Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly.

Several immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defence1-5. Here we studied an antiphage defence system in bacteria, comprising a ubiquitin-like protein, ubiquitin-conjugating enzymes E1 and E2, and a deubiquitinase. We show that during phage infection, this system specifically conjugates the ubiquitin-like protein to the phage central tail fibre, a protein at the tip of the tail that is essential for tail assembly as well as for recognition of the target host receptor. Following infection, cells encoding this defence system release a mixture of partially assembled, tailless phage particles and fully assembled phages in which the central tail fibre is obstructed by the covalently attached ubiquitin-like protein. These phages show severely impaired infectivity, explaining how the defence system protects the bacterial population from the spread of phage infection. Our findings demonstrate that conjugation of ubiquitin-like proteins is an antiviral strategy conserved across the tree of life.

A mechanism of ferritin crystallization revealed by cryo-STEM tomography.

Protein crystallization is important in structural biology, disease research and pharmaceuticals. It has recently been recognized that nonclassical crystallization-involving initial formation of an amorphous precursor phase-occurs often in protein, organic and inorganic crystallization processes1-5. A two-step nucleation theory has thus been proposed, in which initial low-density, solvated amorphous aggregates subsequently densify, leading to nucleation4,6,7. This view differs from classical nucleation theory, which implies that crystalline nuclei forming in solution have the same density and structure as does the final crystalline state1. A protein crystallization mechanism involving this classical pathway has recently been observed directly8. However, a molecular mechanism of nonclassical protein crystallization9-15 has not been established9,11,14. To determine the nature of the amorphous precursors and whether crystallization takes place within them (and if so, how order develops at the molecular level), three-dimensional (3D) molecular-level imaging of a crystallization process is required. Here we report cryogenic scanning transmission microscopy tomography of ferritin aggregates at various stages of crystallization, followed by 3D reconstruction using simultaneous iterative reconstruction techniques to provide a 3D picture of crystallization with molecular resolution. As crystalline order gradually increased in the studied aggregates, they exhibited an increase in both order and density from their surface towards their interior. We observed no highly ordered small structures typical of a classical nucleation process, and occasionally we observed several ordered domains emerging within one amorphous aggregate, a phenomenon not predicted by either classical or two-step nucleation theories. Our molecular-level analysis hints at desolvation as the driver of the continuous order-evolution mechanism, a view that goes beyond current nucleation models, yet is consistent with a broad spectrum of protein crystallization mechanisms.

Variability in the age of schooling contributes to the link between literacy and numeracy in Côte d'Ivoire.

Literacy and numeracy are correlated throughout development, however, our understanding of this relation is limited. We explored the predictors of literacy and numeracy covariance (i.e., shared fluency between literacy and numeracy) in children (N = 1167, girls = 563) in rural Côte d'Ivoire, with specific focus on how developmental timing of instruction may relate to covariance. Many Ivorian children experience late enrollment and grade repetition, leading to variation in age-for-grade; participants were between grades 1 to 6, but their ages ranged from 5 to 15 (M = 9.19, SD = 2.07). Phonological awareness, numerical magnitude, ordinality, working memory, and inhibitory control were cognitive predictors of covariance. Age-for-grade was negatively related to covariance suggesting that covariance is related to timing of instruction.

Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap.

Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access 3D volumes on the scale of 1 micron with a resolution of nanometers, making it ideal for this task. Here we introduce two relevant advances: (a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and (b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy. Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to-isotropic resolution in the reconstruction without averaging. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.

Teacher depressive symptoms and children's school readiness in Ghana.

This study investigated associations between kindergarten teachers' (N = 208) depressive symptoms and students' (Ghanaian nationals, N = 1490, Mage  = 5.8) school-readiness skills (early literacy, early numeracy, social-emotional skills, and executive function) across 208 schools in Ghana over one school year. Teachers' depressive symptoms in the fall negatively predicted students' overall school-readiness skills in the spring, controlling for school-readiness skills in the fall. These results were primarily driven by social-emotional skills (r = .1-.3). There was evidence of heterogeneity by students' fall skill levels; teacher depressive symptoms predicted more negative spring overall school readiness for children who had higher fall school-readiness skills. Findings underscore the importance of teachers' mental health in early childhood education globally, with implications for policy and practice.

Three-dimensional deconvolution processing for STEM cryotomography.

The complex environment of biological cells and tissues has motivated development of three-dimensional (3D) imaging in both light and electron microscopies. To this end, one of the primary tools in fluorescence microscopy is that of computational deconvolution. Wide-field fluorescence images are often corrupted by haze due to out-of-focus light, i.e., to cross-talk between different object planes as represented in the 3D image. Using prior understanding of the image formation mechanism, it is possible to suppress the cross-talk and reassign the unfocused light to its proper source post facto. Electron tomography based on tilted projections also exhibits a cross-talk between distant planes due to the discrete angular sampling and limited tilt range. By use of a suitably synthesized 3D point spread function, we show here that deconvolution leads to similar improvements in volume data reconstructed from cryoscanning transmission electron tomography (CSTET), namely a dramatic in-plane noise reduction and improved representation of features in the axial dimension. Contrast enhancement is demonstrated first with colloidal gold particles and then in representative cryotomograms of intact cells. Deconvolution of CSTET data collected from the periphery of an intact nucleus revealed partially condensed, extended structures in interphase chromatin.

Toward Compositional Contrast by Cryo-STEM.

Electron microscopy (EM) is the most versatile tool for the study of matter at scales ranging from subatomic to visible. The high vacuum environment and the charged irradiation require careful stabilization of many specimens of interest. Biological samples are particularly sensitive due to their composition of light elements suspended in an aqueous medium. Early investigators developed techniques of embedding and staining with heavy metal salts for contrast enhancement. Indeed, the Nobel Prize in 1974 recognized Claude, de Duve, and Palade for establishment of the field of cell biology, largely due to their developments in separation and preservation of cellular components for electron microscopy. A decade later, cryogenic fixation was introduced. Vitrification of the water avoids the need for dehydration and provides an ideal matrix in which the organic macromolecules are suspended; the specimen represents a native state, suddenly frozen in time at temperatures below -150 °C. The low temperature maintains a low vapor pressure for the electron microscope, and the amorphous nature of the medium avoids diffraction contrast from crystalline ice. Such samples are extremely delicate, however, and cryo-EM imaging is a race for information in the face of ongoing damage by electron irradiation. Through this journey, cryo-EM enhanced the resolution scale from membranes to molecules and most recently to atoms. Cryo-EM pioneers, Dubochet, Frank, and Henderson, were awarded the Nobel Prize in 2017 for high resolution structure determination of biological macromolecules.A relatively untapped feature of cryo-EM is its preservation of composition. Nothing is added and nothing removed. Analytical spectroscopies based on electron energy loss or X-ray emission can be applied, but the very small interaction cross sections conflict with the weak exposures required to preserve sample integrity. To what extent can we interpret quantitatively the pixel intensities in images themselves? Conventional cryo-transmission electron microscopy (TEM) is limited in this respect, due to the strong dependence of the contrast transfer on defocus and the absence of contrast at low spatial frequencies.Inspiration comes largely from a different modality for cryo-tomography, using soft X-rays. Contrast depends on the difference in atomic absorption between carbon and oxygen in a region of the spectrum between their core level ionization energies, the so-called water window. Three dimensional (3D) reconstruction provides a map of the local X-ray absorption coefficient. The quantitative contrast enables the visualization of organic materials without stain and measurement of their concentration quantitatively. We asked, what aspects of the quantitative contrast might be transferred to cryo-electron microscopy?Compositional contrast is accessible in scanning transmission EM (STEM) via incoherent elastic scattering, which is sensitive to the atomic number Z. STEM can be regarded as a high energy, low angle diffraction measurement performed pixel by pixel with a weakly convergent beam. When coherent diffraction effects are absent, that is, in amorphous materials, a dark field signal measures quantitatively the flux scattered from the specimen integrated over the detector area. Learning to interpret these signals will open a new dimension in cryo-EM. This Account describes our efforts so far to introduce STEM for cryo-EM and tomography of biological specimens. We conclude with some thoughts on further developments.

Development, Validity, and Cross-Context Equivalence of the Child Food Insecurity Experiences Scale for Assessing Food Insecurity of School-Age Children and Adolescents.

BACKGROUND: Children ages 6 to 17 years can accurately assess their own food insecurity, whereas parents are inaccurate reporters of their children's experiences of food insecurity. No globally applicable scale to assess the food insecurity of children has been developed and validated. OBJECTIVES: We aimed to develop a globally applicable, experience-based measure of child and adolescent food insecurity and establish the validity and cross-contextual equivalence of the measure. METHODS: The 10-item Child Food Insecurity Experiences Scale (CFIES) was based on items previously validated from questionnaires from the United States, Venezuela, and Lebanon. Cognitive interviews were conducted to check understanding of the items. The questionnaire then was administered in 15 surveys in 13 countries. Other items in each survey that assessed the household socioeconomic status, household food security, or child psychological functioning were selected as criterion variables to compare to the scores from the CFIES. To investigate accuracy (i.e., criterion validity), linear regression estimated the associations of the CFIES scores with the criterion variables. To investigate the cross-contextual equivalence (i.e., measurement invariance), the alignment method was used based on classical measurement theory. RESULTS: Across the 15 surveys, the mean scale scores for the CFIES ranged from 1.65 to 5.86 (possible range of 0 to 20) and the Cronbach alpha ranged from 0.88 to 0.94. The variance explained by a 1-factor model ranged from 0.92 to 0.99. Accuracy was demonstrated by expected associations with criterion variables. The percentages of equivalent thresholds and loadings across the 15 surveys were 28.0 and 5.33, respectively, for a total percentage of nonequivalent thresholds and loadings of 16.7, well below the guideline of <25%. That is, 83.3% of thresholds and loadings were equivalent across these surveys. CONCLUSIONS: The CFIES provides a globally applicable, valid, and cross-contextually equivalent measure of the experiences of food insecurity of school-aged children and adolescents, as reported by them.

Medium-term protective effects of quality early childhood education during the COVID-19 pandemic in Ghana.

The COVID-19 pandemic led to extended school closures globally. Access to remote learning opportunities during this time was vastly unequal within and across countries. Higher-quality early childhood education (ECE) can improve later academic outcomes, but longer-term effects during crises are unknown. This study provides the first experimental evidence of how previously attending a higher-quality ECE program affected child engagement in remote learning and academic scores during pandemic-related school closures in Ghana. Children (N = 1668; 50.1% male; Mage  = 10.1 years; all Ghanaian nationals) who attended higher-quality ECE at age 4 or 5 years had greater engagement in remote learning (d = .14) in October 2020, but not better language and literacy and math scores. Previous exposure to higher-quality ECE may support educational engagement during crises.

A Complex Systems Network Approach to Quantifying Peer Effects: Evidence From Ghanaian Preprimary Classrooms.

Research on classroom peer effects has focused nearly exclusively on high-income countries and on academic skills. Little is known about peer effects in low-income countries and whether effects differ under different educational environments (e.g., teacher-directed versus child-centered, conditions of concentrated advantage or disadvantage). Based on a data set of Ghanaian preprimary classrooms in the Greater Accra Region collected in the 2015-2016 school year, we use complex system networks with multilevel modeling to study the presence and magnitude of peer effects. Results corroborated small statistically significant effects on academic and nonacademic skills (d = .06-.10). Peer effects on literacy were larger for children in public schools, who are relatively more disadvantaged than their private school counterparts. Teacher-directivity intensity did not moderate peer effects.

Depressive and anxiety symptoms in early childhood education teachers: Relations to professional well-being and absenteeism.

This study investigated how early childhood education teachers' (N = 444) depressive and anxiety symptoms predicted their professional well-being outcomes and absenteeism over the course of one school year in Ghana. Higher anxiety and depressive symptoms predicted lower job motivation and job satisfaction and higher levels of emotional exhaustion at the end of the school year. Increased depressive symptoms were further associated with more days absent over the course of the school year. Findings point to the importance of considering teachers' mental health for early educational quality. Implications for policy and practice are discussed.

Household economic instability: Constructs, measurement, and implications.

A growing body of research demonstrates the multiple dimensions and dynamism of family income and employment. The metrics of household economic instability and their associations with household characteristics and hardship require further examination in order to compare across studies, subgroups, and historical periods. This paper empirically examines and compares commonly used measures of income and employment instability, how these measures inter-relate, vary by household characteristics, and how they predict household hardship. Using longitudinal data from the 2008 panel of the Survey of Income and Program Participation (SIPP), and focusing on households with children, this study examined a range of descriptive measures of economic instability, including in income, earnings, public assistance benefits, and employment status, and how these measures related to each other. Results indicate that overall rates of income and employment instability were high, particularly among less-educated families, those with young children, and those who did not own a home. Economic instability, particularly decreases in employment, was associated with increased household hardship three months later. Findings also show that the source of income included in the instability measure affects the patterns identified and conclusions drawn, whereas the specific type of measure used matters less. Results highlight the instability of public assistance benefits and suggest that safety net programs must take economic instability into account when designing programs and benefits.

Crystals of Benzamide, the First Polymorphous Molecular Compound, Are Helicoidal.

The growth of spontaneously twisted crystals is a common but poorly understood phenomenon. An analysis of the formation of twisted crystals of a metastable benzamide polymorph (form II) crystallizing from highly supersaturated aqueous and ethanol solutions is given here. Benzamide, the first polymorphic molecular crystal reported (1832), would have been the first helicoidal crystal observed had the original authors undertaken an analysis by light microscopy. Polymorphism and twisting frequently concur as they are both associated with high thermodynamic driving forces for crystallization. Optical and electron microscopies as well as electron and powder X-ray diffraction reveal a complex lamellar structure of benzamide form II needle-like crystals. The internal stress produced by the overgrowth of lamellae is shown to be able to create a twist moment that is responsible for the observed non-classical morphologies.

Socioeconomic Status in Pediatric Health Research: A Scoping Review.

OBJECTIVE: To conduct a scoping review of the literature to describe current conceptualization and measurement of socioeconomic status in pediatric health research. STUDY DESIGN: Four databases were used to identify relevant studies, followed by selection and data extraction. Inclusion criteria for studies were the following: enrolled subjects <18 years old, included a health-related outcome, published from 1999 to 2018, and explicitly measured socioeconomic status (SES). RESULTS: Our literature search identified 1768 publications and 1627 unique records. After screening for duplication and relevance, 228 studies satisfied the inclusion criteria, with 75% (n = 170) published since 2009. There were 52 unique singular measures and an additional 20 composite measures. Income-related measures were used in 65% of studies (n = 147) and measures of education in 42% (n = 95). The majority of studies using census-derived variables or insurance status were conducted within the previous 10 years. CONCLUSIONS: Pediatric studies use a variety of SES measures, which limits comparisons between studies. Few studies provide an evidenced-based rationale that connects the SES indicator to the health outcome, but the majority of studies do find a significant impact of SES on outcomes. SES should be comprehensively studied so that meaningful measures can be used to identify specific SES mechanisms that impact child health.

The role of executive function and social-emotional skills in the development of literacy and numeracy during preschool: a cross-lagged longitudinal study.

The majority of evidence on the interplay between academic and non-academic skills comes from high-income countries. The aim of this study was to examine the bidirectional associations between Ghanaian children's executive function, social-emotional, literacy, and numeracy skills longitudinally. Children (N = 3,862; M age = 5.2 years at time 1) were assessed using direct assessment at three time points over the course of two school years. Controlling for earlier levels of the same skill, early executive function predicted higher subsequent literacy and numeracy skills, and early literacy and numeracy skills predicted higher subsequent executive function, indicating that the development of executive function and academic skills is inter-related and complementary over time. Early literacy and numeracy predicted subsequent social-emotional skills, but early social-emotional skills did not predict subsequent literacy and numeracy skills. The findings provide longitudinal evidence on children's learning and development in West Africa and contribute to a global understanding of the relations between various developmental skills over time.

Longitudinal causal impacts of preschool teacher training on Ghanaian children's school readiness: Evidence for persistence and fade-out.

Preschool programs have expanded rapidly in low- and middle-income countries, but there are widespread concerns about whether they are of sufficient quality to promote children's learning and development. We conducted a large school-randomized control trial ('Quality Preschool for Ghana' - QP4G) of a one-year teacher training and coaching program, with and without parental-awareness meetings, designed to improve preschool quality and child development. We followed 3,435 children in 240 schools in the Greater Accra Region of Ghana, a country with universal pre-primary education. A previous study reported positive impacts of teacher training (but not teacher training plus parental-awareness meetings) at the end of the implementation year on some dimensions of classroom quality, teacher well-being, and children's school readiness (Wolf et al., [2019] Journal of Research on Educational Effectiveness, 12, 10-37). The present study analyzed a new round of data collected 1 year after the end of implementation to assess (a) the extent of persistence in impacts on child development and (b) whether such impacts vary by select child, household, and school characteristics. We found impacts of the teacher training intervention on children's overall school readiness were sustained (d = 0.13), but were only marginally statistically significant. When broken down by domain, impacts on social-emotional skills specifically persisted. Persistent negative effects of teacher training plus parental-awareness meetings varied by the literacy status of the male parent such that negative impacts were concentrated in children in households with non-literate male heads.

Literacy acquisition in multilingual educational contexts: Evidence from Coastal Kenya.

Literacy is a powerful tool against poverty, leading to further education and vocational success. In sub-Saharan Africa, schoolchildren commonly learn in two languages-African and European. Multiple early literacy skills (including phonological awareness and receptive language) support literacy acquisition, but this has yet to be empirically tested in sub-Saharan Africa, where learning contexts are highly multilingual, and children are often learning to read in a language they do not speak at home. We use longitudinal data from 1,100 schoolchildren spanning three groups of native languages [Mijikenda languages (Digo, Duruma, Chonyi, and Giriama), Kiswahili, Kikamba] in coastal Kenya (language of instruction: Kiswahili and English). We find that baseline phonological awareness and receptive language are differentially important in predicting literacy skills in English and in Kiswahili, and these relations are moderated by the degree of shared cross-linguistic features between home and school languages. Importantly, the relative importance of these factors changes over development. Implications for language development and literacy acquisition in linguistically diverse contexts are discussed.

Household Socioeconomic Status and Parental Investments: Direct and Indirect Relations With School Readiness in Ghana.

This study examines how parent socioeconomic status (SES) directly and indirectly predicts children's school readiness through pathways of parental investment. Data come from direct assessments with preschool children and surveys with their primary caregivers in Ghana at the start of the 2015-2016 school year (N = 2,137; Mage  = 5.2 years). Results revealed SES-related gaps in all parental investment characteristics and child school readiness skills. Preschool involvement served as the primary mediating mechanism in the path from SES to most school readiness skills, though it did not predict executive function. The number of books in the household was marginally positively predictive of early literacy, whereas at-home stimulation was negatively related to motor, literacy, and numeracy skills.

Distinct biological events generated by ECM proteolysis by two homologous collagenases.

It is well established that the expression profiles of multiple and possibly redundant matrix-remodeling proteases (e.g., collagenases) differ strongly in health, disease, and development. Although enzymatic redundancy might be inferred from their close similarity in structure, their in vivo activity can lead to extremely diverse tissue-remodeling outcomes. We observed that proteolysis of collagen-rich natural extracellular matrix (ECM), performed uniquely by individual homologous proteases, leads to distinct events that eventually affect overall ECM morphology, viscoelastic properties, and molecular composition. We revealed striking differences in the motility and signaling patterns, morphology, and gene-expression profiles of cells interacting with natural collagen-rich ECM degraded by different collagenases. Thus, in contrast to previous notions, matrix-remodeling systems are not redundant and give rise to precise ECM-cell crosstalk. Because ECM proteolysis is an abundant biochemical process that is critical for tissue homoeostasis, these results improve our fundamental understanding its complexity and its impact on cell behavior.