Improvement of immune dysregulation in individuals with long COVID at 24-months following SARS-CoV-2 infection.

This study investigates the humoral and cellular immune responses and health-related quality of life measures in individuals with mild to moderate long COVID (LC) compared to age and gender matched recovered COVID-19 controls (MC) over 24 months. LC participants show elevated nucleocapsid IgG levels at 3 months, and higher neutralizing capacity up to 8 months post-infection. Increased spike-specific and nucleocapsid-specific CD4+ T cells, PD-1, and TIM-3 expression on CD4+ and CD8+ T cells were observed at 3 and 8 months, but these differences do not persist at 24 months. Some LC participants had detectable IFN-γ and IFN-ß, that was attributed to reinfection and antigen re-exposure. Single-cell RNA sequencing at the 24 month timepoint shows similar immune cell proportions and reconstitution of naïve T and B cell subsets in LC and MC. No significant differences in exhaustion scores or antigen-specific T cell clones are observed. These findings suggest resolution of immune activation in LC and return to comparable immune responses between LC and MC over time. Improvement in self-reported health-related quality of life at 24 months was also evident in the majority of LC (62%). PTX3, CRP levels and platelet count are associated with improvements in health-related quality of life.

The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome.

Nascent polypeptide chains can induce translational stalling to regulate gene expression. This is exemplified by the E. coli secretion monitor (SecM) arrest peptide that induces translational stalling to regulate expression of the downstream encoded SecA, an ATPase that co-operates with the SecYEG translocon to facilitate insertion of proteins into or through the cytoplasmic membrane. Here we present the structure of a ribosome stalled during translation of the full-length E. coli SecM arrest peptide at 2.0 Å resolution. The structure reveals that SecM arrests translation by stabilizing the Pro-tRNA in the A-site, but in a manner that prevents peptide bond formation with the SecM-peptidyl-tRNA in the P-site. By employing molecular dynamic simulations, we also provide insight into how a pulling force on the SecM nascent chain can relieve the SecM-mediated translation arrest. Collectively, the mechanisms determined here for SecM arrest and relief are also likely to be applicable for a variety of other arrest peptides that regulate components of the protein localization machinery identified across a wide range of bacteria lineages.

RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity.

Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.

Smart labels based on polyvinyl alcohol incorporated with chitosan nanoparticles loaded with grape extract: Functionality, stability and food application.

Anthocyanins (ACNs) are natural compounds with potential applications due to their colorimetric response to pH. Due to their sensitivity to various environmental factors, nanoencapsulation with biopolymers is a successful strategy for stabilizing ACNs. In this work ACNs were extracted from grape skins and encapsulated into chitosan (CS) nanoparticles by ionic gelation using sodium tripolyphosphate (TPP) as a cross-linking agent. CS nanoparticles loaded with ACNs had particle sizes between 291 and 324 nm and polydispersity index around 0.3. The encapsulation efficiency of ACNs was approximately 60 %; and encapsulated anthocyanins (ACN-NPs) exhibited color change properties under different pH conditions. pH-sensitive labels based on polyvinyl alcohol (PVA) were prepared by the casting method. The effect of incorporating ACN-NPs on the physical, structural, and pH-sensitive properties of PVA labels was evaluated, and its application as shrimp freshness indicator was studied. The nanoencapsulation protected ACNs against heat and light treatments, preserving the original purple color. When applying the label, visible changes from red to blue until reaching yellow were observed with the change in the quality of the shrimp at the refrigeration temperature. The results suggest that PVA labels containing ACNs encapsulated in C-NPs can be used as smart packaging labels in the food industry.

Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes.

Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.

Household concentrations and female and child exposures to air pollution in peri-urban sub-Saharan Africa: measurements from the CLEAN-Air(Africa) study.

BACKGROUND: Relatively clean cooking fuels such as liquefied petroleum gas (LPG) emit less fine particulate matter (PM2·5) and carbon monoxide (CO) than polluting fuels (eg, wood, charcoal). Yet, some clean cooking interventions have not achieved substantial exposure reductions. This study evaluates determinants of between-community variability in exposures to household air pollution (HAP) across sub-Saharan Africa. METHODS: In this measurement study, we recruited households cooking primarily with LPG or exclusively with wood or charcoal in peri-urban Cameroon, Ghana, and Kenya from previously surveyed households. In 2019-20, we conducted monitoring of 24 h PM2·5 and CO kitchen concentrations (n=256) and female cook (n=248) and child (n=124) exposures. PM2·5 measurements used gravimetric and light scattering methods. Stove use monitoring and surveys on cooking characteristics and ambient air pollution exposure (eg, walking time to main road) were also administered. FINDINGS: The mean PM2·5 kitchen concentration was five times higher among households cooking with charcoal than those using LPG in the Kenyan community (297 µg/m3, 95% CI 216-406, vs 61 µg/m3, 49-76), but only 4 µg/m3 higher in the Ghanaian community (56 µg/m3, 45-70, vs 52 µg/m3, 40-68). The mean CO kitchen concentration in charcoal-using households was double the WHO guideline (6·11 parts per million [ppm]) in the Kenyan community (15·81 ppm, 95% CI 8·71-28·72), but below the guideline in the Ghanaian setting (1·77 ppm, 1·04-2·99). In all communities, mean PM2·5 cook exposures only met the WHO interim-1 target (35 µg/m3) among LPG users staying indoors and living more than 10 min walk from a road. INTERPRETATION: Community-level variation in the relative difference in HAP exposures between LPG and polluting cooking fuel users in peri-urban sub-Saharan Africa might be attributed to differences in ambient air pollution levels. Thus, mitigation of indoor and outdoor PM2·5 sources will probably be critical for obtaining significant exposure reductions in rapidly urbanising settings of sub-Saharan Africa. FUNDING: UK National Institute for Health and Care Research.

Three-Coordinate Nickel and Metal-Metal Interactions in a Heterometallic Iron-Sulfur Cluster.

Biological multielectron reactions often are performed by metalloenzymes with heterometallic sites, such as anaerobic carbon monoxide dehydrogenase (CODH), which has a nickel-iron-sulfide cubane with a possible three-coordinate nickel site. Here, we isolate the first synthetic iron-sulfur clusters having a nickel atom with only three donors, showing that this structural feature is feasible. These have a core with two tetrahedral irons, one octahedral tungsten, and a three-coordinate nickel connected by sulfide and thiolate bridges. Electron paramagnetic resonance (EPR), Mössbauer, and superconducting quantum interference device (SQUID) data are combined with density functional theory (DFT) computations to show how the electronic structure of the cluster arises from strong magnetic coupling between the Ni, Fe, and W sites. X-ray absorption spectroscopy, together with spectroscopically validated DFT analysis, suggests that the electronic structure can be described with a formal Ni1+ atom participating in a nonpolar Ni-W σ-bond. This metal-metal bond, which minimizes spin density at Ni1+, is conserved in two cluster oxidation states. Fe-W bonding is found in all clusters, in one case stabilizing a local non-Hund state at tungsten. Based on these results, we compare different M-M interactions and speculate that other heterometallic clusters, including metalloenzyme active sites, could likewise store redox equivalents and stabilize low-valent metal centers through metal-metal bonding.

Synaptic wiring motifs in posterior parietal cortex support decision-making.

The posterior parietal cortex exhibits choice-selective activity during perceptual decision-making tasks1-10. However, it is not known how this selective activity arises from the underlying synaptic connectivity. Here we combined virtual-reality behaviour, two-photon calcium imaging, high-throughput electron microscopy and circuit modelling to analyse how synaptic connectivity between neurons in the posterior parietal cortex relates to their selective activity. We found that excitatory pyramidal neurons preferentially target inhibitory interneurons with the same selectivity. In turn, inhibitory interneurons preferentially target pyramidal neurons with opposite selectivity, forming an opponent inhibition motif. This motif was present even between neurons with activity peaks in different task epochs. We developed neural-circuit models of the computations performed by these motifs, and found that opponent inhibition between neural populations with opposite selectivity amplifies selective inputs, thereby improving the encoding of trial-type information. The models also predict that opponent inhibition between neurons with activity peaks in different task epochs contributes to creating choice-specific sequential activity. These results provide evidence for how synaptic connectivity in cortical circuits supports a learned decision-making task.

Structural basis of ribosomal 30S subunit degradation by RNase R.

Protein synthesis is a major energy-consuming process of the cell that requires the controlled production1-3 and turnover4,5 of ribosomes. Although the past few years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3' to 5' exonuclease ribonuclease R (RNase R). The structures reveal that RNase R binds at first to the 30S platform to facilitate the degradation of the functionally important anti-Shine-Dalgarno sequence and the decoding-site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S subunit, and this is overcome by a major structural rearrangement of the 30S head, involving the loss of ribosomal proteins. RNase R parallels this movement and relocates to the decoding site by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also indicate that the enzyme alone is sufficient for complete degradation of 30S subunits. Collectively, our results provide a mechanistic basis for the degradation of 30S mediated by RNase R, and reveal that RNase R targets orphaned 30S subunits using a dynamic mechanism involving an anchored switching of binding sites.

Erratum: Prevalence and distribution of selected cervical human papillomavirus types in HIV infected and HIV uninfected women in South Africa, 1989-2021: A narrative review.

[This corrects the article DOI: 10.4102/sajid.v37i1.363.].

Peptidyl-tRNA hydrolase is the nascent chain release factor in bacterial ribosome-associated quality control.

Rescuing stalled ribosomes often involves their splitting into subunits. In many bacteria, the resultant large subunits bearing peptidyl-tRNAs are processed by the ribosome-associated quality control (RQC) apparatus that extends the C termini of the incomplete nascent polypeptides with polyalanine tails to facilitate their degradation. Although the tailing mechanism is well established, it is unclear how the nascent polypeptides are cleaved off the tRNAs. We show that peptidyl-tRNA hydrolase (Pth), the known role of which has been to hydrolyze ribosome-free peptidyl-tRNA, acts in concert with RQC factors to release nascent polypeptides from large ribosomal subunits. Dislodging from the ribosomal catalytic center is required for peptidyl-tRNA hydrolysis by Pth. Nascent protein folding may prevent peptidyl-tRNA retraction and interfere with the peptide release. However, oligoalanine tailing makes the peptidyl-tRNA ester bond accessible for Pth-catalyzed hydrolysis. Therefore, the oligoalanine tail serves not only as a degron but also as a facilitator of Pth-catalyzed peptidyl-tRNA hydrolysis.

Smart Pasta Design: Tailoring Formulations for Technological Excellence with Sprouted Quinoa and Kiwicha Grains.

The pursuit of developing healthier pasta products without compromising technological properties involves a strategic approach via the customization of raw material formulations and the integration of grain germination and extrusion processes. This study explores the impact of incorporating sprouts from quinoa (Chenopodium quinoa Willd) and kiwicha (Chenopodium pallidicaule Aellen) on the physicochemical properties of pasta by employing a centroid mixture design. The desirability function was utilized to identify the optimal ingredient proportions necessary to achieve specific objectives. The study identified optimal formulations for two pasta variations: pasta with the substitution of sprouted quinoa and cushuro powder (PQC), and pasta with partial substitution of sprouted kiwicha and cushuro powder (PKC). The optimal formulation for PKC was determined as 70% wheat flour (WF), 15% sprouted kiwicha flour (SKF), and 15% cushuro powder (CuP), with a desirability score of 0.68. Similarly, for PQC, the optimal formulation comprised 79% WF, 13% sprouted quinoa flour (SQF), and 8% CuP, with a desirability of 0.63. The optimized pasta formulation exhibited longer cooking times (10 and 8 min), increased weight gain (235% and 244%), and minimal loss of solids (1.4 and 1.2%) for PQC and PKC, respectively. Notably, firmness (2.8 and 2.6 N) and breaking strength values (2 and 2.7 N) for PQC and PKC pasta formulations, respectively, were comparable to those of the control sample (2.7 N and 2.6 N for firmness and fracturability, respectively). This research underscores the potential of tailored formulations and innovative processes to enhance the nutritional profile of pasta while maintaining key technological attributes.

The relationship between cardiorespiratory fitness and blood pressure among airline pilots: a mediation analysis of body composition.

OBJECTIVE: Blood pressure (BP), cardiorespiratory fitness (CRF), and body composition are independently associated with health outcomes, yet the relationship between these variables has not been explored among airline pilots. The aim of this study was to evaluate the relationship between CRF and BP, and further examine whether the relationship is mediated by body composition. METHODS: A cross-sectional study was conducted among 356 airline pilots in New Zealand. We measured height, body mass, BP, waist circumference, skinfolds, and CRF (via a WattBike cycle ergometer submaximal VO 2max test). Partial correlation coefficients were estimated to examine the relationships between all variables while controlling for age and sex. Haye's PROCESS macro and the Sobel test were utilized for the mediation analysis. RESULTS: All body composition variables (body mass index, waist circumference and body fat percentage) were positively correlated with all BP variables (systolic pressure, diastolic pressure and mean arterial pressure) ( P  < 0.001). CRF was negatively correlated with all body composition and BP variables ( P  < 0.001). The Sobel test and indirect effect were significant ( P  < 0.001), confirming that all body composition variables partially mediate the relationship between CRF and all blood pressure variables. CONCLUSION: Lower CRF is associated with higher blood pressure, and body composition partially mediates the relationship between these health risk factors. These findings highlight the importance of physical fitness and healthy body composition in the management of blood pressure among this occupational group.

Enhancing Nutritional Profile of Pasta: The Impact of Sprouted Pseudocereals and Cushuro on Digestibility and Health Potential.

We hypothesized that optimizing the formulation of pasta by incorporating sprouted pseudocereal flours, specifically quinoa (Chenopodium quinoa Willd) or kiwicha (Amaranthus caudatus L.) and cushuro (Nostoc sphaericum Vaucher ex Bornet & Flahault) flours, could offer the potential to simultaneously enhance nutritional quality and health-promoting properties in pasta. In this study, our objective was to optimize the formulation of composite flour (a ternary blend of wheat, sprouted pseudocereal, and cushuro flours) using a mixture composite design to maximize total soluble phenolic compounds (TSPC), γ-aminobutyric acid (GABA), antioxidant activity, and mineral bioaccesilability by reducing phytic acid (PA) content. Two optimal formulations were identified: one consisting of 79% wheat flour (WF), 13% SQF, and 8% CuF (oPQC), and the other composed of 70% WF, 15% SKF, and 15% CuF (oPKC). These optimized pastas exhibited reduced starch content and notably higher levels of total dietary fiber (1.5-3.61-fold), protein (1.16-fold), fat (1.3-1.5-fold), ash (2.2-2.7-fold), minerals (K, Na, Fe, Zn, Mg, Mn, and Ca), PA (3-4.5-fold), TSPC (1.3-1.9-fold), GABA (1.2-2.6-fold), and ORAC (6.5-8.7-fold) compared to control pasta (100% WF). Notably, the glycemic index of oPQC (59.8) was lower than that of oPKC (54.7) and control pasta (63.1). The nutritional profile of the optimized pasta was largely retained after cooking, although some significant losses were observed for soluble dietary fiber (18.2-44.0%), K (47.5-50.7%), Na (42.5-63.6), GABA (41.68-51.4%), TSPC (8-18%), and antioxidant activity (45.4-46.4%). In vitro digestion of cooked oPQC and oPKC demonstrated higher bioaccessible content of GABA (6.7-16.26 mg/100 g), TSPC (257.7-261.8 mg GAE/100 g), Ca (58.40-93.5 mg/100 g), and Fe (7.35-7.52 mg/100 g), as well as antioxidant activity (164.9-171.1 µmol TE/g) in intestinal digestates compared to control pasta. These findings suggest that the incorporation of sprouted pseudocereals and cushuro flour offers a promising approach to enhance the nutritional quality and bioactive content of wheat-based pasta, potentially providing health benefits beyond traditional formulations.

5-((3-Amidobenzyl)oxy)nicotinamides as SIRT2 Inhibitors: A Study of Constrained Analogs.

SIRT2 is a member of NAD+-dependent sirtuins and its inhibition has been proposed as a promising therapeutic approach for treating human diseases, including neurodegenerative diseases, cancer, and infections. Expanding SIRT2 inhibitors based on the 3-aminobenzyloxy nicotinamide core structure, we have synthesized and evaluated constrained analogs and selected stereoisomers. Our structure-activity relationship (SAR) study has revealed that 2,3-constrained (S)-isomers possess enhanced in vitro enzymatic inhibitory activity against SIRT2 and retain excellent selectivity over SIRT1 and SIRT3, provided that a suitable ring A is used. This current study further explores SIRT2 inhibitors based on the 3-aminobenzyloxy nicotinamide scaffold and contributes to the discovery of potent, selective SIRT2 inhibitors that have been actively pursued for their potential therapeutic applications.

Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales.

Deserts represent an extreme challenge for photosynthetic life. Despite their aridity, they are often inhabited by diverse microscopic communities of cyanobacteria. These organisms are commonly found in lithic habitats, where they are partially sheltered from extremes of temperature and UV radiation. However, living under the rock surface imposes additional constraints, such as limited light availability, and enrichment of longer wavelengths than are typically usable for oxygenic photosynthesis. Some cyanobacteria from the genus Chroococcidiopsis can use this light to photosynthesize, in a process known as far-red light photoacclimation, or FaRLiP. This genus has commonly been reported from both hot and cold deserts. However, not all Chroococcidiopsis strains carry FaRLiP genes, thus motivating our study into the interplay between FaRLiP and extreme lithic environments. The abundance of sequence data and strains provided the necessary material for an in-depth phylogenetic study, involving spectroscopy, microscopy, and determination of pigment composition, as well as gene and genome analyses. Pigment analyses revealed the presence of red-shifted chlorophylls d and f in all FaRLiP strains tested. In addition, eight genus-level taxa were defined within the encompassing Chroococcidiopsidales, clarifying the phylogeny of this long-standing polyphyletic order. FaRLiP is near universally present in a generalist genus identified in a wide variety of environments, Chroococcidiopsis sensu stricto, while it is rare or absent in closely related, extremophile taxa, including those preferentially inhabiting deserts. This likely reflects the evolutionary process of gene loss in specialist lineages.

Albuminuria Screening in People With Type 2 Diabetes in a Managed Care Organization.

Introduction: Albuminuria-an increased amount of urine albumin, in milligrams, adjusted for grams of urine creatinine-is an early marker of diabetic kidney disease. Several new classes of medications are now available that effectively lower albuminuria levels with the potential to delay or prevent the progression of diabetic kidney disease. However, screening for albuminuria in the U.S. is low in population-based studies (<10% to ∼50% at most). In this study, we examine whether screening for albuminuria was improved in an integrated model of healthcare delivery following the recommendations of the National Committee for Quality Assurance mandate (an umbrella group for the managed healthcare industry) to screen for albuminuria. Methods: We examined screening for albuminuria over a 2-year period among people with Type 2 diabetes in a U.S. HMO with an electronic medical record, onto which automated laboratory ordering for albuminuria could be added when a patient appeared at the laboratory (for any reason) if albuminuria testing had not been obtained within the previous 365 days. Participants under this plan received diabetes education at no cost and panel managers to guide their diabetes care. Logistic regression using data from 2020 and 2021, separately, evaluated the relationship between patient characteristics and the likelihood of albuminuria screening. Results: There were 20,688 and 22,487 participants with Type 2 diabetes mellitus in 2020 and 2021, respectively, who were analyzed. Approximately 80% were screened for albuminuria in both years. African American participants and those aged >64 years were more likely to have completed albuminuria screening. Screened individuals had lower HbA1c, blood pressure, and low-density lipoprotein cholesterol levels than those who were not screened. Conclusions: In an integrated healthcare model, it is possible to achieve consistently high rates of albuminuria screening in people with Type 2 diabetes, especially in groups at high risk for kidney disease.