Biology subjects

Borges, F.

Publications and source records attributed to Borges, F..

11 recordsLinked to original sources

bioRxiv2026

Discovery of Novel Ligands for Cryptococcus neoformans

Fungal pathogens are an escalating global public health concern, particularly in the context of invasive and opportunistic infections. Cryptococcosis, primarily caused by Cryptococcus neoformans var. grubii, can manifest as acute, subacute, or chronic disease, affecting multiple organs and frequently leading to life-threatening meningitis in immunocompromised individuals. Given the limited antifungal therapeutic strategies and the emergence of resistance and toxicity-related constraints, the development of novel anti-cryptococcal agents remains an urgent priority. In this study, a library of innovative hybrids (5a-f) based on the 3-hydroxypyridin-4(1H)-one scaffold was developed. Their antimicrobial activity was evaluated towards a panel of clinically relevant Gram-positive (methicillin-resistant Staphylococcus aureus - MRSA) and Gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii), as well as fungal species Candida albicans and Cryptococcus neoformans var. grubbi. Cytotoxicity was assessed in HEK293 and HepG2 cell lines, and haemolytic profile was determined to evaluate safety. In addition, iron-chelating capacity and lipophilic properties were also investigated. All compounds formed stable complexes with iron(III) and were non-toxic at concentrations up to 25 M. Lipophilicity studies showed that compounds in series 1 (5a-c) exhibited lower lipophilicity than those in Series 2 (5d-f), mainly due to the regioisomeric position of the hydroxyl group on the 2-methyl-4-pyridone scaffold; specifically, the C3-substitution pattern in Series 2 that enhances the hydrophobic character compared to the C5-substitution in Series 1. Fluorination further increased lipophilicity in both series. Notably, compounds 5c-5f emerged as potent, selective, and non-toxic antifungal agents against Cryptococcus neoformans var. grubii (MIC < 16 {micro}g/mL; CC50 > 32 {micro}g/mL; HC10 > 32 {micro}g/mL). Their distinct structural features appear to play a key role in antifungal selectivity, supporting the potential of these 3-hydroxypyridin-4(1H)-one-based hybrids as promising approach for the development of novel therapeutics for cryptococcal meningitis.

pharmacology and toxicology↗

bioRxiv2025

Micronuclear collapse under oxidative stress drives amphisome-mediated export of DNA in Parkinson disease

The diversity of extracellular vesicle (EV) subpopulations and their impact on intercellular communication are increasingly recognized, but how organelle dysfunction shapes EV content in neurodegenerative diseases remains unclear. Mitochondrial and lysosomal functional defects are hallmarks of Parkinsons disease (PD). Here we uncover a novel pathway linking this dysfunctional axis to EV remodeling and immune activation. We show that mitochondrial reactive oxygen species (ROS) induce genomic instability and micronuclei formation in PD fibroblasts, with ruptured micronuclei being sequestered into amphisomes and exported through small EVs. These EVs are enriched in oxidized mitochondrial and nuclear DNA, which potently stimulate microglial inflammatory responses. Mechanistically, this work identifies micronuclei not as passive byproducts of genome instability but as active intermediates in EV cargo loading. Importantly, treatment with the mitochondria-targeted antioxidant AntiOxCIN4 elicited a mitohormetic response, enhancing ATM-mediated DNA damage repair, restoring mitochondrial dynamics, and improving lysosomal function. This reduced the incorporation of oxidized DNA into EVs and blunted their pro-inflammatory activity. Together, our findings reveal a previously unrecognized mechanism by which mitochondrial-lysosomal dysfunction drives the release of DNA-enriched EVs that fuel neuroinflammation in a neurodegenerative context. Targeting mitochondrial quality control to limit oxidized cargo in EVs emerges as a potential strategy to mitigate early inflammatory events in PD.

neuroscience↗

bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗

bioRxiv2024

Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization

Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping can be used as a model engineering approach to investigate the dynamics of communities during serial propagations. In this study, 26 raw milk samples were used to generate lineages of 6 communities obtained by serial propagation. Bacterial community structures were analyzed by metabarcoding and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high inter-lineage variability of community structures as well as diverse acidification properties. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure. ImportanceMicrobiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy blacksloping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.

microbiology↗

bioRxiv2023

Pseudouridine guides germline small RNA transport and epigenetic inheritance

Epigenetic modifications that arise during plant and animal development, such as DNA and histone modification, are mostly reset during gamete formation, but some are inherited from the germline including those marking imprinted genes1. Small RNAs guide these epigenetic modifications, and some are also inherited by the next generation2,3. In C. elegans, these inherited small RNAs have poly (UG) tails4, but how inherited small RNAs are distinguished in other animals and plants is unknown. Pseudouridine ({Psi}) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop novel assays to detect {Psi} in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs and their precursors. We also detect substantial enrichment in germline small RNAs, namely epigenetically activated siRNAs (easiRNAs) in Arabidopsis pollen, and piwi-interacting piRNAs in mouse testis. In pollen, pseudouridylated easiRNAs are localized to sperm cells, and we found that PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with {Psi} and is required for transport of easiRNAs into sperm cells from the vegetative nucleus. We further show that Exportin-t is required for the triploid block: chromosome dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, {Psi} has a conserved role in marking inherited small RNAs in the germline. One-Sentence SummaryPseudouridine marks germline small RNAs in plants and mammals, impacting epigenetic inheritance via nuclear transport.

genetics↗

bioRxiv2021

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We have identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing hybridization barriers in crosses between different Capsella species, thus potentially emerging as a novel strategy for producing triploids and interspecific hybrids with high agronomical interest. One sentence summaryGenome-wide loss of DNA methylation induced by 5-Azacytidine allows bypassing interploidy and interspecific hybridization barriers in Arabidopsis and Capsella.

plant biology↗

bioRxiv2020

The Arabidopsis "retrovirome" and its regulation by epigenetically activated small RNA

In Arabidopsis, LTR-retrotransposons are activated by mutations in the chromatin remodeler DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21-22nt epigenetically activated siRNAs (easiRNAs) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like-particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. Next generation short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive catalog of active LTR-retrotransposons without the need for mapping transposition, and independent of genomic copy number. Linear replication intermediates of a functionally intact copia element EVADE revealed multiple central polypurine tracts (cPPT), a feature shared with HIV where cPPT promote nuclear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon "suicide" by auto-integration within the VLP. easiRNA targeted EVADE genomic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethylation. VLP DNA-seq provides a comprehensive landscape of LTR-retrotransposons, and their control at transcriptional, post-transcriptional and reverse transcriptional levels.

genomics↗

bioRxiv2019

Functional role of Polymerase IV during pollen development in Capsella

In Arabidopsis thaliana, the DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE 3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-dependent DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically-activated siRNAs (easiRNAs) that likely silence TEs by post-transcriptional mechanisms. Despite this proposed functional role, loss of Pol IV function in Arabidopsis does not cause a discernable pollen defect. Here, we show that loss of NRPD1, encoding the largest subunit of Pol IV in the Brassicaceae Capsella rubella, causes post-meiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were depleted in Capsella nrpd1 microspores. In wild-type background, we found that the same TEs produced 21/22-nt and 24-nt siRNAs, leading us to propose that Pol IV is generating the direct precursors for 21-24-nt siRNAs, which are targeted by different DICERs. Arrest of Capsella nrpd1 microspores was accompanied by deregulation of genes targeted by Pol IV-dependent siRNAs. The distance of TEs to genes was much closer in Capsella rubella compared to Arabidopsis thaliana, providing a possible explanation for the essential role of Pol IV for pollen development in Capsella. Our study in Capsella uncovers a functional requirement of Pol IV in microspores, emphasizing the relevance of investigating different plant models. One-sentence summaryLoss of Polymerase IV function in Capsella rubella causes microspore arrest, revealing an important functional role of Polymerase IV during pollen development. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Claudia Kohler (Claudia.Kohler@slu.se)

plant biology↗

bioRxiv2019

CompScore: boosting structure-based virtual screening performance by incorporating docking scoring functions components into consensus scoring

Consensus scoring has become a commonly used strategy within structure-based virtual screening (VS) workflows with improved performance compared to those based in a single scoring function. However, no research has been devoted to analyze the worth of docking scoring functions components in consensus scoring. We implemented and tested a method that incorporates docking scoring functions components into the setting of high performance VS workflows. This method uses genetic algorithms for finding the combination of scoring components that maximizes the VS enrichment for any target. Our methodology was validated using a dataset that contains ligands and decoys for 102 targets that has been widely used in VS validation studies. Results show that our approach outperforms other methods for all targets. It also boosts the initial enrichment performance of the traditional use of whole scoring functions in consensus scoring by an average of 45%. CompScore is freely available at: http://bioquimio.udla.edu.ec/compscore/

bioinformatics↗

bioRxiv2017

microRNA-triggered transposon small RNAs mediate genome dosage response

Chromosome dosage plays a significant role in reproductive isolation and speciation in both plants and animals, but underlying mechanisms are largely obscure1. Transposable elements can promote hybridity through maternal small RNA2, and have been postulated to regulate dosage response via neighboring imprinted genes3,4. Here, we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of LTR-retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21 to 22-nucleotide small RNA in a dose dependent fashion via RNA polymerase IV. We show that these epigenetically activated small-interfering RNAs (easiRNAs) mediate hybridization barriers between diploid seed parents and tetraploid pollen parents (\"the triploid block\"), and that natural variation for miR845 may account for \"endosperm balance\" allowing formation of triploid seeds. Targeting the PBS with small RNA is a common mechanism for transposon control in mammals and plants, and provides a uniquely sensitive means to monitor chromosome dosage and imprinting in the developing seed.

plant biology↗

bioRxiv2017

Epigenetic activation of meiotic recombination in Arabidopsis centromeres via loss of H3K9me2 and non-CG DNA methylation

Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis centromeres are suppressed for crossovers, as recombination in these regions can cause chromosome mis-segregation. Plant centromeres are surrounded by repetitive, transposon-dense heterochromatin that is epigenetically silenced by histone 3 lysine 9 dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. Here we show that disruption of Arabidopsis H3K9me2 and non-CG DNA methylation pathways increases meiotic DNA double strand breaks (DSBs) within centromeres, whereas crossovers increase within pericentromeric heterochromatin. Increased pericentromeric crossovers in H3K9me2/non-CG mutants occurs in both inbred and hybrid backgrounds, and involves the interfering crossover repair pathway. Epigenetic activation of recombination may also account for the curious tendency of maize transposon Ds to disrupt CHROMOMETHYLASE3 when launched from proximal loci. Thus H3K9me2 and non-CG DNA methylation exert differential control of meiotic DSB and crossover formation in centromeric and pericentromeric heterochromatin.

genomics↗