Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements.

In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.

Quantitative 1H Nuclear Magnetic Resonance Assay for the Rapid Detection of Pyrazinamide Resistance in Mycobacterium tuberculosis from Sputum Samples.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the 10 leading killer diseases in the world. At least one-quarter of the population has been infected, and there are 1.3 million deaths annually. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains challenges TB treatments. One of the drugs widely used in first- and second-line regimens is pyrazinamide (PZA). Statistically, 50% of MDR and 90% of XDR clinical strains are resistant to PZA, and recent studies have shown that its use in patients with PZA-resistant strains is associated with higher mortality rates. Therefore, the is an urgent need for the development of an accurate and efficient PZA susceptibility assay. PZA crosses the M. tuberculosis membrane and is hydrolyzed to its active form, pyrazinoic acid (POA), by a nicotinamidase encoded by the pncA gene. Up to 99% of clinical PZA-resistant strains have mutations in this gene, suggesting that this is the most likely mechanism of resistance. However, not all pncA mutations confer PZA resistance, only the ones that lead to limited POA production. Therefore, susceptibility to PZA may be addressed simply by its ability to form, or not, POA. Here, we present a nuclear magnetic resonance method to accurately quantify POA directly in the supernatant of sputum cultures collected from TB patients. The ability of the clinical sputum culture to hydrolyze PZA was determined, and the results were correlated with the results of other biochemical and molecular PZA drug susceptibility assays. The excellent sensitivity and specificity values attained suggest that this method could become the new gold standard for the determination of PZA susceptibility.

Preclinical examination of early-onset thalamic-cortical seizures after hemispheric stroke.

OBJECTIVE: Ischemic stroke is one of the main causes of death and disability worldwide and currently has limited treatment options. Electroencephalography (EEG) signals are significantly affected in stroke patients during the acute stage. In this study, we preclinically characterized the brain electrical rhythms and seizure activity during the hyperacute and late acute phases in a hemispheric stroke model with no reperfusion. METHODS: EEG signals and seizures were studied in a model of hemispheric infarction induced by permanent occlusion of the middle cerebral artery (pMCAO), which mimics the clinical condition of stroke patients with permanent ischemia. Electrical brain activity was also examined using a photothrombotic (PT) stroke model. In the PT model, we induced a similar (PT group-1) or smaller (PT group-2) cortical lesion than in the pMCAO model. For all models, we used a nonconsanguineous mouse strain that mimics human diversity and genetic variation. RESULTS: The pMCAO hemispheric stroke model exhibited thalamic-origin nonconvulsive seizures during the hyperacute stage that propagated to the thalamus and cortex. The seizures were also accompanied by progressive slowing of the EEG signal during the acute phase, with elevated delta/theta, delta/alpha, and delta/beta ratios. Cortical seizures were also confirmed in the PT stroke model of similar lesions as in the pMCAO model, but not in the PT model of smaller injuries. SIGNIFICANCE: In the clinically relevant pMCAO model, poststroke seizures and EEG abnormalities were inferred from recordings of the contralateral hemisphere (noninfarcted hemisphere), emphasizing the reciprocity of interhemispheric connections and that injuries affecting one hemisphere had consequences for the other. Our results recapitulate many of the EEG signal hallmarks seen in stroke patients, thereby validating this specific mouse model for the examination of the mechanistic aspects of brain function and for the exploration of the reversion or suppression of EEG abnormalities in response to neuroprotective and anti-epileptic therapies.

Stably stratified Taylor-Couette flows.

Stably stratified Taylor-Couette flow has attracted much attention due to its relevance as a canonical example of the interplay among rotation, stable stratification, shear and container boundaries, as well as its potential applications in geophysics and astrophysics. In this article, we review the current knowledge on this topic, highlight unanswered questions and propose directions for future research. This article is part of the theme issue 'Taylor-Couette and related flows on the centennial of Taylor's seminal Philosophical transactions paper (Part 2)'.

Morphological and metabolic profiling of a tropical-adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor.

Potato (Solanum tuberosum L.) is one of the world's most important crops, but it is facing major challenges due to climatic changes. To investigate the effects of intermittent drought on the natural variability of plant morphology and tuber metabolism in a novel potato association panel comprising 258 varieties we performed an augmented block design field study under normal irrigation and under water-deficit and recovery conditions in Ica, Peru. All potato genotypes were profiled for 45 morphological traits and 42 central metabolites via nuclear magnetic resonance. Statistical tests and norm of reaction analysis revealed that the observed variations were trait specific, that is, genotypic versus environmental. Principal component analysis showed a separation of samples as a result of conditional changes. To explore the relational ties between morphological traits and metabolites, correlation-based network analysis was employed, constructing one network for normal irrigation and one network for water-recovery samples. Community detection and difference network analysis highlighted the differences between the two networks, revealing a significant correlational link between fumarate and plant vigor. A genome-wide association study was performed for each metabolic trait. Eleven single nucleotide polymorphism (SNP) markers were associated with fumarate. Gene Ontology analysis of quantitative trait loci regions associated with fumarate revealed an enrichment of genes regulating metabolic processes. Three of the 11 SNPs were located within genes, coding for a protein of unknown function, a RING domain protein and a zinc finger protein ZAT2. Our findings have important implications for future potato breeding regimes, especially in countries suffering from climate change.

Transcervical Foley Balloon Plus Vaginal Misoprostol versus Vaginal Misoprostol Alone for Cervical Ripening in Nulliparous Obese Women: A Multicenter, Randomized, Comparative-Effectiveness Trial.

OBJECTIVE: Nulliparous obese women are at increased risk of labor induction and cesarean delivery (CD). We sought to determine whether the combination of a transvaginal Foley balloon plus misoprostol prostaglandin E1 (PGE1) is superior to misoprostol alone in reducing the risk for CD. STUDY DESIGN: We undertook a multicenter, open-label, comparative-effectiveness randomized clinical trial of nulliparous obese women with unfavorable cervix (Bishop's score ≤ 6) undergoing labor induction from January 2016 to June 2018 at three tertiary centers. Those at <32 weeks' gestation, premature rupture of membranes, stillbirth, and major fetal anomalies were excluded. Women were randomized 1:1 to either a combination of Foley balloon and misoprostol or misoprostol alone. Once Bishop's score was >6, further management was deferred to treating physicians. Primary outcome was the rate of CD. Secondary maternal outcomes included duration of induction-to-delivery interval, occurrence of tachysystole, clinical chorioamnionitis, need for operative vaginal delivery, as well as a composite of maternal morbidity (postpartum endometritis, surgical-site infection, venous thromboembolism, need for transfusion, intensive care unit admission, and maternal death). Secondary neonatal outcomes included need for neonatal intensive care unit admission, transient tachypnea of the newborn, respiratory distress syndrome, meconium aspiration syndrome, culture-proven sepsis, neonatal seizures, and a composite of neonatal morbidity (Apgar's score ≤7 at 5 minutes, umbilical artery cord pH ≤7.10, birth injury, perinatal death). With the rate of CD rate being 53% at Children's Memorial Herman Hospital among nulliparous obese women who underwent induction of labor at ≥32 weeks and met our inclusion criteria; 250 women (125 women per group) were required to answer the study question. All analyses were by intention to treat. RESULTS: Of the 236 women randomized, 113 (48%) were allocated to group 1 (combined Foley and PGE1) and 123 (52%) to group 2 (PGE1 alone). The rate of CD was similar between the groups (45 vs. 43%, p = 0.84, relative risk [RR]: 1.03, 95% CI: 0.75-1.42). There was no difference in the occurrence of tachysystole that resulted in fetal heart rate abnormalities between the groups (8.8 vs. 16.2%, p = 0.09, RR: 0.54, 95% CI: 0.27-1.11). The total duration of the induction-to-delivery interval was also similar between the groups (24.8 ± 13.8 vs. 24.5 ± 14.0 hours, p = 0.87) regardless of the mode of delivery. No differences were seen in the indications for CD and secondary maternal or neonatal outcomes. CONCLUSION: In this trial of nulliparous obese women undergoing labor induction, cervical ripening with combined Foley balloon and PGE1 resulted in similar CD rates than ripening with vaginal PGE1 alone. KEY POINTS: · Nulliparous obese women are at increased risk for cesarean delivery.. · Combined intravaginal misoprostol-Foley balloon versus misoprostol alone resulted in similar rates of cesarean delivery.. · Further research is warranted to determine the optimal cervical ripening strategy in this population..

Study of the Acetylation Pattern of Chitosan by Pure Shift NMR.

Chitosan is a biodegradable, antibacterial, and nontoxic biopolymer used in a wide range of applications including biotechnology, pharmacy, and medicine. The physicochemical and biological properties of chitosan have been associated with parameters such as the degree of polymerization (DP) and the fraction of acetylation (FA). New methods are being developed to yield chitosans of specific acetylation patterns, and, recently, a correlation between biological activity and the distribution of the acetylated units (PA: pattern of acetylation) has been demonstrated. Although there are numerous well-established methods for the determination of DP and FA values, this is not the case for PA. The methods available are either not straightforward or not sensitive enough, limiting their use for routine analysis. In this study, we demonstrate that by applying HOmodecoupled Band-Selective (HOBS) decoupling NMR on signals assigned by multidimensional Pure Shift NMR methods, PA can be easily and accurately determined on various chitosan samples. This novel methodology-easily implemented for routine analysis-could become a standard for chitosan PA assessment. In addition, by applying Spectral Aliased Pure Shift HSQC, the analysis was enhanced with the determination of triads.

Cutaneous metaplastic synovial cyst in Ehlers-Danlos syndrome.

Classic Ehlers-Danlos syndrome (EDS) is a connective tissue disorder characterized by laxity. The skin, as one of the organs involved, shows hyperextensibility, which makes it prone to trauma. In this context, it would seem logical for cutaneous synovial metaplasia, which is considered a form of repair, to be commonly found in cases of EDS. However, there are only two previously published cases of synovial metaplasia in EDS. We present a third case in a 56-year-old woman with painful redundant skin in both elbows and knees for whom a skin fold of the left elbow was removed to relieve her symptoms. The biopsy showed preservation of the elastic and collagen fibers. The main alteration was the evidence of dermal cystic spaces lined by fibrinoid rests with focal pseudopapillary projections. However, in some zones the cellular lining was preserved, and it was composed of vimentin-positive, fibroblast-like flat, elongated cells, as well as CD68-positive macrophages. No birefringent particles were found in an examination under polarized light.

Spatiotemporal Organization of Correlated Local Activity within Global Avalanches in Slowly Driven Interfaces.

We study the jerky response of slowly driven fronts in disordered media, just above the depinning transition. We focus on how spatially disconnected clusters of internally correlated activity lead to large-scale velocity fluctuations in the form of global avalanches and identify three different ways in which local activity clusters may organize within a global avalanche, depending on the distance to criticality. Our analysis provides new scaling relations between the power-law exponents of the statistical distributions of sizes and durations of local bursts and global avalanches. Fluid fronts of imbibition in heterogeneous media are taken as a case study to validate these scaling relations.

Predicting Steady Shear Rheology of Condensed-Phase Monomolecular Films at the Air-Water Interface.

Predicting the non-Newtonian shear response of soft interfaces in biophysical systems and engineered products has been compromised by the use of linear (Newtonian) constitutive equations. We present a generalized constitutive equation, with tractable material properties, governing the response of Newtonian and non-Newtonian interfaces subjected to a wide range of steady shear. With experiments spanning six decades of shear rate, we capture and unify divergent reports of shear-thinning behavior of monomolecular films of the lipid dipalmitoylphosphatidylcholine, the primary constituent of mammalian cell walls and lung surfactant, at near-physiological packing densities.

Surface shear viscosity as a macroscopic probe of amyloid fibril formation at a fluid interface.

Amyloidogenesis of proteins is of wide interest because amyloid structures are associated with many diseases, including Alzheimer's and type II diabetes. Dozens of different proteins of various sizes are known to form amyloid fibrils. While there are numerous studies on the fibrillization of insulin induced by various perturbations, shearing at fluid interfaces has not received as much attention. Here, we present a study of human insulin fibrillization at room temperature using a deep-channel surface viscometer. The hydrodynamics of the bulk flow equilibrates in just over a minute, but the proteins at the air-water interface exhibit a very slow development during which the surface (excess) shear viscosity deduced from a Newtonian surface model increases slightly over a period of a day and a half. Then, there is a very rapid increase in the surface shear viscosity to effectively unbounded levels as the interface becomes immobilized. Atomic force microscopy shows that fibrils appear at the interface after it becomes immobilized. Fibrillization in the bulk does not occur until much later. This has been verified by concurrent atomic force microscopy and circular dichroism spectroscopy of samples from the bulk. The immobilized interface has zero in-plane shear rate, however due to the bulk flow, there is an increase in the strength of the normal component of the shear rate at the interface, implicating this component of shear in the fibrillization process ultimately resulting in a thick weave of fibrils on the interface. Real-time detection of fibrillization via interfacial rheology may find utility in other studies of proteins at sheared interfaces.

Diverging Fluctuations of the Lyapunov Exponents.

We show that in generic one-dimensional Hamiltonian lattices the diffusion coefficient of the maximum Lyapunov exponent diverges in the thermodynamic limit. We trace this back to the long-range correlations associated with the evolution of the hydrodynamic modes. In the case of normal heat transport, the divergence is even stronger, leading to the breakdown of the usual single-function Family-Vicsek scaling ansatz. A similar scenario is expected to arise in the evolution of rough interfaces in the presence of suitably correlated background noise.

Shear-induced amyloid fibrillization: the role of inertia.

Agitation of protein is known to induce deleterious effects on protein stability and structure, with extreme agitation sometimes resulting in complete aggregation into amyloid fibrils. Many mechanisms have been proposed to explain how protein becomes unstable when subjected to flow, including alignment of protein species, shear-induced unfolding, simple mixing, or fragmentation of existing fibrils to create new seeds. Here a shearing flow was imposed on a solution of monomeric human insulin via a rotating Couette device with a small hydrophobic fluid interface. The results indicate that even very low levels of shear are capable of accelerating amyloid fibril formation. Simulations of the flow suggest that the shear enhances fibrillization kinetics when flow inertia is non-negligible and the resulting meridional circulation allows for advection of bulk protein to the hydrophobic interface.

Flow-induced 2D protein crystallization: characterization of the coupled interfacial and bulk flows.

Two-dimensional crystallization of the protein streptavidin, crystallizing below a biotinylated lipid film spread on a quiescent air-water interface is a well studied phenomenon. More recently, 2D crystallization induced by a shearing interfacial flow has been observed at film surface pressures significantly lower than those required in a quiescent system. Here, we quantify the interfacial and bulk flow associated with 2D protein crystallization through numerical modeling of the flow along with a Newtonian surface model. Experiments were conducted over a wide range of conditions resulting in a state diagram delineating the flow strength required to induce crystals for various surface pressures. Through measurements of the velocity profile at the air-water interface, we found that even in the cases where crystals are formed, the macroscopic flow at the interface is well described by the Newtonian model. However, the results show that even in the absence of any protein in the system, the viscous response of the biotinylated lipid film is complicated and strongly dependent on the strength of the flow. This observation suggests that the insoluble lipid film plays a key role in flow-induced 2D protein crystallization.

Bacterial colonization of a fumigated alkaline saline soil.

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m(-1), and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8%) compared to the unfumigated soil (34.2%), while that of the Bacteroidetes decreased from 16.2% in the unfumigated soil to 8.8% in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7% in the unfumigated soil to 25.7%. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.

Papular mucinosis of the breast after radiation therapy.

Localized papular mucinosis is a type of mucinosis induced by several different causes. However, to the best of our knowledge, prior radiation therapy has not been reported to be related to papular mucinosis. We present a case of a 47-year-old woman who had undergone an operation for a breast carcinoma 2 years earlier and received local radiotherapy in the affected breast. Currently, she presents multiple erythematous papules that are caused by abundant dermal mucin deposits. We discuss some potential differential diagnoses.

Synchronizing spatio-temporal chaos with imperfect models: a stochastic surface growth picture.

We study the synchronization of two spatially extended dynamical systems where the models have imperfections. We show that the synchronization error across space can be visualized as a rough surface governed by the Kardar-Parisi-Zhang equation with both upper and lower bounding walls corresponding to nonlinearities and model discrepancies, respectively. Two types of model imperfections are considered: parameter mismatch and unresolved fast scales, finding in both cases the same qualitative results. The consistency between different setups and systems indicates that the results are generic for a wide family of spatially extended systems.

Lyapunov vectors and excited energy states of the directed polymer in random media.

The scaling behavior of the excited energy states of the directed polymer in random media is analyzed numerically. We find that the spatial correlations of polymer energies scale as ∼k^{-δ} for small enough wave numbers k with a nontrivial exponent δ≈1.3. The equivalence between the stochastic-field equation that describes the partition function of the directed polymer and that governing the time evolution of infinitesimal perturbations in space-time chaos is exploited to connect this exponent δ with the spatial correlations of the Lyapunov vectors reported in the literature. The relevance of our results for other problems involving optimization in random systems is discussed.

Fragility of Kardar-Parisi-Zhang universality class in the presence of temporally correlated noise.

We study numerically a family of surface growth models that are known to be in the universality class of the Kardar-Parisi-Zhang equation when driven by uncorrelated noise. We find that, in the presence of noise with power-law temporal correlations with exponent θ, these models exhibit critical exponents that differ both quantitatively and qualitatively from model to model. The existence of a threshold value for θ below which the uncorrelated fixed point is dominant occurs for some models but not for others. In some models the dynamic exponent z(θ) is a smooth decreasing function, while it has a maximum in other cases. Despite all models sharing the same symmetries, critical exponents turn out to be strongly model dependent. Our results clearly show the fragility of the universality class concept in the presence of long-range temporally correlated noise.

Linear mixed-effect models for correlated response to process electroencephalogram recordings.

A data set of clinical studies of electroencephalogram recordings (EEG) following data acquisition protocols in control individuals (Eyes Closed Wakefulness - Eyes Open Wakefulness, Hyperventilation, and Optostimulation) are quantified with information theory metrics, namely permutation Shanon entropy and permutation Lempel Ziv complexity, to identify functional changes. This work implement Linear mixed-effects models (LMEMs) for confirmatory hypothesis testing. The results show that EEGs have high variability for both metrics and there is a positive correlation between them. The mean of permutation Lempel-Ziv complexity and permutation Shanon entropy used simultaneously for each of the four states are distinguishable from each other. However, used separately, the differences between permutation Lempel-Ziv complexity or permutation Shanon entropy of some states were not statistically significant. This shows that the joint use of both metrics provides more information than the separate use of each of them. Despite their wide use in medicine, LMEMs have not been commonly applied to simultaneously model metrics that quantify EEG signals. Modeling EEGs using a model that characterizes more than one response variable and their possible correlations represents a new way of analyzing EEG data in neuroscience.