Biology subjects

Gil, A.

Publications and source records attributed to Gil, A..

14 recordsLinked to original sources

bioRxiv2026

Stealth CAR-Tregs evade CD3 antibody therapy and skew immune responses toward regulation

Organ transplantation standard of care relies on lifelong immunosuppression, increasing infection and malignancy risks. An emerging approach using Chimeric Antigen Receptor Regulatory T cells (CAR-Tregs) targeting donor antigens, allows the suppression of alloimmune responses while preserving protective immunity. However, transplant recipients harbor a substantial pool of alloreactive memory T-cells, limiting CAR-Tregs tolerance-promoting effect. To address this challenge, our strategy combines selective depletion of activated T-cells, using non-mitogenic CD3 antibody therapy, with HLA-A2-targeted-CAR-Treg therapy. We established that T-cell receptor alpha chain (TRAC) deletion does not impair CAR-Treg antigen-specific activation, expansion, or their transcriptomic, phenotypic, epigenetic, and functional profiles. TRAC-/-CAR-Tregs exhibit robust protection from CD3 antibody depletion in circulation and peripheral tissues, whereas most TRAC+/+CAR-T cells are eliminated. Importantly, TRAC+/+CAR-T cells that escape CD3 antibody mediated depletion exhibit a transcriptomic signature consistent with T-cell exhaustion. Our findings demonstrate that CD3 antibody therapy provides an in vivo survival advantage to TRAC-/-CAR-Tregs, thereby shifting the immune balance toward regulation. This approach might enhance the translational potential of CAR-Treg therapy by reducing the required cell dose needed for clinical efficacy.

immunology↗

bioRxiv2026

High-throughput screen identifies a potent MCU activator boosting cardiac contractile bioenergetics

Mitochondrial Ca2+ uptake through the mitochondrial calcium uniporter complex (MCUc) couples intracellular Ca2+ signaling to energy metabolism and cellular function. Despite its physiological importance, potent and selective pharmacological activators of the MCU complex remain scarce, and existing compounds show modest specificity. Here, we screened 1,280 bioactive compounds and identified CGP7930 as a potent activator of mitochondrial Ca2+ uptake. Mechanistically, the compound required MICU1, but not MICU2, to exert its effects. Molecular docking, non-covalent interaction analysis, and site-directed mutagenesis identified Gln304 and Val307 in MICU1 as critical determinants of compound activity. In addition to directly stimulating MCU activity, CGP7930 increased mitochondria-endoplasmic reticulum contact sites, suggesting an additional mechanism to facilitate inter-organellar Ca2+ transfer. CGP7930 promoted Ca2+-dependent activation of mitochondrial energy metabolism in cardiomyocytes and boosted the contractile performance of the mice hearts. This effect was MCU-dependent, as hearts from MCU KO mice failed to increase the ventricular contraction force upon CGP7930 perfusion. Molecular docking, non-covalent interaction analysis, and site-directed mutagenesis identified Gln304 and Val307 in MICU1 as critical determinants of compound activity.

biochemistry↗

bioRxiv2026

Exploring the relationship between dolphins and fisheries: uncovering the spatial and temporal patterns that influence potential conflicts along Portugal's north coast

The north coast of mainland Portugal supports a strong dolphin presence and extensive fishing activity, increasing the likelihood of interactions, such as bycatch. This study provides an initial assessment of potential conflict areas, using automatic identification system (AIS) data from Global Fishing Watch. To this end, sighting data from the ATLANTIDA project (2021-2024) on the common dolphin (Delphinus delphis) were used to describe spatiotemporal patterns of occurrence and encounter rates, and to predict their association with fishing effort to identify and map areas of potential overlap. A generalised additive model (GAM) was then applied, integrating environmental, spatial, temporal, and fisheries-related variables to identify the main predictors of species occurrence. Common dolphins were frequently observed during the summer, with an average encounter rate of 3.662 sightings/km. This high encounter rate may be associated with factors such as sea surface temperature, diet, and purse seine fishing activity. The maps showed a spatial overlap between fishing grounds and areas of common dolphin occurrence. Fishing effort was nearly identical between locations with sightings (2.00 h/km{superscript 2}) and those without (1.62 h/km{superscript 2}), suggesting that dolphins are not actively avoiding fishing areas but may instead frequent them due to shared habitat preferences. The best-fitted GAM indicated that encounters were related to year, latitude, fishing effort, depth, sea surface temperature, and season. There was an increase in occurrence over the years and a decrease with increasing fishing effort and sea surface temperature, possibly linked to changes in prey availability, although broad confidence intervals warrant cautious interpretation. Despite some limitations encountered in this study, we believe our findings provide valuable insights into the relationship between dolphin occurrence, environmental conditions, and fishing activities in the area, establishing an important baseline for future conservation and fisheries management efforts.

ecology↗

bioRxiv2026

Time to Potential Collision: A Dynamic Approach To Study Vessel-Whale Close Encounters

Vessel-whale collisions are a growing global concern and remain challenging to quantify. Therefore, the use of proxies, such as Close Encounters (CEs) that comprise Surprise Encounters (SEs) and Near-Miss Events (NMEs), has been proposed and widely employed to assess collision risk. To better understand this risk in the Eastern North Atlantic, where maritime traffic is intensive, this study aimed to redefine and quantify CEs, and to assess detectability-related variables that may affect CE identification. CEs were assessed using a cetacean occurrence dataset collected between 2012 and 2024 on board cargo ships and oceanographic vessels. CEs thresholds were redefined based on Time to Potential Collision (TPC), rather than distance alone (as described in literature), to allow a more dynamic, risk-based, and speed-sensitive approach. In total, 1226 sightings of whales (baleen, sperm, and beaked whales) were recorded, of which 37.4% were classified as SEs and 2.0% as NMEs. The sperm whale, Physeter macrocephalus, was the species most frequently involved in CEs (13.9% of all CEs), followed by the Cuviers beaked whale, Ziphius cavirostris (11.8%). A Generalized Additive Model was used to assess the influence of detectability-related variables (i.e., meteorological conditions, whale taxa, vessel characteristics, and Marine Mammals Observers (MMOs) experience) on TPC. Significantly lower TPC values were observed with beaked whales, cargo ships, poor visibility conditions, and less experienced MMOs. The results of this study provide an CEs assessment in this region and contribute to the ongoing efforts to standardize CE quantification, by using TPC as a metric. This work also highlights the importance of decreased speeds and the presence of experienced MMOs on board to increase detection probability and TPC, thereby potentially minimizing collision risk.

ecology↗

bioRxiv2025

Evaluating the Influence of Disease-Gene Associations in the Significance of Disease Modules through the lens of Network Medicine

The rapid expansion of genomic and biomedical data has paved the way for constructing complex disease networks, offering new insights into disease mechanisms and therapeutic target identification. Central to these networks are disease modules, which are constructed from seed genes that are prioritized based on their relevance to a given disease. Gene prioritization aims to rank genes based on their strength of association with a disease. Resources like DisGeNET, integrated within DISNET knowledge base, assigns a Gene-Disease Association (GDA) score that reflects the confidence in the association between a gene and a disease. This study investigates how both disease module sizes and GDA scores influence the statistical significance of these modules. By characterizing disease modules, filtering the data based on their GDA score thresholds, and analysing the relationship between their size, GDA score, and significance, potential cutoffs for robust module construction are estimated. Our findings suggest that disease modules filtered to include GDA scores above 0.3 and module sizes greater than 10 tend to be significant. These insights provide guidance for optimal gene prioritization and module selection, ultimately enhancing strategies for target identification and drug repurposing in network medicine.

bioinformatics↗

bioRxiv2025

New insights into the metabolomic signatures of spontaneously hypertensive rats

BACKGROUNDHypertension is a major risk factor associated with cardiovascular diseases and one of the leading causes of premature death. Hypertension has no obvious clinical signs; therefore, the identification of new biomarkers for the early detection of people at risk is needed to prevent hypertension and its further complications. Metabolomics is a useful tool for studying in vivo metabolic profiles that better understand the pathogenesis of diseases such as hypertension. This work aimed to explore the plasma and urinary non-targeted metabolic profile of 16-week-old spontaneously hypertensive rats (SHR) to identify new metabolomic profiles associated with hypertensive phenotypical characteristics that allow early diagnosis of patients at risk. METHODSPlasma and 24-hours urine samples were collected from 10 SHR and 10 age-matched normotensive Wistar-Kyoto 16-week-old male rats. Plasma and urinary metabolic profiles were investigated using high-performance liquid chromatography quadrupole time of flight coupled to mass spectroscopy followed by multivariate statistical analysis. The mummichog pathway enrichment analysis was used to integrate metabolomics data into biological contexts. RESULTSA total of 16 differential metabolites were found in plasma and 13 differential metabolites in urine from SHR compared to normotensive rats. Differences in some microbiota-derived metabolites suggest changes in the gut microbiota associated with hypertension in our experimental model. The mummichog algorithm has recognized that hypertensive metabolism is associated with the altered metabolism of steroid hormones, bile acid and purines. CONCLUSIONSThis work highlights the importance of metabolomics as a tool for the identification of biomarkers in the early detection of hypertension, a condition that represents a significant risk to cardiovascular health. The findings suggest that hypertension is associated with alterations in the metabolism of steroid hormones, bile acids and purines, as well as metabolites derived from the intestinal microbiota. These results not only contribute to a better understanding of the pathogenesis of hypertension but also open the door to future research in humans that could facilitate more accurate and earlier diagnoses, thus helping to prevent serious complications associated with this disease.

biochemistry↗

bioRxiv2024

Vibrio are a potential source of novel colistin-resistance genes in European coastal environments

Colistin is a widespread last resort antibiotic for treatment of multidrug-resistant bacteria. The recent worldwide emergence of colistin resistance (Col-R) conferred by mcr-1 in human pathogens has raised concern, but the putative sources and reservoirs of novel mcr genes in the marine environment remain underexplored. We observed a high prevalence of Col-R, particularly in Vibrio isolated from European coastal waters by using a unique stock of specific-pathogen-free (SPF) oysters as a bioaccumulator. The high sequence diversity found in the mcr/eptA gene family was geographically structured, particularly for three novel eptA gene variants, which were restricted to the Mediterranean (France, Spain) and occurred as a dgkA-eptA operon controlled by the RstA/RstB two component system. By analyzing 29427 Vibrionaceae genome assemblies, we showed that this mechanism of intrinsic resistance is prevalent and specific to the Harveyi clade, which includes strains of Vibrio parahaemolyticus and Vibrio alginolyticus causing infections in humans. The operon conferred colistin-resistance when transferred to sensitive non-Vibrio strains. While mcr-and arn-based Col-R mechanisms were also identified, the widespread presence of eptA gene variants in Vibrio suggests they play a key role in intrinsic resistance to colistin. Beyond these ancient eptA gene copies having evolved with the Vibrio lineage, we also identified mobile eptA paralogues that have been recently transferred between and within Vibrio clades. This highlights Vibrio as a potential source of Col-R mechanisms, emphasizing the need for enhanced surveillance to prevent colistin-resistant infections in coastal areas.

microbiology↗

bioRxiv2024

Environmental DNA as a complementary tool for biodiversity monitoring: A multi-technique and multi-trophic approach to investigate cetacean distribution and feeding ecology

The use of environmental DNA (eDNA) to assess the presence of biological communities has emerged as a promising monitoring tool in the marine conservation landscape. Moreover, advances in Next-Generation Sequencing techniques, such as DNA metabarcoding, enable multi-species detection in mixed samples, allowing the study of complex ecosystems such as oceanic ones. We aimed at using these molecular-based techniques to characterise cetacean communities, as well as potential prey in the northern coast of Mainland Portugal. During seasonal campaigns, we collected seawater samples, along with visual records of cetacean occurrence. The eDNA extracted from 64 environmental samples was sequenced in an Illumina platform, with universal primers targeting marine vertebrates. Five cetacean species were identified by molecular detection: common dolphin (Delphinus delphis), bottlenose dolphin (Tursiops truncatus), Rissos dolphin (Grampus griseus), harbour porpoise (Phocoena phocoena) and fin whale (Balaenoptera physalus). Overall, except for the fin whale (not sighted during the campaigns), this cetacean community composition was similar to that obtained through visual monitoring, and the complementary results suggest their presence in the region all year round. In addition, the positive molecular detections of B. physalus are of special relevance since there are no visual records reported in the area. The detection of multiple known preys of the identified dolphins indicates they use these coastal areas for feeding purposes. While this methodological approach remains in a development stage, the present work highlights the benefits of using eDNA to study marine communities, with specific applications for research on cetacean distribution and feeding ecology, ultimately serving as the baseline of a methodological approach for biodiversity monitoring and marine conservation.

ecology↗

bioRxiv2022

Co-evolution of human influenza A and Epstein Barr virus-specific CD8 ex vivo memory T cell receptor BV repertoires with increasing age

CD8 memory T cells are generated during primary infection with intracellular pathogens, such as viruses. These cells play an important role in the protection of the host upon re-infection with the same pathogen. In this study, we compare CD8 memory T cell receptor (TCR) BV repertoires directly ex vivo for two common human viruses, influenza A virus (IAV), an RNA virus that frequently re-infects due to a high rate of genetic mutation, and Epstein-Barr virus (EBV), a DNA virus, which persists in B cells for life, in the 95% of people that become infected. In cross- sectional and longitudinal studies of EBV seropositive, HLA-A2+, young (18-22 years), middle age (25-59 years), and older (>60 years) donors, we demonstrate that CD8 memory TCR repertoires to three immunodominant epitopes, known to have cross-reactive responses, IAV- M158-66 (M1), EBV-BMLF1280-288 (BM), and EBV-BRLF109-117 (BR) co-evolve as individuals age. Cross-sectional studies showed that IAV-M1- and both EBV-specific repertoires narrowed their TRBV usage with increasing age manifesting to different degrees for each epitope. In fact, narrowing of EBV-BM and EBV-BR-specific TRBV usage correlated with increasing age. IAV- M1-specific TRBV usage was significantly narrowed by middle-age. There was evidence that TRBV usage was changing with increasing age. For instance, IAV-M1-specific dominant BV19 usage appeared to become bimodal showing either high or low frequency of usage in the older age group, while BV30 usage frequency directly correlated with age. For the EBV epitope-specific responses there was preferential usage of particular TRBV and changes in the hierarchy of BV family usage in the different age groups. There appeared to be focusing of the TRBV repertoire by all 3 epitopes to three common BV in the older donors, which would be consistent with retention of crossreactive TCR suggesting co-evolution. Longitudinal studies tracking two donors over 14- 15 years (middle age to older) showed that there were continuous modulations in the TCR repertoire of IAV-M1, EBV-BM and EBV-BR-specific responses over time. There was evidence that acute IAV infection could contribute to these changes in TCR repertoire. This could be occurring by the TCR cross-reactivity that is known to exist between these 3 epitopes, and which appeared to be enhanced during acute IAV infection based on increased usage of common shared TRBV. These studies suggest that virus-specific TCR repertoires change over time as individuals age leading to narrowing of the repertoire favoring retention of potentially crossreactive TCR.

immunology↗

bioRxiv2020

SwarmTCR: a computational approach to predict the specificity of T Cell Receptors

MotivationComputationally predicting the specificity of T cell receptors can be a powerful tool to shed light on the immune response against infectious diseases and cancers, autoimmunity, cancer immunotherapy, and immunopathology. With more T cell receptor sequence data becoming available, the need for bioinformatics approaches to tackle this problem is even more pressing. Here we present SwarmTCR, a method that uses labeled sequence data to predict the specificity of T cell receptors using a nearest-neighbor approach. SwarmTCR works by optimizing the weights of the individual CDR regions to maximize classification performance. ResultsWe compared the performance of SwarmTCR against a state-of-the-art method (TCRdist) and showed that SwarmTCR performed significantly better on epitopes EBV-BRLF1300, EBV-BRLF1109, NS4B214-222 with single cell data and epitopes EBV-BRLF1300, EBV-BRLF1109, IAV-M158 with bulk sequencing data ( and {beta} chains). In addition, we show that the weights returned by SwarmTCR are biologically interpretable. AvailabilitySwarmTCR is distributed freely under the terms of the GPL-3 license. The source code and all sequencing data are available at GitHub (https://github.com/thecodingdoc/SwarmTCR) Contactdghersi@unomaha.edu

bioinformatics↗

bioRxiv2020

Epstein Barr virus epitope/MHC interaction combined with convergent recombination drive selection of diverse T cell receptor a and b repertoires

Recognition modes of individual T cell receptors (TCR) are well studied, but factors driving the selection of TCR repertoires from primary through persistent human virus infections are less well understood. Using deep sequencing, we demonstrate a high degree of diversity of EBV-specific clonotypes in acute infectious mononucleosis. Only 9% of unique clonotypes detected in AIM persisted into convalescence; the majority (91%) of unique clonotypes detected in AIM were not detected in convalescence and were seeming replaced by equally diverse "de-novo" clonotypes. The persistent clonotypes had a greater probability of being generated than non-persistent due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter CDR3 regions with fewer nucleotide additions (i.e. sequences closer to germline). Moreover, the two most immunodominant HLA-A2-restricted EBV epitopes, BRLF1109 and BMLF1280, show highly distinct antigen-specific public (i.e. shared between individuals) features. In fact, TCR CDR3 motifs played a dominant role, while TCR{beta} played a minimal role, in the selection of TCR repertoire to an immunodominant EBV epitope, BRLF1. This contrasts with the majority of previously reported repertoires, which appear to be selected either on TCR{beta} CDR3 interactions with peptide/MHC or in combination with TCR CDR3. Understanding of how TCR/peptide/MHC complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer. ImportanceSeveral lines of evidence suggest that TCR and {beta} repertoires play a role in disease outcomes and treatment strategies during viral infections in transplant patients, and in cancer and autoimmune disease therapy. Our data suggests that it is essential that we understand the basic principles of how to drive optimum repertoires for both TCR chains, and {beta}. We address this important issue by characterizing the CD8 TCR repertoire to a common persistent human viral infection (EBV), which is controlled by appropriate CD8 T cell responses. The ultimate goal would be to determine if the individuals who are infected asymptomatically develop a different TCR repertoire than those that develop the immunopathology of AIM. Here, we begin by doing an in depth characterization of both CD8 T cell TCR and {beta} repertoires to two immunodominant EBV epitopes over the course of AIM identifying potential factors that may be driving their selection.

immunology↗

bioRxiv2019

Ancient genomes reveal early Andean farmers selected common beans while preserving diversity

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations [1, 2]. Farmers selected desirable phenotypic traits, such as improved energy accumulation, palatability of seeds or reduced natural shattering [3], while leading domesticated populations through several more or less gradual demographic contractions [2, 4]. As a consequence, erosion of wild genetic variation [5] is typical of modern cultivars making them highly susceptible to pathogens, pests and environmental change [6,7]. The loss of genetic diversity hampers further crop improvement programs to increase food production in a changing world, posing serious threats to food security [8,9]. Using both ancient and modern seeds, we analyzed the temporal dynamic of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) that occurred in the Southern Andes. Here we show that most domestic traits were selected for prior to 2,500 years ago, with no or only minor loss of whole-genome variation. In fact, i) all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable - at least as variable as a modern genome from the wild; the genetic erosion that we observe in modern cultivars is therefore a recent process that occurred in the last centuries; ii) the majority of changes at coding genes that differentiate wild and domestic genomes are already present in the ancient genomes analyzed here. Considering that most desirable phenotypic traits are likely controlled by multiple polymorphic genes [10], a likely explanation of this decoupling of selection and genomic erosion is that early farmers applied a relatively weak selection pressure [2] by using many phenotypically similar but genomically diverse individuals as breeders. Selection strategies during the last few centuries were probably less sustainable and produced further improvements focusing on few plants carrying the traits of interest, at the cost of marked genetic erosion.

genomics↗

bioRxiv2018

High diversity, turnover, and structural constraints characterize TCR α and β repertoire selection

Recognition modes of individual T-cell receptors (TCR) are well studied, but how TCR repertoires are selected during acute through persistent human virus infections is less clear. Here, we show that persistent EBV-specific clonotypes account for only 9% of unique clonotypes but are highly expanded in acute infectious mononucleosis, and have distinct antigen-specific public features that drive selection into convalescence. The other 91% of highly diverse unique clonotypes disappear and are replaced in convalescence by equally diverse \"de-novo\" clonotypes. These broad fluctuating repertoires lend plasticity to antigen recognition and potentially protect against T-cell clonal loss and viral escape.

immunology↗

bioRxiv2017

Demonstration of de novo chemotaxis in E. coli using a real-time, quantitative, and digital-like approach

Chemotaxis is the movement of an organism in response to an external chemical stimulus. This system enables bacteria to sense their immediate environment and adapt to changes in its chemical composition. Bacterial chemotaxis is mediated by chemoreceptors, membrane proteins that bind an effector and transduce the signal to the downstream proteins. From a synthetic biology perspective, the natural chemotactic repertoire is of little use since bacterial chemoreceptors have evolved to sense specific ligands that either benefit or harm the cell. Here we demonstrate that using a combined computational design approach together with a quantitative, real-time, and digital detection approach, we can rapidly design, manufacture, and characterize a synthetic chemoreceptor in E. coli for histamine (a ligand for which there are no known chemoreceptors). First, we employed a computational protocol that uses the Rosetta bioinformatics software together with high threshold filters to design mutational variants to the native Tar ligand binding domain that target histamine. Second, we tested different ligand-chemoreceptors pairs with a novel chemotaxis assay, based on optical reflectance interferometry of porous silicon (PSi) optical transducers, enabling label-free quantification of chemotaxis by monitoring real-time changes in the optical readout (expressed as the effective optical thickness, EOT). We found that different ligands can be characterized by an individual set of fingerprints in our assay. Namely, a binary, digital-like response in EOT change (i.e. positive or negative) that differentiates between attractants and repellants, the amplitude of change of EOT response, and the rate by which steady state in EOT change is reached. Using this assay, we were able to positively identify and characterize a single mutational chemoreceptor variant for histamine that mediated chemotaxis comparably to the natural Tar-aspartate system. Our results demonstrate the possibility of not only expanding the natural chemotaxis repertoire, but also provide a new quantitative assay by which to characterize the efficacy of the chemotactic response.

synthetic biology↗