Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

SPATA2 regulates the activation of RIPK1 by modulating linear ubiquitination.

Stimulation of cells with TNFα leads to the formation of the TNF-R1 signaling complex (TNF-RSC) to mediate downstream cellular fate decision. Activation of the TNF-RSC is modulated by different types of ubiquitination and may lead to cell death, including apoptosis and necroptosis, in both RIPK1-dependent and RIPK1-independent manners. Spata2 (spermatogenesis-associated 2) is an adaptor protein recruited into the TNF-RSC to modulate the interaction between the linear ubiquitin chain assembly complex (LUBAC) and the deubiquitinase CYLD (cylindromatosis). However, the mechanism by which Spata2 regulates the activation of RIPK1 is unclear. Here, we report that Spata2-deficient cells show resistance to RIPK1-dependent apoptosis and necroptosis and are also partially protected against RIPK1-independent apoptosis. Spata2 deficiency promotes M1 ubiquitination of RIPK1 to inhibit RIPK1 kinase activity. Furthermore, we provide biochemical evidence for the USP domain of CYLD and the PUB domain of the SPATA2 complex preferentially deubiquitinating the M1 ubiquitin chain in vitro. Spata2 deficiency also promotes the activation of MKK4 and JNK and cytokine production independently of RIPK1 kinase activity. Spata2 deficiency sensitizes mice to systemic inflammatory response syndrome (SIRS) induced by TNFα, which can be suppressed by RIPK1 inhibitor Nec-1s. Thus, Spata2 can regulate inflammatory response and cell death in both RIPK1-dependent and RIPK1-independent manners.

RNA target highlights in CASP15: Evaluation of predicted models by structure providers.

The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who provided experimental structures to challenge the predictors. In this article, these scientists offer a unique and valuable analysis of both the successes and areas for improvement in the predicted models. All 10 RNA-only targets yielded predictions topologically similar to experimentally determined structures. For one target, experimentalists were able to phase their x-ray diffraction data by molecular replacement, showing a potential application of structure predictions for RNA structural biologists. Recommended areas for improvement include: enhancing the accuracy in local interaction predictions and increased consideration of the experimental conditions such as multimerization, structure determination method, and time along folding pathways. The prediction of RNA-protein complexes remains the most significant challenge. Finally, given the intrinsic flexibility of many RNAs, we propose the consideration of ensemble models.

Three types of HLA-G+ extravillous trophoblasts that have distinct immune regulatory properties.

During pregnancy, invading HLA-G+ extravillous trophoblasts (EVT) play a key role in placental development, uterine spiral artery remodeling, and prevention of detrimental maternal immune responses to placental and fetal antigens. Failures of these processes are suggested to play a role in the development of pregnancy complications, but very little is known about the underlying mechanisms. Here we present validated methods to purify and culture primary HLA-G+ EVT from the placental disk and chorionic membrane from healthy term pregnancy. Characterization of HLA-G+ EVT from term pregnancy compared to first trimester revealed their unique phenotypes, gene expression profiles, and differing capacities to increase regulatory T cells (Treg) during coculture assays, features that cannot be captured by using surrogate cell lines or animal models. Furthermore, clinical variables including gestational age and fetal sex significantly influenced EVT biology and function. These methods and approaches form a solid basis for further investigation of the role of HLA-G+ EVT in the development of detrimental placental inflammatory responses associated with pregnancy complications, including spontaneous preterm delivery and preeclampsia.

Switch-associated adverse events: focus on olanzapine.

OBJECTIVES:: Switching between different antipsychotic therapies is a frequent occurrence in the management of patients with schizophrenia and other psychotic disorders. This paper provides a review of the principles of antipsychotic switching and discusses pharmacological principles underlying adverse events that occur while switching olanzapine to another antipsychotic medication. It offers suggestions for management of switch-associated adverse events in clinical settings. CONCLUSIONS:: Few publications explore olanzapine switch-related adverse events, the underlying pharmacological principles and appropriate switching strategies to minimise the risk of adverse events. There is still a need for further studies to verify existing knowledge and assist in the development of 'gold standard' guidelines that outline appropriate switching strategies and duration of the switching process to reduce and avoid adverse events.

Mesenchymal stem cells protect neurons against hypoxic-ischemic injury via inhibiting parthanatos, necroptosis, and apoptosis, but not autophagy.

Cellular therapy with mesenchymal stem cells (MSCs) protects cortical neurons against hypoxic-ischemic injury of stroke. Although sorts of efforts have been made to confirm the neuroprotective effect of MSCs on neurons against hypoxic-ischemic injury, the mechanism is until now far away from clear. Here in this study, oxygen-glucose deprivation (OGD)-injured neuron model was applied to mimic the neuronal hypoxic-ischemic injury in vitro. Co-culturing with MSCs in a transwell co-culture system, the OGD injured neurons were rescued by 75.0 %. Further data demonstrated that co-culturing with MSCs protected the cortical neurons from the OGD-induced parthanatos by alleviating apoptosis-inducing factor (AIF) nuclear translocation; attenuated the neuronal necroptosis by down-regulating the expression of the two essential kinases in necroptosis, receptor interacting protein kinase1 (RIP1) and 3 (RIP3); rescued the neurons from apoptosis by deactivating caspase-3; whilst performed no significant influence on OGD-induced neuronal autophagy, according to its failed regulation on Beclin1. In conclusion, MSCs potentially protect the cortical neurons from OGD-injury in vitro, through rescuing neurons from the cell death of parthanatos, necroptosis, and apoptosis, but not autophagy, which could provide some evidence to the mechanism explanation on stem cell treatment for ischemic stroke.

Remineralization of early caries by chewing sugar-free gum: a clinical study using quantitative light-induced fluorescence.

PURPOSE: To determine whether sugar-free gum can provide remineralization and caries control of active enamel caries lesions compared to baseline (before gum chewing) and to a no-gum group, following daily chewing for 12 weeks by school children; to determine whether chewing frequency can affect the extent of remineralization. METHOD: A pragmatic cluster-randomized controlled clinical trial with schools as the unit of randomization was employed. Three schools in Chengdu, PR China comprised the clusters. The study was approved by the Internal Review Board of Sichuan University. 177 school children, 8-13 years old, with at least one visible white-spot lesion were enrolled in the study. Each of the three clusters was randomly assigned to one of three groups: (1) no gum; (2) chew 2 pieces of sugar-free gum for 20 minutes, 3x per day; (3) chew 2 pieces of sugar-free gum for 12 minutes, 5x per day. White-spot lesions were examined by quantitative light-induced fluorescence (QLF) at baseline and after 4, 8, and 12 weeks of treatment. RESULTS: 155 subjects completed the study. Of them, the mean values of fluorescence loss at baseline were 9.52, 9.83 and 9.17 for no-gum group, 3x per day group and 5x per day group, respectively. For the area, the mean values at baseline were 2.52, 2.61 and 2.57 mm2 for no-gum group, 3x per day group and 5x per day group, respectively. For AQ, the mean values at baseline were -27.91, -28.29 and -29.67 for no-gum group, 3x per day group and 5x per day group, respectively. To adjust for differences in groups at baseline, ANCOVA was used. After 12-weeks, for all QLF metrics, the absolute values of 5x per day group were the lowest and the no gum group was the highest; the differences among three groups were statistically significant (P < 0.05). For AQ, which was accepted as the most useful metrics of QLF system, the adjusted mean values at 12 weeks were -26.35, -19.81 and -17.58 for no-gum group, 3x per day group and 5x per day group, respectively. There were significant differences between groups.

Early pregnancy maternal blood pressure and risk of preeclampsia: Does the association differ by parity? Evidence from 14,086 women across 7 countries.

OBJECTIVE: To determine if the relationship between blood pressure (BP) before 16 weeks' gestation and subsequent onset of preeclampsia differs by parity, and by history of hypertensive disorders of pregnancy (HDP) in parous women. STUDY DESIGN: Data from two studies were pooled. First, routinely collected clinical data from three metropolitan hospitals in Sydney, Australia (2017-2020), where BP was measured as part of routine clinical care using validated mercury-free sphygmomanometers. Second, prospectively collected research data from the INTERBIO-21st Study, conducted in six countries, investigating the epidemiology of fetal growth restriction and preterm birth, where BP was measured by dedicated research staff using an automated machine validated for use in pregnancy. MAIN OUTCOME: Adjusted odds ratios (aOR) (95% confidence interval (CI)) for the association of systolic BP (SBP), diastolic BP (DBP) and mean arterial pressure (MAP) with preeclampsia were obtained from logistic regression models. Models were adjusted for age, smoking, body mass index, previous hypertension, previous diabetes, and previous preeclampsia. Interactions for parity, and history of HDP in parous women were included. RESULTS: There were 14,086 pregnancies (Sydney = 11008, INTERBIO-21st = 3078) in the pooled analyses, 6914 (49 %) were parous, of which 414 (6.0 %) had a history of HDP. Nulliparous women had a higher risk of preeclampsia (2.6 %) compared with parous women (1.5 %): [aOR (95 %CI) 3.61 (2.67, 4.94)], as did parous women with a history of HDP (15.0 %) compared with no history (0.7 %) [12.70 (8.02, 20.16)]. MAP before 16 weeks' gestation (mean [SD] 78.8[8.6] mmHg) was more strongly associated than SBP or DBP with development of preeclampsia in parous women [2.22 (1.81, 2.74)] per SD higher MAP] compared with nulliparous women [1.58 (1.34, 1.87)] (p for interaction 0.013). There were no significant differences on the effect of blood pressure on preeclampsia in parous women by history of HDP (p for interaction 0.5465). CONCLUSION: The risk of preeclampsia differs according to parity and history of HDP in a previous pregnancy. Blood pressure in early pregnancy predicts preeclampsia in all groups, although more strongly associated in parous than nulliparous women, but no different in parous women by history of HDP.

A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.

We present an integrated single-cell RNA sequencing atlas of the primary breast tumor microenvironment (TME) containing 236,363 cells from 119 biopsy samples across eight datasets. In this study, we leverage this resource for multiple analyses of immune and cancer epithelial cell heterogeneity. We define natural killer (NK) cell heterogeneity through six subsets in the breast TME. Because NK cell heterogeneity correlates with epithelial cell heterogeneity, we characterize epithelial cells at the level of single-gene expression, molecular subtype, and 10 categories reflecting intratumoral transcriptional heterogeneity. We develop InteractPrint, which considers how cancer epithelial cell heterogeneity influences cancer-immune interactions. We use T cell InteractPrint to predict response to immune checkpoint inhibition (ICI) in two breast cancer clinical trials testing neoadjuvant anti-PD-1 therapy. T cell InteractPrint was predictive of response in both trials versus PD-L1 (AUC = 0.82, 0.83 vs. 0.50, 0.72). This resource enables additional high-resolution investigations of the breast TME.

Biodiversity monitoring for a just planetary future.

Data that influence policy and major investment decisions risk entrenching social and political inequities.

Bridging adaptive management and reinforcement learning for more robust decisions.

From out-competing grandmasters in chess to informing high-stakes healthcare decisions, emerging methods from artificial intelligence are increasingly capable of making complex and strategic decisions in diverse, high-dimensional and uncertain situations. But can these methods help us devise robust strategies for managing environmental systems under great uncertainty? Here we explore how reinforcement learning (RL), a subfield of artificial intelligence, approaches decision problems through a lens similar to adaptive environmental management: learning through experience to gradually improve decisions with updated knowledge. We review where RL holds promise for improving evidence-informed adaptive management decisions even when classical optimization methods are intractable and discuss technical and social issues that arise when applying RL to adaptive management problems in the environmental domain. Our synthesis suggests that environmental management and computer science can learn from one another about the practices, promises and perils of experience-based decision-making. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Improving the patient decision-making experience for cataract surgery during the COVID-19 era.

OBJECTIVE: To explore whether video-based patient decision aids (VBPDAs) for cataract surgery consultation can enhance a patient's decision-making process while upholding safety regulations during the coronavirus disease 2019 (COVID-19) pandemic. DESIGN: Single-centre consecutive case study. PARTICIPANTS: 147 patients, with an average age of 70 years, who came in for a cataract surgery consult were enrolled in this study. METHODS: All patients watched part 1 of the VBPDA outlining the process of cataract surgery and the decisions involved. Patients then underwent cataract surgery consultation with an ophthalmologist. Afterward, if the patient was indicated for surgery, part 2 of the VBPDA was played. At the end of the visit, all patients completed a survey assessing the effects of COVID-19 safety precautions on their appointment. In addition, patients who had gone forward with surgery complete the Decisional Conflict Scale (DCS). RESULTS: For patients proceeding with cataract surgery, the median DCS score was 9.38 (range, 0-54.69, min-max) on a scale from 0 to 100 (low-high decisional conflict). A DCS score <25 indicates low decisional conflict (n = 76, 68.47%) and a score >25 indicates feeling unsure (n = 35, 31.53%). The DCS also can be separated into various subscales: the informed subscale (median = 8.33; min-max = 0-66.67), values subscale (16.67, 0-58.33), support subscale (8.33, 0-50.00), uncertainty subscale (8.33, 0-83.33), and effective decision subscale (0, 0-37.50). CONCLUSION: Our study found VBPDAs to be an effective tool to enhance the patient decision-making process for cataract surgery during the COVID-19 era.

Cushing Syndrome due to Adrenocortical Carcinoma During Pregnancy.

Cushing syndrome resulting from adrenocortical carcinoma in pregnancy is exceedingly rare. There are no validated guidelines to establish a diagnosis or guide management in pregnancy. We provide a case of a 31-year-old woman presenting for management of diabetes in pregnancy who appeared cushingoid. She was subsequently diagnosed with ACTH-independent Cushing syndrome and experienced preterm labor at 33 weeks' gestation, delivering a healthy infant. Four weeks postpartum, the patient underwent a left adrenalectomy and was subsequently diagnosed with adrenocortical carcinoma.

Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically-determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus SARS-CoV-2, resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4-6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across the studied human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9-8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4-9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities, with implications for potential protein-binding modes and therapeutic targets.

Ab Interno XEN Gel Stent Implantation in Eyes with Previous Tube Shunt Surgery.

Purpose: After tube shunt surgery, many factors may contribute to insufficient filtration over time, prompting further intervention to achieve optimal intraocular pressure (IOP) control. This study explores whether ab interno XEN gel stent implantation could be a viable approach in eyes that need further IOP reduction after tube shunt surgery. Methods: This is a retrospective, single-surgeon case series on ab interno XEN45 gel stent implantation in eyes that had previous tube shunt surgery. Main outcome measures were IOP and number of glaucoma medications at the pre-operative visit, post-operative week (POW) 1, and post-operative month (POM) 1, 3, 6, and 12. Adverse events and further interventions were noted. Surgery outcome was qualified as absolute success (IOP ≤ 18mmHg or ≥ 20% IOP reduction without glaucoma medications), qualified success (IOP ≤ 18mmHg or ≥ 20% IOP reduction with glaucoma medications), or failure (IOP > 18mmHg and < 20% IOP reduction with maximum tolerated glaucoma medications). Results: 7 eyes from 6 patients were included in this study. IOP was reduced from 23.9 ± 5.3 mmHg (mean ± standard deviation) pre-operatively to 14.0 ± 5.3 mmHg at POM12 (p < 0.05). Number of glaucoma medications was reduced from 4.3 ± 1.3 pre-operatively to 1.6 ± 1.6 at POM12 (p < 0.05). Hypotony and choroidal effusion were noted in one case which resolved before POM1. Bleb needling was required in 3 of the 7 eyes (43%), with one eye requiring needling twice. By POM12, 2 of 7 eyes (29%) achieved absolute success, 4 eyes (57%) qualified success, and 1 eye (14%) was qualified as failure. Conclusion: Ab interno XEN gel stent can effectively reduce IOP and number of glaucoma medications after failed tube shunt surgery. Nonetheless, further interventions such as bleb needling may still be required to optimize IOP control.

Naegleria fowleri: Protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba.

Naegleria fowleri is a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain's frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen's high mortality is the lack of sensitivity of N. fowleri to current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets from N. fowleri. The genes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged in N. fowleri research. In 2017, 178 N. fowleri protein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.

Distinct nutritional and endocrine regulation of prothoracic gland activities underlies divergent life history strategies in Manduca sexta and Drosophila melanogaster.

Life history trade-offs lead to various strategies that maximize fitness, but the developmental mechanisms underlying these alternative strategies continue to be poorly understood. In insects, trade-offs exist between size and developmental time. Recent studies in the fruit fly Drosophila melanogaster have suggested that the steroidogenic prothoracic glands play a key role in determining the timing of metamorphosis. In this study, the nutrient-dependent growth and transcriptional activation of prothoracic glands were studied in D. melanogaster and the tobacco hornworm Manduca sexta. In both species, minimum viable weight (MVW) was associated with activation of ecdysteroid biosynthesis genes and growth of prothoracic gland cells. However, the timing of MVW attainment in M. sexta is delayed by the presence of the sesquiterpenoid hormone, juvenile hormone (JH), whereas in D. melanogaster it is not. Moreover, in D. melanogaster, the transcriptional regulation of ecdysteroidogenesis becomes nutrient-independent at the MVW/critical weight (CW) checkpoint. In contrast, in M. sexta, starvation consistently reduced transcriptional activation of ecdysteroid biosynthesis genes even after CW attainment, indicating that the nature of CW differs fundamentally between the two species. In D. melanogaster, the prothoracic glands dictate the timing of metamorphosis even in the absence of nutritional inputs, whereas in M. sexta, prothoracic gland activity is tightly coupled to the nutritional status of the body, thereby delaying the onset of metamorphosis before CW attainment. We propose that selection for survival under unpredictable nutritional availability leads to the evolution of increased modularity in both morphological and endocrine traits.

Recognizing Cardiovascular Risk After Preeclampsia: The P4 Study.

Background There is increased risk of hypertension, early cardiovascular disease, and premature mortality in women who have had preeclampsia. This study was undertaken to determine the upper limit of normal blood pressure (BP) 6 months postpartum and the frequency of women with prior preeclampsia who had BP above these limits, as part of the P4 (Post-Partum Physiology, Psychology and Pediatric) follow-up study. Methods and Results BP was measured by sphygmomanometer, 24-hour ambulatory BP monitoring, and non-invasive central BP at 6 months postpartum in 302 women who had normotensive pregnancy and 90 who had preeclampsia. The upper limit of normal BP (mean+2 SD) for women with normotensive pregnancy was 122/79 mm Hg for routine BP, 115/81 mm Hg for central BP, and 121/78 mm Hg for 24-hour ambulatory BP monitoring. Traditional normal values detected only 3% of women who had preeclampsia as having high BP 6 months postpartum whereas these new values detected between 13% and 19%. Women with preeclampsia had greater body mass index (27.8 versus 25.0, P<0.001) and left ventricular wall thickness but similar augmentation index. They also had lower high-density lipoprotein (59±15 versus 65±16 mg/dL, P=0.002), higher triglycerides (77±51 versus 61±35 mg/dL, P=0.005), and higher homeostatic model assessment score (2.1±1.8 versus 1.3±1.9, P<0.001). Conclusions Clinicians wishing to detect high BP in these women should be aware of the lower than usual upper limit of normal for this young cohort and where possible should use 24-hour ambulatory BP monitoring to detect these changes. This may define a subgroup of women who had preeclampsia for whom targeted BP lowering therapy would be successful. Registration URL: https://anzctr.org.au/Trial/Registration/TrialReview.aspx?id=365295&isReview=true; Unique identifier: ACTRN12613001260718.

Author Correction: A next-generation tumor-targeting IL-2 preferentially promotes tumor-infiltrating CD8+ T-cell response and effective tumor control.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.