevance in COVID-19 progression.

immunology↗

bioRxiv2023

Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution

Understanding the genetic mechanisms underpinning the differentiation of osteoblasts, the bone producing cells, has far reaching implications for skeletal diseases and evolution. To this end, it is crucial to characterize osteoblastic regulatory landscape in a diverse array of distantly-related vertebrate species. By comparing of the ATAC-seq profile of Xenopus tropicalis (Xt) osteoblasts to liver, heart and lung control tissues, we identified 524 promoters and 6,750 distal regions whose chromatin is specifically open in osteoblasts. Nucleotide composition, Gene Ontology, and RNA-Seq confirmed that the identified elements correspond to bona fide osteogenic transcriptional enhancers, and TFBS enrichment revealed a well-conserved regulatory logic with mammals. Amongst the 357 Xt osteoblast-specific enhancers aligning to homologous human loci, 127 map to regions annotated as enhancers. Phenotype predictions based on the genes neighbouring these conserved enhancers are tightly related to impaired skeletal development. In addition, six conserved enhancers are located at loci associated to craniosynostosis (mx2, tcf12), osteopoikilosis (lemd3), osteopenia (gorab), skeletal dysplasia (flnb) and craniofacial abnormalities (gpc4). From an evolutionary perspective, the elephant shark genome aligns to 53 Xt osteoblast-specific enhancers that are also conserved and annotated as enhancers in humans, revealing an ancestral osteogenic role for the ATOH8, IRX3, NFAT, NFIB and MEF2C transcription factors, as well as for the FGF, IHH and BMP/TGFb signalling pathways. As the absence of bone in sharks is a derived feature, we propose that, in this lineage, the osteogenic regulatory network has been maintained for its function in odontoblasts. Our data argues in favour of a common origin for dentine and bone, and provides a glimpse into the key regulatory elements and upstream activators that drove the formation of an ancient type of mineralized tissue in the vertebrates that inhabited the oceans more than 460 million years ago. Author SummaryDuring animal embryogenesis, distinct type of tissues are formed and assembled, resulting in an integrated, functional organism. During this process, cells must make important decisions, which largely rely on an accurate use of their genetic material. Here, we have studied how the genome "knows" that it must participate to the formation of the bone tissue in a frog animal model. We therefore identified important genomic regions that are involved in driving the expression of genes involved in the formation of a mineralized skeleton. On the one hand, we show that some of these regions are also present in humans, and, therefore, skeletal pathologies could be studied in the frog model at a genetic level. On the other hand, we also identify regions that are present in the genome of a shark, which allows us to propose an evolutionary framework for the early evolutionary origin of the vertebrate skeleton.

genomics↗

bioRxiv2023

Secretory and transcriptomic responses of mantle cells to low pH in the Pacific oyster (Crassostrea gigas)

Since the Industrial Revolution, the concentration of atmospheric carbon dioxide (CO2) due to anthropogenic activities has increased at unprecedented rates. One-third of the atmospheric anthropogenic CO2 emissions are dissolved in the oceans affecting the chemical equilibrium of seawater, which in turn leads to a decrease in pH and carbonate ion (CO32-) concentration, a phenomenon known as ocean acidification (OA). This chemical disequilibrium can be detrimental to marine organisms (e.g., mollusks) that fabricate mineralized structures based on calcium carbonate (CaCO3). Most studies on the effect of reduced pH in seawater have been conducted on the early developmental stages of shell-building invertebrates, neglecting how adult individuals face OA stress. Here, we evaluate histological, secretory, and transcriptional changes in the mantle of adult oysters (Crassostrea gigas) exposure to ambient (8.0 {+/-} 0.2) and reduced (7.6 {+/-} 0.2) pH during 20 days. Most histological observations did not show differences in terms of mantle cell morphology. However, Alcian Blue/PAS staining revealed significant differences in the number of Alcian Blue positive cells in the mantle edge, suggesting a decrease in the secretory activity in this morphogenetic zone. Transcriptomic analysis revealed 172 differentially expressed genes (DEGs) between mantle tissues from adult oysters kept in normal and reduced pH conditions. Almost 18% of the DEGs encode secreted proteins that are likely to be contributing to shell fabrication and patterning. 17 of 31 DEGs encoding secreted proteins correspond to oyster-specific genes, highlighting the fact that molluscan shell formation is underpinned by a rapidly evolving secretome. The GO analysis of DEGs encoding secreted proteins showed that they are involved in the cellular response to stimulus, response to stress, protein binding, and ion binding, suggesting these biological processes and molecular functions are altered by OA. This study demonstrates that histology and gene expression profiling can advance our understanding of the cellular and molecular mechanisms underlying adult oyster tolerance to low pH conditions.

molecular biology↗

bioRxiv2021

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering much of their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context and discrepancies between molecular divergence times and fossil evidence. We employ seventeen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace--a multidimensional representation of node ages--and use it to explore the effects of using alternative gene samples, models of molecular evolution, and clock priors. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models shows little effects. The choice of loci shows an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships among sand dollars and their close relatives, showing that the genus Apatopygus represents a relict lineage with a deep Jurassic origin. Surprisingly, the origin of sand dollars is confidently dated to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

evolutionary biology↗

bioRxiv2018

Evolutionary implications of the first microRNA- and piRNA complement of Lepidodermella squamata (Gastrotricha)

Gastrotrichs - hairy bellies - are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g. microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a multi-omics approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA-and piRNA complements along with the RNAi protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA and protein data support a close relationship of gastrotrichs and flatworms.

evolutionary biology↗

bioRxiv2018

Changes in the neuropeptide complement correlate with nervous system architectures in xenacoelomorphs

Neuropeptides are essential neurosecretory signaling molecules common in protostomes and deuterostomes (together Nephrozoa). Not much, however, is known about the neuropeptide complement of the sister group Xenacoelomorpha. This group is comprised of the three clades Xenoturbella, Nemertodermatida, and Acoela, which differ strongly in their nervous system anatomy. In order to reconstruct the ancestral bilaterian neuropeptide complement and gain insights into neuropeptide evolution within Xenacoelomorpha, we analyzed transcriptomes of 13 acoels, nemertodermatids, and Xenoturbella species. Together with motif searches, similarity searches, mass spectrometry and phylogenetic analyses of neuropeptide precursors and neuropeptide receptors, we reconstruct the xenacoelomorph neuropeptide complement. Our comparison of xenacoelomorph GPCRs with cnidarian and nephrozoan neuropeptide receptors shows that the neuropeptide signaling diversified into at least 20 ancestral peptidergic systems in the lineage to Bilateria. We find that Xenoturbella species possess many of the ancestral bilaterian peptidergic systems and only a few clade-specific neuropeptides. Nemertodermatids seem to have nearly the complete complement of ancestral bilaterian systems and several novel neuropeptides. Acoels show an extensive loss of conserved bilaterian systems, but gained the highest number of novel and group-specific neuropeptides. While it is difficult to correlate the emergence of the bilaterian neuropeptide complement with the evolution of centralized nervous systems, we find a correlation between nervous system novelties and the expansion of taxon-specific neuropeptides in Xenacoelomorpha.

evolutionary biology↗