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Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.

Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.

Modern nano-engineered pesticides have great promise for agriculture due to their extended, low dose release profiles that are intended to increase effectiveness but reduce environmental harm. Whether nanopesticides, including copper (Cu) formulations, cause reduced levels of toxicity to non-target aquatic organisms is unclear but important to assess. Predicting how aquatic species respond to incidental exposure to Cu-based nanopesticides is challenging because of the expected very low concentrations in the environment, and the two forms of exposure that may occur, namely to Cu ions and Cu nanoparticles. We conducted Cu speciation, tissue uptake, and 7-day toxicity laboratory experiments to test how a model estuarine organism, the amphipod Leptocheirus plumulosus, responded to two popular Cu-based nanopesticides, CuPRO and Kocide, and conventional CuCl2. Exposure concentrations ranged from 0 to 2.5 ppm, which were similar to those found in estuarine water located downstream of agricultural fields. Cu dissolution rates were much slower for the nanopesticides than the ionic formula, and Cu body burden in amphipods increased approximately linearly with the nominal exposure concentration. Amphipod survival declined in a normal dose-response manner with no difference among Cu formulations. Growth and movement rates after 7 days revealed no difference among exposure levels when analyzed with conventional statistical methods. By contrast, analysis of respiration rates, inferred from biomass measurements, with a bioenergetic toxicodynamic model indicated potential for population-level effects of exposure to very low-levels of the two nanopesticides, as well as the control contaminant CuCl2. Our results indicate that toxicity assessment of environmental trace pollutant concentrations may go undetected with traditional ecotoxicological tests. We present a process integrating toxicity test results and toxicodynamic modeling that can improve our capacity to detect and predict environmental impacts of very low levels of nanomaterials released into the environment.

Family engagement can take many different formats, including community events. In this study, the researchers designed an event to encourage multigenerational family involvement using STEM (science, technology, engineering, and mathematics) and DAT (developmentally appropriate theater). The study was also designed in an outside environment to encourage interactions with nature and outdoor physical activity. The researchers found that families enjoyed the event and understood the academic and social benefits of nature and arts based education. Overall, this study continues a conversation focused on the importance of engaging families in nature and art based activities.

Interleukin-37 (IL-37), a member of the IL-1 family of cytokines, is a fundamental suppressor of innate and acquired immunities. Here, we used an integrative approach that combines biophysical, biochemical, and biological studies to elucidate the unique characteristics of IL-37. Our studies reveal that single amino acid mutations at the IL-37 dimer interface that result in the stable formation of IL-37 monomers also remain monomeric at high micromolar concentrations and that these monomeric IL-37 forms comprise higher antiinflammatory activities than native IL-37 on multiple cell types. We find that, because native IL-37 forms dimers with nanomolar affinity, higher IL-37 only weakly suppresses downstream markers of inflammation whereas lower concentrations are more effective. We further show that IL-37 is a heparin binding protein that modulates this self-association and that the IL-37 dimers must block the activity of the IL-37 monomer. Specifically, native IL-37 at 2.5 nM reduces lipopolysaccharide (LPS)-induced vascular cell adhesion molecule (VCAM) protein levels by ∼50%, whereas the monomeric D73K mutant reduced VCAM by 90% at the same concentration. Compared with other members of the IL-1 family, both the N and the C termini of IL-37 are extended, and we show they are disordered in the context of the free protein. Furthermore, the presence of, at least, one of these extended termini is required for IL-37 suppressive activity. Based on these structural and biological studies, we present a model of IL-37 interactions that accounts for its mechanism in suppressing innate inflammation.

Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.

[This corrects the article DOI: 10.1038/s41523-018-0074-6.].

Clinical isolates of Yersinia, Klebsiella, and Escherichia coli frequently secrete the small molecule metallophore yersiniabactin (Ybt), which passivates and scavenges transition metals during human infections. YbtT is encoded within the Ybt biosynthetic operon and is critical for full Ybt production in bacteria. However, its biosynthetic function has been unclear because it is not essential for Ybt production by the in vitro reconstituted nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) pathway. Here, we report the structural and biochemical characterization of YbtT. YbtT structures at 1.4-1.9 Å resolution possess a serine hydrolase catalytic triad and an associated substrate chamber with features similar to those previously reported for low-specificity type II thioesterases (TEIIs). We found that YbtT interacts with the two major Ybt biosynthetic proteins, HMWP1 (high-molecular-weight protein 1) and HMWP2 (high-molecular-weight protein 2), and hydrolyzes a variety of aromatic and acyl groups from their phosphopantetheinylated carrier protein domains. In vivo YbtT titration in uropathogenic E. coli revealed a distinct optimum for Ybt production consistent with a tradeoff between clearing both stalled inhibitory intermediates and productive Ybt precursors from HMWP1 and HMWP2. These results are consistent with a model in which YbtT maintains cellular Ybt biosynthesis by removing nonproductive, inhibitory thioesters that form aberrantly at multiple sites on HMWP1 and HMWP2.

After implementation of a new standards-based grading initiative in one school district, research revealed five prominent issues, and corresponding resolutions were developed to address needed changes in assessment practices.

There is increasing evidence that thirdhand exposure to e-cigarette vapor (e-vapor) can have detrimental effects on the lungs. However, whether maternal exposure during pregnancy results in harmful changes to the offspring is unknown. Using two different e-cigarette settings (low vs. high power), BALB/c mice were subjected to thirdhand e-vapor (e-vapor deposited onto towels, towels changed daily) in the absence or presence of nicotine, before, during, and after pregnancy. Male adult offspring were then infected with mouse-adapted influenza A virus (A/PR/8/34 H1N1; Flu) and lung and bone marrow immune cell responses were assessed 7 days postinfection. Maternal thirdhand exposure to low-power (MLP) or high-power (MHP) e-vapor with nicotine (MLP + NIC and MHP + NIC, respectively) increased the percentage of lung immune cells and neutrophils in the bone marrow. Interestingly, Flu-infected offspring from MLP + NIC and MHP + NIC groups had lower percentages of lung alveolar macrophages and more pronounced increases in neutrophils in the bone marrow, when compared with offspring from MSham Flu controls. Flu infection also decreased the percentage of lung CD4+ T cells and increased the percentage of lung CD8+ T cells, irrespective of maternal exposure (MLP −/+ NIC and MHP −/+ NIC). Significantly, both MLP + NIC and MHP + NIC resulted in blunted activation of lung CD4+ T cells, but only MLP + NIC caused blunted activation of lung CD8+ T cells. Together, we show for the first time that maternal thirdhand exposure to e-vapor results in significant, long-lived effects on lung and bone marrow immune cell responses in offspring at baseline and response to Flu infection. NEW & NOTEWORTHY: Maternal exposure to environmental residues of e-cigarette use has significant effects on immune cell responses in the lungs and bone marrow of offspring at both baseline and in response to influenza A virus (Flu) infection. [ABSTRACT FROM AUTHOR]

SUMMARY: This study uses crisis management and organizational culture theories to understand how audit engagement leaders' responses to challenges during the COVID-19 pandemic provide insight into audit firm culture. Semi-structured interviews with 22 U.S. audit engagement leaders during and after the pandemic reveal consistencies and inconsistencies among the organizational mechanisms used to convey and embed underlying cultural values. We find that audit engagement leaders consistently espouse and reinforce professionalism and commercialism as strong values of audit firm culture. However, in maintaining both of these values during the pandemic, leaders respond inconsistently to learning and development, as well as auditors' mental health and well-being, despite their potential long-term impacts on professionalism and commercialism, suggesting that these are weaker cultural values. The findings reveal the short-term myopia of the audit profession on audit quality and firm profitability. Our findings have important implications for research and practice. JEL Classifications: M40; M42. [ABSTRACT FROM AUTHOR]

This study explored the practices of Grade 3 teachers in Cataingan East District, employing an Explanatory-Sequential Study design to identify strategies, assess efficacy, address challenges, and determine support needs. Quantitative analysis scrutinized socio-demographic profiles, teaching strategies, and effectiveness perceptions, while qualitative inquiry through thematic analysis delved into challenges and support mechanisms. Participants included 21 elementary teachers from Cataingan East District, predominantly female, married, and experienced, representing diverse backgrounds. Commonly used strategies such as Vocabulary Instruction and Interactive Read-Aloud were identified, with potential enhancements suggested for areas like Literature Circles. Phonics Instruction emerged as highly effective. Challenges included student reading levels, learning styles, resource scarcity, waning student interest, and parental involvement. Teachers articulated requisites for enhanced literacy instruction, including conducive environments, tutoring support, parental involvement, ongoing training, ample resources, and mentorship opportunities. Recommendations emphasized supporting teacher professional development, fostering collaborative instructional approaches, ensuring sustained support and resource availability, developing targeted interventions, and nurturing a supportive teaching environment. These insights advocated tailored initiatives aimed at empowering Grade 3 teachers, optimizing teaching practices, and addressing systemic challenges in literacy instruction, ultimately fostering student success and promoting holistic educational development. [ABSTRACT FROM AUTHOR]

This tutorial demonstrates the use of information geometry tools in analyzing environmental parameter sensitivities in underwater acoustics. Sensitivity analyses quantify how well data can constrain model parameters, with application to inverse problems like geoacoustic inversion. A review of examples of parameter sensitivity methods and their application to problems in underwater acoustics is given, roughly grouped into "local" and "non-local" methods. Local methods such as Fisher information and Cramér-Rao bounds have important connections to information geometry. Information Geometry combines the fields of information theory and differential geometry by interpreting a model as a Riemannian manifold, known as the model manifold, that encodes both local and global parameter sensitivities. As an example, 2-dimensional model manifold slices are constructed for the Pekeris waveguide with sediment attenuation, for a vertical array of hydrophones. This example demonstrates how effective, reduced-order models emerge in certain parameter limits, which correspond to boundaries of the model manifold. This example also demonstrates how the global structure of the model manifold influences the local sensitivities quantified by the Fisher information matrix. This paper motivates future work to utilize information geometry methods for experimental design and model reduction applied to more complex modeling scenarios in underwater acoustics. [ABSTRACT FROM AUTHOR]

Matrix isolation infrared spectroscopy was used to characterize a 1:1 complex of methanol (CH3OH) and benzene (C6H6). Co-deposition experiments with CH3OH and C6H6 were performed at 17–20 K using nitrogen and argon as the matrix gases. Several new infrared peaks in the co-deposition spectra were observed near the fundamental absorptions of the CH3OH and C6H6 parent molecules and these new peaks have been attributed to CH3OH–C6H6 complexe. Experiments were also performed with isotopic CD3OD and C6D6 and the corresponding infrared peaks of the isotopologue complexes have also been observed. Theoretical calculations were performed for the CH3OH–C6H6 complex using the M06-2X, ωB97X-D, MP2, and CCSD(T) methods with the aug-cc-pVDZ and aug-cc-pVTZ basis sets. Full geometry optimizations followed by vibrational frequency calculations were performed for several initial starting geometries and three stable minima were found for the CH3OH–C6H6 complex. The first has the CH3OH above the C6H6 ring with the OH hydrogen interacting with the π cloud of the ring (H–π complex), the second has the CH3OH above the C6H6 ring with the OH oxygen interacting with one or two of the C–H bonds of the ring (CH–O 1 complex), and the third has the CH3OH towards the side of the C6H6 ring with the OH oxygen interacting with two of the C–H bonds of the ring (CH–O 2 complex). The H–π complex structure is predicted to be the lower energy structure by ∼8 kJ/mol compared to the two CH–O structures. Comparing the theoretically predicted infrared spectra for the optimized CH3OH–C6H6 complex structures to the experimentally observed infrared peaks in argon and nitrogen matrices, it is concluded that in the argon matrices only the H–π complex structure is being observed, whereas in the nitrogen matrices the H–π complex and CH–O 1 complex structures are being observed. [ABSTRACT FROM AUTHOR]

This article presents a methodology for program managers to effectively monitor and control scope, schedule, and cost in programs that use the Rolling Wave lifecycle. It explains the differences between predictive and adaptive lifecycles and discusses the challenges of scaling up the Rolling Wave methodology for program management. The article also addresses the interdependencies between multiple projects within a program and suggests a structural solution to manage them. It introduces a program-level dashboard that includes various tools for project management, such as a Gantt chart view, an Early Warning System, a change order report, and a display of upcoming tasks and late starts. The article emphasizes the importance of communication and updates among project managers to minimize disruptions and manage risk and quality. [Extracted from the article]

Homelessness increases the risk of acquiring an infectious disease. We conducted a systematic review of the literature to identify quantitative data related to infectious diseases and homelessness. We searched Google Scholar, PubMed, and SCOPUS for quantitative literature published from January 2003 through December 2022 in English from the United States and Canada. We excluded literature on vaccine-preventable diseases and HIV because these diseases were recently reviewed. Of the 250 articles that met inclusion criteria, more than half were on hepatitis C virus or Mycobacterium tuberculosis. Other articles were on COVID-19, respiratory syncytial virus, Staphylococcus aureus, group A Streptococcus, mpox (formerly monkeypox), 5 sexually transmitted infections, and gastrointestinal or vectorborne pathogens. Most studies showed higher prevalence, incidence, or measures of risk for infectious diseases among people experiencing homelessness as compared with people who are housed or the general population. Although having increased published data that quantify the infectious disease risks of homelessness is encouraging, many pathogens that are known to affect people globally who are not housed have not been evaluated in the United States or Canada. Future studies should focus on additional pathogens and factors leading to a disproportionately high incidence and prevalence of infectious diseases among people experiencing homelessness. [ABSTRACT FROM AUTHOR]

The author uses his father's autobiographical writings about the small-town, baseball experiences of his youth as background for discussing the significant cultural shifts that have dramatically changed the nature of the game from a free-play experience for neighborhood kids to an organized youth-league sport. In contrast to his father's day, the author claims that the playfulness of youth baseball has become nearly extinct. After a brief overview to define the essence of play, the author explains how his father's kind of free, unstructured, deliberate play has been diminished by complex cultural and social shifts such as rationalization, suburban sprawl, and changing child-development philosophies. He concludes that the continual decline these forces have created in free play will not only significantly influence the future of baseball as a sport but also the quality of children's growth, development, and health.