Ancestral ribonucleases back in motion for evolutionary-dynamics guided protein design.

The dynamics behavior of a protein is essential for its functionality. Here, Doucet et al. demonstrate how the evolutionary analysis of conformational pathways within a protein family serves to identify common core scaffolds that accommodate branch-specific functional regions controlled by flexibility switches, offering a model for evolutionary-dynamics based protein design.

MINERVA: A Facile Strategy for SARS-CoV-2 Whole-Genome Deep Sequencing of Clinical Samples.

Analyzing the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from clinical samples is crucial for understanding viral spread and evolution as well as for vaccine development. Existing RNA sequencing methods are demanding on user technique and time and, thus, not ideal for time-sensitive clinical samples; these methods are also not optimized for high performance on viral genomes. We developed a facile, practical, and robust approach for metagenomic and deep viral sequencing from clinical samples. We demonstrate the utility of our approach on pharyngeal, sputum, and stool samples collected from coronavirus disease 2019 (COVID-19) patients, successfully obtaining whole metatranscriptomes and complete high-depth, high-coverage SARS-CoV-2 genomes with high yield and robustness. With a shortened hands-on time from sample to virus-enriched sequencing-ready library, this rapid, versatile, and clinic-friendly approach will facilitate molecular epidemiology studies during current and future outbreaks.

Potential Contributions of Human Endogenous Retroviruses in Innate Immune Memory.

The phenomenon wherein innate immune cells adopt long-term inflammatory phenotypes following the first stimuli is named trained immunity and can improve host defense against infections. Transcriptional and epigenetic reprogramming are critical mechanisms of trained immunity; however, the regulatory networks are not entirely clear at present. The human endogenous retroviruses (HERVs) provide large amounts of transcriptional regulators in the regulatory pathways. In this study, we analyzed published large omics data to explore the roles of such "dark matter" of the human genome in trained and tolerant macrophages. We collected 80 RNA sequencing data and 62 sequencing data to detect histone modifications and active regulatory regions from nine published studies on trained and tolerant macrophages. By analyzing the characteristics of transcription and epigenetic modification of HERVs, as well as their association with gene expression, we found that 15.3% of HERVs were transcribed nonrandomly from noncoding regions and enriched in specific HERV families and specific chromosomes, such as chromosomes 11, 15, 17, and 19, and they were highly related with the expression of adjacent genes. We found that 295 differentially expressed HERVs are located in 50-kbp flanking regions of 142 differentially expressed genes. We found epigenetic changes of these HERVs and that overlap with predicted enhancers and identified 35 enhancer-like HERVs. The related genes were highly involved in the activation and inflammatory responses, such as the TLR pathway. Other pathways including phosphoinositide signaling and transport of folate and K+ might be also related with trained immunity, which require further study. These results demonstrated that HERVs might play important roles in trained immunity.

Discovery of charge order in a cuprate Mott insulator.

Copper oxide superconductors universally exhibit multiple forms of electronically ordered phases that break the native translational symmetry of the CuO2 planes. In underdoped cuprates with correlated metallic ground states, charge/spin stripes and incommensurate charge density waves (CDWs) have been experimentally observed over the years, while early theoretical studies also predicted the emergence of a Coulomb-frustrated 'charge crystal' phase in the very lightly doped, insulating limit of CuO2 planes. Here, we search for signatures of CDW order in very lightly hole-doped cuprates from the 123 family RBa2Cu3O7 - δ (RBCO; R: Y or rare earth), by using resonant X-ray scattering, electron transport, and muon spin rotation measurements to resolve the electronic and magnetic ground states fully. Specifically, Pr is used to substitute Y at the R-site to systematically suppress the superconductivity and access the extremely low hole-doping regime of the cuprate phase diagram without changing the oxygen stoichiometry. X-ray scattering data taken on Pr-doped YBCO thin films reveal an in-plane CDW order that follows the same linear evolution of wave vector versus hole concentration as oxygen-underdoped YBCO but extends all the way to the insulating and magnetically ordered Mott limit. Combined with the recent observation of charge crystal phase on an insulating surface of Bi2Sr2CaCu2O8 + z, our results in RBCO suggest that this electronic symmetry breaking is universally present in very lightly doped CuO2 planes. These findings bridge the gap between the Mott insulating state and the underdoped metallic state and underscore the prominent role that Coulomb-frustrated electronic phase separation plays among all cuprates.

SADS-CoV nsp1 inhibits the STAT1 phosphorylation by promoting K11/K48-linked polyubiquitination of JAK1 and blocks the STAT1 acetylation by degrading CBP.

The newly discovered zoonotic coronavirus swine acute diarrhea syndrome coronavirus (SADS-CoV) causes acute diarrhea, vomiting, dehydration, and high mortality rates in newborn piglets. Although SADS-CoV uses different strategies to evade the host's innate immune system, the specific mechanism(s) by which it blocks the interferon (IFN) response remains unidentified. In this study, the potential of SADS-CoV nonstructural proteins (nsp) to inhibit the IFN response was detected. The results determined that nsp1 was a potent antagonist of IFN response. SADS-CoV nsp1 efficiently inhibited signal transducer and activator of transcription 1 (STAT1) phosphorylation by inducing Janus kinase 1 (JAK1) degradation. Subsequent research revealed that nsp1 induced JAK1 polyubiquitination through K11 and K48 linkages, leading to JAK1 degradation via the ubiquitin-proteasome pathway. Furthermore, SADS-CoV nsp1 induced CREB-binding protein degradation to inhibit IFN-stimulated gene production and STAT1 acetylation, thereby inhibiting STAT1 dephosphorylation and blocking STAT1 transport out of the nucleus to receive antiviral signaling. In summary, the results revealed the novel mechanisms by which SADS-CoV nsp1 blocks the JAK-STAT signaling pathway via the ubiquitin-proteasome pathway. This study yielded valuable findings on the specific mechanism of coronavirus nsp1 in inhibiting the JAK-STAT signaling pathway and the strategies of SADS-CoV in evading the host's innate immune system.

Chronic Neuronal Inactivity Utilizes the mTOR-TFEB Pathway to Drive Transcription-Dependent Autophagy for Homeostatic Up-Scaling.

Activity-dependent changes in protein expression are critical for neuronal plasticity, a fundamental process for the processing and storage of information in the brain. Among the various forms of plasticity, homeostatic synaptic up-scaling is unique in that it is induced primarily by neuronal inactivity. However, precisely how the turnover of synaptic proteins occurs in this homeostatic process remains unclear. Here, we report that chronically inhibiting neuronal activity in primary cortical neurons prepared from embryonic day (E)18 Sprague Dawley rats (both sexes) induces autophagy, thereby regulating key synaptic proteins for up-scaling. Mechanistically, chronic neuronal inactivity causes dephosphorylation of ERK and mTOR, which induces transcription factor EB (TFEB)-mediated cytonuclear signaling and drives transcription-dependent autophagy to regulate αCaMKII and PSD95 during synaptic up-scaling. Together, these findings suggest that mTOR-dependent autophagy, which is often triggered by metabolic stressors such as starvation, is recruited and sustained during neuronal inactivity to maintain synaptic homeostasis, a process that ensures proper brain function and if impaired can cause neuropsychiatric disorders such as autism.SIGNIFICANCE STATEMENT In the mammalian brain, protein turnover is tightly controlled by neuronal activation to ensure key neuronal functions during long-lasting synaptic plasticity. However, a long-standing question is how this process occurs during synaptic up-scaling, a process that requires protein turnover but is induced by neuronal inactivation. Here, we report that mTOR-dependent signaling, which is often triggered by metabolic stressors such as starvation, is "hijacked" by chronic neuronal inactivation, which then serves as a nucleation point for transcription factor EB (TFEB) cytonuclear signaling that drives transcription-dependent autophagy for up-scaling. These results provide the first evidence of a physiological role of mTOR-dependent autophagy in enduing neuronal plasticity, thereby connecting major themes in cell biology and neuroscience via a servo loop that mediates autoregulation in the brain.

Effects of moderate/vigorous activity on 3-year body composition changes in postmenopausal women: a target trial emulation.

Background and Objective Postmenopausal women tend to experience significant changes in body composition, particularly abdominal adipose tissue (AAT) deposition patterns, which are hypothesized to be critical factors influencing future cardiometabolic disease risk. Physical activity has a demonstrable effect on body composition and overall health. However, there is little evidence for how different intensities and durations of physical activity over a sustained period of time influence AAT patterns and other measures of body composition in postmenopausal women. We emulated a target trial of physical activity interventions, including the 2018 Physical Activity Guidelines for Americans recommendations, on 3-year changes in AAT and body composition. Methods We analyzed observational data from 4,451 postmenopausal women aged 50-79 years in the Women's Health Initiative (WHI) to emulate a three-year target trial of adhering to increasing minutes of moderate (at least 15, 30, 75, 150, 300 minutes/week) and vigorous (at least 15, 30, 75, 150 minutes/week) physical activity aligned with the physical activity guidelines. All participants had repeated whole body Dual X-Ray Absorptiometry (DXA) scans with derived abdominal visceral (VAT) and subcutaneous adipose tissue (SAT). The measured differences in average levels of VAT, SAT, and other body composition measures determined at end of follow-up were estimated with the parametric-g formula. Results Over 3 years, interventions of increasing minutes of moderate activity would result in dose-dependent reductions in abdominal VAT, SAT, and overall body fat, and increases in lean soft tissue, with the greatest estimated benefit at the 2018 physical activity guideline recommendation of 150 mins/wk or more. Compared to no intervention, if all participants had adhered to at least 150 mins/wk of moderate physical activity, they would have 16.8 cm2 lower VAT (95% CI -23.1, -10.4), 26.8 cm2 lower SAT (95% CI -36.3, -17.3), 1.3% lower total body fat% (95% CI -1.8, -0.7), 1.2 % higher total lean soft tissue% (95% CI 0.7, 1.8), and 2.6 kg lower total bodyweight (95% CI -3.6, -1.5). We saw similar patterns in our vigorous-intensity activity interventions - if all participants adhered to at least 150 mins/wk, they would have experienced 6.7 cm2 lower VAT (95% CI -17.7, 4.3), 13.3 cm2 lower SAT (95% CI -28.8, 2.1), 1.0 % lower total body fat percent (95% CI -2.0, 0.0 ), % higher total lean soft tissue percent (95% CI) and a 0.9 kg lower total bodyweight (95% CI -2.7, 0.8). Conclusion This hypothetical emulated intervention indicated that postmenopausal women who adhere to physical activity guideline recommendations would experience beneficial changes in abdominal VAT, SAT, and overall body composition over 3 years. The study results underscore the imperative to explore further how physical activity may serve as a potential determinant of body composition.

E3 ubiquitin ligase COP1-mediated CEBPB ubiquitination regulates the inflammatory response of macrophages in sepsis-induced myocardial injury.

CCAAT/enhancer-binding protein beta (CEBPB) has been associated with sepsis. However, its role in sepsis-induced myocardial injury (SIMI) remains ill-defined. This research was designed to illustrate the involvement of CEBPB in SIMI and its upstream modifier. The transcriptomic changes in heart biopsies of mice that had undergone polymicrobial sepsis were downloaded from the GEO dataset for KEGG enrichment analysis. CEBPB, on the TNF signaling pathway, was significantly enhanced in the myocardial tissues of mice with SIMI. Downregulation of CEBPB alleviated SIMI, as evidenced by minor myocardial injury and inflammatory manifestations. Moreover, ubiquitination modification of CEBPB by constitutive photomorphogenesis protein 1 homolog (COP1) led to the degradation of CEBPB and inhibited inflammatory responses in macrophages. Upregulation of COP1 protected against SIMI in mice overexpressing CEBPB. Collectively, our findings demonstrated that COP1 protected the heart against SIMI through the ubiquitination modification of CEBPB, which might be a novel therapeutic approach in the future.

Coexistence of Interacting Charge Density Waves in a Layered Semiconductor.

Coexisting orders are key features of strongly correlated materials and underlie many intriguing phenomena from unconventional superconductivity to topological orders. Here, we report the coexistence of two interacting charge-density-wave (CDW) orders in EuTe_{4}, a layered crystal that has drawn considerable attention owing to its anomalous thermal hysteresis and a semiconducting CDW state despite the absence of perfect Fermi surface nesting. By accessing unoccupied conduction bands with time- and angle-resolved photoemission measurements, we find that monolayers and bilayers of Te in the unit cell host different CDWs that are associated with distinct energy gaps. The two gaps display dichotomous evolutions following photoexcitation, where the larger bilayer CDW gap exhibits less renormalization and faster recovery. Surprisingly, the CDW in the Te monolayer displays an additional momentum-dependent gap renormalization that cannot be captured by density-functional theory calculations. This phenomenon is attributed to interlayer interactions between the two CDW orders, which account for the semiconducting nature of the equilibrium state. Our findings not only offer microscopic insights into the correlated ground state of EuTe_{4} but also provide a general nonequilibrium approach to understand coexisting, layer-dependent orders in a complex system.

Effects of PGE1 on the ERS pathway in neonatal rats with hyperoxic lung injury.

BACKGROUND: With the increase in the number of low birth weight infants, oxygen therapy is more widely used. However, chronic high-concentration oxygen environments lead to hyperoxic lung injury in children, which in turn leads to bronchopulmonary dysplasia (BPD). PGE1 is widely used in the clinic for its ability to inhibit inflammation and improve circulation. Therefore, we further investigated whether PGE-1 has a therapeutic effect on hyperoxic lung injury. METHODS: Hyperoxic lung injury model was adopted for investigating the interventional effects and underlying mechanisms of intraperitoneal injection of prostaglandin E1 (PGE-1) on hyperoxic lung injury in newborn rats via relevant experimental techniques, such as Diff-Quick staining, lung wet dry specific gravity measurements, HE staining, TUNEL staining, ELISA, and the Western blot method. RESULTS: Inflammatory and apoptotic cells in the PGE1-treated group were significantly lower than those in the hyperoxic lung injury group (p < 0.05); and the contents of IL-1ß, IL-6 and TNF-α in the treated group were significantly lower than those in the model group (p < 0.05). Caspase-3, CHOP, GRP78 and Bcl-2/Bax protein expression in the treatment group was significantly lower than that in the model group (p < 0.05). CONCLUSION: PGE-1 has a therapeutic effect on hyperoxic lung injury in neonatal rats. IMPACT: PGE1 treatment reduces levels of inflammatory cells and pro-inflammatory cytokines and decreases apoptosis. PGE1 has a therapeutic effect on BPD through the endoplasmic reticulum stress pathway. This study offers the possibility of PGE1 for the treatment of BPD.