Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.

High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in nonstructural protein 14 (nsp14), which excises nucleotides including antiviral drugs misincorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here, we determined a 1.6-Å resolution crystal structure of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) ExoN in complex with its essential cofactor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. We also show that the ExoN activity can rescue a stalled RNA primer poisoned with sofosbuvir and allow RdRp to continue its extension in the presence of the chain-terminating drug, biochemically recapitulating proofreading in SARS-CoV-2 replication. Molecular dynamics simulations further show remarkable flexibility of multidomain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA binding to support its exonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN-nsp10 complex serves as a platform for future development of anticoronaviral drugs or strategies to attenuate the viral virulence.

Hispidulin exerts a protective effect against oleic acid induced-ARDS in the rat via inhibition of ACE activity and MAPK pathway.

This study investigates the protective role of Hispidulin on acute respiratory distress syndrome (ARDS) in rats. Rats were divided into three groups: control, ARDS, ARDS+ Hispidulin. The ARDS models were established by injecting rats with oleic acid. Hispidulin (100 mg/kg) was injected i.p. an hour before ARDS. Myeloperoxidase (MPO), Interleukin-8 (IL-8), Mitogen-activated protein kinases (MAPK), Lipid Peroxidation (LPO), Superoxide Dismutase (SOD), Glutathione (GSH), and Angiotensin-converting enzyme (ACE) were determined by ELISA. Tumor necrosis factor-alpha (TNF-α) expression was described by RT-qPCR. Caspase-3 immunostaining was performed to evaluate apoptosis. Compared with the model group, a significant decrease was observed in the MPO, IL-8, MAPK, ACE, LPO levels, and TNF-α expression in the ARDS+ Hispidulin group. Moreover, reduced caspase-3 immunoreactivity and activity of ACE were detected in the Hispidulin+ARDS group. The protective effect of Hispidulin treatment may act through inhibition of the ACE activity and then regulation of inflammatory cytokine level and alteration of apoptosis.

Protective effect of melatonin and ascorbic acid combination on sepsis-induced lung injury: An Experimental study.

This study investigated the synergistic protective effects of melatonin (MEL) and ascorbic acid (vitamin C, ASA) in treating sepsis-induced lung injury in rats. Rats were divided into five groups: control, cecal ligation and puncture (CLP), CLP + MEL, CLP + ASA and CLP + MEL + ASA. The effects of MEL (10 mg/kg), ASA (100 mg/kg) and their combination on oxidative stress, inflammation and histopathology were evaluated in septic rats' lung tissues. Sepsis-induced oxidative stress and inflammation were evident through increased levels of malondialdehyde (MDA), myeloperoxidase (MPO), total oxidant status (TOS) and oxidative stress index (OSI); decreased levels of superoxide dismutase (SOD), glutathione (GSH), catalase (CAT) and glutathione peroxidase (GPx); and elevated levels of tumour necrosis factor-α (TNF-α) and interleukin-1 ß (IL-1ß) in the lung tissue. Treatment with MEL, ASA and their combination significantly improved antioxidant capacity and reduced oxidative stress, with the combination treatment being more effective. The combination treatment also significantly reduced TNF-α and IL-1ß levels and improved peroxisome proliferator-activated receptor (PPAR), arylesterase (ARE) and paraoxonase (PON) levels in the lung tissue. Histopathological examination showed reduced oedema and lymphocyte infiltration with a lung tissue appearance similar to the control group. Immunohistochemical staining for caspase 3 demonstrated reduced immune positivity in the treatment groups. In conclusion, this study supports the potential synergistic protective effects of MEL and ASA in treating sepsis-induced lung injury. The combination therapy could effectively reduce oxidative stress, inflammation and improve antioxidant capacity in septic rats, suggesting a promising strategy for treating sepsis-induced lung injury.

Technology Trends for Massive MIMO towards 6G.

At the dawn of the next-generation wireless systems and networks, massive multiple-input multiple-output (MIMO) in combination with leading-edge technologies, methodologies, and architectures are poised to be a cornerstone technology. Capitalizing on its successful integration and scalability within 5G and beyond, massive MIMO has proven its merits and adaptability. Notably, a series of evolutionary advancements and revolutionary trends have begun to materialize in recent years, envisioned to redefine the landscape of future 6G wireless systems and networks. In particular, the capabilities and performance of future massive MIMO systems will be amplified through the incorporation of cutting-edge technologies, structures, and strategies. These include intelligent omni-surfaces (IOSs)/intelligent reflecting surfaces (IRSs), artificial intelligence (AI), Terahertz (THz) communications, and cell-free architectures. In addition, an array of diverse applications built on the foundation of massive MIMO will continue to proliferate and thrive. These encompass wireless localization and sensing, vehicular communications, non-terrestrial communications, remote sensing, and inter-planetary communications, among others.

Functional and Structural Insights into a Vif/PPP2R5 Complex Elucidated Using Patient HIV-1 Isolates and Computational Modeling.

Human immunodeficiency virus type 1 (HIV-1) Vif recruits a cellular ubiquitin ligase complex to degrade antiviral APOBEC3 enzymes (APOBEC3C-H) and PP2A phosphatase regulators (PPP2R5A to PPP2R5E). While APOBEC3 antagonism is the canonical function of HIV-1 Vif, this viral accessory protein is also known to trigger G2/M cell cycle arrest. Vif initiates G2/M arrest by degrading multiple PPP2R5 family members, an activity prevalent among diverse HIV-1 and simian immunodeficiency virus (SIV) isolates. Here, computational protein-protein docking was used to delineate a Vif/CBF-ß/PPP2R5 complex in which Vif is predicted to bind the same PPP2R5 surface as physiologic phosphatase targets. This model was tested using targeted mutagenesis of amino acid residues within or adjacent to the putative interface to show loss or retention, respectively, of Vif-induced PPP2R5 degradation activity. Additionally, expression of a peptide that mimics cellular targets of PPP2R5s robustly inhibited Vif-mediated degradation of PPP2R5A but not APOBEC3G. Moreover, live-cell imaging studies examining Vif-mediated degradation of PPP2R5A and APOBEC3G within the same cell revealed that PPP2R5A degradation kinetics are comparable to those of APOBEC3G with a half-life of roughly 6 h postinfection, demonstrating that Vif can concurrently mediate the degradation of distinct cellular substrates. Finally, experiments with a panel of patient-derived Vif isolates indicated that PPP2R5A degradation activity is common in patient-derived isolates. Taken together, these results support a model in which PPP2R5 degradation and global changes in the cellular phosphoproteome are likely to be advantageous for viral pathogenesis.IMPORTANCE A critical function of HIV-1 Vif is to counteract the family of APOBEC3 innate immune proteins. It is also widely accepted that Vif induces G2/M cell cycle arrest in several different cell types. Recently, it has been shown that Vif degrades multiple PPP2R5 phosphoregulators to induce the G2/M arrest phenotype. Here, computational approaches are used to test a structural model of the Vif/PPP2R5 complex. In addition, imaging studies are used to show that Vif degrades these PPP2R5 substrates in roughly the same time frame as APOBEC3 degradation and that this activity is prevalent in patient-derived Vif isolates. These studies are important by further defining PPP2R5 proteins as a bona fide substrate of HIV-1 Vif.

The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release.

Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen-deuterium exchange MS provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic, thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors.

Determinants of Oligonucleotide Selectivity of APOBEC3B.

APOBEC3B (A3B) is a prominent source of mutation in many cancers. To date, it has been difficult to capture the native protein-DNA interactions that confer A3B's substrate specificity by crystallography due to the highly dynamic nature of wild-type A3B active site. We use computational tools to restore a recent crystal structure of a DNA-bound A3B C-terminal domain mutant construct to its wild type sequence, and run molecular dynamics simulations to study its substrate recognition mechanisms. Analysis of these simulations reveal dynamics of the native A3Bctd-oligonucleotide interactions, including the experimentally inaccessible loop 1-oligonucleotide interactions. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose show a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B, starting from the DNA-bound open state, experience a rapid and consistent closure of the binding site, reaching conformations incompatible with substrate binding. This study reveals a more realistic and dynamic view of the wild type A3B binding site and provides novel insights for structure-guided design efforts for A3B.

Ensemble Docking in Drug Discovery.

Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that is used in docking candidate ligands. This approach is now well established in the field of early-stage drug discovery. This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling.

Dynamics and Molecular Mechanisms of p53 Transcriptional Activation.

The "guardian of the genome", p53, functions as a tumor suppressor that responds to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Mutation of p53 disrupts its tumor suppressor function, leading to various types of human cancers. One particular mutant, R175H, is a structural mutant that inactivates the DNA damage response pathway and acquires oncogenic functions that promotes both cancer and drug resistance. Our current work aims to understand how p53 wild-type function is disrupted due to the R175H mutation. We use a series of atomistic integrative models built previously from crystal structures of the full-length p53 tetramer bound to DNA and model the R175H mutant using in silico site-directed mutagenesis. Explicitly solvated all-atom molecular dynamics (MD) simulations on wild-type and the R175H mutant p53 reveal insights into how wild-type p53 searches and recognizes DNA, and how this mechanism is disrupted as a result of the R175H mutation. Specifically, our work reveals the optimal quaternary DNA binding mode of the DNA binding domain and shows how this binding mode is altered via symmetry loss as a result of the R175H mutation, indicating a recognition mechanism that is reminiscent of the asymmetry seen in wild type p53 binding to nonspecific genomic elements. Altogether our work sheds new light into the hitherto unseen molecular mechanisms governing transcription factor, DNA recognition.

RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting.

Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3' processome in uridylation of gRNA precursors and mature guide RNAs. Along with KPAP1 poly(A) polymerase, RET1 also participates in mRNA translational activation. RET1 is divergent from human TUTases and is essential for parasite viability in the mammalian host and the insect vector. Given its robust in vitro activity, RET1 represents an attractive target for trypanocide development. Here, we report high-resolution crystal structures of the RET1 catalytic core alone and in complex with UTP analogs. These structures reveal a tight docking of the conserved nucleotidyl transferase bi-domain module with a RET1-specific C2H2 zinc finger and RNA recognition (RRM) domains. Furthermore, we define RET1 region required for incorporation into the 3' processome, determinants for RNA binding, subunit oligomerization and processive UTP incorporation, and predict druggable pockets.

The investigation of the sludge reduction efficiency and mechanisms in oxic-settling-anaerobic (OSA) process.

This paper aims to provide a full understanding of the sludge reduction mechanisms in the oxic-settling-anaerobic (OSA) process and presents an evaluation of the sludge reduction efficiencies and sludge characteristics in this process compared to the conventional activated sludge process. Fifty-eight percent reduction in observed yield in the OSA process was achieved compared to the control system at the end of the operational period with no deterioration of effluent quality. The settleability of sludge in the OSA process was also found to be better than that of the control system in terms of sludge volume index. In long-term operation, capillary suction time and specific resistance to filtration values confirmed that the OSA process showed good filterability characteristics. The results of batch experiments showed that higher endogenous respiration in the systems might lead to lower sludge production and that energy uncoupling had only a limited impact on sludge reduction.

Parental socioeconomic status and the neural basis of arithmetic: differential relations to verbal and visuo-spatial representations.

We examined the relation of parental socioeconomic status (SES) to the neural bases of subtraction in school-age children (9- to 12-year-olds). We independently localized brain regions subserving verbal versus visuo-spatial representations to determine whether the parental SES-related differences in children's reliance on these neural representations vary as a function of math skill. At higher SES levels, higher skill was associated with greater recruitment of the left temporal cortex, identified by the verbal localizer. At lower SES levels, higher skill was associated with greater recruitment of right parietal cortex, identified by the visuo-spatial localizer. This suggests that depending on parental SES, children engage different neural systems to solve subtraction problems. Furthermore, SES was related to the activation in the left temporal and frontal cortex during the independent verbal localizer task, but it was not related to activation during the independent visuo-spatial localizer task. Differences in activation during the verbal localizer task in turn were related to differences in activation during the subtraction task in right parietal cortex. The relation was stronger at lower SES levels. This result suggests that SES-related differences in the visuo-spatial regions during subtraction might be based in SES-related verbal differences.

Parents' Talk About Letters With Their Young Children.

A literacy-related activity that occurs in children's homes-talk about letters in everyday conversations-was examined using data from 50 children who were visited every 4 months between 14 and 50 months. Parents talked about some letters, including those that are common in English words and the first letter of their children's names, especially often. Parents' focus on the child's initial was especially strong in families of higher socioeconomic status, and the extent to which parents talked about the child's initial during the later sessions of the study was related to the children's kindergarten reading skill. Conversations that included the child's initial were longer than those that did not, and parents presented a variety of information about this letter.

A tale of two hands: children's early gesture use in narrative production predicts later narrative structure in speech.

Speakers of all ages spontaneously gesture as they talk. These gestures predict children's milestones in vocabulary and sentence structure. We ask whether gesture serves a similar role in the development of narrative skill. Children were asked to retell a story conveyed in a wordless cartoon at age five and then again at six, seven, and eight. Children's narrative structure in speech improved across these ages. At age five, many of the children expressed a character's viewpoint in gesture, and these children were more likely to tell better-structured stories at the later ages than children who did not produce character-viewpoint gestures at age five. In contrast, framing narratives from a character's perspective in speech at age five did not predict later narrative structure in speech. Gesture thus continues to act as a harbinger of change even as it assumes new roles in relation to discourse.

Effects of age and language on co-speech gesture production: an investigation of French, American, and Italian children's narratives.

The aim of this paper is to compare speech and co-speech gestures observed during a narrative retelling task in five- and ten-year-old children from three different linguistic groups, French, American, and Italian, in order to better understand the role of age and language in the development of multimodal monologue discourse abilities. We asked 98 five- and ten-year-old children to narrate a short, wordless cartoon. Results showed a common developmental trend as well as linguistic and gesture differences between the three language groups. In all three languages, older children were found to give more detailed narratives, to insert more comments, and to gesture more and use different gestures--specifically gestures that contribute to the narrative structure--than their younger counterparts. Taken together, these findings allow a tentative model of multimodal narrative development in which major changes in later language acquisition occur despite language and culture differences.

Investigating the individual and combined effects of coenzyme Q10 and vitamin C on CLP-induced cardiac injury in rats.

Sepsis-induced cardiac injury represents a major clinical challenge, amplifying the urgency for effective therapeutic interventions. This study aimed to delve into the individual and combined prophylactic effects of Vitamin C (Vit C) and Coenzyme Q10 (CoQ10) against inflammatory heart injury in a cecal ligation and puncture (CLP) induced polymicrobial sepsis rat model. Thirty adult female Sprague-Dawley rats were randomly divided into five groups: Control, CLP, Vitamin C, CoQ10, and Vit C + CoQ10, each consisting of six rats. Treatments were administered orally via gavage for 10 days prior to the operation. Eighteen hours post-sepsis induction, the animals were euthanized, and specimens were collected for analysis. The study examined variations in oxidative (TOS, OSI, MDA, MPO) and antioxidative markers (TAS, SOD, CAT, GSH), histopathological changes, inflammatory cytokine concentrations (TNF-α, IL-1ß), nitric oxide (NO) dynamics, and cardiac indicators such as CK-MB. Impressively, the combined regimen markedly diminished oxidative stress, and antioxidative parameters reflected notable enhancements. Elevated NO levels, a central player in sepsis-driven inflammatory cascades, were effectively tempered by our intervention. Histological examinations corroborated the biochemical data, revealing diminished cardiac tissue damage in treated subjects. Furthermore, a marked suppression in pro-inflammatory cytokines was discerned, solidifying the therapeutic potential of our intervention. Interestingly, in certain evaluations, CoQ10 exhibited superior benefits over Vit C. Collectively, these findings underscore the potential therapeutic promise of Vit C and CoQ10 combination against septic cardiac injuries in rats.

Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening.

APOBEC3B cytosine deaminase contributes to the mutational burdens of tumors, resulting in tumor progression and therapy resistance. Small molecule APOBEC3B inhibitors have potential to slow or mitigate these detrimental outcomes. Through molecular dynamics (MD) simulations and computational solvent mapping analysis, we identified a novel putative allosteric pocket on the C-terminal domain of APOBEC3B (A3Bctd), and virtually screened the ChemBridge Diversity Set (N~110,000) against both the active and potential allosteric sites. Selected high-scoring compounds were subsequently purchased, characterized for purity and composition, and tested in biochemical assays, which yielded 13 hit compounds. Orthogonal NMR assays verified binding to the target protein. Initial selectivity studies suggest these compounds preferentially target A3Bctd over related deaminase APOBEC3A (A3A), and MD simulations indicate this selectivity may be due to the steric repulsion from H56 that is unique to A3A. Taken together, our studies represent the first virtual screening effort against A3Bctd that has yielded candidate inhibitors suitable for further development.

Phospho-Ser383-Elk-1 is localized to the mitotic spindles during cell cycle and interacts with mitotic kinase Aurora-A.

Elk-1 is a member of the E-twenty-six (ETS) domain superfamily of transcription factors and has been traditionally associated with mitogen-induced immediate early gene transcription upon phosphorylation by mitogen activated protein kinases (ERK/MAPK). Elk-1 is not only upregulated but also phosphorylated in brain tumour cells. However, in this study, we show for the first time that S383-phosphorylated Elk-1 (P-S383-Elk-1) is associated with mitotic spindle poles from metaphase through telophase and relocates to the spindle midbody during cytokinesis, while Thr417Ala mutation is associated with DNA throughout mitosis. Serine 383 phosphorylation appears to be important for polar localization of Elk-1, since exogenous protein including serine-to-alanine mutation was seen to be distributed throughout the spindle fibres. We further show that Elk-1 interacts with the cell cycle kinase Aurora-A, and when Aurora inhibitors are used, P-S383-Elk-1 fails to localize to the poles and remains associated with DNA. Apart from one transcriptional repressor molecule, Kaiso, this is the first time a transactivator was shown to possess such mitotic localization and interaction. The functional significance and detailed mechanism of this cell cycle-related localization of Elk-1 are yet to be determined.

Association of epicardial adipose tissue thickness by echocardiography and hypertension.

OBJECTIVES: Epicardial adipose tissue (EAT) is a component of visceral adiposity with endocrine and paracrine effects. It is also associated with metabolic syndrome (MetS). In this study, we investigated the relationship between EAT thickness and hypertension that is a component of MetS. STUDY DESIGN: Enrolled in this study were 140 hypertensive patients and 60 age- and sex-similar normotensive controls. EAT thickness was measured using 2-D echocardiography from the parasternal long- and short-axis views. EAT thicknesses were compared between patients with hypertension and controls. The effects of hypertension on EAT thickness were evaluated like other components of MetS. RESULTS: EAT thickness was increased in hypertensive patients compared to normotensive controls (6.3 ± 1.7 mm vs. 5.3 ± 1.6 mm; p<0.001). EAT thickness correlated with systolic and diastolic blood pressures (r=0.233, p=0.001; r=0.144, p=0.047, respectively). EAT thickness was further increased in patients with uncontrolled hypertension than in those with controlled hypertension (6.6 ± 1.7 mm vs. 5.9 ± 1.8 mm, p=0.046). When linear regression analysis was performed to assess the effect of hypertension on EAT thickness like the other components of MetS, hypertension (p=0.009, 95% CI 0.236-1.619), waist circumference (p=0.003, 95%CI 0.339-1.640), HDL-cholesterol (p=0.046, 95% CI, -0.054 - 0.001) and blood glucose levels (p=0.007, 95% CI, 0.003-0.002) were found to be independent correlates of EAT thickness. CONCLUSION: EAT thickness is associated with hypertension. Hypertension could be contributing factor for the development of EAT thickness like the other components of MetS.

Protective effect of astaxanthin and metformin in the liver of rats in which the polycystic ovary syndrome model was formed by giving letrozole.

Objectives: In this study, the effects of astaxanthin on liver tissue in rats with polycystic ovary syndrome (PCOS) were evaluated. Materials and Methods: Fifty-four Spraque-Dawley rats were divided into 9 groups: Groups: Control, PCOS, PCOS+Metformin (Met), PCOS+ Astaxanthin (ASX)10, PCOS+ASX20, PCOS+ASX40, PCOS+Met+ASX10, PCOS+Met+ASX20, and PCOS+Met+ASX40. PCOS was induced in female rats by oral administration of letrozole (1 mg/kg) for 21 days. Rats were treated with ASX (10 mg/kg), ASX (20 mg/kg), ASX (40 mg/kg), and metformin (20 mg/kg) for 7 days after PCOS induction. At the end of the experiment, malondialdehyde (MDA) and superoxide dismutase (SOD) levels were measured in the liver tissue. The liver was stained with hematoxylin/eosin for histological examination. Additionally, NF-kB and caspase 3 were analyzed immunohistochemically. Results: A remarkable abnormality was observed in the biochemical and histological parameters in the liver tissue of the PCOS model rats. Astaxanthin dose-dependently normalized the MDA level. Additionally, astaxanthin showed a protective effect by increasing the SOD level and increasing its antioxidant activities. We observed that administration of astaxanthin in addition to metformin applied in the standard was more effective. Caspase 3 and NF-kB immune positivity was lower in the groups given astaxanthin compared with PCOS. Histologically, it was observed that astaxanthin improved the deteriorated liver morphology in the letrozole-induced PCOS group. Conclusion: According to our results, it was observed that astaxanthin had antioxidant, anti-inflammatory and anti-apoptotic effects on PCOS in the treatment groups. Therefore, it was concluded that astaxanthin may have a protective effect against PCOS side effects.