Opposite variations in fumarate and malate dominate metabolic phenotypes of Arabidopsis salicylate mutants with abnormal biomass under chilling.

In chilling conditions (5°C), salicylic acid (SA)-deficient mutants (sid2, eds5 and NahG) of Arabidopsis thaliana produced more biomass than wild type (Col-0), whereas the SA overproducer cpr1 was extremely stunted. The hypothesis that these phenotypes were reflected in metabolism was explored using 600 MHz (1) H nuclear magnetic resonance (NMR) analysis of unfractionated polar shoot extracts. Biomass-related metabolic phenotypes were identified as multivariate data models of these NMR 'fingerprints'. These included principal components that correlated with biomass. Also, partial least squares-regression models were found to predict the relative size of plants in previously unseen experiments in different light intensities, or relative size of one genotype from the others. The dominant signal in these models was fumarate, which was high in SA-deficient mutants, intermediate in Col-0 and low in cpr1 at 5°C. Among signals negatively correlated with biomass, malate was prominent. Abundance of transcripts of the FUM2 cytosolic fumarase (At5g50950) showed strong positive correlation with fumarate levels and with biomass, whereas no significant differences were found for the FUM1 mitochondrial fumarase (At2g47510). It was confirmed that the morphological effects of SA under chilling find expression in the metabolome, with a role of fumarate highlighted.

The metabolic transition during disease following infection of Arabidopsis thaliana by Pseudomonas syringae pv. tomato.

The outcome of bacterial infection in plants is determined by the ability of the pathogen to successfully occupy the apoplastic space and deliver a constellation of effectors that collectively suppress basal and effector-triggered immune responses. In this study, we examined the metabolic changes associated with establishment of disease using analytical techniques that interrogated a range of chemistries. We demonstrated clear differences in the metabolome of Arabidopsis thaliana leaves infected with virulent Pseudomonas syringae within 8 h of infection. In addition to confirmation of changes in phenolic and indolic compounds, we identified rapid alterations in the abundance of amino acids and other nitrogenous compounds, specific classes of glucosinolates, disaccharides, and molecules that influence the prevalence of reactive oxygen species. Our data illustrate that, superimposed on defence suppression, pathogens reconfigure host metabolism to provide the sustenance required to support exponentially growing populations of apoplastically localized bacteria. We performed a detailed baseline study reporting the metabolic dynamics associated with bacterial infection. Moreover, we have integrated these data with the results of transcriptome profiling to distinguish metabolomic pathways that are transcriptionally activated from those that are post-transcriptionally regulated.

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity.

The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.

Co-ordinated expression of amino acid metabolism in response to N and S deficiency during wheat grain filling.

Increasing demands for productivity together with environmental concerns about fertilizer use dictate that the future sustainability of agricultural systems will depend on improving fertilizer use efficiency. Characterization of the biological processes responsible for efficient fertilizer use will provide tools for crop improvement under reduced inputs. Transcriptomic and metabolomic approaches were used to study the impact of nitrogen (N) and sulphur (S) deficiency on N and S remobilization from senescing canopy tissues during grain filling in winter wheat (Triticum aestivum). Canopy tissue N was remobilized effectively to the grain after anthesis. S was less readily remobilized. Nuclear magnetic resonance (NMR) metabolite profiling revealed significant effects of suboptimal N or S supply in leaves but not in developing grain. Analysis of amino acid pools in the grain and leaves revealed a strategy whereby amino acid biosynthesis switches to the production of glutamine during grain filling. Glutamine accumulated in the first 7 d of grain development, prior to conversion to other amino acids and protein in the subsequent 21 d. Transcriptome analysis indicated that a down-regulation of the terminal steps in many amino acid biosynthetic pathways occurs to control pools of amino acids during leaf senescence. Grain N and S contents increased in parallel after anthesis and were not significantly affected by S deficiency, despite a suboptimal N:S ratio at final harvest. N deficiency resulted in much slower accumulation of grain N and S and lower final concentrations, indicating that vegetative tissue N has a greater control of the timing and extent of nutrient remobilization than S.

Correlating Cleaning Thoroughness with Effectiveness and Briefly Intervening to Affect Cleaning Outcomes: How Clean Is Cleaned?

OBJECTIVES: The most efficient approach to monitoring and improving cleaning outcomes remains unresolved. We sought to extend the findings of a previous study by determining whether cleaning thoroughness (dye removal) correlates with cleaning efficacy (absence of molecular or cultivable biomaterial) and whether one brief educational intervention improves cleaning outcomes. DESIGN: Before-after trial. SETTING: Newly built community hospital. INTERVENTION: 90 minute training refresher with surface-specific performance results. METHODS: Dye removal, measured by fluorescence, and biomaterial removal and acquisition, measured with culture and culture-independent PCR-based assays, were clandestinely assessed for eight consecutive months. At this midpoint, results were presented to the cleaning staff (intervention) and assessments continued for another eight consecutive months. RESULTS: 1273 surfaces were sampled before and after terminal room cleaning. In the short-term, dye removal increased from 40.3% to 50.0% (not significant). For the entire study period, dye removal also improved but not significantly. After the intervention, the number of rooms testing positive for specific pathogenic species by culturing decreased from 55.6% to 36.6% (not significant), and those testing positive by PCR fell from 80.6% to 53.7% (P = 0.016). For nonspecific biomaterial on surfaces: a) removal of cultivable Gram-negatives (GN) trended toward improvement (P = 0.056); b) removal of any cultivable growth was unchanged but acquisition (detection of biomaterial on post-cleaned surfaces that were contaminant-free before cleaning) worsened (P = 0.017); c) removal of PCR-based detection of bacterial DNA improved (P = 0.046), but acquisition worsened (P = 0.003); d) cleaning thoroughness and efficacy were not correlated. CONCLUSION: At this facility, a minor intervention or minimally more aggressive cleaning may reduce pathogen-specific contamination, but not without unintended consequences.

Relationships among cleaning, environmental DNA, and healthcare-associated infections in a new evidence-based design hospital.

OBJECTIVE: Hospital environments influence healthcare-associated infection (HAI) patterns, but the role of evidenced-based design (EBD) and residual bacterial DNA (previously thought to be clinically inert) remain incompletely understood. METHODS: In a newly built EBD hospital, we used culture-based and culture-free (molecular) assays, pulsed-field gel electrophoresis (PFGE), and whole-genome sequencing (WGS) to determine: (1) patterns of environmental contamination with target organisms (TOs) and multidrug-resistant (MDR) target organisms (MDR-TOs); (2) genetic relatedness between environmentally isolated MDR-TO and those from HAIs; and (3) correlation between surface contamination and HAIs. RESULTS: A total of 1,273 high-touch surfaces were swabbed before and after terminal cleaning during 77 room visits. Of the 2,546 paired swabs, 47% had cultivable biomaterial and 42% had PCR-amplifiable DNA. The ratios of TOs detected to surfaces assayed were 85 per 1,273 for the culture-based method and 106 per 1,273 for the PCR-based method. Sinks, toilet rails, and bedside tables most frequently harbored biomaterial. Although cleaned surfaces were less likely to have cultivable TOs than precleaned surfaces, they were not less likely to harbor bacterial DNA. The rate of MDR-TOs to surfaces swabbed was 0.1% (3/2546). Although environmental MDR-TOs and MDR-TOs from HAIs were genetically related by PFGE, WGS revealed that they were unrelated. Environmental levels of cultivable Enterococcus spp. and E. coli DNA were positively correlated with infection incidences (P<.04 and P<.005, respectively). CONCLUSION: MDR-TOs were rarely detected during surveillance and were not implicated in HAIs. The roles of environmental DNA and EBD, particularly with respect to water-associated fixtures or the potential suppression of cultivable environmental MDR-TOs, warrant multicenter investigations.

How the legal system should change as a result of converging technologies.

A forecast is given for how the legal system will change to meet some of the challenges for improvement that converging technologies raise for society.

Tissue preparation using Arabidopsis.

The ability to track changes in the levels of many metabolites in plants has great utility in a number of biological contexts. A metabolomics experiment usually requires the comparison of different varieties in either a functional genomics context or in response to perturbation by an external treatment. Such treatments can result in subtle changes in the final chemical signature of the plant tissue, and therefore, any unwanted variance produced in the generation of that tissue must be minimised. Procedures for plant growth, harvesting, preparation of extracts, and the subsequent collection of data have been optimised to minimise experimental variation within the dataset. This chapter describes in detail how to generate reproducible Arabidopsis tissue suitable for a typical plant metabolomics experiment. Issues concerned with tissue sampling, harvesting, and storage are also discussed.

An inter-laboratory comparison demonstrates that [H]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection.

In any metabolomics experiment, robustness and reproducibility of data collection is of vital importance. These become more important in collaborative studies where data is to be collected on multiple instruments. With minimisation of variance in sample preparation and instrument performance it is possible to elucidate even subtle differences in metabolite fingerprints due to genotype or biological treatment. In this paper we report on an inter laboratory comparison of plant derived samples by [(1)H]-NMR spectroscopy across five different sites and within those sites utilising instruments with different probes and magnetic field strengths of 9.4 T (400 MHz), 11.7 T (500 MHz) and 14.1 T (600 MHz). Whilst the focus of the study is on consistent data collection across laboratories, aspects of sample stability and the requirement for sample rotation within the NMR magnet are also discussed. Comparability of the datasets from participating laboratories was exceptionally good and the data were amenable to comparative analysis by multivariate statistics. Field strength differences can be adjusted for in the data pre-processing and multivariate analysis demonstrating that [(1)H]-NMR fingerprinting is the ideal technique for large scale plant metabolomics data collection requiring the participation of multiple laboratories.

Association between television viewing and poor diet quality in young children.

OBJECTIVE: To examine the association between television/video (TV) viewing and markers of diet quality among 3-year-old children. METHODS: We studied 613 boys and 590 girls, age 3 years old, who were participants in Project Viva. Each mother reported the number of hours her child watched TV on an average weekday and weekend day in the past month, from which we calculated a weighted mean. The main outcomes were intakes of selected foods and nutrients from a validated food frequency questionnaire. In linear regression models we adjusted for mother's sociodemographic information, parental body mass index (BMI), and child's age, sex, race/ethnicity, BMI z-score, sleep duration, and breast feeding duration. RESULTS: Mean (standard deviation, SD) age of subjects was 3.2 (0.2) years; 372 children (31%) were non-white and 151 (13%) had a household income < $40 000, and 330 mothers (28%) had completed less than a college degree. Mean (SD) TV viewing was 1.7 (1.0) hours per day. For each 1-hour increment of TV viewing per day, we found higher intakes of sugar-sweetened beverages (0.06 servings/day [95% CI 0.03, 0.10]), fast food (0.32 servings/month [95% CI 0.16, 0.49]), red and processed meat (0.06 servings/day [95% CI 0.02, 0.09]), total energy intake (48.7 kcal/day [95% CI 18.7, 78.6]), and percent energy intake from trans fat (0.05 [95% CI 0.03, 0.07]). We found lower intakes of fruit and vegetables (-0.18 servings/day [95% CI -0.32, -0.05]), calcium (-24.6 mg/day [95% CI -41.0, -8.1]), and dietary fiber (-0.44 g/day [95% CI -0.65, -0.22]). CONCLUSIONS: Among 3-year-olds, more TV viewing is associated with adverse dietary practices. Interventions to reduce TV viewing in this age group may lead to improved diet quality.

Assessing the postoperative patient: philosophy, knowledge and theory.

The assessment of the postoperative patient is critical in identifying the patient's current condition and to monitor any complications that might occur. However, many nurses fail to realize the implications that philosophical paradigms, knowledge and theoretical concepts bring to the assessment practice and the manner in which assessment is conducted; in particular, within 24 h after surgery. This article seeks to explore the usefulness of philosophy, knowledge and theory as they relate to nursing assessment of the postoperative patient within the initial 24 h after surgery. It is the duty of nurses to select and effectively apply appropriate philosophical dimensions, knowledge and theories in practice and critically evaluate these areas with respect to assessment of the postoperative patient, thus aiming for a holistic assessment of the patient.