Biology subjects

Santos, F.

Publications and source records attributed to Santos, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Dynamic TET1 repression coordinates activation of macroH2A.2-poised bivalent genes during neuroectoderm differentiation

Cell state transitions involve changes in gene expression programs in conjunction with epigenetic regulation occurring in chromatin. Bivalent chromatin, marked by overlapping active H3K4me3 and repressive H3K27me3, poises key developmental genes during pluripotency for cell type-specific activation during differentiation. However, the molecular mechanisms that activate bivalent genes during lineage commitment remain poorly understood. Here, we elucidate how the cytosine dioxygenase TET1 promotes neuroectoderm differentiation through dynamic chromatin binding and a non-catalytic repressor function. Through a hypothesis-free screen for TET1 chromatin complex partners, we find that TET1 physically interacts with macroH2A.2 and H2A.X on chromatin. Integrated multi-omic analyses reveal that the non-catalytic repressor function of TET1 and a novel activating function of the H2A variant macroH2A.2 together promote a poised transcriptional state within bivalent chromatin during pluripotency. Upon pluripotency exit, TET1 disengages from macroH2A.2-marked early neuroectoderm genes to permit their activation, while remaining bound as a repressor at mesoendoderm and late neural genes to prevent alternative cell state transitions. Furthermore, TET1 retention at accessible primed enhancers supports neural program activation. Together, our findings reveal a noncanonical functional interplay within bivalent chromatin between TET1 and macroH2A.2 that maintains a poised state during pluripotency and predicts selective gene activation during neuroectoderm specification.

developmental biology↗

bioRxiv2026

Forest degradation reshapes trophic functioning in vertebrate food webs across Amazonian forests

The Amazon is a mosaic of ecosystems, accounting for 13% of all known species globally, and responsible for providing a variety of ecosystem services, including a key role in global climate regulation. However, 18% of the Amazon forest cover has been lost completely and a further 38% degraded, threatening biodiversity and millions of local livelihoods. Currently, little is known about how this impacts the functioning of ecological communities. Here, we combine an energetic approach with biodiversity metrics to quantify ecosystem functioning in mammal and bird food webs across Amazonia, along a gradient of forest degradation linked to road proximity. We show that even under relatively low disturbance, ecosystem functions shift: carnivory increases closer to roads, driven by generalist species that persist under these conditions, whereas herbivory declines mainly due to reduced herbivore biomass and species richness. This suggests that processes associated with forest degradation can alter energy flow even where biodiversity metrics remain relatively unchanged, highlighting energetic approaches as sensitive indicators of ecosystem disruption.

ecology↗

bioRxiv2026

Coupled effects of salinity and host phylogeny on niche breadth and viral evolution from seawater to salt saturation

Virus-host interactions are fundamental drivers of microbial community structure, yet whether viral ecological niches are confined within individual host niches (nested host niche scenario) or span multiple hosts and exceed any single host niche (expanded host niche scenario) remains poorly understood. To explore these patterns, we characterized prokaryotic and viral distributions and predicted virus-host interactions along a salinity gradient at Bras del Port salterns (Spain), ranging from seawater (3.6% salinity) to salt saturation (39.0%). We analyzed metagenomes and viromes from six ponds supplemented by 27 additional published viromes from the same hypersaline system, recovering 170 metagenome-assembled genomes (MAGs) dereplicated at the genomospecies level (MAGs clustered at 95 % average nucleotide identity), approximately 55,000 viral operational taxonomic units (vOTUs), and nearly 4,000 predicted virus-host pairs. Viruses exhibited broader niches than their putative hosts at the highest salinities, while at lower salinities the pattern was reversed or inconsistent depending on the site, and niche breadths of both viruses and hosts increased steadily toward higher salinities. Host taxonomy at the class level and below was the primary driver of viral genomic clustering, explaining more variance than salinity provenance (approximately 30% vs. approximately 19%), while the contribution of salinity to viral genomic composition appeared indirect, mediated through the salinity-driven distribution of distinct host classes rather than direct environmental filtering of viral sequences. Together, these findings support the expanded host niche scenario as the predominant virus-host interaction strategy, with evolutionary and ecological dynamics jointly shaped by salinity and host identity.

microbiology↗

bioRxiv2026

Beyond Pulsing Dyes: Are Flickers the Language of the Mitochondrial Network?

Mitochondrial membrane potential ({Delta}{Psi}m) is central to ATP production, ion homeostasis, and cell survival, reflecting the functional state of the inner mitochondrial membrane and oxidative phosphorylation. Accurate assessment of {Delta}{Psi}m is therefore essential for understanding mitochondrial physiology and dysfunction in health, ageing, and disease. Lipophilic cationic fluorescent dyes, such as TMRM and TMRE, are widely used to monitor {Delta}{Psi}m in live cells, enabling high-temporal-resolution imaging of both steady-state membrane potential and dynamic fluctuations. Beyond stable bioenergetic measurements, live-cell imaging reveals transient, reversible depolarisation events, known as mitochondrial "flickers." These events, observed across multiple cell types and imaging platforms, are often associated with brief openings of the mitochondrial permeability transition pore (mPTP) and may represent regulated mitochondrial excitability, rather than irreversible damage. While excessive or synchronised depolarisations may signal mitochondrial injury, transient flickers are increasingly viewed as potential signalling mechanisms within the mitochondrial network. This work discusses methodological considerations for {Delta}{Psi}m imaging, the biological significance of mitochondrial flickers, and the importance of distinguishing physiological events from probe- and light-induced artefacts, highlighting the emerging concept of mitochondria as dynamic and communicative bioenergetic networks.

cell biology↗

bioRxiv2026

Metagenomic insights into microbial mediation of Caulerpa prolifera invasion in a coastal lagoon

Opportunistic seaweeds of the genus Caulerpa have benefited from human-driven environmental change to expand within coastal lagoons, frequently displacing native seagrasses. In the Mar Menor lagoon (southeastern Spain), Caulerpa prolifera has progressively expanded since the 1970s, coinciding with the decline of the native seagrass Cymodocea nodosa. Sediments colonized by Ca. prolifera are characterized by elevated sulfide concentrations, which are toxic to seagrasses. Because sulfide is microbially produced, these sediment communities likely shape the competition between Ca. prolifera and Cy. nodosa. However, their metabolic potential and activity remain poorly understood. Here, we examined the taxonomic composition and functional capabilities of sediment microbial communities using 12 paired metagenomes and metatranscriptomes from areas dominated by either Ca. prolifera or Cy. nodosa. Caulerpa-associated sediments displayed a higher potential for organic matter degradation and sulfate reduction. Several metagenome-assembled genomes (MAGs) encoded enzymes putatively involved in the degradation of pectin-like polysaccharides characteristic of the Caulerpa cell wall. Comparison of metagenomic and metatranscriptomic data further revealed that the most abundant MAGs were not necessarily the most transcriptionally active. This finding challenges the common assumption that ecological importance is primarily determined by abundance and highlights the potential contribution of less abundant microorganisms to biogeochemical cycling. Further, 97 of the 100 most highly expressed genes lacked functional annotation. Recombinant production and functional characterization of the protein encoded by the most highly expressed gene in the analyzed sediments revealed that it is an enzyme able to breakdown endogenous bacterial peptidoglycan. Collectively, these results underscore the importance of integrating metagenomics and metatranscriptomics with experimental validation to achieve a more comprehensive understanding of microbial functional capabilities, an integration that is still uncommon in the microbial ecology field.

microbiology↗

bioRxiv2025

Metabolic fluctuations explain allometric scaling diversity

Metabolic scaling, the relationship between energy use and body size, has long been treated as a universal law of life. However, extensive variation in scaling exponents across species challenges this assumption. Here, we show that such scaling can emerge spontaneously from stochastic cellular growth dynamics, without postulating any fixed relationship between mass and metabolism. In our framework, ontogeny is a nonequilibrium thermodynamic process in which energy is continuously dissipated and redistributed among fluctuating cellular states. When applied across diverse life histories, the model reproduces the observed range of metabolic exponents, revealing that scaling diversity arises naturally from fundamental thermodynamic constraints on stochastic, energy-dissipating growth.

ecology↗

bioRxiv2025

Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns

Hypersaline environments, due to their discrete and geographically isolated nature, constitute ideal systems for studying evolutionary patterns and microbial diversification, and especially here when contrasting coastal with inland systems. Based on metagenomic comparisons of 25 hypersaline sites across 11 countries, we explored the influence of environmental factors, ionic composition, and geographic distance on their microbial community structures and taxa diversification. Our results revealed that microbial communities from coastal environments were taxonomically and functionally more similar to each other than to those from inland sites. A distance-decay relationship in the genetic relatedness, significantly more pronounced for the coastal sites, was observed among reconstructed metagenome-assembled genomes (MAGs), clearer at distances below 400 km, but still detectable across global scales up to 20,000 km. The 484 MAGs recovered, representing 284 distinct species, revealed a striking global ubiquity, with 62.5% of the species showed cosmopolitanism as were detected across multiple sites. The higher taxonomic and genetic similarity of coastal environments over the inland sites seems to reflect an environmental connection that may be related to the ocean current dynamics. Most cosmopolitan species showed clear allopatric differentiation, although few cases of a single globally dominant genomovar (average nucleotide identity, ANI > 99.8%) were also observed, especially for some Haloquadratum species. The findings suggest that coastal hypersaline systems are loosely constrained by geographic isolation, with clear signals of allopatric speciation at the mesoscale (tenths to hundreds of kilometers) that become blurrier at larger scales.

microbiology↗

bioRxiv2025

Biological context modulates virus-host dynamics and diversification

Virus-host interactions are fundamental to microbial ecology and evolution, yet they are often studied in simplified systems. To assess the impact of biological complexity, we examined the halophilic bacterium Salinibacter ruber strain M1 and the EM1 virus, a bacteriophage that infects M1, in the presence of additional strains and viruses. In the short term, the presence of a biotic background delayed population-level lysis and reduced EM1 production. In the long term, both M1 and EM1 persisted across all conditions, but their evolutionary trajectories diverged. The virus accumulated many mutations, showed reduced infectivity against its native host, and expanded its host range in the presence of other viruses, highlighting a role of virus-virus interactions in promoting diversification. In contrast, the host accumulated more mutations when evolving with other bacterial strains. Taken together, these findings demonstrate that biological complexity shapes both the ecological dynamics and evolutionary trajectories of virus-host interactions.

microbiology↗

bioRxiv2025

Predictors of extinction risk in large tropical forest mammals: from global to local

Studies can only guide conservation if their findings are informative at the scales at which practitioners and policymakers operate. Yet, it is rarely tested whether large-scale studies reach similar conclusions to the smaller-scale studies on which conservation traditionally relies. We examine whether predictors of extinction risk are consistent across global, regional, and local scales, for 210 tropical forest mammal species ([≥] 1 kg) that existed during the last 130,000 years, in 64 tropical forests, across three biogeographical realms. We found consistent predictors of extinction risk (body mass, generation length, diet, brain volume and scansoriality) when analyses differed only in their spatial resolution. However, predictors differed when analyses also varied in their temporal extent. Macroecological findings about extinction risk can, thus, inform conservation at smaller scales, but they risk misidentifying threatened species if differences in temporal extent are not recognised.

ecology↗

bioRxiv2025

Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis

Inflammation in the pancreas drives acinar-to-ductal metaplasia (ADM), a progenitor-like state that can be hijacked by mutant Kras in the formation of pancreatic cancer (PDAC). How these cell fate decisions vary according to KRAS mutation remains poorly understood. To define mutation-specific lineage reversion and tumor initiation, we implement novel Ptf1a-TdTomato mice and multiple KRAS mutants across an array of genetic, pharmacologic, and inflammatory perturbations in vivo. Whereas KRASG12D co-opts injury to enable lineage reversion, enhancer reprogramming, and tumor initiation, KRASG12R/V can initiate but not sustain dedifferentiated and neoplastic transcriptional and epigenetic programs. We find the KRASG12R/V defects consist of a failure to invoke robust EGFR signaling and activate Rac1/Vav1, with constitutive Akt activation in vivo sufficient to rescue the tumorigenic potential of KRASG12R. As the marked heterogeneity among KRAS variants begins early in tumorigenesis, these data are crucial to understanding mutation-specific oncogenic trajectories and directing the implementation of KRAS-directed therapeutics. SIGNIFICANCEDefining how KRAS mutants drive distinct outcomes in human pancreatic cancer is critical for developing allele-specific therapeutic approaches. This study unveils a hierarchy among KRASG12D, KRASG12V, and KRASG12R to drive tumor initiation, owing to heterogeneous activation of EGFR, PI3K/AKT, and RAC1 signaling, thus revealing mutation-specific evolutionary paths in pancreatic tumorigenesis.

cancer biology↗

bioRxiv2024

Episomal virus maintenance enables bacterial population recovery from infection and virus-bacterial coexistence

Hypersaline environments harbor the highest concentrations of virus-like particles (VLPs) reported for aquatic ecosystems. The substantial densities of both microbial populations and VLPs challenge traditional explanations of top-down control exerted by viruses. At close to saturation salinities, prokaryotic populations are dominated by Archaea and the bacterial clade Salinibacter. In this work we examine the episomal maintenance of a virus within a Salinibacter ruber host. We found that infected cultures of Sal. ruber M1 developed a population-level resistance and underwent systematic and reproducible recovery post infection that was counter-intuitively dependent on the multiplicity of infection (MOI), where higher MOI led to better host outcomes. Furthermore, we developed a nonlinear population dynamics model that successfully reproduced the qualitative features of the recovery. This suggests that the maintenance of the virus episomally, often referred to as pseudolysogeny, and lysis inhibition allow for host-virus co-existence under high MOI infections. Our results emphasize the ecological importance of exploring a spectrum of viral infection strategies beyond the conventional binary of lysis or lysogeny.

microbiology↗

bioRxiv2024

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

genomics↗

bioRxiv2024

Metabolic and age-associated epigenetic barriers during direct reprogramming of mouse fibroblasts into induced cardiomyocytes

Heart disease is the leading cause of mortality in developed countries novel regenerative procedures are warranted for improving patients well fare. Direct cardiac conversion (DCC) can create induced cardiomyocytes (iCMs) and besides holding great promise, lacks clinical effectiveness for cardiac regeneration as metabolic and age-associated barriers remains elusive. Here, we identify by histone post-translational analysis that DCC triggers major age-dependent alterations in the epigenetic landscape. Metabolomics revealed decrease abundance of anabolic metabolites related to TCA cycle and glutaminolysis and profound mitochondrial network remodeling, with increased elongation and interconnectivity and reliance in mitochondrial respiration in iCMs. Importantly, adult-derived iCMs present increase accumulation of oxidative stress in the mitochondria and pharmacological activation of mitophagy increase DCC of adult fibroblasts in vitro. Metabolic modulation in vitro and dietary manipulations in vivo improves DCC efficiency and are accompanied by significant alterations in the histone acetylation and methylation landscape and mitochondria homeostasis. Our study provides evidence that metaboloepigenetics as a direct role in cell fate transitions driving direct cardiac conversion into iCMs, highlighting the potential use of metabolic modulation in increasing cardiac regenerative strategies.

cell biology↗

bioRxiv2024

The moon's influence on the activity of tropical forest mammals

Changes in lunar illumination alter the balance of risks and opportunities for animals at night, influencing activity patterns and species interactions. Our knowledge about behavioral responses to moonlight is incomplete, yet it can serve to assess and predict how species respond to environmental changes such as light pollution or loss of canopy cover. As a baseline, we wish to examine if and how wildlife responds to the lunar cycle in some of the darkest places inhabited by terrestrial mammals: the floors of tropical forests. We quantified the prevalence and direction of activity responses to the moon in tropical forest mammal communities. Using custom Bayesian multinomial logistic regression models, we analyzed long-term camera trapping data on 88 mammal species from 17 protected forests on three continents. We also tested the hypothesis that nocturnal species are more prone to avoiding moonlight, as well as quantified diel activity shifts in response to moonlight. We found that, apparent avoidance of moonlight (lunar phobia, 16% of species) is more common than apparent attraction (lunar philia, 3% of species). The three species exhibiting lunar philia followed diurnal or diurnal-crepuscular activity patterns. Lunar phobia, detected in 14 species, is more pronounced with higher degree of nocturnality, and is disproportionately common among rodents. Strongly lunar phobic species were less active during moonlit nights, which in most cases also decreases their total daily activity. Our findings indicate that moonlight influences animal behavior even beneath the forest canopy. This suggests that such impacts may be exacerbated in degraded and fragmented forests. Additionally, the effect of artificial light on wild communities is becoming increasingly apparent. Our study offers empirical data from protected tropical forests as a baseline for comparison with more disturbed areas, together with a robust approach for detecting activity shifts in response to environmental change. Open Research statement: The data and code for performing the analyses described in this article are available at https://github.com/richbi/TropicalMoon.

ecology↗

bioRxiv2024

Knowledge Innovation Ecosystem for the Promotion of User-Centre Health Innovations: Living Lab Methodology and Lessons Learned Through the Proposal of Standard Good Practices

Living Labs, experiencing a global surge in popularity over the past years, demands standardized guidance through the development of widely accepted good practices. While challenging due to the complex and evolving nature of Living Labs, this task remains essential. These knowledge innovation ecosystems facilitate a diverse array of interconnected and interacting end-users and stakeholder partners who engage collaboratively to co-create, embed, and/or leverage end-user-centric breakthroughs at one or more innovation phases within a real-world context. Based on the development of six Living Labs in the health domain, this study proposes a more general yet critical set of Living Labs good practices, emphasizing the importance of strong initial marketing and promotion strategies for Living Labs open calls, enforcing gender equality, carefully selecting stakeholders, devising and implementing effective framework strategies for end-user engagement and value creation, ensuring value creation for all Living Labs partners, prolonging the long-term viability of the Living Lab project, promoting and disseminating impactful actions and results, fostering environmental sustainability, and processing results data for Living Lab performance evaluation.

scientific communication and education↗

bioRxiv2023

Development and Validation of an MRI-Derived Head-Neck Finite Element Model

PurposeThis study aimed to develop and validate a magnetic resonance imaging (MRI)-based biofidelic head-neck finite element (FE) model comprised of scalp, skull, CSF, brain, dura mater, pia mater, cervical vertebrae, and discs, 14 ligaments, and 42 neck muscles. MethodsWe developed this model using head and neck MRI images of a healthy male participant and by implementing a novel meshing algorithm to create finer hexahedral mesh structures of the brain. The model was validated by replicating four experimental studies: NBDLs high acceleration profile, Itos frontal impact cervical vertebrae study, Alshareefs brain sonomicrometry study, and Nahums impact study. ResultsThe results showed reasonable geometrical fidelity. Our simulated brain displacement and cervical disc strain results were close to their experimental counterparts. The intracranial pressure and brain stress data of our head-only model (excluding neck structures and constraining the base of the skull) were similar to Nahums reported results. As neck structures were not considered in Nahums study, the FE results of our head-neck model showed slight discrepancies. Notably, the addition of neck structures (head-neck model) reduced brain stress values and uncovered the brains intracranial pressure dynamics, which the head-only model failed to capture. Nevertheless, the FE simulation results showed a good agreement (r > 0.97) between the kinematic responses of the head-neck model and NBDLs experimental results. ConclusionThe developed head-neck model can accurately replicate the experimental results and has the potential to be used as an efficient computational tool for brain and head injury biomechanics research. Statements and DeclarationsThis work was primarily supported by the U.S. Department of Homeland Security (70RSAT21CB0000023). The MRI data acquisition was supported by the Texas Tech Neuroimaging Center.

bioengineering↗

bioRxiv2021

GLP is critical for oogenesis exhibiting a G9A-independent role in transcriptional repression

GLP (EHMT1) is a multifunctional protein, best known for its role as an H3K9me1 and H3K9me2 methyltransferase through its reportedly obligatory dimerization with G9A (EHMT2). Here, we investigate the role of GLP in the oocyte in comparison to G9A using oocyte-specific conditional knockout mouse models (G9a cKO, Glp cKO, G9a-Glp cDKO). Loss of GLP in Glp cKO and G9a-Glp cDKO oocytes re-capitulated meiotic defects observed in the G9a cKO; however, there was a significant impairment in oocyte maturation and developmental competence in Glp cKO and G9a-Glp cDKO oocytes beyond that observed in the G9a cKO. Consequently, loss of GLP in oogenesis results upon fertilisation in mid-gestation embryonic lethality. To assess the molecular functions of GLP and G9A, we applied a multi-omics approach, supported by immunofluorescence, to identify changes in epigenomic, transcriptomic and proteomic signatures in cKO oocytes. H3K9me2 was equally depleted in all cKO oocytes, whereas H3K9me1 was decreased only upon loss of GLP. The transcriptome, DNA methylome and proteome were markedly more affected in G9a-Glp cDKO than G9a cKO oocytes, with transcriptional de-repression associated with increased protein abundance and gains in genic DNA methylation in G9a-Glp cDKO oocytes. Together, our findings suggest that GLP contributes to transcriptional repression in the oocyte, independent of G9A, and is critical for oogenesis and oocyte developmental competence.

developmental biology↗

bioRxiv2021

Modelling human zygotic genome activation in 8C-like cells in vitro

The remodelling of the epigenome and transcriptome of the fertilised oocyte to establish totipotency in the zygote and developing embryo is one of the most critical processes in mammalian embryogenesis. Zygotic or embryonic genome activation (ZGA, EGA) in the 2-cell embryo in mouse, and the 8-cell embryo in humans, constitutes the first major wave of transcription. Failure to initiate ZGA leads to developmental defects, and contributes to the high attrition rates of human pre-implantation embryos. Due to limitations in cell numbers and experimental tractability, the mechanisms that regulate human embryonic genome activation in the totipotent embryo remain poorly understood. Here we report the discovery of human 8-cell like cells (8CLCs) specifically among naive embryonic stem cells, but not primed pluripotent cells. 8CLCs express ZGA marker genes such as ZSCAN4, LEUTX and DUXA and their transcriptome closely resembles that of the 8-cell human embryo. 8-cell like cells reactivate 8-cell stage specific transposable elements such as HERVL and MLT2A1 and are characterized by upregulation of the DNA methylation regulator DPPA3. 8CLCs show reduced SOX2 protein, and can be identified based on expression of the novel ZGA-associated protein markers TPRX1 and H3.Y in vitro. Overexpression of the transcription factor DUX4. as well as spliceosome inhibition increase ZGA-like transcription and enhance TPRX1+ 8CLCs formation. Excitingly, the in vitro identified 8CLC marker proteins TPRX1 and H3.Y are also expressed in 8-cell human embryos at the time of genome activation and may thus be relevant in vivo. The discovery of 8CLCs provides a unique opportunity to model and manipulate human ZGA-like transcriptional programs in vitro, and might provide critical functional insights into one of the earliest events in human embryogenesis in vivo. HighlightsO_LIZGA markers and transposable elements are expressed in 8CLCs among naive human stem cells C_LIO_LIThe transcription factor DUX4 and spliceosome inhibition induce ZGA-like transcription C_LIO_LI8CLC marker proteins TPRX1 and H3.Y are expressed in nuclei of 8-cell human embryos C_LIO_LI8CLCs serve as a novel in vitro model for human ZGA C_LI

molecular biology↗