Rli51 Attenuates Transcription of the Listeria Pathogenicity Island 1 Gene mpl and Functions as a Trans-Acting sRNA in Intracellular Bacteria.

Listeria pathogenicity island 1 (LIPI-1) is a genetic region containing a cluster of genes essential for virulence of the bacterial pathogen Listeria monocytogenes. Main virulence factors in LIPI-1 include long 5' untranslated regions (5'UTRs), among which is Rli51, a small RNA (sRNA) in the 5'UTR of the Zn-metalloprotease-coding mpl. So far, Rli51 function and molecular mechanisms have remained obscure. Here, we show that Rli51 exhibits a dual mechanism of regulation, functioning as a cis- and as a trans-acting sRNA. Under nutrient-rich conditions, rli51-mpl transcription is prematurely terminated, releasing a short 121-nucleotide-long sRNA. Rli51 is predicted to function as a transcription attenuator that can fold into either a terminator or a thermodynamically more stable antiterminator. We show that the sRNA Rli21/RliI binds to a single-stranded RNA loop in Rli51, which is essential to mediate premature transcription termination, suggesting that sRNA binding could stabilize the terminator fold. During intracellular infection, rli51 transcription is increased, which generates a higher abundance of the short Rli51 sRNA and allows for transcriptional read-through into mpl. Comparative intracellular bacterial transcriptomics in rli51-null mutants and the wild-type reference strain EGD-e suggests that Rli51 upregulates iron-scavenging proteins and downregulates virulence factors from LIPI-1. MS2 affinity purification confirmed that Rli51 binds transcripts of the heme-binding protein Lmo2186 and Lmo0937 in vivo. These results prove that Rli51 functions as a trans-acting sRNA in intracellular bacteria. Our research shows a growth condition-dependent mechanism of regulation for Rli51, preventing unintended mpl transcription in extracellular bacteria and regulating genes important for virulence in intracellular bacteria.

Interactions between Stress Levels and Hormonal Responses Related to Sports Performance in Pro Women's Basketball Team.

The testosterone to cortisol ratio (T:C ratio) is a measure of whether elite athletes are recovering from their training. This study described this hormone balance stress in elite women's basketball. (1) Objectives: to analyse the fluctuation of T:C ratio over a 16-week period and explore itis relation to their athletic performance. The participants characteristics were: (height: 177.6 ± 6.4 cm; body mass: 77.808 ± 12.396 kg age: 26.0 ± 5.9 years; and a playing experience of 14.7 ± 2.9 years with 5.0 ± 1.2 years at the elite level. The T:C ratio at Time 1 is: 4.0 ± 2.4 (n = 12); and at Time 2 is: 5.1 ± 4.3 (n = 12). (2) Methods: during 16 weeks of competition, participants underwent analysis of blood samples to assess various biochemical parameters including hormone levels. In addition, their athletic performance was assessed with the following tests: jumping (SJ, CMJ, ABK, DJ); throwing test with a medicine ball (3 kg); Illinois COD agility test; sprint repeatability with change of direction; 20-m speed test without change of direction; and Yo-yo intermittent endurance test IET (II). (3) Results: The main alterations observed were an increase in T levels (1.687%) and a decrease in C levels (-7.634%) between moments, with an improvement (26.366%) in the T:C ratio. Improvements were also observed in some of the tests developed, such as jumping (SJ: 11.5%, p = 0.029; CMJ: 10.5%, p = 0.03; DJ: 13.0%, p = 0.01), upper body strength (MBT: 5.4%, p = 0.03), translation ability (20 m: -1.7%), repeated sprint ability (RSA: -2.2%), as well as intermittent endurance test (Yy (IET): 63.5%, p = 0.01), with significant changes in some of the performance tests. (4) Conclusions: T:C ratio may differ in a manner unrelated to training volume, showing some variation. These results may be attributed to the accumulation of psychophysiological stress during the season.

Isavuconazole Pharmacokinetics in Critically Ill Patients: Relationship with Clinical Effectiveness and Patient Safety.

Isavuconazole is used to treat fungal infections. This study aims to describe isavuconazole pharmacokinetics in critically ill patients and evaluate their relationship with clinical efficacy and patient safety. We conducted a prospective, observational study in patients treated with intravenous isavuconazole. Samples were collected at predose (Cmin), 1 h (Cmax) and 12 h (C50) after the last dose. The plasma concentration was determined by high-performance liquid chromatography. The relationship between plasma concentration and clinical and microbiological outcomes and safety was evaluated. The influence of covariates (age, sex, weight, SAPS3, creatinine, liver enzymes and extracorporeal devices: continuous renal replacement therapy (CRRT) and extracorporeal membrane oxygenation (ECMO)) was analysed. Population pharmacokinetic modelling was performed using NONMEN®. A total of 71 isavuconazole samples from 24 patients were analysed. The mean Cmin was 1.76 (1.02) mg/L; 87.5% reached the optimal therapeutic target and 12.5% were below 1 mg/L. Population pharmacokinetics were best described by a one-compartment model with first-order elimination. No factor had a significant impact on the plasma concentration or pharmacokinetic parameters. Thus, isavuconazole could be safely used in a critically ill population, even in those treated with CRRT and ECMO, from a pharmacokinetic standpoint. Therefore, routine therapeutic drug monitoring may not be strictly necessary in daily clinical practice.

Statistical Interdependence between Daily Precipitation and Extreme Daily Temperature in Regions of Mexico and Colombia.

We study the statistical interdependence between daily precipitation and daily extreme temperature for regions of Mexico (14 climatic stations, period 1960-2020) and Colombia (7 climatic stations, period 1973-2020) using linear (cross-correlation and coherence) and nonlinear (global phase synchronization index, mutual information, and cross-sample entropy) synchronization metrics. The information shared between these variables is relevant and exhibits changes when comparing regions with different climatic conditions. We show that precipitation and temperature records from La Mojana are characterized by high persistence, while data from Mexico City exhibit lower persistence (less memory). We find that the information exchange and the level of coupling between the precipitation and temperature are higher for the case of the La Mojana region (Colombia) compared to Mexico City (Mexico), revealing that regions where seasonal changes are almost null and with low temperature gradients (less local variability) tend to display higher synchrony compared to regions where seasonal changes are very pronounced. The interdependence characterization between precipitation and temperature represents a robust option to characterize and analyze the collective dynamics of the system, applicable in climate change studies, as well as in changes not easily identifiable in future scenarios.

Patient safety, what does clinical simulation and teaching innovation contribute?

Clinical simulation in Intensive Care Medicine is a crucial tool to strengthen patient safety. It focuses on the complexity of the Intensive Care Unit, where challenging clinical situations require rapid decision making and the use of invasive techniques that can increase the risk of errors and compromise safety. Clinical simulation, by mimicking clinical contexts, is presented as essential for developing technical and non-technical skills and enhancing teamwork in a safe environment, without harm to the patient. in situ simulation is a valuable approach to practice in realistic environments and to address latent security threats. Other simulation methods as virtual reality and tele-simulation are gaining more and more acceptance. Herein, we provide current data on the clinical utility of clinical simulation related to improved safety in the practice of techniques and procedures, as well as improvements of teamwork performance and outcomes. Finally, we propose the needs for future research.

Relative impact of three growth conditions on the Escherichia coli protein acetylome.

Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).

Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29.

The genome-organizing protein p6 of Bacillus subtilis bacteriophage φ29 plays an essential role in viral development by activating the initiation of DNA replication and participating in the early-to-late transcriptional switch. These activities require the formation of a nucleoprotein complex in which the DNA adopts a right-handed superhelix wrapping around a multimeric p6 scaffold, restraining positive supercoiling and compacting the viral genome. Due to the absence of homologous structures, prior attempts to unveil p6's structural architecture failed. Here, we employed AlphaFold2 to engineer rational p6 constructs yielding crystals for three-dimensional structure determination. Our findings reveal a novel fold adopted by p6 that sheds light on its self-association mechanism and its interaction with DNA. By means of protein-DNA docking and molecular dynamic simulations, we have generated a comprehensive structural model for the nucleoprotein complex that consistently aligns with its established biochemical and thermodynamic parameters. Besides, through analytical ultracentrifugation, we have confirmed the hydrodynamic properties of the nucleocomplex, further validating in solution our proposed model. Importantly, the disclosed structure not only provides a highly accurate explanation for previously experimental data accumulated over decades, but also enhances our holistic understanding of the structural and functional attributes of protein p6 during φ29 infection.

Simplicial complex entropy for time series analysis.

The complex behavior of many systems in nature requires the application of robust methodologies capable of identifying changes in their dynamics. In the case of time series (which are sensed values of a system during a time interval), several methods have been proposed to evaluate their irregularity. However, for some types of dynamics such as stochastic and chaotic, new approaches are required that can provide a better characterization of them. In this paper we present the simplicial complex approximate entropy, which is based on the conditional probability of the occurrence of elements of a simplicial complex. Our results show that this entropy measure provides a wide range of values with details not easily identifiable with standard methods. In particular, we show that our method is able to quantify the irregularity in simulated random sequences and those from low-dimensional chaotic dynamics. Furthermore, it is possible to consistently differentiate cardiac interbeat sequences from healthy subjects and from patients with heart failure, as well as to identify changes between dynamical states of coupled chaotic maps. Our results highlight the importance of the structures revealed by the simplicial complexes, which holds promise for applications of this approach in various contexts.

Structural and Functional Retinal Changes in Patients with Mild Cognitive Impairment with and without Diabetes.

Our objective is to analyze retinal changes using optical coherence tomography angiography (OCT-A) in patients with mild cognitive impairment (MCI) to characterize structural and vascular alterations. This cross-sectional study involved 117 eyes: 39 eyes from patients with MCI plus diabetes (DM-MCI), 39 eyes from patients with MCI but no diabetes (MCI); and 39 healthy control eyes (C). All patients underwent a visual acuity measurement, a structural OCT, an OCT-A, and a neuropsychological examination. Our study showed a thinning of retinal nerve fiber layer thickness (RNFL) and a decrease in macular thickness when comparing the MCI-DM group to the C group (p = 0.008 and p = 0.016, respectively). In addition, an increase in arteriolar thickness (p = 0.016), a reduction in superficial capillary plexus density (p = 0.002), and a decrease in ganglion cell thickness (p = 0.027) were found when comparing the MCI-DM group with the MCI group. Diabetes may exacerbate retinal vascular changes when combined with mild cognitive impairment.

Influence of Bentonite Particles on the Mechanical Properties of Polyester-Sisal Fiber Composites.

As a part of the mission to create materials that are more environmentally friendly, we present the following proposal, in which a study of the mechanical properties of composite materials comprising a polyester resin with sisal fiber and bentonite particles was conducted. Sisal fiber was added to a matrix in percentages ranging from 5% to 45% in relation to the polyester resin weight, while bentonite remained fixed at 7% in relation to the polyester resin weight. The specimens were manufactured by compression molding. The mechanical properties were analyzed by tensile, bending, impact, stepped creep, and relaxation tests. In addition, energy-dispersive X-ray spectroscopy and scanning electron microscopy analyses were carried out to analyze the composition and heterogeneity of the structure of the composite material. The results obtained showed that 7% of bentonite added to the matrix affects the tensile strength. Flexural strength increased by up to 21% in the specimens with a 20% addition of sisal fiber, while the elastic modulus increased by up to 43% in the case of a 20% addition of sisal fiber. The viscoelastic behavior was improved, while the relaxation stress was affected.

Sensing preferences for prokaryotic solute binding protein families.

Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three-dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron-chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.

Development of an Epoxy Matrix Hybrid Composite with Astrocaryum Aculeatum (Tucumã) Endocarp and Kaolin from the Amazonas State in Brazil.

Composites with natural lignocellulosic fillers are being cited as a viable and sustainable alternative to conventional materials, as they combine lower costs with lower weight. In many tropical countries, such as Brazil, there is a considerable amount of lignocellulosic waste that is improperly discarded, which causes pollution of the environment. The Amazon region has huge deposits of clay silicate materials in the Negro River basin, such as kaolin, which can be used as fillers in polymeric composite materials. This work investigates a new composite material (ETK) made of epoxy resin (ER), powdered tucumã endocarp (PTE), and kaolin (K), without coupling agents, with the aim of producing a composite with lower environmental impact. The ETK samples, totaling 25 different compositions, were prepared by cold molding. Characterizations of the samples were performed using a scanning electron microscope (SEM) and a Fourier-transform infrared spectrometer (FTIR). In addition, the mechanical properties were determined via tensile, compressive, three-point flexural and impact tests. The FTIR and SEM results showed an interaction between ER, PTE, and K, and the incorporation of PTE and K reduced the mechanical properties of the ETK samples. Nonetheless, these composites can be considered potential materials to be used for sustainable engineering applications in which high mechanical strength is not a main requirement of the material.

Programa de Mentoría: acompañando tus primeros pasos hacia la excelencia científica / Mentoring Programme: Guiding your first steps towards scientific excellence

El primer Programa de Mentoría de SEMICYUC tiene como objetivo apoyar la carrera investigadora de los miembros más jóvenes de la Sociedad. Como beneficios añadidos está la adquisición de nuevas capacidades de investigación y/o clínicas, incrementar la capacidad de reflexión y fomentar el desarrollo de la próxima generación de líderes en la investigación. Este proyecto no sería posible sin el equipo excepcional de mentores o expertos investigadores dispuestos a emprender el viaje con los jóvenes aprendices. El presente artículo expone las bases de dicho programa, además de proponer futuros cambios en haz de una mejora continua (AU)

SEMICYUC's first Mentoring Programme aims to support the research careers of the Society's youngest members. Added benefits include acquiring new research and/or clinical skills, increasing the ability of critical thought, and fostering the development of the next generation of research leaders. This project would not be possible without the exceptional team of mentors or research experts willing to embark on the journey with the young trainees. This article sets out the foundations of such a programme and proposes future changes for continuous improvement (AU)

Study of NIT domain-containing chemoreceptors from two global phytopathogens and identification of NIT domains in eukaryotes.

Bacterial signal transduction systems are typically activated by the binding of signal molecules to receptor ligand binding domains (LBDs), such as the NIT LBD. We report here the identification of the NIT domain in more than 15,000 receptors that were present in 30 bacterial phyla, but also in 19 eukaryotic phyla, expanding its known phylogenetic distribution. The NIT domain formed part of seven receptor families that either control transcription, mediate chemotaxis or regulate second messenger levels. We have produced the NIT domains from chemoreceptors of the bacterial phytopathogens Pectobacterium atrosepticum (PacN) and Pseudomonas savastanoi (PscN) as individual purified proteins. High-throughput ligand screening using compound libraries revealed a specificity for nitrate and nitrite binding. Isothermal titration calorimetry experiments showed that PacN-LBD bound preferentially nitrate ( K D = 1.9 µM), whereas the affinity of PscN-LBD for nitrite ( K D = 2.1 µM) was 22 times higher than that for nitrate. Analytical ultracentrifugation experiments indicated that PscN-LBD is monomeric in the presence and absence of ligands. The R182A mutant of PscN did not bind nitrate or nitrite. This residue is not conserved in the NIT domain of the Pseudomonas aeruginosa chemoreceptor PA4520, which may be related to its failure to bind nitrate/nitrite. The magnitude of P. atrosepticum chemotaxis towards nitrate was significantly greater than that of nitrite and pacN deletion almost abolished responses to both compounds. This study highlights the important role of nitrate and nitrite as signal molecules in life and advances our knowledge on the NIT domain as universal nitrate/nitrite sensor module.

Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors.

Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.

Effect of Nanometric Particles of Bentonite on the Mechanical Properties of a Thermoset Polymeric Matrix Reinforced with Hemp Fibers.

The influence of the addition of bentonite nanoparticles on the tensile and flexural strength of a thermosetting polymer matrix composite material reinforced with hemp fibers was de-terminated. All composites were manufactured with 5% of bentonite in the polymer mass-weight ratios and 10 to 45 wt% of fibers with a step of 5%. For mechanical characterization, tensile and flexural tests were performed: scanning electron microscopy and energy-dispersive X-ray spectroscopy analyses were carried out. The tensile strength of the samples containing bentonite compared to the polymer samples with the fiber addition was affected for all fiber addition percentages, except for 35% while the flexural resistance improved with the addition of bentonite in the percentages of 20, 30, 35, and 45% of fiber addition. With the addition of bentonite, the maximum values of tensile and flexural strength were both obtained for the 35% addition of fibers, with values of 34.28 MPa and 98.04 MPa, respectively. The presence of bentonite favored the rigidity of the material to traction and bending, which was reflected through an increase in the elastic modulus compared to the composite that only had fiber. The maximum values obtained were 9065 MPa in tension and 8453 MPa in flexion for the 40% and 35% of addition of fiber, respectively. Microscopy showed a good distribution of fibers in the matrix, the absence of internal porosities, and a good interaction between matrix and reinforcement.

Mentoring Programme: Guiding your first steps towards scientific excellence.

SEMICYUC's first Mentoring Programme aims to support the research careers of the Society's youngest members. Added benefits include acquiring new research and/or clinical skills, increasing the ability of critical thought, and fostering the development of the next generation of research leaders. This project would not be possible without the exceptional team of mentors or research experts willing to embark on the journey with the young trainees. This article sets out the foundations of such a programme and proposes future changes for continuous improvement.

Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria.

Bacteria have evolved a sophisticated array of signal transduction systems that allow them to adapt their physiology and metabolism to changing environmental conditions. Typically, these systems recognize signals through dedicated ligand binding domains (LBDs) to ultimately trigger a diversity of physiological responses. Nonetheless, an increasing number of reports reveal that signal transduction receptors also bind antagonists to inhibit responses mediated by agonists. The mechanisms by which antagonists block the downstream signaling cascade remain largely unknown. To advance our knowledge in this field, we used the LysR-type transcriptional regulator AdmX as a model. AdmX activates the expression of an antibiotic biosynthetic cluster in the rhizobacterium Serratia plymuthica. AdmX specifically recognizes the auxin phytohormone indole-3-acetic acid (IAA) and its biosynthetic intermediate indole-3-pyruvic acid (IPA) as signals. However, only IAA, but not IPA, was shown to regulate antibiotic production in S. plymuthica. Here, we report the high-resolution structures of the LBD of AdmX in complex with IAA and IPA. We found that IAA and IPA compete for binding to AdmX. Although IAA and IPA binding does not alter the oligomeric state of AdmX, IPA binding causes a higher degree of compactness in the protein structure. Molecular dynamics simulations revealed significant differences in the binding modes of IAA and IPA by AdmX, and the inspection of the three-dimensional structures evidenced differential agonist- and antagonist-mediated structural changes. Key residues for auxin binding were identified and an auxin recognition motif defined. Phylogenetic clustering supports the recent evolutionary emergence of this motif specifically in plant-associated enterobacteria. IMPORTANCE Although antagonists were found to bind different bacterial signal transduction receptors, we are still at the early stages of understanding the molecular details by which these molecules exert their inhibitory effects. Here, we provide insight into the structural changes resulting from the binding of an agonist and an antagonist to a sensor protein. Our data indicate that agonist and antagonist recognition is characterized by small conformational differences in the LBDs that can be efficiently transmitted to the output domain to modulate the final response. LBDs are subject to strong selective pressures and are rapidly evolving domains. An increasing number of reports support the idea that environmental factors drive the evolution of sensor domains. Given the recent evolutionary history of AdmX homologs, as well as their narrow phyletic distribution within plant-associated bacteria, our results are in accordance with a plant-mediated evolutionary process that resulted in the emergence of receptor proteins that specifically sense auxin phytohormones.

Key Factors Associated With Pulmonary Sequelae in the Follow-Up of Critically Ill COVID-19 Patients.

INTRODUCTION: Critical COVID-19 survivors have a high risk of respiratory sequelae. Therefore, we aimed to identify key factors associated with altered lung function and CT scan abnormalities at a follow-up visit in a cohort of critical COVID-19 survivors. METHODS: Multicenter ambispective observational study in 52 Spanish intensive care units. Up to 1327 PCR-confirmed critical COVID-19 patients had sociodemographic, anthropometric, comorbidity and lifestyle characteristics collected at hospital admission; clinical and biological parameters throughout hospital stay; and, lung function and CT scan at a follow-up visit. RESULTS: The median [p25-p75] time from discharge to follow-up was 3.57 [2.77-4.92] months. Median age was 60 [53-67] years, 27.8% women. The mean (SD) percentage of predicted diffusing lung capacity for carbon monoxide (DLCO) at follow-up was 72.02 (18.33)% predicted, with 66% of patients having DLCO<80% and 24% having DLCO<60%. CT scan showed persistent pulmonary infiltrates, fibrotic lesions, and emphysema in 33%, 25% and 6% of patients, respectively. Key variables associated with DLCO<60% were chronic lung disease (CLD) (OR: 1.86 (1.18-2.92)), duration of invasive mechanical ventilation (IMV) (OR: 1.56 (1.37-1.77)), age (OR [per-1-SD] (95%CI): 1.39 (1.18-1.63)), urea (OR: 1.16 (0.97-1.39)) and estimated glomerular filtration rate at ICU admission (OR: 0.88 (0.73-1.06)). Bacterial pneumonia (1.62 (1.11-2.35)) and duration of ventilation (NIMV (1.23 (1.06-1.42), IMV (1.21 (1.01-1.45)) and prone positioning (1.17 (0.98-1.39)) were associated with fibrotic lesions. CONCLUSION: Age and CLD, reflecting patients' baseline vulnerability, and markers of COVID-19 severity, such as duration of IMV and renal failure, were key factors associated with impaired DLCO and CT abnormalities.