SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis.

The recent discovery of SPINDLY (SPY)-catalyzed protein O-fucosylation revealed a novel mechanism for regulating nucleocytoplasmic protein functions in plants. Genetic evidence indicates the important roles of SPY in diverse developmental and physiological processes. However, the upstream signal controlling SPY activity and the downstream substrate proteins O-fucosylated by SPY remain largely unknown. Here, we demonstrated that SPY mediates sugar-dependent growth in Arabidopsis (Arabidopsis thaliana). We further identified hundreds of O-fucosylated proteins using lectin affinity chromatography followed by mass spectrometry. All the O-fucosylation events quantified in our proteomic analyses were undetectable or dramatically decreased in the spy mutants, and thus likely catalyzed by SPY. The O-fucosylome includes mostly nuclear and cytosolic proteins. Many O-fucosylated proteins function in essential cellular processes, phytohormone signaling, and developmental programs, consistent with the genetic functions of SPY. The O-fucosylome also includes many proteins modified by O-linked N-acetylglucosamine (O-GlcNAc) and by phosphorylation downstream of the target of rapamycin (TOR) kinase, revealing the convergence of these nutrient signaling pathways on key regulatory functions such as post-transcriptional/translational regulation and phytohormone responses. Our study identified numerous targets of SPY/O-fucosylation and potential nodes of crosstalk among sugar/nutrient signaling pathways, enabling future dissection of the signaling network that mediates sugar regulation of plant growth and development.

SECRET AGENT O-GlcNAcylates Hundreds of Proteins Involved in Diverse Cellular Processes in Arabidopsis.

O-GlcNAcylation is a critical post-translational modification of proteins observed in both plants and animals and plays a key role in growth and development. While considerable knowledge exists about over 3000 substrates in animals, our understanding of this modification in plants remains limited. Unlike animals, plants possess two putative homologs: SECRET AGENT (SEC) and SPINDLY, with SPINDLY also exhibiting O-fucosylation activity. To investigate the role of SEC as a major O-GlcNAc transferase in plants, we utilized lectin-weak affinity chromatography enrichment and stable isotope labeling in Arabidopsis labeling, quantifying at both MS1 and MS2 levels. Our findings reveal a significant reduction in O-GlcNAc levels in the sec mutant, indicating the critical role of SEC in mediating O-GlcNAcylation. Through a comprehensive approach, combining higher-energy collision dissociation and electron-transfer high-energy collision dissociation fragmentation with substantial fractionations, we expanded our GlcNAc profiling, identifying 436 O-GlcNAc targets, including 227 new targets. The targets span diverse cellular processes, suggesting broad regulatory functions of O-GlcNAcylation. The expanded targets also enabled exploration of crosstalk between O-GlcNAcylation and O-fucosylation. We also examined electron-transfer high-energy collision dissociation fragmentation for site assignment. This report advances our understanding of O-GlcNAcylation in plants, facilitating further research in this field.

Uncovering the proximal proteome of CTR1 through TurboID-mediated proximity labeling.

Protein-protein interactions play a crucial role in driving cellular processes and enabling appropriate physiological responses in organisms. The plant hormone ethylene signaling pathway is complex and regulated by the spatiotemporal regulation of its signaling molecules. Constitutive Triple Response 1 (CTR1), a key negative regulator of the pathway, regulates the function of Ethylene-Insensitive 2 (EIN2), a positive regulator of ethylene signaling, at the endoplasmic reticulum (ER) through phosphorylation. Our recent study revealed that CTR1 can also translocate from the ER to the nucleus in response to ethylene and positively regulate ethylene responses by stabilizing EIN3. To gain further insights into the role of CTR1 in plants, we used TurboID-based proximity labeling and mass spectrometry to identify the proximal proteomes of CTR1 in Nicotiana benthamiana. The identified proximal proteins include known ethylene signaling components, as well as proteins involved in diverse cellular processes such as mitochondrial respiration, mRNA metabolism, and organelle biogenesis. Our study demonstrates the feasibility of proximity labeling using the N. benthamiana transient expression system and identifies the potential interactors of CTR1 in vivo, uncovering the potential roles of CTR1 in a wide range of cellular processes.

A nuclear configuration interaction approach to study nuclear spin effects: an application to ortho- and para-3 He2 @C60.

We introduce a non-orthogonal configuration interaction approach to investigate nuclear quantum effects on energies and densities of confined fermionic nuclei. The Hamiltonian employed draws parallels between confined systems and many-electron atoms, where effective non-Coulombic potentials represent the interactions of the trapped particles. One advantage of this method is its generality, as it offers the potential to study the nuclear quantum effects of various confined species affected by effective isotropic or anisotropic potentials. As a first application, we analyze the quantum states of two 3 He atoms encapsulated in C60 . At the Hartree-Fock level, we observe the breaking of spin and spatial symmetries. To ensure wavefunctions with the correct symmetries, we mix the broken-symmetry Hartree-Fock states within the non-orthogonal configuration interaction expansion. Our proposed approach predicts singly and triply degenerate ground states for the singlet (para-3 He2 @C60 ) and triplet (ortho-3 He2 @C60 ) nuclear spin configurations, respectively. The ortho-3 He2 @C60 ground state is 5.69 cm-1 higher in energy than the para-3 He2 @C60 ground state. The nuclear densities obtained for these states exhibit the icosahedral symmetry of the C60 embedding potential. Importantly, our calculated energies for the lowest 85 states are in close agreement with perturbation theory results based on a harmonic oscillator plus rigid rotor model of 3 He2 @C60 .

Electron superhalogens as positronium superhalogens.

Positronium (Ps) exhibits the ability to form energetically stable complexes with atoms and molecules before annihilation occurs. In particular, F, a halogen, shows the highest reported positronium binding energy (2.95 eV) in the periodic table. Superhalogens are defined as molecules with electron affinities exceeding that of Cl (3.61 eV), the atom with the highest electron affinity. Building upon the concept of superhalogens, we can define Ps-superhalogens as molecules with Ps binding energies surpassing that of F. This study explores structural and energetic aspects of positronium and positron binding to neutral and anionic superhalogen molecules of the MXk+1 family (M = Li, Na, Be, Mg, B, Al, Si, P; X = F, Cl, Br), respectively and where k represents the highest formal valence of M. We perform multicomponent MP2 calculations for positron systems, which reveal how positron affinities vary with the type and number of halogen atoms present. The analysis of the results emphasizes the predominant role of electrostatic interactions in determining the positron affinity, with negligible effects of electronic and geometric relaxation upon positron attachment. We predict the energetic stability of 22 of the 24 PsMXk+1 complexes with respect to the chemically relevant dissociation channels: e+ emission, Ps emission and M-X bond breaking. Our findings reveal six MFk+1 systems that qualify as Ps-superhalogens, showing a positronium binding energy exceeding 2.95 eV. Of these, AlF4 stands out by setting a new record for the highest positronium binding energy among neutral molecules, reaching 4.36 eV.

Mechanistic Insight into the Internalization, Distribution, and Autophagy Process of Manganese Nanoparticles in Capsicum annuum L.: Evidence from Orthogonal Microscopic Analysis.

Orthogonal techniques were used to track manganese nanoparticles (MnNPs) in Capsicum annuum L. leaf tissue and cell compartments and subsequently to explain the mechanism of uptake, translocation, and cellular interaction. C. annuum L was cultivated and foliarly exposed to MnNPs (100 mg/L, 50 mL/per leaf) before analysis by using scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS) as well as dark-field hyperspectral and two-photon microscopy. We visualized the internalization of MnNP aggregates from the leaf surface and observed particle accumulation in the leaf cuticle and epidermis as well as spongy mesophyll and guard cells. These techniques enabled a description of how MnNPs cross different plant tissues as well as selectively accumulate and translocate in specific cells. We also imaged abundant fluorescent vesicles and vacuoles containing MnNPs, indicating likely induction of autophagy processes in C. annuum L., which is the bio-response upon storing or transforming the particles. These findings highlight the importance of utilizing orthogonal techniques to characterize nanoscale material fate and distribution with complex biological matrices and demonstrate that such an approach offers a significant mechanistic understanding that can inform both risk assessment and efforts aimed at applying nanotechnology to agriculture.

Optimizing Quantum Control Pulses with Gaussian Process Priors: The Spectral Way.

This study presents the Gaussian Process Prior Optimization for Pulse Shaping (GPPOPS) methodology, a novel approach to pulse shaping engineering. Its main objective is to efficiently identify laser pulse shapes that can achieve a desired task encoded in a cost function while being experimentally implementable. The AlH+ molecule was utilized as a test case to find pulse shapes that maximized vibronic transitions. The results demonstrate that optimal pulses can be readily implemented using current laser technology and that their control capabilities can withstand noise. The study emphasizes the benefits of constructing a surrogate approach to the control landscape during the optimization process. This approach is expected to be versatile, efficient and readily implementable in the laboratory. Its demonstrated robustness to noise sets it apart from other numerical pulse shaping engineering methods. By reducing the required experimental labor, this method has the potential to facilitate breakthroughs in quantum engineering.

Parent-youth convergence (and divergence) in reports about pediatric quality of life.

PURPOSE: Researchers and service providers typically assess pediatric Health-Related Quality of Life (HRQOL) by collecting independent reports from parents and youth. An emerging body of work indicates that patterns of parent-youth reports yield information germane to understanding youth outcomes. We identified patterns of HRQOL among youth and their parents seeking mental health treatment and examined links between agreement patterns and mental and physical health functioning. METHODS: Participants included 227 youth (mean age = 14.40 years, SD = 2.42; 63% female) and parent dyads presenting at a mood disorders clinic between 2013 and 2020. We assessed HRQOL using parallel youth and parent forms of the Pediatric Quality of Life Inventory Generic Core Scales. We also assessed youth clinical correlates of depression, suicidal ideation, and impairment, as well as health information via electronic health record (e.g., psychotropic medication usage, BMI). RESULTS: Latent class analysis showed three parent-youth reporting patterns: Low-Low (LL), High-High (HH), and Parent Low-Youth High (PL-YH). Relative to youth in the HH group, youth in the LL and PL-YH groups reported significantly greater depressive symptoms and had higher rates of suicidal ideation and psychotropic medication use. In addition, youth in the LL group reported significantly greater levels of impairment. CONCLUSIONS: Parent-youth patterns of HRQOL reporting can reveal clinically meaningful information and indicate poorer functioning for certain groups (LL, PL-YH) of youth. These findings have implications for improving accuracy of risk assessments that leverage HRQOL data.

Multicomponent wavefunction-in-DFT embedding for positronium molecules.

This work presents an extension of the projector operator embedding scheme of Manby et al. [J. Chem. Theory Comput. 8, 2564 (2012)] in a multicomponent (MC) framework. Here, a molecular system containing electrons and other types of quantum species is divided into a wavefunction (WF) subsystem of interest and a density functional theory (DFT) environment. The WF-in-DFT partition decreases computational costs by partially truncating the WF subsystem basis set at the cost of introducing a controllable embedding error. To explore the applicability of the MC extension, third-order propagator-in-DFT calculations were performed for positron-anion complexes for alkoxides and carboxylates with carbon chains of different sizes. For these systems, it was found that selecting a WF subsystem with the positron and only the oxygen atoms caused an error of 0.1 eV or lower in positron-binding energies, while reducing between 33% and 55% the basis set size. The reduction of computational costs achieved with the embedding scheme allowed us to improve molecular positron-binding energy predictions by performing complete basis set limit extrapolations. Combining the WF-in-DFT embedding and the complete basis set extrapolation, positronium aliphatic alkoxides were predicted to be energetically stable by 0.3 eV with respect to Ps emission. Similarly, positronium carboxylates, both aromatic and aliphatic, were predicted to be stable by 1.3 eV.

Introduction to the Special Issue. A Dozen Years of Demonstrating That Informant Discrepancies are More Than Measurement Error: Toward Guidelines for Integrating Data from Multi-Informant Assessments of Youth Mental Health.

Validly characterizing youth mental health phenomena requires evidence-based approaches to assessment. An evidence-based assessment cannot rely on a "gold standard" instrument but rather, batteries of instruments. These batteries include multiple modalities of instrumentation (e.g., surveys, interviews, performance-based tasks, physiological readings, structured clinical observations). Among these instruments are those that require soliciting reports from multiple informants: People who provide psychometrically sound data about youth mental health (e.g., parents, teachers, youth themselves). The January 2011 issue of the Journal of Clinical Child and Adolescent Psychology (JCCAP) included a Special Section devoted to the most common outcome of multi-informant assessments of youth mental health, namely discrepancies across informants' reports (i.e., informant discrepancies). The 2011 JCCAP Special Section revolved around a critical question: Might informant discrepancies contain data relevant to understanding youth mental health (i.e., domain-relevant information)? This Special Issue is a "sequel" to the 2011 Special Section. Since 2011, an accumulating body of work indicates that informant discrepancies often contain domain-relevant information. Ultimately, we designed this Special Issue to lay the conceptual, methodological, and empirical foundations of guidelines for integrating multi-informant data when informant discrepancies contain domain-relevant information. In this introduction to the Special Issue, we briefly review the last 12 years of research and theory on informant discrepancies. This review highlights limitations inherent to the most commonly used strategies for integrating multi-informant data in youth mental health. We also describe contributions to the Special Issue, including articles about informant discrepancies that traverse multiple content areas (e.g., autism, implementation science, measurement validation, suicide).

The Operations Triad Model and Youth Mental Health Assessments: Catalyzing a Paradigm Shift in Measurement Validation.

Researchers strategically assess youth mental health by soliciting reports from multiple informants. Typically, these informants (e.g., parents, teachers, youth themselves) vary in the social contexts where they observe youth. Decades of research reveal that the most common data conditions produced with this approach consist of discrepancies across informants' reports (i.e., informant discrepancies). Researchers should arguably treat these informant discrepancies as domain-relevant information: data relevant to understanding youth mental health domains (e.g., anxiety, depression, aggression). Yet, historically, in youth mental health research as in many other research areas, one set of paradigms has guided interpretations of informant discrepancies: Converging Operations and the Multi-Trait Multi-Method Matrix (MTMM). These paradigms (a) emphasize shared or common variance observed in multivariate data, and (b) inspire research practices that treat unique variance (i.e., informant discrepancies) as measurement confounds, namely random error and/or rater biases. Several yearsw ago, the Operations Triad Model emerged to address a conceptual problem that Converging Operations does not address: Some informant discrepancies might reflect measurement confounds, whereas others reflect domain-relevant information. However, addressing this problem requires more than a conceptual paradigm shift beyond Converging Operations. This problem necessitates a paradigm shift in measurement validation. We advance a paradigm (Classifying Observations Necessitates Theory, Epistemology, and Testing [CONTEXT]) that addresses problems with using the MTMM in youth mental health research. CONTEXT optimizes measurement validity by guiding researchers to leverage (a) informants that produce domain-relevant informant discrepancies, (b) analytic procedures that retain domain-relevant informant discrepancies, and (c) study designs that facilitate detecting domain-relevant informant discrepancies.

Revealing Giant Exciton Fine-Structure Splitting in Two-Dimensional Perovskites Using van der Waals Passivation.

Organic-inorganic layered perovskites are currently some of the most promising 2D van der Waals materials. Low crystal quality usually broadens the exciton line width, obscuring the fine structure of the exciton in conventional photoluminescence experiments. Here, we propose a mechanical approach to reducing the effect of spectral diffusion by means of hBN capping on layered perovskites, revealing the exciton fine structure. We used a stochastic model to link the reduction of the spectral line width with the population of charge fluctuation centers present in the organic spacer. van der Waals forces between both lattices cause the partial clamping of the perovskite organic spacer molecules, and hence the amplitude of the overall spectral diffusion effect is reduced. Our work provides a low-cost solution to the problem of accessing important fine-structure excitonic state information, along with an explanation of the important carrier dynamics present in the organic spacer that affect the quality of the optical emission.

Radiation use efficiency increased over a century of maize (Zea mays L.) breeding in the US corn belt.

In the absence of stress, crop growth depends on the amount of light intercepted by the canopy and the conversion efficiency [radiation use efficiency (RUE)]. This study tested the hypothesis that long-term genetic gain for grain yield was partly due to improved RUE. The hypothesis was tested using 30 elite maize hybrids commercialized in the US corn belt between 1930 and 2017. Crops grown under irrigation showed that pre-flowering crop growth increased at a rate of 0.11 g m-2 year-1, while light interception remained constant. Therefore, RUE increased at a rate of 0.0049 g MJ-1 year-1, translating into an average of 3 g m-2 year-1 of grain yield over 100 years of maize breeding. Considering that the harvest index has not changed for crops grown at optimal density for the hybrid, the cumulative RUE increase over the history of commercial maize breeding in the USA can account for ~32% of the documented yield trend for maize grown in the central US corn belt. The remaining RUE gap between this study and theoretical maximum values suggests that a yield improvement of a similar magnitude could be achieved by further increasing RUE.

The Relationship Between Harmful Alcohol Use and Antiretroviral Non-adherence in People Accessing HIV Treatment in Cape Town, South Africa: An Event-Level Analysis.

Harmful alcohol consumption can significantly compromise adherence to antiretroviral therapy (ART). Prior research has identified aggregate relationships between alcohol use and ART non-adherence, largely relying on concurrent assessment of these domains. There is relatively limited evidence on more nuanced day-level associations between alcohol use and ART non-adherence, despite potentially important clinical implications. We recruited adults with HIV treatment adherence challenges and harmful alcohol use (n = 53) from HIV care in South Africa. We examined relationships between alcohol use and same and next day ART adherence, accounting for the role of weekends/holidays and participant demographics, including gender. Results demonstrated that ART adherence was significantly worse on weekend/holiday days. Next day adherence was significantly worse in the context of weekend alcohol use and among men. These results suggest the importance of tailoring intervention strategies to support ART adherence during weekend drinking and for men engaged in heavy episodic drinking.

Assessing the Mental Health of Maltreated Youth with Child Welfare Involvement Using Multi-Informant Reports.

Researchers often question the validity of multi-informant assessments among adolescents with child welfare involvement. Yet, within other clinical populations, prior research finds that multi-informant reports have a discernable structure characterized by discrete patterns of agreement and disagreement. This structure "tracks" contextual displays of behavior and clinical severity. We examined the structure of multi-informant reports (i.e., adolescent, caregiver, teacher) of adolescent externalizing and internalizing problems in a sample of adolescents with a history of child welfare involvement. Across problem domains and informants, reporting patterns mirrored those observed in other clinical populations, and displayed characteristics robustly present in meta-analytic work on cross-informant correspondence. Specifically, informants agreed more on reports of externalizing problems than internalizing problems and caregiver-teacher dyads agreed more than adolescent-caregiver dyads. Overall, we found robust, replicable patterns of multi-informant reports among child welfare involved adolescents. These reporting patterns may facilitate use and interpretation of multi-informant evidence-based assessments among this population.

Applying a Chemogeographic Strategy for Natural Product Discovery from the Marine Cyanobacterium Moorena bouillonii.

The tropical marine cyanobacterium Moorena bouillonii occupies a large geographic range across the Indian and Western Tropical Pacific Oceans and is a prolific producer of structurally unique and biologically active natural products. An ensemble of computational approaches, including the creation of the ORCA (Objective Relational Comparative Analysis) pipeline for flexible MS1 feature detection and multivariate analyses, were used to analyze various M. bouillonii samples. The observed chemogeographic patterns suggested the production of regionally specific natural products by M. bouillonii. Analyzing the drivers of these chemogeographic patterns allowed for the identification, targeted isolation, and structure elucidation of a regionally specific natural product, doscadenamide A (1). Analyses of MS2 fragmentation patterns further revealed this natural product to be part of an extensive family of herein annotated, proposed natural structural analogs (doscadenamides B-J, 2-10); the ensemble of structures reflect a combinatorial biosynthesis using nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) components. Compound 1 displayed synergistic in vitro cancer cell cytotoxicity when administered with lipopolysaccharide (LPS). These discoveries illustrate the utility in leveraging chemogeographic patterns for prioritizing natural product discovery efforts.

Protective Factors Associated with Daily Affective Reactivity and Instability During Adolescence.

The daily emotional experiences of adolescents are dynamic, vary significantly across individuals, and are crucial to their psychological adjustment, warranting a need to identify factors that promote adaptive affective responses to stressors and attenuated affective instability. The objective of this study, therefore, was to examine protective factors linked to individual differences in daily affective reactivity and instability utilizing a daily diary design in a national sample of 100 U.S. adolescents (13-17 years; 40% girls; 79% White). Adolescents completed a baseline survey and then 14 daily online surveys. Better mother-adolescent communication predicted lower negative affect reactivity, whereas greater use of problem-focused coping strategies predicted higher positive affect reactivity. Greater trait resilience and instrumental support seeking predicted lower negative affect instability. Conversely, more emotional support seeking predicted higher negative affect instability. No factors were associated with positive affect instability, and father-adolescent communication was unrelated to daily affective reactivity and instability. The findings implicate specific protective factors associated with distinct aspects of affective reactivity and instability.

Imaging practice in low-grade gliomas among European specialized centers and proposal for a minimum core of imaging.

OBJECTIVE: Imaging studies in diffuse low-grade gliomas (DLGG) vary across centers. In order to establish a minimal core of imaging necessary for further investigations and clinical trials in the field of DLGG, we aimed to establish the status quo within specialized European centers. METHODS: An online survey composed of 46 items was sent out to members of the European Low-Grade Glioma Network, the European Association of Neurosurgical Societies, the German Society of Neurosurgery and the Austrian Society of Neurosurgery. RESULTS: A total of 128 fully completed surveys were received and analyzed. Most centers (n = 96, 75%) were academic and half of the centers (n = 64, 50%) adhered to a dedicated treatment program for DLGG. There were national differences regarding the sequences enclosed in MRI imaging and use of PET, however most included T1 (without and with contrast, 100%), T2 (100%) and TIRM or FLAIR (20, 98%). DWI is performed by 80% of centers and 61% of centers regularly performed PWI. CONCLUSION: A minimal core of imaging composed of T1 (w/wo contrast), T2, TIRM/FLAIR, PWI and DWI could be identified. All morphologic images should be obtained in a slice thickness of ≤ 3 mm. No common standard could be obtained regarding advanced MRI protocols and PET. IMPORTANCE OF THE STUDY: We believe that our study makes a significant contribution to the literature because we were able to determine similarities in numerous aspects of LGG imaging. Using the proposed "minimal core of imaging" in clinical routine will facilitate future cooperative studies.

The any particle molecular orbital grid-based Hartree-Fock (APMO-GBHF) approach.

The any particle molecular orbital grid-based Hartree-Fock approach (APMO-GBHF) is proposed as an initial step to perform multi-component post-Hartree-Fock, explicitly correlated, and density functional theory methods without basis set errors. The method has been applied to a number of electronic and multi-species molecular systems. Results of these calculations show that the APMO-GBHF total energies are comparable with those obtained at the APMO-HF complete basis set limit. In addition, results reveal a considerable improvement in the description of the nuclear cusps of electronic and non-electronic densities.

Assessment and the Journal of Clinical Child and Adolescent Psychology's Evidence Base Updates Series: Evaluating the Tools for Gathering Evidence.

In 2014, Michael Southam-Gerow and Mitch Prinstein launched the Evidence Base Updates series. As invited contributors, authors of Evidence Base Updates articles offer the field an invaluable resource: regular evaluations of the latest data on tools for addressing the mental health needs of children and adolescents. Until now, authors of Evidence Base Updates articles have focused exclusively on evaluating treatment techniques. In this article, we outline how the Evidence Base Updates series will evolve to also include evaluations of assessment techniques. In our treatment-focused updates, contributors follow strict criteria when evaluating the evidence. Following these criteria allows authors of Evidence Base Updates articles to provide mental health professionals with clear "take-home messages" about the evidence underlying the treatments evaluated. Similarly, we outline the criteria that authors will follow when preparing Evidence Base Updates articles that evaluate assessments. We also highlight the formats of these articles, which will include evaluations of condition-focused measures (e.g., anxiety, conduct problems); transdiagnostic constructs (e.g., parenting, rumination); specific, widely used measures that cut across conditions; and updates on field-wide considerations regarding measurement (e.g., clinical utility, incremental validity).