Biology subjects

Quintana, F.

Publications and source records attributed to Quintana, F..

5 recordsLinked to original sources

bioRxiv2026

Cytokine-mediated activation of exhausted T cells

CD8 T cell exhaustion during chronic infection and cancer is marked by impaired effector function and limited responsiveness to stimulation. While memory CD8 T cells can be activated TCR-independently by IL-12 and IL-18, it remains unclear whether exhausted cells, despite diminished TCR responsiveness, retain this cytokine-driven effector capacity. Here, we show that IL-12 and IL-18 stimulation induce robust IFN{gamma} production in exhausted CD8 T cells from chronic LCMV Cl13 infection, exceeding responses to antigen-specific stimulation. This activation does not result in upregulation of Tox, suggesting engagement of transcriptional circuits distinct from those promoting exhaustion. Single-cell transcriptomics revealed an innate acting T cell (TIA)-specific gene signature enriched within exhausted populations in chronic infection and tumor-infiltrating lymphocytes, particularly at the interface of intermediate and terminal exhaustion. Using heterologous Legionella pneumophila infection, we confirmed in vivo bystander responsiveness of exhausted CD8 T cells, reducing bacterial burden, highlighting their functional capacity. Our findings demonstrate that exhausted CD8 T cells retain inducible effector capacity through IL-12 and IL-18 stimulation, providing new insights into possible routes to activate exhausted T cells.

immunology↗

bioRxiv2025

Neuronal activity promotes repair by microglial reprogramming following demyelination

Microglia, the resident immune cells of the central nervous system (CNS), play a multifaceted role in neurological disorders. In multiple sclerosis (MS), a chronic demyelinating and neurodegenerative disease, microglia contribute to inflammation and tissue damage, but can also support repair by clearing myelin debris, limiting inflammation and promoting remyelination and neuroprotection. The timely transition from their pro-inflammatory to pro-regenerative states is essential for effective repair and, in chronic MS, persistent, defective microglial activation contributes to disease progression. Yet, the mechanisms underlying the microglial switch remain largely unknown. In this study, we demonstrate that neuronal activity can modulate microglial signature at the onset of remyelination in MS models, in a pattern-dependent manner. Transcriptomic analyses reveal a downregulation of pro-inflammatory, disease-associated microglial signatures alongside an upregulation of genes associated with oxidative phosphorylation and lipid metabolism, indicative of a shift toward pro-regenerative states following physiological activity enhancement. This activity-dependent reprogramming also extends to infiltrating monocytes and macrophages, collectively fostering a microenvironment favoring repair.

neuroscience↗

bioRxiv2025

Inter-tool analysis of a NIST dataset for assessing baseline nucleic acid sequence screening

Nucleic acid synthesis is a dual-use technology that can benefit fields such as biology, medicine, and information storage. However, synthetic nucleic acids could also potentially be used negligently and ultimately cause harm, or be used with malicious intent to cause harm. Thus, this technology needs to be appropriately safeguarded. Sequence screening is one component of a biosecurity protocol for preventing such harm and consists of differentiating Sequences of Concern (SOCs) from benign sequences that are not associated with pathogenicity or toxicity. There exist many fit-for-purpose tools that have been developed for DNA synthesis sequence screening. However, questions remain regarding their performance with respect to consistency of screening. To aid in determining if screening tools are harmonized in regard to baseline sequence screening, NIST constructed a test dataset based on current screening recommendations. NIST then sent blinded datasets to sequence screening tool developers for testing. Overall, there was a general agreement between the tools and NIST assignments of the sequences and all tools had a baseline performance of greater than 95% sensitivity and 97% accuracy. Disagreement on specific sequences largely arose from single tools and could be traced to differences in defining a SOC and/or methodological differences in screening algorithms.

bioinformatics↗

bioRxiv2024

Magellanic penguins balance navigation with foraging opportunities in complex current regimes

Animals navigating in fluid environments often face lateral forces from wind or water currents that challenge travel efficiency and route accuracy. We investigated how 27 Magellanic penguins (Spheniscus magellanicus) adapt their navigation strategies to return to their colony amid regional tidal ocean currents. Using GPS-enhanced dead-reckoning loggers and high-resolution ocean current data, we reconstructed penguin travel vectors during foraging trips to assess their responses to variable currents during their colony-bound movements. By integrating estimates of energy costs and prey pursuits, we found that birds balanced direct navigation with current-driven drift: in calm currents, they maintained precise line-of-sight headings to their colony. In stronger currents, they aligned their return with lateral flows, which increased travel distance, but at minimal energy costs, and provided them with increased foraging opportunities. Since the lateral tidal currents always reversed direction over the course of return paths, the penguins return paths were consistently S-shaped but still resulted in the birds returning efficiently to their colonies. These findings suggest that Magellanic penguins can sense current drift and use it to optimize energy expenditure by maintaining overall directional accuracy while capitalizing on foraging opportunities.

animal behavior and cognition↗

bioRxiv2022

The role of wingbeat frequency and amplitude in flight power

Body-mounted accelerometers provide a new prospect for estimating power use in flying birds, as the signal varies with the two major kinematic determinants of aerodynamic power: wingbeat frequency and amplitude. Yet wingbeat frequency is sometimes used as a proxy for power output in isolation. There is therefore a need to understand which kinematic parameter birds vary and whether this is predicted by flight mode (e.g., accelerating, ascending/descending flight), speed or morphology. We investigate this using high-frequency acceleration data from (i) 14 species flying in the wild, (ii) two species flying in controlled conditions in a wind tunnel and (iii) a review of experimental and field studies. While wingbeat frequency and amplitude were positively correlated, R2 values were generally low, supporting the idea that parameters can vary independently. Indeed, birds were more likely to modulate wingbeat amplitude for more energy-demanding flight modes, including climbing and take-off. Nonetheless, the striking variability even within species and flight types, highlights the complexity of describing the kinematic relationships, which appear sensitive to both the biological and physical context. Notwithstanding this acceleration metrics that incorporate both kinematic parameters should be more robust proxies for power than wingbeat frequency alone.

biophysics↗