Biology subjects

Antunes, C.

Publications and source records attributed to Antunes, C..

6 recordsLinked to original sources

bioRxiv2026

15-deoxy-Δ12,14-prostaglandin J2 limits Salmonella infection through regulation of host TLR4 signaling and inflammasome activation

Enteric infections caused by Salmonella enterica remain a major global health concern and are increasingly associated with antimicrobial resistance. Therefore, new strategies to combat this important pathogen are needed. The interactions between S. enterica and the human host have been the subject of intense investigation over the last several decades, yet new findings continue to emerge. We previously showed that 15-deoxy-{Delta}12,14-prostaglandin J2 (15d-PGJ2) reduces Salmonella colonization of macrophages, but the mechanisms underlying this protective effect were still unknown. Here, we demonstrate that 15d-PGJ2 limits Salmonella infection by suppressing TLR4 signaling and inflammasome activation. Treatment with 15d-PGJ2 reduced TLR4 expression, NF-{kappa}B activation, iNOS, COX-2, nitric oxide production, IL-1{beta} release, and inflammasome-related targets, including NLRP3 and caspase-1 activity, while only partially reversing macrophage polarization. Combined treatment with the TLR4 antagonist TAK-242 further reduced bacterial colonization of and IL-1{beta} release by macrophages, supporting the involvement of TLR4 signaling in the effects of 15d-PGJ2. During mouse infections, 15d-PGJ2 reduced bacterial burdens in a tissue-dependent manner. Together, these findings demonstrate that 15d-PGJ2 limits Salmonella infection through selective modulation of TLR4 signaling and inflammasome activation.

microbiology↗

bioRxiv2026

In silico structural analysis of EthA substitutions for ranking priority mutations leading to ethionamide resistance in Mycobacterium tuberculosis

BackgroundTuberculosis (TB) is the second-leading cause of deaths from infectious agents and remains a global health threat. Ethionamide (ETH) is a prodrug used in regimens for multidrug-resistant TB, and, partly due to side effects that can lead to low treatment adhesion, resistance arises. Changes in EthA, the monooxygenase that activates ETH, are the main mechanism of resistance. Yet, of hundreds of EthA substitutions found in resistant isolates, only a handful have been annotated as resistance determinants. ResultsAn in silico analysis was carried out on a previously described panel of Mycobacterium tuberculosis clinical isolates for which genomes and ETH susceptibility testing results were available. EthA substitutions were mapped, revealing the existence of hotspots in its sequence. Visualization of the hotspots in the EthA structural model shows that they cluster in three regions, including ligand binding pockets. Models were built of twenty-three variants found in resistant isolates and changes in local configuration was mapped to identify investigate impact on ETH activation. Information from these models contributed to establishing five criteria for scoring whether substitutions are most likely to lead to resistance. Using these criteria, EthA D58G was selected and its expression is shown to increase growth in high ETH concentrations. ConclusionFunctionally relevant regions of EthA are revealed and point out priority substitutions for functional studies, enhancing identification and detection of substitutions not been previously associated with resistance.

molecular biology↗

bioRxiv2025

Enterocloster citroniae and related gut microbiome species modulate Vibrio cholerae biofilm formation through the production of bioactive small molecules

Cholera is a diarrheal disease that affects millions of people globally. Although the causative agent, Vibrio cholerae, has been extensively studied in isolation, investigation of its interactions with the gut microbiota started relatively recently. We and others previously showed that microbiota-derived metabolites significantly influence V. cholerae behavior. By investigating how an organic extract of human feces affects V. cholerae gene expression, we showed that gut metabolites strongly suppress swimming motility, a trait important for host colonization. Interestingly, extracts of pure cultures of a gut commensal, Enterocloster citroniae, recapitulated this inhibition. Here, we present a comprehensive examination of the effect of small molecules produced by E. citroniae and related species on V. cholerae behavior. We show that E. citroniae small molecules inhibit motility by various V. cholerae strains, and that several phylogenetically related species produce this activity, although the magnitude of the effect varies between strains. Using biofilm formation assays in static and flow conditions, we show that V. cholerae strongly induces biofilm formation in response to E. citroniae metabolites. Transcriptome and reporter analyses showed that several genes involved in synthesis of an extracellular polysaccharide are induced by E. citroniae metabolites. Lastly, we show that V. cholerae interactions with host cells are also modulated by this commensal. These findings advance our understanding of microbiome-pathogen interactions and how commensal bacteria influence V. cholerae virulence through the production of small molecules. In the future, this knowledge may be used to design novel microbiome-based therapeutic approaches to combat cholera and other infections. ImportanceThe human gut is home to a dense and rich community of microbes termed microbiota. This community has critical functions for host health, including protection against enteric pathogens. Despite this important role, we have only recently scratched the surface of the interactions that occur between members of the microbiota and pathogenic invaders. Cholerae is a disease that still causes significant morbidity and mortality worldwide. Studying how the causative agent, Vibrio cholerae, interacts with the microbiota will have implications not only for our understanding of this important microbial community, but may also lead to the development of new therapeutic strategies against cholera and potentially other infectious diseases.

microbiology↗

bioRxiv2025

Population-specific bycatch risks in two vulnerable anadromous clupeids: insights from otolith microchemistry

Otolith microchemistry analysis revealed that bycatch of European shads--allis shad Alosa alosa (L. 1758) and twaite shad Alosa fallax (Lacepede 1803)-- in western Iberian commercial fisheries removes individuals from a wide array of natal origins, with the most abundant source rivers suffering the heaviest losses. Spatial variation in bycatch risk was evident: specific marine areas exhibited high natal-origin diversity, reflecting complex dispersal. A. alosa showed extensive medium- and long-distance movements-- including rare longitudinal displacements along the Cantabrian slope--and greater natal origin diversity than A. fallax, whose dispersal was largely restricted to middle-distance, latitudinal migrations. In both species, bycatches were dominated by the most abundant continental populations--Mondego and Minho for A. alosa, and Ulla and Minho for A. fallax--suggesting that these rivers function as source populations exporting individuals to sink populations through marine dispersal. Despite their differing dispersal ranges, both species displayed dual resident-dispersive contingents coexisting within the same populations, reflecting an interplay of river proximity, philopatry and resource availability. The stronger philopatry and constrained range of A. fallax imply heightened vulnerability to localized bycatch pressure near natal rivers, whereas A. alosas broader dispersal and higher origin diversity expose multiple populations to risk at a regional scale. These species-specific dispersal capacities and metapopulation structures critically shape bycatch vulnerability. Incorporating natal-origin and dispersal data into transnational, ecosystem-based management--such as targeted temporal or spatial fishing restrictions at mixing hotspots--will be essential to safeguard metapopulation dynamics, mitigate bycatch mortality, and maintain ecological connectivity among European shad populations.

ecology↗

bioRxiv2025

Detection of diadromous fish using environmental DNA: prospects for its use in conservation of endangered species occurring in Portugal

The high economic value and cultural relevance of diadromous fish make them primary targets for traditional fisheries, that need effective management to ensure the long-term survival of their populations. In Portugal, these species are experiencing a marked decline, primarily due to habitat loss and fragmentation, alongside pollution and overfishing. Accurate monitoring is therefore essential to strengthen the management of diadromous fish within Portuguese ecosystems. Advancements in monitoring methodologies could benefit from more sensitive approaches, such as environmental DNA (eDNA) analysis, which is increasingly recognized as a valuable complement to conventional fish monitoring. However, eDNA-based tools remain largely absent and untested in Portugals monitoring and management of diadromous fish. This study reviews literature on eDNA-based detection of diadromous fish species and discusses key methodological aspects influencing the detection efficiency, including sample processing (e.g., water filtration), DNA extraction methods, marker regions and primers, approach and platforms. A particular focus is placed on diadromous fishes occurring in Portugal, which includes several endangered species, and the prospects of using eDNA to monitor them. We also report a pilot study comparing specific assays and DNA metabarcoding in eDNA-based detection of sea lamprey in the Minho River watershed. By consolidating current literature, this work underscores the potential of eDNA to strengthen diadromous fish conservation in Portugal and offers insights to support the integration of eDNA-based tools into national monitoring frameworks. Although our study focuses on Portuguese species, the approaches and insights discussed are broadly applicable and can inform conservation efforts in other regions facing similar challenges. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/645525v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@d5f332org.highwire.dtl.DTLVardef@5171b0org.highwire.dtl.DTLVardef@ff1993org.highwire.dtl.DTLVardef@1e8264f_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2018

Mammalian Cell Entry domains are required for bile resistance and virulence in Salmonella

MCE domains were first reported in Mycobacteria as having a role in Mammalian Cell Entry, with subsequent studies showing their importance during infection. Here, we have examined the function of MCE proteins in Salmonella Typhimurium during mammalian infection. We report that MCE proteins are required for Salmonella virulence, but that this is not related to decreased adherence, entry or survival in mammalian cells. Instead, we reveal that MCE proteins are required for Salmonella bile resistance, in particular to withstand bile salts such as cholate and deoxycholate. Based on our previous work in Escherichia coli, and other studies that have reported roles for MCE proteins in membrane biogenesis, we propose that Salmonella lacking MCE domains have a defective outer membrane that results in bile sensitivity and decreased virulence in vivo. These results suggest that MCE domains mediate fundamental aspects of bacterial membrane physiology as opposed to a proposed direct role in mammalian cell entry, explaining their conservation across both pathogenic and non-pathogenic bacteria.

microbiology↗