Biology subjects

Ramos, F.

Publications and source records attributed to Ramos, F..

7 recordsLinked to original sources

bioRxiv2025

Common origin for effector and regulatory Follicular and Tissue-Adapted CD4+ T cells in Non-Small Cell Lung Cancer

Tumor-invaded lymph nodes (LNs) serve as critical hubs for anti-tumor immunity, yet their role in orchestrating immune responses remains poorly understood. Using integrated single-cell RNA sequencing, T cell receptor sequencing, and chromatin accessibility profiling, we analyzed CD4+ T cells from matched blood, tumor-invaded LNs, and tumors of treatment-naive non-small cell lung cancer patients. We identified distinct immunological landscapes across these compartments. Compared to blood, tumor-invaded LNs and tumors were enriched for follicular regulatory T cells (Treg-Tfr), conventional T cell subsets with Tfh-like characteristics (Tconv-Tfh and Tconv-CXCL13), and tissue-resident memory Tregs (Treg-Trm). These populations share a BATF-dependent transcriptional program that governs T-cell activation and tissue adaptation, while simultaneously engaging distinct, subset-specific regulatory networks. Integrative TCR-RNA analysis revealed that tumor-reactive, neoantigen-specific T cell clones were enriched within these subsets and demonstrated extensive LN-tumor clonal sharing, indicating active recirculation between compartments. Through clonal coupling analysis and trajectory inference, we uncovered that Treg-Tfr cells function as multipotent progenitors that bifurcate into tissue-resident Treg-Trm or into ex-Tregs adopting a Tfh-like CXCL13+ ewector phenotype. Remarkably, follicular CD4+ T subsets from LNs and tumor were transcriptionally and epigenetically similar and localized to analogous germinal center niches. These findings establish tumor-invaded LNs as functional extensions of the tumor microenvironment that generate and maintain tumor-reactive CD4+ lineages. The identification of tissue-resident Treg-Tfr plasticity reveals a critical developmental checkpoint that could be therapeutically targeted to redirect immunosuppressive programs toward anti-tumor ewector responses.

immunology↗

bioRxiv2025

Give It Time: Green Anacondas Show Prolonged Behavioral Responses to Enclosure Enhancements

Information about green anacondas (Eunectes murinus) in human care is limited, especially concerning their behavior, welfare, and overall well-being. To help bridge this knowledge gap, this study evaluated how exhibit design enhancements influence E. murinus behavior. The aim was to assess immediate behavioral changes following enclosure modifications and investigate potential habituation over time, ultimately evaluating the effectiveness and longevity of the behavioral changes induced by the improved environment. Systematic observations were divided into three phases: before enclosure improvements, immediately after these modifications, and three weeks later. Enclosure modifications focused on areas less frequented by the anacondas during Phase 1. Results revealed decreased inactivity in Phase 2 and more balanced space use in Phase 3, with anacondas occupying previously underutilized areas, including the terrariums vertical dimension. Interaction with exhibit enhancement items increased in the studys final phase, where a decrease in engagement would be anticipated due to habituation. These results suggested the anacondas required additional time to acclimate to the modifications, even though environmental factors may have contributed to these changes. This study highlights how enclosure enhancements may benefit green anacondas welfare while underlining the importance of providing sufficient acclimation time to accurately evaluate the animals complete behavioral response. Simple SummaryGreen anacondas (Eunectes murinus) remain largely understudied, particularly in terms of their behavior and welfare in human care. To address this knowledge gap, improvements were made to the enclosure of green anacondas in captivity, and their behaviors were observed before and after the modifications. The observations were divided into three phases: before the changes (Phase 1), immediately after (Phase 2), and approximately three weeks later (Phase 3). The modifications focused on areas that were rarely utilized during Phase 1. After the improvements, the anacondas became more active and used their enclosure more evenly, including at varying heights. The anacondas interacted more with the new enclosure features after the three weeks, when increased disinterest would have been expected, although environmental conditions may have influenced these changes. These findings show how enclosure modifications may help enhance the welfare of green anacondas and emphasize the need for research that allows enough time for the animals to fully adjust, ensuring a complete understanding of their response.

animal behavior and cognition↗

bioRxiv2022

Identification and quantification of α- and β-amanitin in wild mushrooms by HPLC-UV-EC and HPLC-DAD-MS detection

Amatoxins are a group of highly toxic peptides, which include - and {beta}-amanitin, found in several species of mushrooms (e.g. Amanita phalloides). Due to their high hepatotoxicity, they account for most deaths occurring after mushrooms ingestion. The determination of - and {beta}- amanitin content in wild mushrooms is invaluable for treating cases involving poisoning. In the present study, we have developed and validated an analytical method based on high-performance liquid chromatography, with in-line ultraviolet and electrochemical detection (HPLC-UV-EC), for the rapid quantification of - and {beta}-amanitin in wild mushroom samples collected from the Inner Center of Portugal. A reproducible and simple solid-phase extraction (SPE) using OASIS(R) PRIME HLB cartridges was used for sample pre-treatment, followed by chromatographic separation based on the RP-C18 column. The UV and EC chromatograms of - and {beta}-amanitin were recorded at 305 nm and +0.600 V vs. Ag/AgCl, respectively. The linear quantification for both amanitins was in the range of 0.5-20.0 g{middle dot}mL-1 (R2 > 0.999). The LOD, calculated based on the calibration curve, was similar for UV and EC detection (0.12-0.33 g ml.-1). Intra-day and inter-day precision were less than 13%, and the recovery ratios ranged from 89% to 117%. Nine Amanita species and five edible mushrooms were analysed by HPLC-UV-EC, and HPLC-DAD-MS confirmed the identification of amatoxins. We find high - and {beta}-amanitin content in A. phalloides and not in the other species analysed. In sum, the developed and validated method provides a simple and fast analysis of - and {beta}-amanitins contents in wild mushrooms and is suitable for screening and routine assessment of mushroom intoxication. HighlightsO_LINew validated method using HPLC-UV-EC to determine - and {beta}-amanitin in wild mushrooms. C_LIO_LIReproducible and fast SPE procedure for small samples. C_LIO_LIEffective sample pre-treatment with the OASIS(R) PRIME HLB SPE cartridge. C_LIO_LIIdentification and quantification of - and {beta}-amanitin in wild mushroom samples from Portugal. C_LIO_LIHPLC-DAD-MS confirmation of amatoxins present in mushroom samples. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/483521v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@734f7aorg.highwire.dtl.DTLVardef@66d9fforg.highwire.dtl.DTLVardef@720f39org.highwire.dtl.DTLVardef@458e64_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2018

MAU2 and NIPBL variants in Cornelia de Lange syndrome reveal MAU2-independent loading of cohesin and uncover a protective mechanism against early truncating mutations in NIPBL

Cornelia de Lange syndrome (CdLS) is a rare developmental disorder caused by mutations in genes related to the cohesin complex. For its association with chromatin, cohesin depends on a heterodimer formed by NIPBL and MAU2, which interact via their respective N-termini. Variants in NIPBL are the main cause of CdLS and result in NIPBL haploinsufficiency.\n\nUsing CRISPR, we generated cells homozygous for an out-of-frame duplication in NIPBL. Remarkably, alternative translation initiation rescued NIPBL expression in these cells and produced an N-terminally truncated NIPBL that lacks MAU2-interaction domain, causing a dramatic reduction of MAU2 protein levels. Strikingly, this protective mechanism allows nearly normal amounts of cohesin to be loaded onto chromatin in a manner that is independent of functional NIPBL/MAU2 complexes and therefore in contrast to previous findings.\n\nWe also report the first pathogenic variant in MAU2, a deletion of seven amino acids important for wrapping the N-terminus of NIPBL within MAU2. The mutation causes dramatic reduction of MAU2 heterodimerization with NIPBL, hence undermining the stability of both proteins.\n\nOur data confirm NIPBL haploinsufficiency as the major pathogenic mechanism of CdLS and give new insights into the molecular mechanisms responsible for this neurodevelopmental disorder. Our work also unveils an alternative translation-based mechanism that protects cells from out-of-frame variants of NIPBL and that may be of relevance in other genetic conditions.

molecular biology↗

bioRxiv2018

PP4 phosphatase cooperates in recombinational DNA repair by enhancing double-strand break end resection

The role of Rad53 in response to a DNA lesion is central for the accurate orchestration of the DNA damage response. Rad53 activation relies on its phosphorylation by the Mec1 kinase and its own auto-phosphorylation in a manner dependent on the adaptor Rad9. While the mechanism behind Rad53 phosphorylation and activation has been well documented, less is known about the processes that counteract its kinase activity during the response to DNA damage. Here, we describe that PP4 phosphatase dephosphorylates Rad53 during the repair of a double-strand break, a process that impacts on the phosphorylation status of multiple factors involved in the DNA damage response. PP4-dependent Rad53 dephosphorylation stimulates DNA end resection by relieving the negative effect that Rad9 exerts over the Sgs1/Dna2 exonuclease complex. Consequently, elimination of PP4 activity affects DNA resection and repair by single-strand annealing, defects that are bypassed by reducing the hyper-phosphorylation state of Rad53 observed in the absence of the phosphatase. These results confirm that Rad53 is one of the main targets of PP4 during the repair of a DNA lesion and demonstrate that the attenuation of its kinase activity during the initial steps of the repair process is essential to efficiently enhance recombinational DNA repair pathways that depend on long-range resection.

molecular biology↗

bioRxiv2018

Integrated accounts of behavioral and neuroimaging data using flexible recurrent neural network models

Neuroscience studies of human decision-making abilities commonly involve sub-jects completing a decision-making task while BOLD signals are recorded using fMRI. Hypotheses are tested about which brain regions mediate the effect of past experience, such as rewards, on future actions. One standard approach to this is model-based fMRI data analysis, in which a model is fitted to the behavioral data, i.e., a subjects choices, and then the neural data are parsed to find brain regions whose BOLD signals are related to the models internal signals. However, the internal mechanics of such purely behavioral models are not constrained by the neural data, and therefore might miss or mischaracterize aspects of the brain. To address this limitation, we introduce a new method using recurrent neural network models that are flexible enough to be jointly fitted to the behavioral and neural data. We trained a model so that its internal states were suitably related to neural activity during the task, while at the same time its output predicted the next action a subject would execute. We then used the fitted model to create a novel visualization of the relationship between the activity in brain regions at different times following a reward and the choices the subject subsequently made. Finally, we validated our method using a previously published dataset. We found that the model was able to recover the underlying neural substrates that were discovered by explicit model engineering in the previous work, and also derived new results regarding the temporal pattern of brain activity.

neuroscience↗

bioRxiv2018

Models that learn how humans learn: the case of depression and bipolar disorders

Computational models of learning and decision-making processes in the brain play an important role in many domains. Such models typically have a constrained structure and make specific assumptions about the underlying human learning processes; these may make them underfit observed behaviours. Here we suggest an alternative method based on learning-to-learn approaches, using recurrent neural networks (RNNs) as a flexible family of models that have sufficient capacity to represent the complex learning and decision-making strategies used by humans. In this approach, an RNN is trained to predict the next action that a subject will take in a decision-making task, and in this way, learns to imitate the processes underlying subjects choices and their learning abilities. We demonstrate the benefits of this approach with a new dataset containing behaviour of uni-polar depression (n=34), bipolar (n=33) and control (n=34) participants in a two-armed bandit task. The results indicate that the new approach is better than baseline reinforcement-learning methods in terms of overall performance and its capacity to predict subjects choices. We show that the model can be interpreted using off-policy simulations, and thereby provide a novel clustering of subjects learning processes - something that often eludes traditional approaches to modelling and behavioural analysis.

bioinformatics↗