Biology subjects

Luque, D.

Publications and source records attributed to Luque, D..

11 recordsLinked to original sources

bioRxiv2026

Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions

Asgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal bacterial symbiosis, yet the contribution of viruses remains unexplored. Here, for the first time, we visualised unique viruses associated with Asgard archaeal cells. Additionally, we identified the first putative Asgard-archaeal virus satellite, which exhibited genomic interactions involving a bacterium, Stromatodesulfovibrio nilemahensis, providing evidence of a virus-mediated interaction between an Asgard archaeon and a bacterium. Additionally, novel proviruses of S. nilemahensis displayed distinct genomic features where predictions of alternate recombination sites suggested the acquisition of horizontally acquired genes associated with biofilm formation. Further, we comprehensively characterise (pro)viruses associated with this co-culture using high resolution cryo-electron tomography, proximity ligation (Hi-C), and metagenomics. Together, these findings expand the known diversity of Asgard archaeal viruses and establish a foundation for investigating the role of viruses in microbial symbiosis relevant to the emergence of eukaryotic life.

microbiology↗

bioRxiv2026

Engineering a Novel Bacterial Encapsulin for Programmable Surface Functionalization: From Single-Target to Mosaic Nanovaccines

Encapsulins are prokaryotic self-assembling protein nanocages with promise as nanovaccine scaffolds. Their utility as modular platforms require tolerance to surface engineering, high-yield soluble production, formulation stability, and controlled antigen (co-)display. Herein, a previously uncharacterized encapsulin from Alkaliphilus metalliredigens is engineered into a SpyCatcher-decorated nanoscaffold (Am-S) that enables controlled surface display of SpyTagged antigens. Cryo-EM confirms that the native encapsulin forms a T = 1 icosahedral nanocage, and that C-terminal SpyCatcher fusion yields Am-S without compromising nanocage assembly, symmetry, or structural integrity. Notably, Am-S exhibits high-yield soluble production in Escherichia coli, remains monodisperse after freeze-thaw and extended storage, and supports efficient SpyTagged peptide conjugation for single- and multi-antigen display. As a proof-of-concept, Am-S is functionalized with Alzheimers disease-associated amyloid-{beta} and/or hyperphosphorylated tau epitopes to generate single-target nanocages displaying either antigen and dual-target mosaic nanocages co-displaying both. In mice, Am-S antigen display enhances antigen-specific IgG responses relative to free antigens and induces predominantly IgG1-biased humoral immunity. Mosaic nanocages elicit antibodies against both targets, with immune sera selectively recognizing amyloid-{beta}- and phosphorylated tau-associated pathology in ex vivo brain sections from Alzheimers disease mouse models. These findings position Am-S as a manufacturable scaffold for developing multi-targeting nanovaccines against complex diseases.

synthetic biology↗

bioRxiv2025

Structural determinants of rotavirus proteolytic activation

The infectivity of rotavirus (RV), the leading cause of childhood diarrhea, hinges on the activation of viral particles through the proteolysis of the spike protein by trypsin-like proteases in the host intestinal lumen. Despite comprehensive structural characterization of the virus particle, the structural rationale behind the necessity of trypsin digestion of the VP4 protein for infectivity remains poorly understood. In this study, using cryo-electron microscopy (cryo-EM) and advanced image processing techniques, we compared uncleaved and cleaved RV virions and found that the conformation of the non-proteolyzed spike is constrained by the position of loops that surround its structure, linking the lectin domains of the spike head to its body. The proteolysis of these loops removes this structural constraint, thereby enabling the spike to undergo the necessary conformational changes required for cell membrane penetration. Thus, these loops function as regulatory elements to ensure that the spike protein is activated precisely when and where it is needed to facilitate a successful infection.

microbiology↗

bioRxiv2025

The Neural Basis of Habit Formation Measured in Goal-Directed Response Switching

To override ongoing habitual responses requires switching well-learned actions with new goal-directed processing. However, the neural circuits responsible for these processes remain unclear. This study infers habit strength by introducing a novel task capturing the increased cost associated with switching a habitual response. We employed neuroimaging and brain stimulation to examine the dynamic interactions between human brain regions involved in habits and their interference with ongoing incompatible goal-directed behavior. Training S-R links in overtrained stimuli (compared to less trained ones, termed standard-trained stimuli) increased RT switch costs, explained by drift diffusion computations governing both the training and outcome devaluation phases. Training engaged sensorimotor areas and the posterior putamen, whereas standard trained behaviors, recruited the posterior caudate, insula, and prefrontal regions. A cortical network orchestrated habit expression (right S1 with the left anterior insula/prefrontal areas) while also implicating basal ganglia when overriding habits (left premotor with the putamen). Importantly, stimulation of the left premotor played a causal role in habit control, enhancing performance across both the training and devaluation phases. Our findings reveal an interaction between habitual and goal-directed brain regions, highlighting shared neural dynamics when overriding habitual behaviors.

neuroscience↗

bioRxiv2023

Metabolic and mitochondria alterations induced by SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10

Antiviral signaling, immune response and cell metabolism in human body are dysregulated by SARS-CoV-2, the causative agent of the COVID-19. Here, we show that SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10 induce a significant mitochondrial and metabolic reprogramming in A549 lung epithelial cells. While all four ORFs caused mitochondrial fragmentation and altered mitochondrial function, only ORF3a and ORF9c induced a marked structural alteration in mitochondrial cristae. ORF9b, ORF9c and ORF10 induced largely overlapping transcriptomes. In contrast, ORF3a induced a distinct transcriptome, including the downregulation of numerous genes for proteins with critical mitochondrial functions and morphology. Genome-Scale Metabolic Models predicted common and private metabolic flux reprogramming, notably a depressed amino acid metabolism, and an enhanced metabolism of specific lipids distinctly induced by ORF3a. These findings reveal metabolic dependencies and vulnerabilities prompted by SARS-CoV-2 accessory proteins that may be exploited to identify new targets for intervention. One-Sentence SummaryMitochondria and metabolic alterations induced by SARS- CoV-2 accessory proteins ORF3a, ORF9b, ORF9c, ORF10 in pulmonary cells unravel new targets of intervention.

immunology↗

bioRxiv2022

Model-free decision making resists improved instructions and is enhanced by stimulus-response associations

Human behaviour may be thought of as supported by two different computational-learning mechanisms, model-free and model-based respectively. In model-free strategies, stimulus-response associations are strengthened when actions are followed by a reward and weakened otherwise. In model-based learning, previous to selecting an action, the current values of the different possible actions are computed based on a detailed model of the environment. Previous research with the two-stage task suggests that participants behaviour usually shows a mixture of both strategies. But, interestingly, a recent study by da Silva and Hare (2020) found that participants primarily deploy model-based behaviour when they are given detailed instructions about the structure of the task. In the present study, we reproduce this essential experiment. Our results confirm that improved instructions give rise to a stronger model-based component. Crucially, we also found a significant effect of reward that became stronger under conditions that favoured the development of strong stimulus-response associations. This suggests that the effect of reward, often taken as indicator of a model-free component, is related to stimulus-response learning.

neuroscience↗

bioRxiv2022

Equilibrium dynamics of a biomolecular complex analyzed at single-amino acid resolution by cryo-electron microscopy

The biological function of macromolecular complexes depends not only on large-scale transitions between conformations, but also on small-scale conformational fluctuations at equilibrium. This study shows that detailed information on the equilibrium dynamics of a biocomplex obtained from local resolution (LR) data in cryo-electron microscopy (cryo-EM) density maps matches the information obtained in solution by hydrogen-deuterium exchange mass-spectrometry. The structure of the minute virus of mice (MVM) capsid as a model system was determined by cryo-EM, and LR values were found to correlate with both crystallographic B-factors and hydrogen-deuterium exchange values. Once validated, the cryo-EM LR-based approach was used to compare the equilibrium dynamics of wild-type and two mutant MVM capsids. The results revealed a linkage between mechanical stiffening and impaired equilibrium dynamics in a biocomplex. Cryo-EM is emerging as a powerful approach for simultaneously acquiring information on the atomic structure and local equilibrium dynamics of biomolecular complexes.

biophysics↗

bioRxiv2022

Pharmacological inhibition of titan-like cells formation suggests that accumulation of endogenous free radicals that correlate with mitochondrial changes are required to induce this transition in Cryptococcus neoformans

Cryptococcus neoformans is an encapsulated yeast able to cause disease (mainly meningoencephalitis) among immunosuppressed patients, mostly HIV+. This yeast can form the so-called titan cells in vivo, which are cells of an abnormal larger size due to an increase in both the capsule and the cell body size (total size reaching between 50-70 microns). This phenomenon can be partially reproduced in vitro to obtain cells of an intermediate size (25-30 um), which have been denominated titan-like cells. In this work, we have screened 1,520 compounds from the Prestwick Chemical Library and identified off-patent drugs that inhibited titan-like cell formation in vitro. We developed an automated fluorescence-based microscopy assay and identified 64 compounds as possible inhibitors of titan-like cells in vitro. We chose 10 of these compounds to confirm their inhibitory effect and confirmed them as inhibitors of titan-like cells with dose-response curves. Several of the compounds identified had antioxidant properties (i.e., retinoic acid), indicating a possible role of free radicals during titan cell formation. Using fluorescent probes, we found that there was an endogenous accumulation of ROS during cell growth, which was inhibited in the presence of retinoic acid. Furthermore, we found that during titanization, there were significant changes in the mitochondria, which is the main organelle where ROS are produced. We hypothesize that an intracellular increase of free radicals at the mitochondria might be a triggering signal to induce titanization. ImportanceCryptococcus neoformans is an excellent model to investigate fungal pathogenesis. This yeast can produce "titan cells", which are cells of an abnormal larger size that contribute to the persistence of the yeast in the host. In this work, we have used a new approach to characterize them, which is identifying drugs that inhibit this process. We have used a repurposing off- patent drug library, combined with an automatic method to image and analyse fungal cell size. In this way, we have identified many compounds that inhibit this transition. Interestingly, several compounds were antioxidants, allowing us to confirm that endogenous ROS and mitochondrial changes are important for titan cell formation. This work provides new evidences of the mechanisms required for titanization. Furthermore, the future characterization of the inhibitory mechanisms of the identified compounds by the scientific community will contribute to better understand the role of titan cells in virulence.

microbiology↗

bioRxiv2021

Striatal role in everyday life and laboratory developed habits

The dorsolateral striatum plays a critical role in the acquisition and expression of stimulus-response habits that are learned in experimental laboratories. Here, we use meta-analytic procedures to contrast the neural circuits activated by laboratory-acquired habits with those activated by stimulus-response behaviours acquired in everyday-life. We confirmed that newly learned habits rely more on the anterior putamen with activation extending into caudate and nucleus accumbens. Motor and associative components of everyday-life habits were identified. We found that motor-dominant stimulus-response associations developed outside the laboratory primarily engaged posterior dorsal putamen, supplementary motor area (SMA) and cerebellum. Importantly, associative components were also represented in the posterior putamen. Thus, common neural representations for both naturalistic and laboratory-based habits were found in the left posterior and right anterior putamen. These findings suggest a partial common striatal substrate for habitual actions that are performed predominantly by stimulus-response associations represented in the posterior striatum. The overlapping neural substrates for laboratory and everyday-life habits supports the use of both methods for the analysis of habitual behaviour.

neuroscience↗

bioRxiv2020

Four-dimensional characterization of the Babesia divergens asexual life cycle: from the trophozoite to the multiparasite stage

Babesia is an apicomplexan parasite of significance that causes the disease known as babesiosis in domestic and wild animals and in humans worldwide. Babesia infects vertebrate hosts and reproduces asexually by a form of binary fission within erythrocytes/red blood cells (RBCs), yielding a complex pleomorphic population of intraerythrocytic parasites. Seven of them, clearly visible in human RBCs infected with Babesia divergens, are considered the main forms and named single, double and quadruple trophozoites, paired and double paired-pyriforms, tetrad or Maltese Cross, and multiparasite stage. However, these main intraerythrocytic forms coexist with RBCs infected with transient parasite combinations of unclear origin and development. In fact, little is understood about how Babesia builds this complex population during its asexual life cycle. By combining the emerging technique cryo soft X-ray tomography and video microscopy, main and transitory parasites were characterized in a native whole cellular context and at nanometric resolution. As a result, the architecture and kinetic of the parasite population has been elucidated. Importantly, the process of multiplication by binary fission, involving budding, was visualized in live parasites for the first time, revealing that fundamental changes in cell shape and continuous rounds of multiplication occur as the parasites go through their asexual multiplication cycle. Based on these observations, a four-dimensional (4D) asexual life cycle model has been designed highlighting the origin of the tetrad, double paired-pyriform and multiparasite stages and the transient morphological forms that, surprisingly, intersperse in a chronological order between one main stage and the next along the cycle. IMPORTANCEBabesiosis is a disease caused by intraerythrocytic Babesia parasites, which possess many clinical features that are similar to those of malaria. This worldwide disease, is increasing in frequency and geographical range, and has a significant impact on human and animal health. Babesia divergens is one of the species responsible for human and cattle babesiosis causing death unless treated promptly. When B. divergens infects its vertebrate hosts it reproduces asexually within red blood cells. During its asexual life cycle, B. divergens builds a population of numerous intraerythrocytic (IE) parasites of difficult interpretation. This complex population is largely unexplored, and we have therefore combined three and four dimensional (3D and 4D) imaging techniques to elucidate the origin, architecture, and kinetic of IE parasites. Unveil the nature of these parasites have provided a vision of the B. divergens asexual cycle in unprecedented detail and a key step to develop control strategies against babesiosis

microbiology↗

bioRxiv2018

Learned predictiveness acquired through experience prevails over the influence of conflicting verbal instructions in rapid selective attention

Previous studies have provided evidence that selective attention tends to prioritize the processing of stimuli that are good predictors of upcoming events over nonpredictive stimuli. In the present study we explored whether the mechanism responsible for this effect critically reflects the influence of prior experience of predictiveness (history of attentional selection of predictive stimuli), or whether it reflects a more flexible process that can be adapted to new verbally acquired knowledge. Our experiment manipulated participants experience of the predictiveness of different stimuli over the course of trial-by-trial training; we then provided explicit verbal instructions regarding stimulus predictiveness that were designed to be either consistent or inconsistent with the previously established learned predictiveness. The effects of training and instruction on attention to stimuli were measured using a dot probe task. Results revealed a rapid attentional bias towards stimuli experienced as predictive (versus those experienced as nonpredictive), that was completely unaffected by verbal instructions. This was not due to participants failure to recall or use instructions appropriately, as revealed by analyses of their learning about stimuli, and their memory for instructions. Overall, these findings suggest that stimuli experienced as predictive through trial-by-trial training produce a relatively inflexible attentional bias based on prior selection history, which is not (always) easily altered through instructions.

animal behavior and cognition↗