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Abstract Division and differentiation events by which cell populations with specific functions are generated often take place as part of a developmental programme, which can be represented by a sequence of compartments. A compartment is the set of cells with common characteristics; sharing, for instance, a spatial location or a phenotype. Differentiation events are transitions from one compartment to the next. Cells may also die or divide. We consider three different types of division events: (i) where both daughter cells inherit the mother’s phenotype (self-renewal), (ii) where only one of the daughters changes phenotype (asymmetric division), and (iii) where both daughters change phenotype (symmetric division). The self-renewal probability in each compartment determines whether the progeny of a single cell, moving through the sequence of compartments, is finite or grows without bound. We analyse the progeny stochastic dynamics with probability generating functions. In the case of self-renewal, by following one of the daughters after any division event, we may construct lifelines containing only one cell at any time. We analyse the number of divisions along such lines, and the compartment where lines terminate with a death event. Analysis and numerical simulations are applied to a five-compartment model of the gradual differentiation of hematopoietic stem cells and to a model of thymocyte development: from pre-double positive to single positive (SP) cells with a bifurcation to either SP4 or SP8 in the last compartment of the sequence.

Vaccines have historically played a pivotal role in controlling epidemics. Effective vaccines for viruses causing significant human disease, e.g., Ebola, Lassa fever, or Crimean Congo hemorrhagic fever virus, would be invaluable to public health strategies and counter-measure development missions. Here, we propose coverage metrics to quantify vaccine-induced CD8+ T cell-mediated immune protection, as well as metrics to characterize immuno-dominant epitopes, in light of human genetic heterogeneity and viral evolution. Proof-of-principle of our approach and methods are demonstrated for Ebola virus, SARS-CoV-2, and Burkholderia pseudomallei (vaccine) proteins.

Abstract Diversity of the naive T cell repertoire is maintained by competition for stimuli provided by self-peptides bound to major histocompatibility complexes (self-pMHCs). We extend an existing bi-variate competition model to a multi-variate model of the dynamics of multiple T cell clonotypes which share stimuli. In order to understand the late-time behaviour of the system, we analyse: (i) the dynamics until the extinction of the first clonotype, (ii) the time to the first extinction event, (iii) the probability of extinction of each clonotype, and (iv) the size of the surviving clonotypes when the first extinction event takes place. We also find the probability distribution of the number of cell divisions per clonotype before its extinction. The mean size of a new clonotype at quasi-steady state is an increasing function of the stimulus available to it, and a decreasing function of the fraction of stimuli it shares with other clonotypes. Thus, the probability of, and time to, extinction of a new clonotype entering the pool of T cell clonotypes is determined by the extent of competition for stimuli it experiences and by its initial number of cells.

Abstract NK‐cell reactivity against cancer is conceivably suppressed in the tumor microenvironment by the interaction of the inhibitory receptor NKG2A with the non‐classical MHC‐I molecules HLA‐E in humans or Qa‐1b in mice. We found that intratumoral delivery of NK cells attains significant therapeutic effects only if co‐injected with anti‐NKG2A and anti‐Qa‐1b blocking monoclonal antibodies against solid mouse tumor models. Such therapeutic activity was contingent on endogenous CD8 T cells and type‐1 conventional dendritic cells (cDC1). Moreover, the anti‐tumor effects were enhanced upon combination with systemic anti‐PD‐1 mAb treatment and achieved partial abscopal efficacy against distant non‐injected tumors. In xenografted mice bearing HLA‐E‐expressing human cancer cells, intratumoral co‐injection of activated allogeneic human NK cells and clinical‐grade anti‐NKG2A mAb (monalizumab) synergistically achieved therapeutic effects. In conclusion, these studies provide evidence for the clinical potential of intratumoral NK cell‐based immunotherapies that exert their anti‐tumor efficacy as a result of eliciting endogenous T‐cell responses.

The “One Health” approach provides a comprehensive framework for understanding antimicrobial resistance. This perspective is of particular importance in the study of Pseudomonas aeruginosa, as it is not only a pathogen that affects humans but also persists in environmental reservoirs. To assess evolutionary selection for niche-specific traits, a genomic comparison of 749 P. aeruginosa strains from three environments (clinical, aquatic, and soil) was performed. The results showed that the environment does indeed exert selective pressure on specific traits. The high percentage of persistent genome, the lack of correlation between phylogeny and origin of the isolate, and the high intrinsic resistance indicate that the species has a high potential for pathogenicity and resistance, regardless of the reservoir. The flexible genome showed an enrichment of metal resistance genes, which could act as a co-selection of antibiotic resistance genes. In the plasmids, resistance genes were found in multigenic clusters, with the presence of a mobile integron being prominent. This integron was identified in several pathogenic strains belonging to distantly related taxa with a worldwide distribution, showing the risk of rapid evolution of resistance. These results provide a more complete understanding of the evolution of P. aeruginosa, which could help develop new prevention strategies.

SARS-CoV-2 still presents a global threat to human health due to the continued emergence of new strains and waning immunity among vaccinated populations. Therefore, it is still relevant to investigate potential therapeutics, such as therapeutic interfering particles (TIPs). Mathematical and computational modeling are valuable tools to study viral infection dynamics for predictive analysis. Here, we expand on the previous work on SARS-CoV-2 intra-cellular replication dynamics to include defective interfering particles (DIPs) as potential therapeutic agents. We formulate a deterministic model that describes the replication of wild-type (WT) SARS-CoV-2 virus in the presence of DIPs. Sensitivity analysis of parameters to several model outputs is employed to inform us on those parameters to be carefully calibrated from experimental data. We then study the effects of co-infection on WT replication and how DIP dose perturbs the release of WT viral particles. Furthermore, we provide a stochastic formulation of the model that is compared to the deterministic one. These models could be further developed into population-level models or used to guide the development and dose of TIPs.

ABSTRACT Prokaryotic species are composed of multiple clonal lineages coexisting in the same habitat. In recent years, understanding the maintenance of this high intraspecific genetic diversity in asexual microorganisms has been a challenge for microbial ecology. In this study, we investigated the potential ecological role of this genomic heterogeneity in the marine HIMB59 clade. The metagenomic recruitment revealed the presence of three main genomospecies with different ecological distribution patterns within the two defined families. Genomic analysis revealed the presence of a flexible genomic island conserved throughout the order at the same position in the genome and related to phosphate (P) metabolism. The different versions of this island showed a distribution correlated with the concentration of P in the environment but not with the phylogeny at the genomospecies level. At high P availability (>0.5 µM), HIMB59 cells had only the high-affinity phosphate transporter operon (PstSCAB and PhoU). Under conditions of higher P scarcity (

ABSTRACTBO-112 is a poly I:C-based viral mimetic that exerts anti-tumor efficacy when intratumorally delivered in mouse models. Intratumoral BO-112 synergizes in mice with systemic anti-PD-1 mAbs and this combination has attained efficacy in PD1-refractory melanoma patients. We sought to evaluate the anti-tumor efficacy of BO-112 pre-surgically applied in neoadjuvant settings to mouse models. We have observed that repeated intratumoral injections of BO-112 prior to surgical excision of the primary tumor significantly reduced tumor metastasis from orthotopically implanted 4T1-derived tumors and subcutaneous MC38-derived tumors in mice. Such effects were enhanced when combined with systemic anti-PD-1 mAb. The anti-tumor efficacy of this neoadjuvant immunotherapy approach depended on the presence of antigen-specific effector CD8 T cells and cDC1 antigen-presenting cells. Since BO-112 has been successful in phase-two clinical trials for metastatic melanoma, these results provide a strong rationale for translating this pre-surgical strategy into clinical settings, especially in combination with standard-of-care checkpoint inhibitors.

Abstract Lymphocyte populations, stimulated in vitro or in vivo, grow as cells divide. Stochastic models are appropriate because some cells undergo multiple rounds of division, some die, and others of the same type in the same conditions do not divide at all. If individual cells behave independently, then each cell can be imagined as sampling from a probability density of times to division and death. The exponential density is the most mathematically and computationally convenient choice. It has the advantage of satisfying the memoryless property, consistent with a Markov process, but it overestimates the probability of short division times. With the aim of preserving the advantages of a Markovian framework while improving the representation of experimentally-observed division times, we consider a multi-stage model of cellular division and death. We use Erlang-distributed (or, more generally, phase-type distributed) times to division, and exponentially distributed times to death. We classify cells into generations, using the rule that the daughters of cells in generation n are in generation $$n+1$$ n + 1 . In some circumstances, our representation is equivalent to established models of lymphocyte dynamics. We find the growth rate of the cell population by calculating the proportions of cells by stage and generation. The exponent describing the late-time cell population growth, and the criterion for extinction of the population, differs from what would be expected if N steps with rate $$\lambda$$ λ were equivalent to a single step of rate $$\lambda /N$$ λ / N . We link with a published experimental dataset, where cell counts were reported after T cells were transferred to lymphopenic mice, using Approximate Bayesian Computation. In the comparison, the death rate is assumed to be proportional to the generation and the Erlang time to division for generation 0 is allowed to differ from that of subsequent generations. The multi-stage representation is preferred to a simple exponential in posterior distributions, and the mean time to first division is estimated to be longer than the mean time to subsequent divisions.

Background: Pseudomonas aeruginosa shows resistance to several antibiotics and often develops such resistance during patient treatment. Objective: Develop an in vitro model, using clinical isolates of P. aeruginosa, to compare the ability of the imipenem and imipenem/relebactam to generate resistant mutants to imipenem and to other antibiotics. Perform a genotypic analysis to detect how the selective pressure changes their genomes. Methods: The antibiotics resistance was studied by microdilution assays and e-test, and the genotypic study was performed by NGS. Results: The isolates acquired resistance to imipenem in an average of 6 days, and to imipenem/relebactam in 12 days (p value = 0.004). After 30 days of exposure, 75% of the isolates reached a MIC > 64 mg/L for imipenem and 37.5% for imipenem/relebactam (p value = 0.077). The 37.5% and the 12.5% imipenem/relebactam mutants developed resistance to piperacillin/tazobactam and ceftazidime, respectively, while the 87.5% and 37.5% of the imipenem mutants showed resistance to these drugs (p value = 0.003, p value = 0.015). The main biological processes altered by the SNPs were the glycosylation pathway, transcriptional regulation, histidine kinase response, porins, and efflux pumps. Discussion: The addition of relebactam delays the generation of resistance to imipenem and limits the cross-resistance to other beta-lactams. The clinical relevance of this phenomenon, which has the limitation that it has been performed in vitro, should be evaluated by stewardship programs in clinical practice, as it could be useful in controlling multi-drug resistance in P. aeruginosa.

Bacteriophages selectively infect and kill their target bacterial host, being a promising approach to controlling zoonotic bacteria in poultry production. To ensure confidence in its use, fundamental questions of safety and toxicity monitoring of phage therapy should be raised. Due to its high specificity, a minimal impact on the gut ecology is expected; however, more in-depth research into key parameters that influence the success of phage interventions has been needed to reach a consensus on the impact of bacteriophage therapy in the gut. In this context, this study aimed to investigate the interaction of phages with animals; more specifically, we compared the caecum microbiome and metabolome after a Salmonella phage challenge in Salmonella-free broilers, evaluating the role of the phage administration route. To this end, we employed 45 caecum content samples from a previous study where Salmonella phages were administered via drinking water or feed for 24 h from 4, 5 to 6-weeks-old broilers. High-throughput 16S rRNA gene sequencing showed a high level of similarity (beta diversity) but revealed a significant change in alpha diversity between broilers with Salmonella-phage administered in the drinking water and control. Our results showed that the phages affected only a few genera of the microbiota’s structure, regardless of the administration route. Among these, we found a significant increase in Streptococcus and Sellimonas in the drinking water and Lactobacillus, Anaeroplasma and Clostridia_vadinBB60_group in the feed. Nevertheless, the LC-HRMS-based metabolomics analyses revealed that despite few genera were significantly affected, a substantial number of metabolites, especially in the phage administered in the drinking water were significantly altered (64 and 14 in the drinking water and feed groups, respectively). Overall, our study shows that preventive therapy with bacteriophages minimally alters the caecal microbiota but significantly impacts their metabolites, regardless of the route of administration.

Three-dimensional food printing is one of the modern techniques for food customization. The difficulty of this technique lies in the formulation of new matrices. These new formulations must have good extrusion characteristics and, at the same time, maintain the structure once printed. These qualities are related to textural and rheological properties. Printability studies are those whose objective is to know the above properties. Some authors have correlated printability with rheological and physicochemical parameters. The aim of this study was to characterize three gels to test prediction models and to determine the most important rheological and textural parameters (G′, G″, Tanδ, maxF, average) in printability. The formulations studied were bovine gelatin (4%) with kappa-carrageenan (0.5%) (Gb + K), porcine gelatin (5%) plus iota-carrageenan (2%) (Gp + I), and methylcellulose (4%) (MC). The samples were characterized by an oscillatory test for the rheological properties and an extrusion test for the textural properties. In addition, the density was obtained to apply the predictive models and correlate the rheological and textural parameters to determine their influence. Gp + I and Gb + K showed higher values of maximum force in the extrusion test than MC, but MC had less deviation in the mean force during the test. All the samples showed a predominantly elastic behavior and damping factor (Tanδ) between 0.14 (Gb + K) and 0.37 (MC). It was observed that the tangent of the phase angle (Tanδ) had a large positive influence on the maximum and average force studied in the extrusion tests. The sample results did not match 100% with the predictions made from the models. It was possible to print samples that were higher in height without obtaining deformations over time of more than 5%. Further work is needed to optimize models and parameters for more accurate prediction.

Concern about food waste has become a major global concern. The waste generated by the agri-food industry poses an environmental challenge. However, the development of 3D printing technology offers an opportunity to address this problem. By incorporating food waste into inks, it can create personalized food tailored to individual needs. The aim of this study is the valorization of orange by-products (OBP) in 3D printed gels to obtain a final product in the form of a fiber-enriched snack. Gelatin gels were printed with different concentrations of apricot pulp (30, 50, and 70%) and OBP was added. These gels were subjected to a freeze-drying process. The rheology of the gels before and after printing, the printing precision, and the post-treatment of the freeze-dried product, including color, shear force, and the presence of bioactive compounds, were evaluated. The addition of OBP resulted in an increase in the elasticity (997–1242u) of the samples and improved the printability of them. However, an increase in the hardness (173–184u) was observed in the freeze-dried samples. The use of OBP not only improves the printability of the gels but also enables obtaining fiber-enriched snacks, which could contribute to the reduction in food waste and the promotion of healthy and sustainable food.

Abstract Endosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.

Tuberculosis (TB) remains a major health problem worldwide, and the emergence of multi-resistant strains to first-line drugs has become the biggest obstacle to its treatment. On the other hand, the incidence of non-tuberculous mycobacteria (NTM) in humans has increased remarkably in recent years. The search for new and better treatments against mycobacterial infections is a constant at the global level. Hence, in this study, we propose to investigate the antimycobacterial effect of the extracts and major compounds of Hedeoma drummondii against clinical isolates of Mycobacterium tuberculosis and non-tuberculous mycobacteria: M. abscessus, M. fortuitum, M. intracellulare, and M. gordonae. To determine the antimycobacterial activity, a microdilution assay was used to establish the minimum inhibitory concentration (MIC) of the different strains of Mycobacterium. The methanolic extract presented the best activity against M. tuberculosis, inhibiting ten of the twelve strains analyzed at a concentration < 2500 µg/mL; meanwhile, the hexanic extract presented the best activity against non-tuberculous mycobacteria (NTM) by inhibiting eight of the ten strains studied at ≤625 µg/mL. Moreover, there is a strong positive correlation between the antimycobacterial activity of pulegone and the hexanic extract against non-tuberculous strains, so this compound could serve as a predictability marker against these types of microorganisms.

The process of 3D food printing is a rapidly growing field that involves the use of specialized 3D printers to produce food items with complex shapes and textures. This technology allows the creation of customized, nutritionally balanced meals on demand. The objective of this study was to evaluate the effect of apricot pulp content on printability. Additionally, the degradation of bioactive compounds of gels before and after printing was evaluated to analyze the effect of the process. For this proposal, physicochemical properties, extrudability, rheology, image analysis, Texture Profile Analysis (TPA), and bioactive compounds content were evaluated. The rheological parameters lead to higher mechanical strength and, thus, a decrease in elastic behavior before and after 3D printing as the pulp content increases. An increase in strength was observed when the pulp content increased; thus, sample gels with 70% apricot pulp were more rigid and presented better buildability (were more stable in their dimensions). On the other hand, a significant (p < 0.05) degradation of total carotenoid content after printing was observed in all samples. From the results obtained, it can be said that the gel with 70% apricot pulp food ink was the best sample in terms of printability and stability.

ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen and a major cause of nosocomial infections. The global spread of carbapenem-resistant strains is growing rapidly and has become a major public health challenge. Imipenem-relebactam (I/R) is a novel carbapenem-beta-lactamase inhibitor combination that can overcome carbapenem resistance. In this study, we aimed to understand the mechanism underlying resistance to imipenem and imipenem-relebactam. For this purpose, we performed a genomic comparison of 40 new clinical P. aeruginosa strains with different antibiotic sensitivity patterns as well as the presence/absence of carbapenemases. Results indicated the presence of a reduced flexible genome (15% total) mostly represented by phages and defense mechanisms against them, showing an important role in evolution and pathogenicity. We found a high diversity of antibiotic resistance genes grouped in small clusters mobilized via integrative and conjugative elements and facilitated by the high homologous recombination detected. Ortholog genes were found in several pathogenic strains from distantly related taxa in different mobile elements with a global distribution. The microdiversity found in those strains without carbapenemases did not reveal a clear pattern that could be associated with carbapenem resistance, suggesting multiple mechanisms of resistance in the core genome. Our results provide new insight into the dynamics and high genomic plasticity by which clinical strains of P. aeruginosa acquire resistance. This knowledge can be applied to other multidrug-resistant microbes to create predictive frameworks for assessing common molecular mechanisms of antibiotic resistance and integrated into new strategies for their prevention. IMPORTANCE The growing emergence and spread of carbapenem-resistant pathogens worldwide exacerbate the clinical challenge of treating these infections. Given the importance of carbapenems for the treatment of infections caused by Pseudomonas aeruginosa, this study aimed to investigate the underlying genomic properties of the clinical isolates that exhibited resistance to imipenem and imipenem-relebactam. This information will enhance our ability to forecast traits of resistant strains and design reliable treatments against this important threat. Our results provide new insight into the dynamics and high genomic plasticity by which clinical strains of P. aeruginosa acquire resistance as well as offers a methodology that can be applied to many other opportunistic pathogens with broad antibiotic resistance.

We present a stochastic mathematical model of the intracellular infection dynamics of Bacillus anthracis in macrophages. Following inhalation of B. anthracis spores, these are ingested by alveolar phagocytes. Ingested spores then begin to germinate and divide intracellularly. This can lead to the eventual death of the host cell and the extracellular release of bacterial progeny. Some macrophages successfully eliminate the intracellular bacteria and will recover. Here, a stochastic birth-and-death process with catastrophe is proposed, which includes the mechanism of spore germination and maturation of B. anthracis. The resulting model is used to explore the potential for heterogeneity in the spore germination rate, with the consideration of two extreme cases for the rate distribution: continuous Gaussian and discrete Bernoulli. We make use of approximate Bayesian computation to calibrate our model using experimental measurements from in vitro infection of murine peritoneal macrophages with spores of the Sterne 34F2 strain of B. anthracis. The calibrated stochastic model allows us to compute the probability of rupture, mean time to rupture, and rupture size distribution, of a macrophage that has been infected with one spore. We also obtain the mean spore and bacterial loads over time for a population of cells, each assumed to be initially infected with a single spore. Our results support the existence of significant heterogeneity in the germination rate, with a subset of spores expected to germinate much later than the majority. Furthermore, in agreement with experimental evidence, our results suggest that most of the spores taken up by macrophages are likely to be eliminated by the host cell, but a few germinated spores may survive phagocytosis and lead to the death of the infected cell. Finally, we discuss how this stochastic modelling approach, together with dose-response data, allows us to quantify and predict individual infection risk following exposure.

Abstract Live 17D is widely used as a prophylactic vaccine strain for yellow fever virus that induces potent neutralizing humoral and cellular immunity against the wild‐type pathogen. 17D replicates and kills mouse and human tumor cell lines but not non‐transformed human cells. Intratumoral injections with viable 17D markedly delay transplanted tumor progression in a CD8 T‐cell‐dependent manner. In mice bearing bilateral tumors in which only one is intratumorally injected, contralateral therapeutic effects are observed consistent with more prominent CD8 T‐cell infiltrates and a treatment‐related reduction of Tregs. Additive efficacy effects were observed upon co‐treatment with intratumoral 17D and systemic anti‐CD137 and anti‐PD‐1 immunostimulatory monoclonal antibodies. Importantly, when mice were preimmunized with 17D, intratumoral 17D treatment achieved better local and distant antitumor immunity. Such beneficial effects of prevaccination are in part explained by the potentiation of CD4 and CD8 T‐cell infiltration in the treated tumor. The repurposed use of a GMP‐grade vaccine to be given via the intratumoral route in prevaccinated patients constitutes a clinically feasible and safe immunotherapy approach.

Three-dimensional (3D) printing is an excellent technology for creating food products of any shape and dimension, with desired flavors and nutritional compositions. This study aimed to evaluate the effect of apricot pulp content on the stability and printability of bovine gelatin gels. °Brix, pH, Texture Profile Analysis (TPA), and image analysis after 3D printing were measured. Bovine gelatin gels (5%) were formulated with different concentrations of apricot pulp (30%, 50%, and 70%), and cylinders of 3 cm in diameter and 1 cm in height were printed. An increase in firmness of the printed gel was observed with the rise in the pulp concentration. Concerning image analysis, it was observed that as the concentration of apricot pulp (AP) in the samples increased, there was minor deformation of the height dimension. There were no significant differences (p > 0.05) in pieces for the cylinder area, and all presented a 12% area deformation. From the results obtained, it can be said that the 70% apricot pulp sample has the best texture profile and is the sample with the slightest deformation.

Cytokines elicit pleiotropic and non-redundant activities despite strong overlap in their usage of receptors, JAKs and STATs molecules. We use IL-6 and IL-27 to ask how two cytokines activating the same signaling pathway have different biological roles. We found that IL-27 induces more sustained STAT1 phosphorylation than IL-6, with the two cytokines inducing comparable levels of STAT3 phosphorylation. Mathematical and statistical modeling of IL-6 and IL-27 signaling identified STAT3 binding to GP130, and STAT1 binding to IL-27Rα, as the main dynamical processes contributing to sustained pSTAT1 levels by IL-27. Mutation of Tyr613 on IL-27Rα decreased IL-27-induced STAT1 phosphorylation by 80% but had limited effect on STAT3 phosphorgylation. Strong receptor/STAT coupling by IL-27 initiated a unique gene expression program, which required sustained STAT1 phosphorylation and IRF1 expression and was enriched in classical Interferon Stimulated Genes. Interestingly, the STAT/receptor coupling exhibited by IL-6/IL-27 was altered in patients with systemic lupus erythematosus (SLE). IL-6/IL-27 induced a more potent STAT1 activation in SLE patients than in healthy controls, which correlated with higher STAT1 expression in these patients. Partial inhibition of JAK activation by sub-saturating doses of Tofacitinib specifically lowered the levels of STAT1 activation by IL-6. Our data show that receptor and STATs concentrations critically contribute to shape cytokine responses and generate functional pleiotropy in health and disease.

BackgroundSARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient’s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group.ResultsStatistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms.ConclusionOur study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.

Mathematical modelling has successfully been used to provide quantitative descriptions of many viral infections, but for the Ebola virus, which requires biosafety level 4 facilities for experimentation, modelling can play a crucial role. Ebola virus modelling efforts have primarily focused on in vivo virus kinetics, e.g., in animal models, to aid the development of antivirals and vaccines. But, thus far, these studies have not yielded a detailed specification of the infection cycle, which could provide a foundational description of the virus kinetics and thus a deeper understanding of their clinical manifestation. Here, we obtain a diverse experimental data set of the Ebola virus infection in vitro, and then make use of Bayesian inference methods to fully identify parameters in a mathematical model of the infection. Our results provide insights into the distribution of time an infected cell spends in the eclipse phase (the period between infection and the start of virus production), as well as the rate at which infectious virions lose infectivity. We suggest how these results can be used in future models to describe co-infection with defective interfering particles, which are an emerging alternative therapeutic.

Summary: IL-7 receptor signaling is essential for the generation and maintenance of conventional T cells. Immunosuppressive Foxp3+ Treg cells, however, express uniquely low amounts of the IL-7-proprietary IL-7Rα so that they are impaired in IL-7 signaling. Because Treg cells depend on IL-2, the loss of IL-7Rα has been considered irrelevant for Treg cells. In contrast, here, we report that IL-7Rα downregulation is necessary to maximize IL-2R signaling. Although IL-7Rα overexpression promoted IL-7 signaling, unexpectedly, IL-2 signaling was suppressed in the same cells. Mechanistically, we found that γc, which is a receptor subunit shared by IL-7R and IL-2R, directly binds and pre-associates with IL-7Rα, thus limiting its availability for IL-2R binding. Consequently, overexpression of signaling-deficient, tailless IL-7Rα proteins inhibited IL-2R signaling, demonstrating that IL-7Rα sequesters γc and suppresses IL-2R signaling by extracellular interactions. Collectively, these results reveal a previously unappreciated regulatory mechanism of IL-2 receptor signaling that is governed by IL-7Rα abundance.

We study the pathogenesis of Francisella tularensis infection with an experimental mouse model, agent-based computation and mathematical analysis. Following inhalational exposure to Francisella tularensis SCHU S4, a small initial number of bacteria enter lung host cells and proliferate inside them, eventually destroying the host cell and releasing numerous copies that infect other cells. Our analysis of disease progression is based on a stochastic model of a population of infectious agents inside one host cell, extending the birth-and-death process by the occurrence of catastrophes: cell rupture events that affect all bacteria in a cell simultaneously. Closed expressions are obtained for the survival function of an infected cell, the number of bacteria released as a function of time after infection, and the total bacterial load. We compare our mathematical analysis with the results of agent-based computation and, making use of approximate Bayesian statistical inference, with experimental measurements carried out after murine aerosol infection with the virulent SCHU S4 strain of the bacterium Francisella tularensis, that infects alveolar macrophages. The posterior distribution of the rate of replication of intracellular bacteria is consistent with the estimate that the time between rounds of bacterial division is less than 6 hours in vivo.

As the ongoing outbreak in the Democratic Republic of Congo illustrates, Ebola virus disease continues to pose a significant risk to humankind and this necessitates the continued development of therapeutic options. One option that warrants evaluation is that of defective genomes; these can potentially parasitize resources from the wild-type virus and may even be packaged for repeated co-infection cycles. Deletion and copy-back defective genomes have been identified and reported in the literature. As a crude, mixed preparation these were found to have limiting effects on cytopathology. Here we have used synthetic virology to clone and manufacture two deletion defective genomes. These genomes were tested with Ebola virus using in vitro cell culture and shown to inhibit viral replication; however, and against expectations, the defective genomes were not released in biologically significant numbers. We propose that EBOV might have yet unknown mechanisms to prevent parasitisation by defective interfering particles beyond the known mechanism that prevents sequential infection of the same cell. Understanding this mechanism would be necessary in any development of a defective interfering particle-based therapy.

Type I interferons (IFNs) are cytokines with both antiviral properties and protective roles in innate immune responses to viral infection. They induce an antiviral cellular state and link innate and adaptive immune responses. Yet, viruses have evolved different strategies to inhibit such host responses. One of them is the existence of viral proteins which subvert type I IFN responses to allow quick and successful viral replication, thus, sustaining the infection within a host. We propose mathematical models to characterise the intra-cellular mechanisms involved in viral protein antagonism of type I IFN responses, and compare three different molecular inhibition strategies. We study the Ebola viral protein, VP35, with this mathematical approach. Approximate Bayesian computation sequential Monte Carlo, together with experimental data and the mathematical models proposed, are used to perform model calibration, as well as model selection of the different hypotheses considered. Finally, we assess if model parameters are identifiable and discuss how such identifiability can be improved with new experimental data.

If viral strains are sufficiently similar in their immunodominant epitopes, then populations of cross-reactive T cells may be boosted by exposure to one strain and provide protection against infection by another at a later date. This type of pre-existing immunity may be important in the adaptive immune response to influenza and to coronaviruses. Patterns of recognition of epitopes by T cell clonotypes (a set of cells sharing the same T cell receptor) are represented as edges on a bipartite network. We describe different methods of constructing bipartite networks that exhibit cross-reactivity, and the dynamics of the T cell repertoire in conditions of homeostasis, infection and re-infection. Cross-reactivity may arise simply by chance, or because immunodominant epitopes of different strains are structurally similar. We introduce a circular space of epitopes, so that T cell cross-reactivity is a quantitative measure of the overlap between clonotypes that recognize similar (that is, close in epitope space) epitopes.

El ocio es un derecho. Todas las personas, sea cual sea su condición, tienen derecho a disfrutar de experiencias de ocio satisfactorias. Sin embargo, cuando hablamos de discapacidad nos encontramos con demasiada frecuencia con programas de ocio organizados según modelos estandarizados orientados a la mera ocupación del tiempo libre, y que no tienen en cuenta la diversidad y la voluntad de los usuarios. El presente artículo estudia las necesidades de las personas autistas para su inclusión plena en los museos y muestra diferentes estudios de caso, para favorecer su presencia normalizada en la sociedad y convertir dichos productos culturales en oferta permanente para los propios museos.

Este trabajo tiene como objetivo agrupar las distintas ocupaciones laborales en diversas categorías en función de la semejanza en los requisitos que presenta cada ocupación en cuanto a competencias lingüísticas. Para ello, se utilizan los datos para las ocupaciones definidas en la O’Net-SOC-2010 para EE.UU. en 2015. Se consideran tres clasificaciones, en función del nivel de desagregación que presentan los datos de O’Net. El análisis se efectúa mediante redes neuronales artificiales, en concreto, los mapas autoorganizativos de Kohonen (SOM). Se pretende así analizar si el nivel de desagregación de las ocupaciones influye en la clasificación de dichas ocupaciones en función del nivel requerido de competencias lingüísticas. La aportación que se realiza es novedosa, ya que, hasta donde conocemos, no existe ningún trabajo previo que utilice los SOM para la clasificación de las ocupaciones laborales considerando las competencias lingüísticas requeridas. Dicho análisis puede ayudar a los investigadores sociales en el estudio del impacto e influencia que presentan los componentes lingüís- ticos del trabajo en la productividad laboral, la empleabilidad de los trabajadores, los resultados empresariales y la generación de ventajas competitivas basadas en el lenguaje, entre otras.

Poly I:C is a powerful immune adjuvant as a result of its agonist activities on TLR-3, MDA5 and RIG-I. BO-112 is a nanoplexed formulation of Poly I:C complexed with polyethylenimine that causes tumor cell apoptosis showing immunogenic cell death features and which upon intratumoral release results in more prominent tumor infiltration by T lymphocytes. Intratumoral treatment with BO-112 of subcutaneous tumors derived from MC38, 4 T1 and B16-F10 leads to remarkable local disease control dependent on type-1 interferon and gamma-interferon. Some degree of control of non-injected tumor lesions following BO-112 intratumoral treatment was found in mice bearing bilateral B16-OVA melanomas, an activity which was enhanced with co-treatment with systemic anti-CD137 and anti-PD-L1 mAbs. More abundant CD8+ T lymphocytes were found in B16-OVA tumor-draining lymph nodes and in the tumor microenvironment following intratumoral BO-112 treatment, with enhanced numbers of tumor antigen-specific cytotoxic T lymphocytes. Genome-wide transcriptome analyses of injected tumor lesions were consistent with a marked upregulation of the type-I interferon pathway. Inspired by these data, intratumorally delivered BO-112 is being tested in cancer patients (NCT02828098).

The homeostasis of T cell populations depends on migration, division and death of individual cells (1). T cells migrate between spatial compartments (spleen, lymph nodes, lung, liver, etc.), where they may divide or differentiate, and eventually die (2). The kinetics of recirculation influences the speed at which local infections are detected and controlled (3). New experimental techniques have been developed to measure the lifespan of cells, and their migration dynamics; for example, fluorescence-activated cell sorting (4), in vitro time-lapse microscopy (5), or in vivo stable isotope labeling (e.g., deuterium) (6). When combined with mathematical and computational models, they allow estimation of rates of migration, division, differentiation and death (6, 7). In this work, we develop a stochastic model of a single cell migrating between spatial compartments, dividing and eventually dying. We calculate the number of division events during a T cell's journey, its lifespan, the probability of dying in each compartment and the number of progeny cells. A fast-migration approximation allows us to compute these quantities when migration rates are larger than division and death rates. Making use of published rates: (i) we analyse how perturbations in a given spatial compartment impact the dynamics of a T cell, (ii) we study the accuracy of the fast-migration approximation, and (iii) we quantify the role played by direct migration (not via the blood) between some compartments.

Despite critical thinking supporting a deeper understanding of the scientific process, university activities prioritize lower cognitive processes, such as remembering skills. Also, it is unclear whether gender biases in interest toward science exist in university science degrees. These hinder students from achieving their goals effectively since students' test scores and motivation improve with project-based learning. The main goal of this study is to examine the influence of active methodology based on research project-based learning (RPBL) on students' overall perception and its variation across gender groups in relation to the acquisition of higher-order cognitive skills. The RPBL activity will consist of a straightforward microbial ecology project in which the students will use conventional and affordable lab equipment. The project will address all higher-order thinking skills levels included in Bloom's taxonomy. We evaluated students' perception of their learning outcomes on lab and cognitive skills, including the effect of gender, using two online surveys we passed before and after the RPBL activity. The results displayed that the students' opinion regarding the project was decidedly favorable. Most of the students view the potential effort required for these activities positively, as it pertains to the subject matter and enhances their learning. However, the gender differences that were observed prior to the project's implementation disappeared once the activity was carried out. Female students lacked confidence in their statistical skills while they had high confidence in their laboratory skills compared to male students. After attending our RPBL activity, female students gained confidence in statistics, and male students gained confidence in laboratory skills. This project reveals that a straightforward and affordable RPBL activity, which would not suppose a substantial additional workload for university lecturers, holds the potential to serve as a valuable tool to eliminate gender segregation, enhancing students' academic self-concept, and improving their prospects for success. Additionally, it emphasizes higher cognitive skills, particularly the critical thinking skills that are essential within the university environment.

Cellular receptors on the cell membrane can bind ligand molecules in the extra-cellular medium to form ligand-bound monomers. These interactions ultimately determine the fate of a cell through the resulting intra-cellular signalling cascades. Often, several receptor types can bind a shared ligand leading to the formation of different monomeric complexes, and in turn to competition for the common ligand. Here, we describe competition between two receptors which bind a common ligand in terms of a bi-variate stochastic process. The stochastic description is important to account for fluctuations in the number of molecules. Our interest is in computing two summary statistics—the steady-state distribution of the number of bound monomers and the time to reach a threshold number of monomers of a given kind. The matrix-analytic approach developed in this manuscript is exact, but becomes impractical as the number of molecules in the system increases. Thus, we present novel approximations which can work under low-to-moderate competition scenarios. Our results apply to systems with a larger number of population species (i.e., receptors) competing for a common resource (i.e., ligands), and to competition systems outside the area of molecular dynamics, such as Mathematical Ecology.

We present a multi-scale model of the within-phagocyte, within-host and population-level infection dynamics of Francisella tularensis, which extends the mechanistic one proposed by Wood et al. (2014). Our multi-scale model incorporates key aspects of the interaction between host phagocytes and extracellular bacteria, accounts for inter-phagocyte variability in the number of bacteria released upon phagocyte rupture, and allows one to compute the probability of response, and mean time until response, of an infected individual as a function of the initial infection dose. A Bayesian approach is applied to parameterize both the within-phagocyte and within-host models using infection data. Finally, we show how dose response probabilities at the individual level can be used to estimate the airborne propagation of Francisella tularensis in indoor settings (such as a microbiology laboratory) at the population level, by means of a deterministic zonal ventilation model.

Genetic differences contribute to variations in the immune response mounted by different individuals to a pathogen. Such differential response can influence the spread of infectious disease, indicating why such diseases impact some populations more than others. Here, we study the impact of population-level genetic heterogeneity on the epidemic spread of different strains of H1N1 influenza. For a population with known HLA class-I allele frequency and for a given H1N1 viral strain, we classify individuals into sub-populations according to their level of susceptibility to infection. Our core hypothesis is that the susceptibility of a given individual to a disease such as H1N1 influenza is inversely proportional to the number of high affinity viral epitopes the individual can present. This number can be extracted from the HLA genetic profile of the individual. We use ethnicity-specific HLA class-I allele frequency data, together with genome sequences of various H1N1 viral strains, to obtain susceptibility sub-populations for 61 ethnicities and 81 viral strains isolated in 2009, as well as 85 strains isolated in other years. We incorporate these data into a multi-compartment SIR model to analyse the epidemic dynamics for these (ethnicity, viral strain) epidemic pairs. Our results show that HLA allele profiles which lead to a large spread in individual susceptibility values can act as a protective barrier against the spread of influenza. We predict that populations skewed such that a small number of highly susceptible individuals coexist with a large number of less susceptible ones, should exhibit smaller outbreaks than populations with the same average susceptibility but distributed more uniformly across individuals. Our model tracks some well-known qualitative trends of influenza spread worldwide, suggesting that HLA genetic diversity plays a crucial role in determining the spreading potential of different influenza viral strains across populations.

CD69 is an early activation marker on the surface of T lymphocytes undergoing activation by cognate antigen. We observed intense expression of CD69 on tumor-infiltrating T-lymphocytes that reside in the hypoxic tumor microenvironment and hypothesized that CD69 could be, at least partially, under the control of the transcriptional hypoxia response. In line with this, human and mouse CD3-stimulated lymphocytes cultured under hypoxia (1% O2) showed increased expression of CD69 at the protein and mRNA level. Consistent with these findings, mouse T lymphocytes that had recently undergone hypoxia in vivo, as denoted by pimonidazole staining, were more frequently CD69+ in the tumor and bone marrow hypoxic tissue compartments. We found evidence for HIF-1α involvement both when using T-lymphocytes from inducible HIF-1α−/− mice and when observing tumor-infiltrating T-lymphocytes in mice whose T cells are HIF-1α−/−. Direct pro-transcriptional activity of HIF-1α on a newly identified hypoxia response element (HRE) found in the human CD69 locus was demonstrated by ChIP experiments. These results uncover a connection between the HIF-1α oxygen-sensing pathway and CD69 immunobiology.

La afectividad y la sexualidad constituyen un aspecto central en la psiquis humana. Sin embargo, en nuestros días se tiende a mostrar una imagen distorsionada de ambas al tener en consideración sólo algunos de sus elementos. Los jóvenes, que están frecuentemente inmersos en una realidad virtual, se encuentran expuestos a dicha imagen, lo cual se opone a que ellos puedan reconocer una afectividad y sexualidad vinculadas íntimamente al quehacer del ser humano. Una sexualidad desvinculada del amor, la razón y los sentimientos conduce a una disociación de la persona. Por esto, es de suma importancia la integración de la esfera racional con la afectiva, pues de lo contrario se corrompe el sentido más verdadero de la sexualidad. El objetivo de esta revisión es mostrar los principales aspectos relacionados con la problemática de la sexualidad en adolescentes, con especial atención en la sexualidad de las jóvenes chilenas. En ellas se observa un inicio cada vez más temprano de la actividad sexual, lo cual origina un aumento del embarazo adolescente, de la deserción escolar y de las enfermedades de transmisión sexual. Considerando las características propias de la adolescencia en cuanto a la toma de decisiones, se analiza el efecto del Programa Teen STAR en relación a los cambios en la conducta sexual y disminución de embarazo en las adolescentes que han participado en dicho programa versus quienes no han participado. Además, se enfatiza la importancia de entregar una formación que incluya todas las áreas de la persona, no limitándose a la entrega de soluciones técnicas o normativas. También se plantea que mediante la educación en la sexualidad la persona por completo adquiriría una educación para el amor, en cuanto se educa para reconocer la verdad de la persona misma; se educa para el reconocimiento y el respeto de sí mismo y del otro. Es dicho reconocimiento lo que permite distinguir entre lo que es verdaderamente bueno de lo que es simplemente deseable