Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.

Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms.

Thermal Liquid Biopsy: A Promising Tool for the Differential Diagnosis of Pancreatic Cystic Lesions and Malignancy Detection.

Pancreatic cystic lesions (PCLs) are a heterogeneous group of lesions with increasing incidence, usually identified incidentally on imaging studies (multidetector computed tomography (MDCT), magnetic resonance imaging (MRI), or endoscopic ultrasound (EUS)) [...

Key factors influencing magnetic nanoparticle-based photothermal therapy: physicochemical properties, irradiation power, and particle concentration .

A collection of magnetic nanoparticles with average particle sizes in the range between 9 and 78 nm were prepared using several synthetic approaches that also provided different particle morphologies (spherical, octahedral and flowers). Some of these particles were also subsequently coated with different molecules in order to generate a set of materials that allowed us to evaluate the impact that the particle size, shape and coating had on the heating capacity of the nanoparticles when exposed to near infrared (NIR) laser light. Moreover, one of the prepared materials (octahedral particles of ∼32 nm coated with dextran) was used to perform an assay to study the possible use of this material in the frame of photothermal treatments to trigger cell death.

Echo chamber formation sharpened by priority users.

On social media platforms, priority users (e.g., verified profiles on X) are users whose posts are promoted by recommendation algorithms.

LLMs and generative agent-based models for complex systems research.

The advent of Large Language Models (LLMs) offers to transform research across natural and social sciences, offering new paradigms for understanding complex systems. In particular, Generative Agent-Based Models (GABMs), which integrate LLMs to simulate human behavior, have attracted increasing public attention due to their potential to model complex interactions in a wide range of artificial environments. This paper briefly reviews the disruptive role LLMs are playing in fields such as network science, evolutionary game theory, social dynamics, and epidemic modeling.

Inhibition of SARS-CoV-2 3CLpro by chemically modified tyrosinase from .

Antiviral compounds are crucial to controlling the SARS-CoV-2 pandemic. Approved drugs have been tested for their efficacy against COVID-19, and new pharmaceuticals are being developed as a complementary tool to vaccines. In this work, a cheap and fast purification method for natural tyrosinase from (AbTyr) fresh mushrooms was developed to evaluate the potential of this enzyme as a therapeutic protein the inhibition of SARS-CoV-2 3CLpro protease activity .

Novel Drug-like HsrA Inhibitors Exhibit Potent Narrow-Spectrum Antimicrobial Activities against .

infection constitutes a silent pandemic of global concern. In the last decades, the alarming increase in multidrug resistance evolved by this pathogen has led to a marked drop in the eradication rates of traditional therapies worldwide. By using a high-throughput screening strategy, in combination with in vitro DNA binding assays and antibacterial activity testing, we identified a battery of novel drug-like HsrA inhibitors with MIC values ranging from 0.

A bitopic agonist bound to the dopamine 3 receptor reveals a selectivity site.

Although aminergic GPCRs are the target for ~25% of approved drugs, developing subtype selective drugs is a major challenge due to the high sequence conservation at their orthosteric binding site. Bitopic ligands are covalently joined orthosteric and allosteric pharmacophores with the potential to boost receptor selectivity and improve current medications by reducing off-target side effects. However, the lack of structural information on their binding mode impedes rational design.

A statistical-physics approach for codon usage optimisation.

The concept of "codon optimisation" involves adjusting the coding sequence of a target protein to account for the inherent codon preferences of a host species and maximise protein expression in that species. However, there is still a lack of consensus on the most effective approach to achieve optimal results. Existing methods typically depend on heuristic combinations of different variables, leaving the user with the final choice of the sequence hit.

BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responses.

Although the Bacille-Calmette-Guérin (BCG) vaccine is used to prevent tuberculosis, it also offers protection against a diverse range of non-mycobacterial infections. However, the underlying protective mechanisms in humans are not yet fully understood. Here, we surveyed at single-cell resolution the gene expression and chromatin landscape of human bone marrow, aspirated before and 90 days after BCG vaccination or placebo.

From unbiased to maximal-entropy random walks on hypergraphs.

Random walks have been intensively studied on regular and complex networks, which are used to represent pairwise interactions. Nonetheless, recent works have demonstrated that many real-world processes are better captured by higher-order relationships, which are naturally represented by hypergraphs. Here we study random walks on hypergraphs.

ISR pathway contribution to tissue specificity of mitochondrial diseases.

Mitochondrial genetic defects caused by whole-body mutations typically affect different tissues in different ways. Elucidating the molecular determinants that cause certain cell types to be primarily affected has become a critical research target within the field. We propose a differential activation of the integrated stress response as a potential contributor to this tissue specificity.

Functional characterization of Fur from the strict anaerobe Clostridioides difficile provides insight into its redox-driven regulatory capacity.

Clostridioides (formerly Clostridium) difficile is a leading cause of infectious diarrhea associated with antibiotic therapy. The ability of this anaerobic pathogen to acquire enough iron to proliferate under iron limitation conditions imposed by the host largely determines its pathogenicity. However, since high intracellular iron catalyzes formation of deleterious reactive hydroxyl radicals, iron uptake is tightly regulated at the transcriptional level by the ferric uptake regulator Fur.

Isolation of Mitochondria for Mitochondrial Supercomplex Analysis from Small Tissue and Cell Culture Samples.

Over the last decades, the evidence accumulated about the existence of respiratory supercomplexes (SCs) has changed our understanding of the mitochondrial electron transport chain organization, giving rise to the proposal of the "plasticity model." This model postulates the coexistence of different proportions of SCs and complexes depending on the tissue or the cellular metabolic status. The dynamic nature of the assembly in SCs would allow cells to optimize the use of available fuels and the efficiency of electron transfer, minimizing reactive oxygen species generation and favoring the ability of cells to adapt to environmental changes.

Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers.

Epistasis among driver mutations is pervasive and explains relevant features of cancer, such as differential therapy response and convergence towards well-characterized molecular subtypes. Furthermore, a growing body of evidence suggests that tumor development could be hampered by the accumulation of slightly deleterious passenger mutations. In this work, we combined empirical epistasis networks, computer simulations, and mathematical models to explore how synergistic interactions among driver mutations affect cancer progression under the burden of slightly deleterious passengers.

Comparison of the function of two novel human dopamine D2 receptor variants identifies a likely mechanism for their pathogenicity.

Two recently discovered DRD2 mutations, c.634A > T, p.Ile212Phe and c.

Pyridoxal 5'-Phosphate Biosynthesis by Pyridox-(am)-ine 5'-Phosphate Oxidase: Species-Specific Features.

Enzymes reliant on pyridoxal 5'-phosphate (PLP), the metabolically active form of vitamin B, hold significant importance in both biology and medicine. They facilitate various biochemical reactions, particularly in amino acid and neurotransmitter metabolisms. Vitamin B is absorbed by organisms in its non-phosphorylated form and phosphorylated within cells via pyridoxal kinase (PLK) and pyridox-(am)-ine 5'-phosphate oxidase (PNPOx).

Model-based impact evaluation of new tuberculosis vaccines in aging populations under different modeling scenarios: the case of China.

Introduction: The slow descent in TB burden, the COVID-19 pandemic, along with the rise of multidrug-resistant strains of , seriously threaten TB control and the goals of the End TB strategy. To fight back, several vaccine candidates are under development, with some of them undergoing the phases 2B and 3 of the development pipeline. The impact of these vaccines on the general population needs to be addressed using disease-transmission models, and, in a country like China, which last year ranked third in number of cases worldwide, and where the population is aging at a fast pace, the impact of TB vaccination campaigns may depend heavily upon the age of targeted populations, the mechanistic descriptions of the TB vaccines and the coupling between TB dynamics and demographic evolution.

The utility of fetal heart rate deceleration's descending slope in searching for a non-National Institute of Child Health and Human Development parameter for the detection of fetal acidosis.

Objective: To identify new parameters predicting fetal acidemia.

Methods: A retrospective case-control study in a cohort of deliveries from a tertiary referral hospital-based cohort deliveries in Zaragoza, Spain between 2018 and 2021 was performed. To predict fetal acidemia, the NICHD categorizations and non-NICHD parameters were analyzed in the electronic fetal monitoring (EFM).

Emergence of innovations in networked populations with reputation-driven interactions.

In this work, we analyze how reputation-based interactions influence the emergence of innovations. To do so, we make use of a dynamic model that mimics the discovery process by which, at each time step, a pair of individuals meet and merge their knowledge to eventually result in a novel technology of higher value. The way in which these pairs are brought together is found to be crucial for achieving the highest technological level.

Routine results of an algorithm for managing the production of blood components.

Background And Objectives: The variability in the number of donations together with a growing demand for platelet concentrates and plasma-derived medicines make us seek solutions aimed at optimizing the processing of blood. Some mathematical models to improve efficiencies in blood banking have been published. The goal of this work is to validate and evaluate an algorithm's impact in the production of blood components in the Blood and Tissues Bank of Aragon (BTBA).

Understanding the role of neutral species by means of high-order interaction in the rock-paper-scissors dynamics.

The existence of neutral species carries profound ecological implications that warrant further investigation. In this paper, we study the impact of neutral species on biodiversity in a spatial tritrophic system of cyclic competition, in which the neutral species are identified as the fourth species that may affect the competition process of the other three species under the rock-paper-scissors (RPS) rule. Extensive simulations showed that neutral species can promote coexistence in a high mobility regime within the system.