Biology subjects

Santos, P.

Publications and source records attributed to Santos, P..

10 recordsLinked to original sources

bioRxiv2025

Coexisting with humans: genomic and behavioural consequences in a small and isolated bear population

Climate and land use change have increased human-wildlife interactions, potentially reducing wild species density and prompting behavioural adaptations to urbanised environments. It is still debated if behavioural responses are mainly the result of phenotypic plasticity or if they were driven by anthropic selective pressures, especially in small populations. Our study focused on the Apennine brown bear population (Ursus arctos marsicanus), which has coexisted with humans in Central Italy for millennia. We characterised genomic diversity and identified adaptation signals distinctive to this population by comparing whole genome resequencing data across the Holarctic species range. We show that Apennine brown bears possess a unique genomic diversity pattern including selective signatures at genes associated with reduced aggressiveness, possibly involving alternative splicing mechanism. Our findings suggest that even in small and long-isolated populations, selection may shape behavioural traits. We hypothesise that human-induced selection has influenced these changes, reducing conflicts and contributing to the long-term persistence of the Apennine bear and its coexistence with humans.

genomics↗

bioRxiv2025

Cross-Species Communication via Fungal Extracellular Vesicles

Extracellular vesicles (EVs) play crucial roles in fungal communication and host immune modulation, representing potential therapeutic targets for fungal infections. This study investigated the role of fungal EVs in both intra- and interspecies communication, focusing on their effects on virulence and immune responses. Co-incubation experiments were performed using EVs derived from Candida albicans and Candida auris to assess interactions with C. albicans planktonic cells and biofilms, as well as Cryptococcus neoformans and Cryptococcus gattii EVs interacting with C. neoformans cultures. EVs were observed associating with recipient cell surfaces, suggesting subsequent internalization. Functional assays revealed that EV exposure led to increased expression of Cap59, Lac1, Ure1, and Erg11 genes, correlating with reduced antifungal susceptibility in both planktonic and biofilm forms. Additionally, EVs facilitated cross-species communication, enhancing biofilm adhesion and dispersion, which underscores their role in phenotypic modulation. Macrophages stimulated with fungal EVs exhibited receptor-specific gene expression changes, notably the upregulation of galectin-3, along with a pro-inflammatory phenotype marked by increased iNOS expression and elevated cytokine levels (IL-1{beta}, IL-6, and IL-8). Collectively, these findings underscore a critical role for fungal EVs in interspecies communication, biofilm regulation, and immune modulation, offering valuable insights into fungal pathogenicity mechanisms. ImportanceCurrently, no vaccines exist to prevent fungal infections, underscoring the need for new therapies. As fungal diseases increase globally, understanding fungal biology is essential to identifying treatment targets. Fungi use EVs to communicate and evade immune responses. EVs mediate cell-cell communication, transporting proteins, polysaccharides, lipids, and nucleic acids - serving as "messages" exchanged within a fungal network. Understanding how these vesicles facilitate communication not only within a single species but also across different fungal species can shed light on their contribution to infection persistence and cross-species adaptability. Moreover, EVs may have a broader role in inter-kingdom communication, influencing how fungi interact with host immune cells. The impact of fungal EVs on human innate immune responses remains a largely underexplored area, with significant gaps in our knowledge. This study aims to examine how fungal EVs affect immune responses and whether their signaling varies across species, potentially revealing new therapeutic targets.

microbiology↗

bioRxiv2025

Inference of human pigmentation from ancient DNA by genotype likelihood

Light eyes, hair and skins probably evolved several times as Homo sapiens dispersed from Africa. In areas with lower UV radiation, light pigmentation alleles increased in frequency because of their adaptive advantage and of other contingent factors such as migration and drift. However, the tempo and mode of their spread is not known. Phenotypic inference from ancient DNA is complicated, both because these traits are polygenic, and because of low sequence depth. We evaluated the effects of the latter by randomly removing reads in two high-coverage ancient samples, the Paleolithic Ust-Ishim from Russia and the Mesolithic SF12 from Sweden. We could thus compare three approaches to pigmentation inference, concluding that, for suboptimal levels of coverage (<8x), a probabilistic method estimating genotype likelihoods leads to the most robust predictions. We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye and hair color evolved over the past 45,000 years. The shift towards lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Copper and Iron ages. We also observed a peak of light eye pigmentation in Mesolithic times, and an accelerated change during the spread of Neolithic farmers over Western Eurasia, although localized processes of gene flow and admixture, or lack thereof, also played a significant role.

genomics↗

bioRxiv2024

Deciphering Cargo Contents in Extracellular Vesicles of Candida haemulonii var. vulnera

ABSTRACTCandida haemulonii comprises a group of pathogenic fungi known for their resistance to primary antifungal treatments. Infections caused by these pathogens present substantial challenges due to the difficulties in accurate identification. Extracellular vesicles (EVs) released by these fungi play a critical role in the pathogen-host interaction, potentially influencing antifungal resistance and virulence. Previous research by our group indicates that EVs contain immunogenic particles capable of impacting the hosts immune response. Understanding the composition of these EVs is crucial for elucidating the mechanisms underlying resistance and virulence in C. haemulonii var. vulnera. This study aims to investigate the contents of EVs from C. haemulonii var. vulnera using proteomic and microRNA sequencing tools, providing insights into their role in adaptation, survival, and the progression of infections. Our findings reveal key proteins transported by EVs, including BMH1, TEF1, CDC19, and PDC11. These proteins are involved in various cellular processes, such as the alteration of cell wall structure, biofilm formation, and facilitation of morphological changes, among others. Additionally, we observed that miRNA-like molecules transported within EVs are linked to the electron transport chain and regulation of the citric acid cycle, which are metabolic processes associated with virulence factors and rapid adaptation to diverse hosts or environments. In this context, our findings provide a novel perspective on fungal EVs, highlighting their potential as targets for therapies. Therefore, these vesicles may reflect the expression levels of regulatory molecules crucial for the survival, pathogenicity, and virulence of C. haemulonii var. vulnera. IMPORTANCEThe study of Candida haemulonii complex holds substantial clinical significance due to its notable resistance to conventional antifungal therapies and the complex challenges inherent in its specific identification. This research focuses on cargo of EVs released by these fungi, which play an essential role in pathogen-host interactions, influencing fungal pathogenicity. EVs contain immunogenic particles that can modulate the hosts immune response. Proteomic and microRNA analyses of EVs from Candida haemulonii var. vulnera have identified key proteins and miRNAs involved in cellular processes such as metabolic adjustment, biofilm formation, and modulation of cytoplasmic functions. These components are essential for the adaptation, survival, and progression of infections. This study offers novel insights into fungal EVs, underscoring their potential as targets for therapeutic intervention. By elucidating the mechanisms underlying the rapid adaptation of Candida haemulonii, the research enhances our understanding of the pathogenicity of this emerging yeast.

microbiology↗

bioRxiv2024

Extracellular vesicles produced during fungal infection in humans are immunologically active

Of the known 1.5 million fungal species, Candida spp., Cryptococcus spp., and Paracoccidioides spp. are the main pathogenic species causing serious diseases with almost two million annual deaths. The diagnosis and treatment of fungal infections are challenging since of the limited access to diagnostic tests and the emergence of antifungal resistance. Extracellular vesicles (EVs) promote the interactions of fungal cells with other organisms and play an important role in the pathogen-host relationship. Owing to the complexity of fungal EVs and the lack of clinical studies on their roles in human infections, we studied the EVs from the serum and urine samples of patients with fungal infections caused by Candida albicans, Cryptococcus neoformans, and Paracoccidioides brasiliensis and determined their roles. Steroids, sphingolipids, and fatty acids were identified as the main secondary metabolites via mass spectrometry analysis. We asked whether these metabolites in EVs could play roles in modulating the host immune response. Our findings revealed the polarization of the proinflammatory profile in murine and human macrophages, with the increased production of cytokines, such as the tumor necrosis factor-, interferon-{gamma}, and interleukin-6, and an increased expression of the inducible nitric oxide synthase gene, a M1 response marker. Therefore, circulating EVs from patients with fungal infections are likely involved in the disease pathophysiology. Our findings provide insights into the roles of EVs in fungal infections in clinical samples and in vitro, suggesting possible targets for systemic mycoses therapy. Significance StatementFungal infections cause approximately 1.6 million deaths annually. Due to therapeutic and diagnostic limitations, it is mandatory to understand and develop new immunological interventions. Despite several in vitro studies on the production of extracellular vesicles (EVs) from fungal pathogens, this study is a pioneer in the identification and characterization of EVs in the course of fungal infection in humans. Our group demonstrated the presence of EVs in clinical samples from patients diagnosed with candidiasis, cryptococcosis, and paracoccidioidomycosis, as well as the EVs interaction produced by host and fungal pathogen with the immune system, resulting in relationships that may be beneficial for the progression or elimination of fungal disease.

microbiology↗

bioRxiv2021

Fungal extracellular vesicles are involved in intraspecies intracellular communication

Fungal infections are associated with high mortality rates in humans. The risk of fungal diseases creates the urgent need to broaden the knowledge base regarding their pathophysiology. In this sense, the role of extracellular vesicles (EVs) has been described to convey biological information and participate in the fungal-host interaction process. EVs play many roles, including cellular physiology, responding to environmental cues, mediating a complex circuit of cellular communication in bidirectional crosstalk with other organisms, and the communication between fungal cells has been speculated. This study demonstrated the intra species uptake of EVs in fungi, including Candida albicans, Aspergillus fumigatus, and Paracoccidioides brasiliensis, and the effects triggered by EVs in fungal cells. In C. albicans, we evaluated the involvement of EVs in yeast to hyphae transition, whilst in P. brasiliensis and A. fumigatus the function of EVs as stress transducers was investigated. Both P. brasiliensis and A. fumigatus were exposed to an inhibitor of glycosylation or UV light, respectively. The results demonstrated the role of EVs in regulating the expression of target genes and phenotype features. The EVs treatment induced cellular proliferation and boosted the transition yeast to hyphal transition in C. albicans, while they enhanced stress signals in A. fumigatus and P. brasiliensis, establishing a role for EVs in fungal intra species communication. Thus, fungal EVs regulate the virulence and adaptive traits in fungal interaction systems as potent message effectors, and understanding their effects and mechanism(s) of action could be exploited in antifungal therapies. Author SummaryExtracellular vesicles (EVs) play an important role in export systems. They act as vehicles for the transference of complex cargoes with broad biological functions, such as proteins, carbohydrates, pigments, nucleic acids, and lipids. EVs can contribute to fungal infection outcomes. The EV content exerts immunomodulatory functions during fungus-host interactions. Furthermore, the participation of EVs in communication between fungal cells has been speculated. This study investigated the capacity of EVs to mediate intra-species in three genera of human pathogenic fungi and established a regulatory function of EVs. We also assessed the features of this regulation by analyzing the cellular morphological aspects of fungi after stimulation with EVs. Our data suggest fungal EVs can function as potent signal mediators that mediate virulence and adaptive responses.

microbiology↗

bioRxiv2020

More rule than exception: Parallel evidence of ancient migrations in grammars and genomes of Finno-Ugric speakers

To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method exclusively based on syntactic data, here we focus on the complex relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis supports three distinct clusters corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL-speakers. Therefore, our study indicates plausible secondary convergence in the syntax of languages of different families, providing evidence that such interference effects were accompanied, and possibly caused, by recognizable processes at the population level. In particular, based on the comparison of modern and ancient genomes, our analysis identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of the FU into Europe.

genomics↗

bioRxiv2020

In silico prediction of ARB resistance: A first step in creating personalized ARB therapy

Angiotensin II type 1 receptor (AT1R) blockers (ARBs) are among the most prescribed drugs. However, ARB effectiveness varies widely, and some patients do not respond to ARB therapy. One reason for the variability between patients is non-synonymous single nucleotide polymorphisms (nsSNPs) within agtr1, the AT1R gene. There are over 100 nsSNPs in the AT1R; therefore, this study embarked on determining which nsSNPs may abrogate the binding of selective ARBs. The crystal structure of olmesartan-bound human AT1R (PDB:4ZUD) served as a template to create an inactive empty AT1R via molecular dynamics simulation (n = 3). All simulations resulted in a smaller ligand-binding pocket than 4ZUD due to the absence of olmesartan in the simulation yet remained inactive with little movement in the receptor core. A single frame representing the average stable AT1R was used as a template to thrice (n = 3) dock each ARB via AutoDock to obtain a predicted affinity from the weighted average of 100 docking simulations. The results were far from known values; thus, an optimization protocol was initiated, resulting in the predicted binding affinities within experimentally determined ranges (n = 6). The empty model AT1R was altered and minimized in Molecular Operating Environment software to represent 103 of the known human AT1R polymorphisms. Each of the eight ARBs was then docked, using the optimized parameters, to each polymorphic AT1R (n = 6). Although each nsSNP has little effect on global AT1R structure, most nsSNPs drastically alter a sub-set of ARBs affinity to the AT1R. Comparisons to previous binding studies suggest that the results have a 60% chance of predicting ARB resistance. Although more biochemical studies and refinement of the model are required to increase the accuracy of the prediction of ARB resistance, personalized ARB therapy based on agtr1 sequence could increase overall ARB effectiveness. Author SummaryThe term "personalized medicine" was coined at the turn of the century, but most medicines are currently prescribed based on disease categories and occasionally racial demographics, but not personalized attributes. In cardiovascular medicine, the personalization of medication is minimal; however, it is accepted that not all patients respond equally to common cardiovascular medications. Here we chose one prominent cardiovascular drug target, the angiotensin receptor, and, using computer modeling, created preliminary models of over 100 known alterations to the angiotensin receptor to determine if the alterations changed the ability of clinically used drugs to interact with the angiotensin receptor. The strength of interaction was compared to the unaltered angiotensin receptor, generating a map predicting which alteration affected each drug. It is expected that in the future, a patients receptors can be sequenced, and maps, such as the one presented here, can be used to select the optimum medication based on the patients genetics. Such a process would allow for the personalization of current medication therapy.

pharmacology and toxicology↗

bioRxiv2019

A cereal aphid effector promotes barley susceptibility in a species-specific manner through suppression of defence gene expression.

Aphids secrete diverse repertoires of effectors into their hosts to promote the infestation process. While \"omics\"-approaches facilitated the identification and comparison of effector repertoires from a number of aphid species, the functional characterization of these proteins has been limited to dicot (model) plants. The bird cherry-oat aphid Rhopalosiphum padi is a pest of cereal crops, including barley. Here, we extended efforts to characterize aphid effectors with regards to their role in promoting susceptibility to the R. padi-barley interaction. We selected 3 R. padi effectors based on sequences similarity to previously characterized M. persicae effectors and assessed their subcellular localisation, expression, and role in promoting plant susceptibility. Expression of R. padi effectors RpC002 and Rp1 in transgenic barley lines enhanced plant susceptibility to R. padi but not M. persicae, for which barley is a poor host. Characterization of Rp1 transgenic barley lines revealed reduced gene expression of plant hormone signalling genes relevant to plant-aphid interactions, indicating this effector enhances susceptibility by suppressing plant defences in barley. Our data suggests that some aphid effectors specifically function when expressed in host species, and feature activities that benefit their corresponding aphid species.

plant biology↗

bioRxiv2019

A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model system

AO_SCPCAPBSTRACTC_SCPCAPGenotyping novel complex multigene systems is particularly challenging in non-model organisms. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification bias. Most next-generation sequencing genotyping pipelines have been validated in non-model systems whereby the real genotype is unknown and the generation of artefacts may be highly repeatable. Further hindering accurate genotyping, the relationship between artefacts and copy number variation (CNV) within a PCR remains poorly described. Here we investigate the latter by experimentally combining multiple known major histocompatibility complex (MHC) haplotypes of a model organism (chicken, Gallus gallus, 43 artificial genotypes with 2-13 alleles per amplicon). In addition to well defined "optimal" primers, we simulated a non-model species situation by designing "naive" primers, with sequence data from closely related Galliform species. We applied a novel open-source genotyping pipeline (ACACIA) to the data, and compared its performance with another, previously published, pipeline. ACACIA yielded very high allele calling accuracy (>98%). Non-chimeric artefacts increased linearly with increasing CNV but chimeric artefacts leveled when amplifying more than 4-6 alleles. As expected, we found heterogeneous amplification efficiency of allelic variants when co-amplifying multiple loci. Using our validated ACACIA pipeline and the example data of this study, we discuss in detail the pitfalls researchers should avoid in order to reliably genotype complex multigene systems. ACACIA and the datasets used in this study are publicly available at GitLab and FigShare (https://gitlab.com/psc_santos/ACACIA and https://figshare.com/projects/ACACIA/66485).

molecular biology↗