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Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consultation with data collectors, data users, instrument manufacturers, and data scientists was undertaken in order to ensure that the reporting format met community needs. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format is published in the U.S. Department of Energy's ESS-DIVE data repository, with documentation and future development efforts being maintained in a version control system.

Soil moisture plays a key role in hydrological, biogeochemical, and energy budgets of terrestrial ecosystems. Accurate soil moisture measurements in remote ecosystems such as the Amazon are difficult and limited because of logistical constraints. Time domain reflectometry (TDR) sensors are widely used to monitor soil moisture and require calibration to convert the TDR's dielectric permittivity measurement (Ka) to volumetric water content (θv). In this study, our objectives were to develop a field-based calibration of TDR sensors in an old-growth upland forest in the central Amazon, to evaluate the performance of the calibration, and then to apply the calibration to determine the dynamics of soil moisture content within a 14.2-m-deep vertical soil profile. Depth-specific TDR calibration using local soils in a controlled laboratory setting yielded a novel Ka–θv third-degree polynomial calibration. The sensors were later installed to their specific calibration depth in a 14.2-m pit. The widely used Ka–θv relationship (Topp model) underestimated the site-specific θv by 22–42%, indicating significant error in the model when applied to these well-structured, clay-rich tropical forest soils. The calibrated wet- and dry-season θv data showed a variety of depth and temporal variations highlighting the importance of soil textural differentiation, root uptake depths, as well as event to seasonal precipitation effects. Data such as these are greatly needed for improving our understanding of ecohydrological processes within tropical forests and for improving models of these systems in the face of changing environmental conditions.

Metadata describe the ancillary information needed for data preservation and independent interpretation, comparison across heterogeneous datasets, and quality assessment and quality control (QA/QC). Environmental observations are vastly diverse in type and structure, can be taken across a wide range of spatiotemporal scales in a variety of measurement settings and approaches, and saved in multiple formats. Thus, well-organized, consistent metadata are required to produce usable data products from diverse environmental observations collected across field sites. However, existing metadata reporting protocols do not support the complex data synthesis and model-data integration needs of interdisciplinary earth system research. We developed a metadata reporting framework (FRAMES) to enable management and synthesis of observational data that are essential in advancing a predictive understanding of earth systems. FRAMES utilizes best practices for data and metadata organization enabling consistent data reporting and compatibility with a variety of standardized data protocols. We used an iterative scientist-centered design process to develop FRAMES, resulting in a data reporting format that incorporates existing field practices to maximize data-entry efficiency. Thus, FRAMES has a modular organization that streamlines metadata reporting and can be expanded to incorporate additional data types. With FRAMES's multi-scale measurement position hierarchy, data can be reported at observed spatial resolutions and then easily aggregated and linked across measurement types to support model-data integration. FRAMES is in early use by both data originators (persons generating data) and consumers (persons using data and metadata). In this paper, we describe FRAMES, identify lessons learned, and discuss areas of future development.

Background: Dietitians at the Oxford Radcliffe Hospital encountering the problem of chyle leakage found a lack of information regarding its dietetic management. This study was undertaken to review the literature and to survey current dietetic practice and medical opinion in the UK. Methods: A postal survey of dietitians and clinicians in relevant specialities at hospitals involved in the clinical training of dietetic students (n = 110) was undertaken. The dietitians' questionnaire examined knowledge and experience of chyle leakage, types of patients treated, dietary therapies employed, responsibilities for prescriptions and outcomes. A different questionnaire was used to assess clinician's opinions on appropriate management. Results: A link between the origin of chyle leakage and the effectiveness of conservative management became apparent from the literature review. Conservative management appears to be most effective in chyle leakage associated with head and neck surgery, and least effective when chyle leakage is associated with malignancy. Completed questionnaires were received from 336 dietitians in 90 training departments and 132 clinicians. Dietitians reported the use of a number of dietary therapies, including low-fat diets. These ranged from minimal long chain triglycerides (LCT) to 'standard' low-fat diets. These were sometimes used in conjunction with medium chain triglycerides (MCT). The use of total parenteral nutrition (TPN) was also reported, either alone or in combination with a 'low-fat diet'. No clear pattern emerged as to when a particular therapy was indicated or should be revised. More than 70% of respondents to the medical survey considered there to be a role for conservative management in the treatment of chyle leakage. TPN appeared to be slightly favoured over minimal-fat (LCT) diet. Dietitians are hampered by the lack of consensus about the optimum nutritional therapy for this condition. This was reflected in the wide variation in the composition of reported dietary regimens. The majority of dietitians who had treated such patients reported the use of 'low-fat' diets, but only 5 (13%) respondents specified a level of fat restriction. Conclusions: The literature suggests that TPN may be the most effective treatment for reducing chyle flow. However, given the risks of TPN an initial trial of minimal-fat (LCT) diet plus MCT is warranted. The need for readily accessible practice guidelines for dietitians is apparent. [ABSTRACT FROM AUTHOR]

OBJECTIVE: Recent reports have suggested that a low glycemic index (GI) diet may have a role in the management of obesity through its ability to increase the satiety value of food and modulate appetite. To date, no long-term clinical trials have examined the effect of dietary GI on body weight regulation. The majority of evidence comes from single-day studies, most of which have been conducted in adults. The purpose of this study was to investigate the effect of 3 test breakfasts-low-GI, low-GI with 10% added sucrose, and high-GI-on ad libitum lunch intake, appetite, and satiety and to compare these with baseline values when habitual breakfast was consumed. METHODS: A 3-way crossover study using block randomization of breakfast type was conducted in a school that already ran a breakfast club. A total of 37 children aged 9 to 12 years (15 boys and 22 girls) completed the study. The proportion of nonoverweight to overweight/obese children was 70:30. Children were divided into 5 groups, and a rolling program was devised whereby, week by week, each group would randomly receive 1 of 3 test breakfasts for 3 consecutive days, with a minimum of 5 weeks between the test breakfasts. Participants acted as their own control. The 3 test breakfasts were devised to match the energy and nutritional content of an individual's habitual breakfast as far as possible. All test breakfasts were composed of fruit juice, cereal, and milk with/without bread and margarine; foods with an appropriate GI value were selected. After each test breakfast, children were instructed not to eat or drink anything until lunchtime, except water and a small serving of fruit supplying approximately 10 g of carbohydrate, which was provided. Breakfast palatability, satiation after breakfast, and satiety before lunch were measured using rating scales based on previously used tools. Lunch was a buffet-style meal, and children were allowed free access to a range of foods. Lunch was served in the school hall where the rest of the schoolchildren were eating. Food intake at lunch was unobtrusively observed and recorded. Leftovers and food swapping were recorded, and plate waste was estimated. Lunch intakes were analyzed using a multilevel regression model for repeated measures data. The likelihood ratio statistic was used to determine whether the type of breakfast eaten had a significant effect on lunch intake after allowing for sex and weight status. RESULTS: The type of breakfast eaten had a statistically significant effect on mean energy intake at lunchtime: lunch intake was lower after low-GI and low-GI with added sucrose breakfasts compared with lunch intake after high-GI and habitual breakfasts (which were high-GI). Overweight and sex did not have a significant effect on lunch intake. Pairwise comparisons among the 3 types of test breakfasts and between each test breakfast and habitual breakfast were made. Lunch intake after the high-GI breakfast was significantly higher than after the low-GI breakfast and low-GI breakfast with added sucrose. The details of the pairwise comparisons were as follows: high-GI versus low-GI = 145 +/- 54 kcal; high-GI versus low-GI plus sucrose = 119 +/- 53 kcal; low-GI plus sucrose versus low-GI = 27 +/- 54 kcal. Lunch intake after the low-GI breakfast and the low-GI breakfast with added sucrose was significantly lower than after the habitual breakfast. The details of the pairwise comparisons were as follows: low-GI versus habitual = -109 +/- 75 kcal; low-GI plus sucrose versus habitual = -83 +/- 75 kcal; high-GI versus habitual = 36 +/- 75 kcal. There were no significant differences between the test breakfasts in immediate satiation. The high-GI breakfasts were rated to be more palatable than the low-GI breakfasts. At lunchtime, hunger ratings were greater after the high-GI breakfast compared with the other 2 test breakfasts on 2 of the 3 experimental days. Prelunch satiety scales were inversely related to subsequent food intake. CONCLUSIONS: These results suggest that low-GI foods eaten at breakfast have a significant impact on food intake at lunch. This is the first study to observe such an effect in a group of normal and overweight children and adds to the growing body of evidence that low-GI foods may have an important role in weight control and obesity management. The potentially confounding effect of differences in the macronutrient and dietary fiber content of the test breakfasts warrants additional study. In addition, the impact of GI on food intake and body weight regulation in the long term needs to be investigated. [ABSTRACT FROM AUTHOR]

The function of transfer RNAs (tRNAs) depends on enzymes that cleave primary transcript ends, add a 3' CCA tail, introduce post-transcriptional base modifications, and charge (aminoacylate) mature tRNAs with the correct amino acid. Maintaining an available pool of the resulting aminoacylated tRNAs is essential for protein synthesis. High-throughput sequencing techniques have recently been developed to provide a comprehensive view of aminoacylation state in a tRNA-specific fashion. However, these methods have never been applied to plants. Here, we treated Arabidopsis thaliana RNA samples with periodate and then performed tRNA-seq to distinguish between aminoacylated and uncharged tRNAs. This approach successfully captured every tRNA isodecoder family and detected expression of additional tRNA-like transcripts. We found that estimated aminoacylation rates and CCA tail integrity were significantly higher on average for organellar (mitochondrial and plastid) tRNAs than for nuclear/cytosolic tRNAs. Reanalysis of previously published human cell line data showed a similar pattern. Base modifications result in nucleotide misincorporations and truncations during reverse transcription, which we quantified and used to test for relationships with aminoacylation levels. We also determined that the Arabidopsis tRNA-like sequences (t-elements) that are cleaved from the ends of some mitochondrial messenger RNAs have post-transcriptionally modified bases and CCA-tail addition. However, these t-elements are not aminoacylated, indicating that they are only recognized by a subset of tRNA-interacting enzymes and do not play a role in translation. Overall, this work provides a characterization of the baseline landscape of plant tRNA aminoacylation rates and demonstrates an approach for investigating environmental and genetic perturbations to plant translation machinery., (© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Photosynthetic acclimation to both warming and elevated CO 2 of boreal trees remains a key uncertainty in modelling the response of photosynthesis to future climates. We investigated the impact of increased growth temperature and elevated CO 2 on photosynthetic capacity (V cmax and J max ) in mature trees of two North American boreal conifers, tamarack and black spruce. We show that V cmax and J max at a standard temperature of 25°C did not change with warming, while V cmax and J max at their thermal optima (T opt ) and growth temperature (T g ) increased. Moreover, V cmax and J max at either 25°C, T opt or T g decreased with elevated CO 2 . The J max /V cmax ratio decreased with warming when assessed at both T opt and T g but did not significantly vary at 25°C. The J max /V cmax increased with elevated CO 2 at either reference temperature. We found no significant interaction between warming and elevated CO 2 on all traits. If this lack of interaction between warming and elevated CO 2 on the V cmax , J max and J max /V cmax ratio is a general trend, it would have significant implications for improving photosynthesis representation in vegetation models. However, future research is required to investigate the widespread nature of this response in a larger number of species and biomes., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

The oxygen fugacity (f O2 ) of convecting upper mantle recorded by ridge peridotites varies by more than four orders of magnitude 1-3 . Although much attention has been given to mechanisms that drive variations in mantle f O2 between tectonic settings 1,3,4 and to comparisons of f O2 between modern rocks and ancient-mantle-derived rocks 5-10 , comparatively little has been done to understand the origins of the high variability in f O2 recorded by peridotites from modern mid-ocean ridge settings. Here we report the petrography and geochemistry of peridotites from the Gakkel Ridge and East Pacific Rise (EPR), including 16 new high-precision determinations of f O2 . Refractory peridotites from the Gakkel Ridge record f O2 more than four orders of magnitude below the mantle average. With thermodynamic and mineral partitioning modelling, we show that excursions to ultralow f O2 can be produced by large degrees of melting at high potential temperature (T p ), beginning in the garnet field and continuing into the spinel field-conditions met during the generation of ancient komatiites but not modern basalts. This does not mean that ambient convecting upper mantle had a lower ferric to ferrous ratio in Archaean times than today nor that modern melting in the garnet field at hotspots produce reduced magmas. Instead, it implies that rafts of ancient, refractory, ultrareduced mantle continue to circulate in the modern mantle while contributing little to modern ridge volcanism., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)