Biology subjects

Castro, F.

Publications and source records attributed to Castro, F..

18 recordsLinked to original sources

bioRxiv2026

CD44-CD206 axis drives dendritic cell loss and immunosuppression in immaturely glycosylated bladder tumours

Antigen-presenting-cell dysfunction drives immune exclusion, but how tumour glycans disable these cells remains incompletely defined. Immature O-glycosylation, marked by Tn and sialyl-Tn antigens, drives myeloid dysfunction in bladder cancer. Transcriptomics and human tumour profiling linked this state to reduced representation of antigen-presenting myeloid cells and attenuated lymphoid-effector programmes. In glycoengineered models, immature O-glycans promoted immunoregulatory macrophage phenotypes and contact-dependent death of monocyte-derived dendritic cells (moDCs), while surviving cells showed impaired maturation and T-cell activation. Tumour-cell CD44 standard isoform was required for DC death, which was accompanied by inflammasome-associated proteins and gasdermin D cleavage, consistent with pyroptosis. Receptor-discovery approaches converged on CD206, which bound immaturely glycosylated CD44. CD206 blockade restored DC viability. In immunocompetent mice, immature glycosylation accelerated tumour growth and depleted conventional DCs, whereas CD206 blockade restrained tumour progression and restored local and nodal myeloid and lymphoid immunity. These findings identify CD44-CD206 as a targetable glycoimmune checkpoint that promotes immune exclusion.

immunology↗

bioRxiv2026

Cldn18 evolution reveals pleiotropic constraints in vertebrate stomach loss

Understanding the origins of anatomical innovations is central to elucidate the evolution of phenotypic diversity, as novel body plans often underpin the colonization of new ecological niches. The stomach, with its acid-secreting glands, evolved in the gnathostome ancestor and has been lost repeatedly. Claudin 18 (CLDN18) is a tight-junction protein that preserves gastric epithelial integrity against extreme H gradients and, in mammals, also acts in the lung through alternative first-exon isoforms. This dual role suggests that pleiotropy may shape the fate of CLDN18 after stomach loss. Here, we provide a detailed analysis of CLDN18 evolution across jawed vertebrates. CLDN18 originated in the gnathostome ancestor and is expressed in the stomach of elasmobranchs. We found no evidence of the gene in chimaeras or lungfishes, two additional agastric lineages, extending the loss of cldn18a previously described in agastric teleosts. Exon 1 architecture indicates a tandem duplication in the Euteleostomi ancestor, whereas stomach- and lung-associated isoforms are partitioned in most tetrapods examined. Monotremes, although agastric, retain only the lung-associated exon 1, consistent with lung function sustaining selection on the locus. Together, these findings reveal a complex evolutionary history involving gene loss, alternative splicing, tissue-specific regulation, and secondary exon loss, highlighting how pleiotropy and regulatory partitioning shaped the evolution of epithelia in jawed vertebrates.

evolutionary biology↗

bioRxiv2025

Whole Genome Assembly of the Atlantic Bluefin Tuna Thunnus thynnus, with Phased Haplotypes

Atlantic bluefin tuna (Thunnus thynnus) are highly migratory fish, the largest tuna in the genus Thunnus. These fish possess a unique suite of traits, including regional endothermy, in their swimming muscle, viscera, brain and eyes that elevates tissue temperatures significantly above ambient water temperatures. Bluefin tuna also have an efficient thunniform locomotory style, involving a fusiform low drag external shape and a novel musculoskeletal system that enhances elastic energy storage. Together the unique swimming form and warm muscle temperatures enable this species to move across large expanses of the ocean. Atlantic bluefin tuna are targeted by high-value international fisheries of over fifty nations. Populations have recovered in recent years and the species is now actively farmed extensively within the Mediterranean Sea and eastern Atlantic. To date, fisheries management and evolutionary studies have been hampered by a lack of genomic resources. Here, we report a novel de novo chromosome-level phased genome assembly for the Atlantic bluefin tuna obtained using PacBio HiFi reads and Dovetail Omni-C scaffolding. This assembly was scaffolded into 24 chromosomes containing 98% of the genes in the BUSCO reference dataset, demonstrating a high level of contiguity with a contig N50 of 26.54 and assembly size of [~]800Mbp. We compare a diploid-resolved (2N) genome assembly of Atlantic bluefin tuna with a haplotype-collapsed (1N) genome assembly from a Pacific bluefin tuna caught in the eastern Pacific off California. We show the two species have a 98.47% sequence identity. These high-quality genomes for northern bluefin tunas provide the genomic tools necessary for improving phylogenomic and evolutionary physiology analyses of this lineage and are important for potential functional assays for population biology of these commercially important species.

evolutionary biology↗

bioRxiv2025

Ghrelin and Mboat4 are lost in Serpentes

Exploring the evolution of gene networks associated with metabolic/energetic homeostasis can yield key insights into the adaptive landscapes governing the physioology of extant lineages. Here, we investigate a key hormonal module of energy metabolism in reptiles. Ghrelin (GHRL), also known as the "hunger hormone", is a multifunctional gastric peptide, involved in appetite, food intake and body weight regulation. We examined the genomes of 112 species comprising members of the Squamata, Testudines, Crocodilia and Rhynchocephalia and provide ample evidence that GHRL was independently lost in snakes, chameleons and toadhead agamas. In accordance, the enzyme responsible for ghrelin acylation and essential for its activity (membrane bound O-acyltransferase domain containing 4), is also eroded in these lineages. We suggest that the loss of this hormonal signalling system parallels critical modifications in energy metabolism, including a lower need to stimulate fatty acid oxidation during fasting in the locomotor muscles of snakes compared to other groups.

evolutionary biology↗

bioRxiv2025

PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era

High-fidelity genome assemblies provide unprecedented opportunities to decipher mechanisms of molecular evolution and phenotype landscapes. Here, we present PseudoChecker2, a command-line version of the web-tool PseudoChecker with expanded functions. It identifies gene loss via drastic mutational events such as premature stop codons, deletions and insertions. It enables the investigation of cross-species genomic datasets through: (i) integration into automated workflows, (ii) multiprocessing capability, and (iii) creation of a functional reference from annotation files. In addition, we introduce PseudoViz, a novel graphical interface designed to help interpret the results of PseudoChecker2 with intuitive visualizations. These tools combine the versatility and automation of a command-line tool with the user-friendliness of a graphical interface to tackle the challenges of the Genome Era. Availability and implementationPseudoChecker2 and PseudoViz are fully available at https://github.com/rresendepinto/PseudoChecker2 and https://github.com/rresendepinto/PseudoViz.

bioinformatics↗

bioRxiv2025

Parallel erosion of a testis-specific Na+/K+ ATPase in three mammalian lineages sheds light into the evolution of spermatozoa energetics

Understanding how extant physiological landscapes arise from novel genetic interactions is key to elucidating phenotypic evolution. Sperm cells exemplify a striking case of functional compartmentalization shaped by molecular adjustments, notably regarding energy metabolism. Here, we examine the impact of gene duplication and loss on the evolution of sperm energetics in mammals. Our findings reveal that the acquisition of an exclusive mechanism controlling the sperm plasma membrane Na+ gradient, critical for glucose uptake, emerged in the ancestor of mammals through gene duplication, which originated the Na+/K+ ATPase transporting subunit alpha 4 transporter (Atp1a4). Furthermore, we demonstrate that testis-specific expression of Atp1a4 was acquired after the divergence from monotremes. Notably, we identify three independent pseudogenization events of Atp1a4, including in pangolins, the naked mole-rat (Heterocephalus glaber) and toothed whales. The recurrent loss of function in Atp1a4 coincides with the erosion of the testis-specific glycolytic pathway in these lineages. Furthermore, enrichment analysis of striped dolphin (Stenella coeruleoalba) and naked mole-rat testis transcriptomes also suggests significant alterations in sperm capacitation processes. Overall, we show that the elaboration of a sodium-dependent glucose uptake wiring was a key innovation in the energetic landscape governing mammalian spermatozoa, with secondary gene loss in three separate lineages pointing to drastic alterations in motility and capacitation processes. Our findings illustrate how metabolic pathways co-shaped by gene duplication and erosion define extant physiological phenotypes. SignificanceThe sperm cell exhibits a distinct morphology, characterized by exceptional functional and energetic compartmentalization between the midpiece and the flagellum. Here, we demonstrate that the evolution of a sodium-dependent glucose uptake mechanism, driven by gene duplication and giving rise to Atp1a4, was a key innovation promoting efficient glucose usage in mammalian sperm. Additionally, we identify independent losses of Atp1a4 in three lineages--pangolins, naked mole-rats, and toothed whales--coinciding with the reduction of glucose-dependent pathways, such as glycolysis. Our findings highlight how gene expansion and erosion shape metabolic pathways, offering insights into the genetic innovations underlying physiological diversity in reproductive biology.

evolutionary biology↗

bioRxiv2025

Correlating High-dimensional longitudinal microbial features with time-varying outcomes with FLORAL

Correlating time-dependent patient characteristics and matched microbiome samples can identify biomarkers in longitudinal microbiome studies. Existing approaches typically repeat a pre-specified modeling approach for all taxonomic features, followed by a multiple testing adjustment step for false discovery rate (FDR) control. In this work, we develop an alternative strategy of using log-ratio penalized generalized estimating equations, which directly models the longitudinal patient characteristic of interest as the outcome variable and treats microbial features as high-dimensional compositional covariates. A cross validation procedure is developed for variable selection and model selection among different working correlation structures. In extensive simulations, the proposed method achieved superior sensitivity over the state-of-the-art methods with robustly controlled FDR. In the analyses of correlating longitudinal dietary intake, bloodstream infection status, and microbial features from matched samples of cancer patients, the proposed method effectively identified gut health indicators and clinically relevant microbial markers, showing robust utilities in real-world applications. The method is implemented under the open-source R package FLORAL, which is available at (https://vdblab.github.io/FLORAL/).

bioinformatics↗

bioRxiv2024

Open Educational Resources for distributed hands-on teaching in molecular biology

The urgent need to develop a more equitable bioeconomy has positioned biotechnology capacity building at the forefront of international priorities. However, in many educational institutions, particularly in low-and middle-income countries, this remains a major challenge due to limited access to reagents, equipment, and technical documentation. In this work, we describe Open Educational Resources (OER) composed of locally produced biological reagents, open source hardware and free software to teach fundamental techniques in biotechnology such as LAMP DNA amplification, RT-PCR RNA detection, enzyme kinetics and fluorescence imaging. The use of locally produced reagents and devices reduces costs by up to one order of magnitude. During the pandemic lockdowns, these tools were distributed nationwide to students homes as a lab-in-a-box for remote teaching of molecular biology. To test their performance, a total of 93 undergraduate students tested these resources during a biochemistry practical course. 27 out of 31 groups ([~]87%) successfully achieved the objectives of the PCR activity, while 28 out of 31 groups ([~]90%) correctly identified the target using LAMP reactions. To assess the potential application in secondary school, we organized three workshops for high school teachers from different institutions across Chile and performed an anonymous questionnaire, obtaining a strong agreement on how these OER broaden teachers perspectives on the techniques and facilitate the teaching of molecular biology topics. This effort was made possible through a close collaboration with open source technology advocates and members of DIYbio communities, whose work is paving the way for low-cost training in biology. All the protocols and design files are available under open source licenses.

molecular biology↗

bioRxiv2022

Convergent Decay of Skin-specific Gene Modules in Pangolins

The Mammalia skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation - Awat1/2, show patterns of inactivation in the stem pangolin branch; while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function, is intact and expressed in the skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated, convergent and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes.

evolutionary biology↗

bioRxiv2022

A de novo transcriptome assembly of the annelid worm Hediste diversicolor

The development of Next-Generation Sequencing (NGS) technologies has revolutionized multiple fields of Biology. The ability to sequence DNA and RNA in an automated, parallel and low-cost approach, was key to boost the applicability and acquisition efficiency of omics resources. In this context, the availability of these tools has become indispensable towards our understanding of biodiversity, deepening our knowledge on the distinct complexity levels, from cells to ecosystems. In this study we comprehensively characterised and annotated a whole-body transcriptome of Hediste diversicolor. This annelid worm species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, this species plays an important role in benthic food webs. The ability of rework sediments through bioturbation activity makes this species essential to the estuarine mechanisms. Here, we used Illumina next-generation sequencing technology, to sequence a total 105 million (M) paired-end (PE) raw reads and produce the first multi-tissue transcriptome assembly of an adult of H. diversicolor. This transcriptome contains 69,335 transcripts with a N50 transcript length of 2,313 bp and a BUSCO gene completeness of 97.7% and 96% (S: 88.2%; D: 7.8%) in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological studies using this species.

genomics↗

bioRxiv2021

A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource

The Atlantic chub mackerel, Scomber colias Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S. colias, produced with Pacbio HiFi long reads and Illumina Paired-End short reads. The estimated genome size is 814 Mb distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4,19 and 3,34 Mb, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3 % of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this is the fourth high-quality genome assembly within the Order Scombriformes and the first in the genus Scomber.

genomics↗

bioRxiv2021

The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: identification of sex-related and lipid biosynthesis genes

Paracentrotus lividus is the most abundant, distributed and desirable echinoid species in Europe. Although, economically important, this species has scarce genomic resources available. Here, we produced and comprehensively characterized the male and female gonad transcriptome of P. lividus. The P. lividus transcriptome assembly has 53,865 transcripts, an N50 transcript length of 1,842 bp and an estimated gene completeness of 97.4% and 95.6% in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses yielded a total of 3371 and 3351 up regulated genes in P. lividus male and female gonad tissues, respectively. Additionally, we analysed and validated a catalogue of pivotal transcripts involved in sexual development and determination (206 transcripts) as well as in biosynthesis and storage of lipids (119 transcripts) in male and female specimens. This study provides a valuable transcriptomic resource and will contribute for the future conservation of the species as well as the exploitation in aquaculture settings. HighlightsAssembly of a reference transcriptome of Paracentrotus lividus gonads. Differential gene expression between males and female gonads of Paracentrotus lividus. Identification and validation of pivotal genes involved in biosynthesis and storage of lipids.

genomics↗

bioRxiv2021

Convergent loss of the necroptosis pathway in disparate mammalian lineages shapes virus countermeasures

Programmed cell death is a vital process in the life cycle of an organism. Necroptosis, an evolutionary restricted form of programmed necrosis, contributes to the innate immune response by killing pathogen-infected cells. This virus-host interaction pathway is organized around two key components: the receptor-interacting protein kinase 3 (RIPK3), which recruits and phosphorylates the mixed lineage kinase-like protein (MLKL), thus inducing cellular plasma membrane rupture and cell death. Critically, the presence of necroptotic inhibitors in viral genomes validates necroptosis as an important host defense mechanism. Here, we show, counterintuitively, that in different mammalian lineages of mammalian, central components of the necroptotic pathway, such as RIPK3 and MLKL genes, are deleted or display inactivating mutations. Frameshifts or premature stop codons are observed in all the studied species of cetaceans and leporids. In carnivores genomes, the MLKL gene is deleted, while in a small number of species from afrotheria and rodentia premature stop codons are observed in RIPK3 and/or MLKL. Interestingly, we also found a strong correlation between the disruption of necroptosis in leporids and cetaceans and the absence of the C-terminal domain of E3-like homologs (responsible for necroptosis inhibition) in their naturally infecting poxviruses. Overall, our study provides the first comprehensive picture of the molecular evolution of necroptosis in mammals. The loss of necroptosis multiple times during mammalian evolution highlights the importance of gene/pathway loss for species adaptation and suggests that necroptosis is not required for normal mammalian development. Moreover, this study highlights a co-evolutionary relationship between poxviruses and their hosts, emphasizing the role of host adaptation in shaping virus evolution.

evolutionary biology↗

bioRxiv2021

Functional or vestigial? The genomics of the pineal gland in Xenarthra

Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e. Linnaeuss two-toed sloth) but undetected in other closely related species (i.e. brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were lost independently. Additionally, by expanding our analysis to 157 mammal genomes we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy, and endorse the use of genomic analyses to ascertain the physiological status of suspected vestigial structures.

genomics↗

bioRxiv2021

A drastic shift in the energetic landscape of toothed whale sperm cells

Mammalia spermatozoa are a notable example of energetic compartmentalization. While mitochondrial oxidative phosphorylation is restricted to the midpiece, sperm-specific glycolysis operates in the flagellum. Consequently, these highly specialized cells exhibit a clear adaptability to fuel substrates. This plasticity is essential to ensure sperm motility, and is known to vary among species. Here we describe an extreme example of spermatozoa-energetics adaptation. We show that toothed whales exhibit impaired sperm glycolysis, due to gene and exon erosion, and demonstrate that dolphin spermatozoa motility depends uniquely on endogenous fatty acid {beta}-oxidation, but not carbohydrates. Our findings substantiate the observation of large mitochondria in spermatozoa, possibly boosting ATP production from endogenous fatty acids. This unique energetic rewiring emphasizes the physiological body reorganisation imposed by the carbohydrate-depleted marine environment.

evolutionary biology↗

bioRxiv2020

Differential Cetacea Circadian Rhythmicity is associated with the molecular erosion of Cortistatin

The ancestors of Cetacea underwent profound morpho-physiological alterations. By displaying an exclusive aquatic existence, cetaceans evolved unique patterns of locomotor activity, vigilant behaviour, thermoregulation and circadian rhythmicity. Deciphering the molecular landscape governing many of these adaptations is key to understand the evolution of phenotypes. Here, we investigate Cortistatin (CORT), a neuropeptide displaying an important role mammalian biorhythm regulation. This neuropeptide is a known neuroendocrine factor, stimulating slow-wave sleep, but also involved in the regulation of energy metabolism and hypomotility inducement. We assessed the functional status of CORT in 139 mammalian genomes (25 orders), including 30 species of Cetacea. Our findings indicate that cetaceans and other mammals with atypical biorhythms, thermal constraints and/or energy metabolism, have accumulated deleterious mutations in CORT. In light of the pleiotropic action of this neuropeptide, we suggest that this inactivation contributed to a plethora of phenotypic adjustments to accommodate adaptive solutions to specific ecological niches.

evolutionary biology↗

bioRxiv2019

Convergent inactivation of the skin-specific C-C motif chemokine ligand 27 in mammalian evolution

The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine receptor (CCR10), which interacts with an epidermal CC chemokine, the skin-specific C-C motif chemokine ligand 27 (CCL27). CCL27 is selectively produced in the skin by keratinocytes, particularly upon inflammation, mediating the adhesion and homing of skin-infiltrating T cells. Here, we examined the evolution and coding condition of Ccl27 in 112 placental mammalian species. Our findings reveal that a number of open reading frame inactivation events such as insertions, deletions, start and stop codon mutations, independently occurred in Cetacea, Pholidota, Sirenia, Chiroptera, and Rodentia, totalizing 18 species. The diverse habitat settings and life-styles of Ccl27-eroded lineages probably implied distinct evolutionary triggers rendering this gene unessential. For example, in Cetacea the rapid renewal of skin layers minimizes the need for an elaborate inflammatory mechanism, mirrored by the absence of epidermal scabs. Our findings suggest that the convergent and independent loss of Ccl27 in mammalian evolution concurred with unique adaptive roads for skin physiology.

evolutionary biology↗

bioRxiv2018

Gut bacterial diversity and physiological traits of Anastrepha fraterculus Brazilian-1 morphotype males are affected by antibiotic treatment

BackgroundThe interaction between gut bacterial symbionts and Tephritidae became the focus of several studies that showed that bacteria contributed to the nutritional status and the reproductive potential of its fruit fly hosts. Anastrepha fraterculus is an economically important fruit pest in South America. This pest is currently controlled by insecticides, which prompt the development of environmentally friendly methods such as the sterile insect technique (SIT). For SIT to be effective, a deep understanding of the biology and sexual behavior of the target species is needed. Although many studies have contributed in this direction, little is known about the composition and role of A. fraterculus symbiotic bacteria. In this study we tested the hypothesis that gut bacteria contribute to nutritional status and reproductive success of A. fraterculus males.\n\nMethodsWild and laboratory-reared males were treated with antibiotics (AB) and provided sugar (S) or sugar plus protein (S+P) as food sources. The effect of AB on the gut bacteria diversity was assessed through DGGE and sequencing of the V6-V9 variable region of the bacterial 16S rRNA gene.\n\nResultsAB affected the bacterial community of the digestive tract of A. fraterculus, in particular bacteria belonging to the Enterobacteriaceae family, which was the dominant bacterial group in the control flies (i.e., non-treated with AB). AB negatively affected parameters directly related to the mating success of laboratory males and their nutritional status. AB also affected males survival under starvation conditions. The effect of AB on the behaviour and nutritional status of the males depended on two additional factors: the origin of the males and the presence of a proteinaceous source in the diet.\n\nConclusionsOur results suggest that A. fraterculus males gut contain symbiotic organisms that are able to exert a positive contribution on A. fraterculus males fitness, although the physiological mechanisms still need further studies.

ecology↗