Nonsugar Sweeteners-Time for Transparency and Caution.

This Viewpoint discusses the growing presence of nonsugar sweeteners (NSSs) in the food supply and mounting concerns about their use, which suggest that disclosure of the amounts of NSS in food and beverages and restrictions on their use in products marketed to children are warranted.

Advancing Equity in the Farm Bill: Opportunities for the Gus Schumacher Nutrition Incentive Program (GusNIP).

The Gus Schumacher Nutrition Incentive Program (GusNIP) is a federally funded grant program that provides nutrition incentives-subsidies for purchasing fruits and vegetables (FV)-to Supplemental Nutrition Assistance Program (SNAP) participants. GusNIP currently advances nutrition equity by improving FV access for people with low incomes, yet inequities exist within GusNIP. We sought to identify inequities in GusNIP at the community, organization, partner, and individual levels and develop recommendations for farm bill provisions to make the program more equitable. In Spring 2021, a group of nutrition incentive experts (n = 11) from across the country convened to discuss opportunities to enhance equity in GusNIP. The iterative recommendation development process included feedback from key stakeholders (n = 15) and focus group participants with GusNIP lived experience (n = 12). Eleven recommendations to advance equity in GusNIP in the farm bill emerged across six categories: (1) increase total GusNIP funding, (2) increase funding and support to lower-resourced organizations and impacted communities, (3) eliminate the match requirement, (4) support statewide expansion, (5) expand and diversify retailer participation, and (6) expand program marketing. Including these recommendations in the upcoming and future farm bills would equitably expand GusNIP for SNAP participants, program grantees, and communities across the country.

Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.

AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca2+-impermeable, or GluA2-lacking and Ca2+-permeable1. Despite their prominent expression throughout interneurons and glia, their role in long-term potentiation and their involvement in a range of neuropathologies2, structural information for GluA2-lacking receptors is currently absent. Here we determine and characterize cryo-electron microscopy structures of the GluA1 homotetramer, fully occupied with TARPγ3 auxiliary subunits (GluA1/γ3). The gating core of both resting and open-state GluA1/γ3 closely resembles GluA2-containing receptors. However, the sequence-diverse N-terminal domains (NTDs) give rise to a highly mobile assembly, enabling domain swapping and subunit re-alignments in the ligand-binding domain tier that are pronounced in desensitized states. These transitions underlie the unique kinetic properties of GluA1. A GluA2 mutant (F231A) increasing NTD dynamics phenocopies this behaviour, and exhibits reduced synaptic responses, reflecting the anchoring function of the AMPAR NTD at the synapse. Together, this work underscores how the subunit-diverse NTDs determine subunit arrangement, gating properties and ultimately synaptic signalling efficiency among AMPAR subtypes.

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.

Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common theme has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows, together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.

How the Gus Schumacher Produce Prescription Program Works: An Adaptation of a Nutrition Incentive Theory of Change.

The United States Department of Agriculture's Gus Schumacher Nutrition Incentive Program (GusNIP) supports nutrition incentive (NI) and produce prescription programs (PPRs). PPRs allow healthcare providers to "prescribe" fruits and vegetables (FVs) to patients experiencing low income and/or chronic disease(s) and who screen positive for food insecurity. We developed a Theory of Change (TOC) that summarizes how and why PPRs work, identifies what the programs hope to achieve, and elucidates the causal pathways necessary to achieve their goals. We created the PPR TOC through an iterative, participatory process that adapted our previously developed GusNIP NI TOC. The participatory process involved food and nutrition security experts, healthcare providers, PPR implementors, and PPR evaluators reviewing the existing NI TOC and suggesting modifications to accurately reflect PPRs. The resulting TOC describes the mechanisms, assumptions, rationale, and underpinnings that lead to successful and equitable outcomes. Modifications of the NI TOC centered around equity and focused on inclusion of healthcare as an additional partner and the importance of health and healthcare utilization as outcomes. The TOC describes how the GusNIP PPR program reaches its goals. This understanding will be useful for PPR developers, implementers, funders, and evaluators for describing the pathways, assumptions, and foundations of successful PPRs.

A Technology-Driven, Healthcare-Based Intervention to Improve Family Beverage Choices: Results from a Pilot Randomized Trial in the United States.

Background: Healthcare-based interventions to address sugary beverage intake could achieve broad reach, but intensive in-person interventions are unsustainable in clinical settings. Technology-based interventions may provide an alternative, scalable approach. Methods: Within an academic health system in the United States that already performs electronic health record-based sugary drink screening, we conducted a pilot randomized trial of a technology-driven family beverage choice intervention. The goal of the intervention was to reduce sugar-sweetened beverage (SSB) and fruit juice (FJ) consumption in 60 parent-child dyads, in which children were 1-8 years old. The pediatrician-initiated intervention consisted of a water promotion toolkit, a video, a mobile phone application, and 14 interactive voice-response phone calls to parents over 6 months. The study was conducted between June 2021 and May 2022. The aim of the pilot study was to assess the potential feasibility and efficacy of the newly developed intervention. Results: Intervention fidelity was excellent, and acceptability was high for all intervention components. Children in both the intervention and the control groups substantially decreased their consumption of SSB and FJ over follow-up (mean combined baseline 2.5 servings/day vs. 1.4/day at 6 months) and increased water consumption, but constrained linear mixed-effects models showed no differences between groups on these measures. Compared to parents in the control group, intervention parents had larger decreases in SSB intake at 3 months (-0.80 (95% CI: -1.54, -0.06, p = 0.03) servings daily), but these differences were not sustained at 6 months. Conclusion: These findings suggest that, though practical to implement in a clinical care setting and acceptable to a diverse participant group, our multicomponent intervention may not be universally necessary to achieve meaningful behavior changes around family beverage choice. A lower-intensity intervention, such as EHR-based clinical screening alone, might be a less resource-intense way for health systems to achieve similar behavioral outcomes. Future studies might therefore explore whether, instead of applying a full intervention to all families whose children overconsume SSB or FJ, a stepped approach, starting with clinical screening and brief counseling, could be a better use of health system resources.

Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology.

Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.

Correction: The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.

[This corrects the article DOI: 10.1371/journal.ppat.1010631.].

Costs, Reach, and Benefits of COVID-19 Pandemic Electronic Benefit Transfer and Grab-and-Go School Meals for Ensuring Youths' Access to Food During School Closures.

Importance: School meals are associated with improved nutrition and health for millions of US children, but school closures due to the COVID-19 pandemic disrupted children's access to school meals. Two policy approaches, the Pandemic Electronic Benefit Transfer (P-EBT) program, which provided the cash value of missed meals directly to families on debit-like cards to use for making food purchases, and the grab-and-go meals program, which offered prepared meals from school kitchens at community distribution points, were activated to replace missed meals for children from low-income families; however, the extent to which these programs reached those who needed them and the programs' costs were unknown. Objective: To assess the proportion of eligible youths who were reached by P-EBT and grab-and-go meals, the amount of meals or benefits received, and the cost to implement each program. Design, Setting, and Participants: This cross-sectional study was conducted from March to June 2020. The study population was all US youths younger than 19 years, including US youths aged 6 to 18 years who were eligible to receive free or reduced-price meals (primary analysis sample). Exposures: Receipt of P-EBT or grab-and-go school meals. Main Outcomes and Measures: The main outcomes were the percentage of youths reached by P-EBT and grab-and-go school meals, mean benefit received per recipient, and mean cost, including implementation costs and time costs to families per meal distributed. Results: Among 30 million youths eligible for free or reduced-price meals, grab-and-go meals reached an estimated 8.0 million (27%) and P-EBT reached 26.9 million (89%). The grab-and-go school meals program distributed 429 million meals per month in spring 2020, and the P-EBT program distributed $3.2 billion in monthly cash benefits, equivalent to 1.1 billion meals. Among those receiving benefits, the mean monthly benefit was larger for grab-and-go school meals ($148; range across states, $44-$176) compared with P-EBT ($110; range across states, $55-$114). Costs per meal delivered were lower for P-EBT ($6.46; range across states, $6.41-$6.79) compared with grab-and-go school meals ($8.07; range across states, $2.97-$15.27). The P-EBT program had lower public sector implementation costs but higher uncompensated time costs to families (eg, preparation time for meals) compared with grab-and-go school meals. Conclusions and Relevance: In this economic evaluation, both the P-EBT and grab-and-go school meal programs supported youths' access to food in complementary ways when US schools were closed during the COVID-19 pandemic from March to June 2020.

Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation.

The phosphatase and tensin homologue deleted on chromosome 10 (PTEN) tumor suppressor gene encodes a tightly regulated dual-specificity phosphatase that serves as the master regulator of PI3K/AKT/mTOR signaling. The carboxy-terminal tail (CTT) is key to regulation and harbors multiple phosphorylation sites (Ser/Thr residues 380-385). CTT phosphorylation suppresses the phosphatase activity by inducing a stable, closed conformation. However, little is known about the mechanisms of phosphorylation-induced CTT-deactivation dynamics. Using explicit solvent microsecond molecular dynamics simulations, we show that CTT phosphorylation leads to a partially collapsed conformation, which alters the secondary structure of PTEN and induces long-range conformational rearrangements that encompass the active site. The active site rearrangements prevent localization of PTEN to the membrane, precluding lipid phosphatase activity. Notably, we have identified phosphorylation-induced allosteric coupling between the interdomain region and a hydrophobic site neighboring the active site in the phosphatase domain. Collectively, the results provide a mechanistic understanding of CTT phosphorylation dynamics and reveal potential druggable allosteric sites in a previously believed clinically undruggable protein.

GPCR kinases generate an APH1A phosphorylation barcode to regulate amyloid-ß generation.

Emerging evidence suggests that G protein-coupled receptor (GPCR) kinases (GRKs) are associated with the pathophysiology of Alzheimer's disease (AD). However, GRKs have not been directly implicated in regulation of the amyloid-ß (Aß) pathogenic cascade in AD. Here, we determine that GRKs phosphorylate a non-canonical substrate, anterior pharynx-defective 1A (APH1A), an integral component of the γ-secretase complex. Significantly, we show that GRKs generate distinct phosphorylation barcodes in intracellular loop 2 (ICL2) and the C terminus of APH1A, which differentially regulate recruitment of the scaffolding protein ß-arrestin 2 (ßarr2) to APH1A and γ-secretase-mediated Aß generation. Further molecular dynamics simulation studies reveal an interaction between the ßarr2 finger loop domain and ICL2 and ICL3 of APH1A, similar to a GPCR-ß-arrestin complex, which regulates γ-secretase activity. Collectively, these studies provide insight into the molecular and structural determinants of the APH1A-ßarr2 interaction that critically regulate Aß generation.

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.

How Does the Gus Schumacher Nutrition Incentive Program Work? A Theory of Change.

Increased fruit and vegetable (FV) intake is associated with decreased risk of nutrition-related chronic diseases. Sociodemographic disparities in FV intake indicate the need for strategies that promote equitable access to FVs. The United States Department of Agriculture's Gus Schumacher Nutrition Incentive Program (GusNIP) supports state and local programs that offer nutrition incentives (NIs) that subsidize purchase of FVs for people participating in the Supplemental Nutrition Assistance Program (SNAP). While a growing body of research indicates NIs are effective, the pathways through which GusNIP achieves its results have not been adequately described. We used an equity-focused, participatory process to develop a retrospective Theory of Change (TOC) to address this gap. We reviewed key program documents; conducted a targeted NI literature review; and engaged GusNIP partners, practitioners, and participants through interviews, workshops, and focus groups in TOC development. The resulting TOC describes how GusNIP achieves its long-term outcomes of increased participant FV purchases and intake and food security and community economic benefits. GusNIP provides NIs and promotes their use, helps local food retailers develop the capacity to sell FVs and accept NIs in accessible and welcoming venues, and supports local farmers to supply FVs to food retailers. The TOC is a framework for understanding how GusNIP works and a tool for improving and expanding the program.

Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.

Cryo-electron microscopy (cryoEM) has become a well established technique with the potential to produce structures of large and dynamic supramolecular complexes that are not amenable to traditional approaches for studying structure and dynamics. The size and low resolution of such molecular systems often make structural modelling and molecular dynamics simulations challenging and computationally expensive. This, together with the growing wealth of structural data arising from cryoEM and other structural biology methods, has driven a trend in the computational biophysics community towards the development of new pipelines for analysing global dynamics using coarse-grained models and methods. At the centre of this trend has been a return to elastic network models, normal mode analysis (NMA) and ensemble analyses such as principal component analysis, and the growth of hybrid simulation methodologies that make use of them. Here, this field is reviewed with a focus on ProDy, the Python application programming interface for protein dynamics, which has been developed over the last decade. Two key developments in this area are highlighted: (i) ensemble NMA towards extracting and comparing the signature dynamics of homologous structures, aided by the recent SignDy pipeline, and (ii) pseudoatom fitting for more efficient global dynamics analyses of large and low-resolution supramolecular assemblies from cryoEM, revisited in the CryoDy pipeline. It is believed that such a renewal and extension of old models and methods in new pipelines will be critical for driving the field forward into the next cryoEM revolution.

Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor.

AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor's ligand-binding domains (LBDs) leads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission and are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs) through currently incompletely resolved mechanisms. Here, electron cryo-microscopy structures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states (at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop ('ß1'), elucidating how this TARP stabilizes specific gating states. We further show how TARPs alter channel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we reveal that the Q/R-editing site couples the channel constriction at the filter entrance to the gate, and forms the major cation binding site in the conduction path. Our results provide a mechanistic framework of how TARPs modulate AMPAR gating and conductance.

Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions.

The emergence of SARS-CoV-2 variants necessitates rational assessment of their impact on the recognition and neutralization of the virus by the host cell. We present a comparative analysis of the interactions of Alpha, Beta, Gamma, and Delta variants with cognate molecules (ACE2 and/or furin), neutralizing nanobodies (Nbs), and monoclonal antibodies (mAbs) using in silico methods, in addition to Nb-binding assays. Our study elucidates the molecular origin of the ability of Beta and Delta variants to evade selected antibodies, such as REGN10933, LY-CoV555, B38, C105, or H11-H4, while being insensitive to others including REGN10987. Experiments confirm that nanobody Nb20 retains neutralizing activity against the Delta variant. The substitutions T478K and L452R in the Delta variant enhance associations with ACE2, whereas P681R promotes recognition by proteases, thus facilitating viral entry. The Ab-specific responses of variants highlight how full-atomic structure and dynamics analyses are required for assessing the response to newly emerging variants.

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.

Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomic molecular dynamics (MD) simulations with the goal of rapidly sampling large and cooperative conformational changes at full atomic resolution. We present here a systematic comparison of the utility and limits of four such hybrid methods that have been introduced in recent years: MD with excited normal modes (MDeNM), collective modes-driven MD (CoMD), and elastic network model (ENM)-based generation, clustering, and relaxation of conformations (ClustENM) as well as its updated version integrated with MD simulations (ClustENMD). We analyzed the predicted conformational spaces using each of these four hybrid methods, applied to four well-studied proteins, triosephosphate isomerase (TIM), 3-phosphoglycerate kinase (PGK), HIV-1 protease (PR) and HIV-1 reverse transcriptase (RT), which provide extensive ensembles of experimental structures for benchmarking and comparing the methods. We show that a rigorous multi-faceted comparison and multiple metrics are necessary to properly assess the differences between conformational ensembles and provide an optimal protocol for achieving good agreement with experimental data. While all four hybrid methods perform well in general, being especially useful as computationally efficient methods that retain atomic resolution, the systematic analysis of the same systems by these four hybrid methods highlights the strengths and limitations of the methods and provides guidance for parameters and protocols to be adopted in future studies.

Sweetened beverage taxes: Economic benefits and costs according to household income.

Taxing sweetened beverages has emerged as an important and effective policy for addressing their overconsumption. However, taxes may place a greater economic burden on people with lower incomes. We assess the degree to which sweetened beverage taxes in three large US cities placed an inequitable burden on populations with lower incomes by assessing spending on beverage taxes by income after taxes have been implemented, as well as any net transfer of funds towards lower income populations once allocation of tax revenue is considered. We find that while lower income populations pay a higher percentage of their income in beverage taxes, there is no difference in absolute spending on beverage taxes per capita, and that there is a sizable net transfer of funds towards programs targeting lower income populations. Thus, when considering both population-level taxes paid and sufficiently targeted allocations of tax revenues, a sweetened beverage tax may have characteristics of an equitable public policy.

Does HMB Enhance Body Composition in Athletes? A Systematic Review and Meta-analysis.

ABSTRACT: Holland, BM, Roberts, BM, Krieger, JW, and Schoenfeld, BJ. Does HMB enhance body composition in athletes? A systematic review and meta-analysis. J Strength Cond Res 36(2): 585-592, 2022-The purpose of this article was to systematically review and meta-analyze the current literature to determine the effects of HMB on body composition in athletes. Studies were deemed eligible for inclusion if they met the following criteria: (a) were an experimental design published in a peer-reviewed, English-language journal; (b) included human athletic populations; (c) assessed body mass (BM), fat mass (FM), or fat-free mass (FFM) using a validated measure; (d) and had a minimum supplementation period of 4 weeks. Separate analyses were performed for BM, FM, and FFM using robust variance random-effects meta-regression for multilevel data structures, with adjustments for small samples. The final analysis of BM comprised a total of 208 subjects from 7 studies. Analysis of FFM and FM encompassed 5 studies comprising 161 subjects and 5 studies comprising 128 subjects, respectively. The principal finding of this analysis suggests HMB may have a small, positive impact on FFM in athletes (0.30 ± 0.13; 95% confidence interval [CI]: -0.07 to 0.68; p = 0.08), although this seems specific to when protein intake is suboptimal (<1.6 g·kg-1·d-1). Consistent with previous research on athletes, HMB demonstrated no significant effect on BM (-0.02 ± 0.04; 95% CI: -0.14 to 0.10; p = 0.70) and a small, nonsignificant effect on FM (-0.33 ± 0.23; 95% CI: -0.96 to 0.31; p = 0.22). More research is required to establish HMB's influence on FFM in athletes. It is also important to consider the dosage of HMB and training parameters of athletes because these will likely influence the efficacy of supplementation.