Hydrophilic interaction chromatography–mass spectrometry for anionic metabolic profiling of urine from antibiotic-treated rats

Hydrophilic interaction chromatography–mass spectrometry (HILIC–MS) was used for anionic metabolic profiling of urine from antibiotic-treated rats to study microbial–host co-metabolism. Rats were treated with the antibiotics penicillin G and streptomycin sulfate for four or eight days and compared to a control group. Urine samples were collected at day zero, four and eight, and analyzed by HILIC–MS. Multivariate data analysis was applied to the urinary metabolic profiles to identify biochemical variation between the treatment groups. Principal component analysis found a clear distinction between those animals receiving antibiotics and the control animals, with twenty-nine discriminatory compounds of which twenty were down-regulated and nine up-regulated upon treatment. In the treatment group receiving antibiotics for four days, a recovery effect was observed for seven compounds after cessation of antibiotic administration. Thirteen discriminatory compounds could be putatively identified based on their accurate mass, including aconitic acid, benzenediol sulfate, ferulic acid sulfate, hippuric acid, indoxyl sulfate, penicillin G, phenol and vanillin 4-sulfate. The rat urine samples had previously been analyzed by capillary electrophoresis (CE) with MS detection and proton nuclear magnetic resonance (1H NMR) spectroscopy. Using CE–MS and 1H NMR spectroscopy seventeen and twenty-five discriminatory compounds were found, respectively. Both hippuric acid and indoxyl sulfate were detected across all three platforms. Additionally, eight compounds were observed with both HILIC–MS and CE–MS. Overall, HILIC–MS appears to be highly complementary to CE–MS and 1H NMR spectroscopy, identifying additional compounds that discriminate the urine samples from antibiotic-treated and control rats.

Collaborative personal profiling for web service ranking and recommendation

Web service is one of the most fundamental technologies in implementing service oriented architecture (SOA) based applications. One essential challenge related to web service is to find suitable candidates with regard to web service consumer’s requests, which is normally called web service discovery. During a web service discovery protocol, it is expected that the consumer will find it hard to distinguish which ones are more suitable in the retrieval set, thereby making selection of web services a critical task. In this paper, inspired by the idea that the service composition pattern is significant hint for service selection, a personal profiling mechanism is proposed to improve ranking and recommendation performance. Since service selection is highly dependent on the composition process, personal knowledge is accumulated from previous service composition process and shared via collaborative filtering where a set of users with similar interest will be firstly identified. Afterwards a web service re-ranking mechanism is employed for personalised recommendation. Experimental studies are conduced and analysed to demonstrate the promising potential of this research.

Development of personalised functional foods needs metabolic profiling

Purpose of review There is growing interest in applying metabolic profiling technologies to food science as this approach is now embedded into the foodomics toolbox. This review aims at exploring how metabolic profiling can be applied to the development of functional foods. Recent findings One of the biggest challenges of modern nutrition is to propose a healthy diet to populations worldwide that must suit high inter-individual variability driven by complex gene-nutrient-environment interactions. Although a number of functional foods are now proposed in support of a healthy diet, a one-size-fits-all approach to nutrition is inappropriate and new personalised functional foods are necessary. Metabolic profiling technologies can assist at various levels of the development of functional foods, from screening for food composition to identification of new biomarkers of food intake to support diet intervention and epidemiological studies. Summary Modern ‘omics’ technologies, including metabolic profiling, will support the development of new personalised functional foods of high relevance to twenty-first-century medical challenges such as controlling the worldwide spread of metabolic disorders and ensuring healthy ageing.

Profiling text comprehension impairments in aphasia

Background: Research in aphasia has focused on acquired dyslexias at the single word level, with a paucity of assessment techniques and rehabilitation approaches for individuals with difficulty at the text level. A rich literature from research with paediatric populations and healthy non-brain damaged, skilled adult readers allows the component processes that are important for text reading to be defined and more appropriate assessments to be devised. Aims: To assess the component processes of text reading in a small group of individuals with aphasia who report difficulties reading at the text level. Do assessments of component processes in reading comprehension reveal distinct profiles of text comprehension? To what extent are text comprehension difficulties caused by underlying linguistic and/or cognitive deficits? Methods & Procedures: Four individuals with mild aphasia who reported difficulties reading at the text level took part in a case-series study. Published assessments were used to confirm the presence of text comprehension impairment. Participants completed a range of assessments to provide a profile of their linguistic and cognitive skills, focusing on processes known to be important for text comprehension. We identified the following areas for assessment: reading speed, language skills (single word and sentence), inferencing, working memory and metacognitive skills (monitoring and strategy use). Outcomes & Results: Performance was compared against age-matched adult control data. One participant presented with a trend for impaired abilities in inferencing, with all other assessed skills being within normal limits. The other three had identified linguistic and working memory difficulties. One presented with a residual deficit in accessing single word meaning that affected text comprehension. The other two showed no clear link between sentence processing difficulties and text comprehension impairments. Across these three, data suggested a link between verbal working memory capacity and specific inferencing skills. Conclusions: Successful text reading relies on a number of component processes. In this paper we have made a start in defining those component processes and devising tasks suitable to assess them. From our results, assessment of verbal working memory and inferencing appears to be critical for understanding text comprehension impairments in aphasia. It is possible that rehabilitation input can capitalize on key meta-cognitive skills (monitoring, strategy use) to support functional reading in the face of existing linguistic, text comprehension and memory impairments.

Nutrimetabonomics: nutritional applications of metabolic profiling

An individual's metabolic phenotype, and ultimately health, is significantly influenced by complex interactions between their genes and the diet. Studying these associations and their downstream biochemical consequences has proven extremely challenging using traditional hypothesis-led strategies. Metabonomics, a systems biology approach, allows the global metabolic response of biological systems to stimuli to be characterised. Through the application of this approach to nutritional-based research, nutrimetabonomics, the biochemical response to dietary inputs is being investigated at greater levels of resolution. This has allowed novel insights to be gained regarding intricate diet-gene interactions and their consequences for health and disease. In this review, we present some of the latest research exploring how nutrimetabonomics can assist in the elucidation of novel biomarkers of dietary behaviour and provide new perspectives on diet-health relationships. The use of this approach to study the metabolic interplay between the gut microbiota and the host is also explored.

A comparative review of skill assessment: performance, prediction and profiling

The assessment of chess players is an increasingly attractive opportunity and an unfortunate necessity. The chess community needs to limit potential reputational damage by inhibiting cheating and unjustified accusations of cheating: there has been a recent rise in both. A number of counter-intuitive discoveries have been made by benchmarking the intrinsic merit of players’ moves: these call for further investigation. Is Capablanca actually, objectively the most accurate World Champion? Has ELO rating inflation not taken place? Stimulated by FIDE/ACP, we revisit the fundamentals of the subject to advance a framework suitable for improved standards of computational experiment and more precise results. Other domains look to chess as the demonstrator of good practice, including the rating of professionals making high-value decisions under pressure, personnel evaluation by Multichoice Assessment and the organization of crowd-sourcing in citizen science projects. The ‘3P’ themes of performance, prediction and profiling pervade all these domains.

Cardiac myocyte gene expression profiling during H2O2-induced apoptosis

High levels of oxidative stress promote cardiac myocyte death, though lower levels are potentially cytoprotective/anabolic. We examined the changes in gene expression in rat neonatal cardiac myocytes exposed to apoptotic (0.2 mM) or nontoxic (0.04 mM) concentrations of H2O2 (2, 4, or 24 h) using Affymetrix microarrays. Using U34B arrays, we identified a ubiquitously expressed, novel H2O2-responsive gene [putative peroxide-inducible transcript 1 (Perit1)], which generates two alternatively spliced transcripts. Using 230 2.0 arrays, H2O2 (0.04 mM) promoted significant changes in expression of only 32 genes, all of which were seen with 0.2 mM H2O2. We failed to detect any increase in the rate of protein synthesis in cardiac myocytes exposed to <0.1 mM H2O2, further suggesting that global, low concentrations of H2O2 are not anabolic in this system. H2O2 (0.2 mM) promoted significant (P < 0.05, >1.75-fold) changes in expression of 649 mRNAs and 187 RNAs corresponding to no established gene. Of the mRNAs, 114 encoded transcriptional regulators including Krüppel-like factors (Klfs). Quantitative PCR independently verified the changes in Klf expression. Thus, H2O2-induced cardiac myocyte apoptosis is associated with dynamic changes in gene expression. The expression of these genes and their protein products potentially influences the progression of the apoptotic response.

A sodar for profiling in a spatially inhomogeneous urban environment

The urban boundary layer, above the canopy, is still poorly understood. One of the challenges is obtaining data by sampling more than a few meters above the rooftops, given the spatial and temporal inhomogeneities in both horizontal and vertical. Sodars are generally useful tools for ground-based remote sensing of winds and turbulence, but rely on horizontal homogeneity (as do lidars) in building up 3-component wind vectors from sampling three or more spatially separated volumes. The time taken for sound to travel to a typical range of 200 m and back is also a limitation. A sodar of radically different design is investigated, aimed at addressing these problems. It has a single vertical transmitted sound pulse. Doppler shifted signals are received from a number of volumes around the periphery of the transmitted beam with microphones which each having tight angular sensitivity at zenith angles slightly off-vertical. The spatial spread of sampled volumes is therefore smaller. By having more receiver microphones than a conventional sodar, the effect of smaller zenith angle is offset. More rapid profiling is also possible with a single vertical transmitted beam, instead of the usual multiple beams.A prototype design is described, together with initial field measurements. It is found that the beam forming using a single dish antenna and the drift of the sound pulse downwind both give rise to reduced performance compared with expectations. It is concluded that, while the new sodar works in principle, the compromises arising in the design mean that the expected advantages have not been realized

Integration of steroid hormone initiated membrane action to genomic function in the brain

Estrogen is a ligand for the estrogen receptor (ER), which on binding 17beta-estradiol, functions as a ligand-activated transcription factor and regulates the transcription of target genes. This is the slow genomic mode of action. However, rapid non-genomic actions of estrogen also exist at the cell membrane. Using a novel two-pulse paradigm in which the first pulse rapidly initiates non-genomic actions using a membrane-limited estrogen conjugate (E-BSA), while the second pulse promotes genomic transcription from a consensus estrogen response element (ERE), we have demonstrated that rapid actions of estrogen potentiate the slower transcriptional response from an ERE-reporter in neuroblastoma cells. Since rapid actions of estrogen activate kinases, we used selective inhibitors in the two-pulse paradigm to determine the intracellular signaling cascades important in such potentiation. Inhibition of protein kinase A (PKA), PKC, mitogen activated protein kinase (MAPK) or phosphatidylinositol 3-OH kinase (PI-3K) in the first pulse decreases potentiation of transcription. Also, our data with both dominant negative and constitutive mutants of Galpha subunits show that Galpha(q) initiates the rapid signaling cascade at the membrane in SK-N-BE(2)C neuroblastoma cells. We discuss two models of multiple kinase activation at the membrane Pulses of estrogen induce lordosis behavior in female rats. Infusion of E-BSA into the ventromedial hypothalamus followed by 17beta-estradiol in the second pulse could induce lordosis behavior, demonstrating the applicability of this paradigm in vivo. A model where non-genomic actions of estrogen couple to genomic actions unites both aspects of hormone action.

Urinary metabolomic profiling to identify biomarkers of a flavonoid-rich and flavonoid-poor fruits and vegetables diet: the FLAVURS trial in adults: the FLAVURS trial

The present study aims to investigate the dose dependent effects of consuming diets enriched in flavonoid-rich and flavonoid-poor fruits and vegetables on the urine metabolome of adults who had a C1.5 fold increased risk of cardiovascular diseases. A single-blind, dose-dependent, parallel randomized controlled dietary intervention was conducted where volunteers (n = 126) were randomly assigned to one of three diets: high flavonoid diet, low flavonoid diet or habitual diet as a control for 18 weeks. High resolution LC– MS untargeted metabolomics with minimal sample cleanup was performed using an Orbitrap mass spectrometer. Putative biomarkers which characterize diets with high and low flavonoid content were selected by state-of-the-art data analysis strategies and identified by HR-MS and HR-MS/MS assays. Discrimination between diets was observed by application of two linear mixedmodels: one including a diet-time interaction effect and the second containing only a time effect. Valerolactones, phenolic acids and their derivatives were among sixteen biomarkers related to the high flavonoid dietary exposure. Four biomarkers related to the low flavonoid diet belonged to the family of phenolic acids. For the first time abscisic acid glucuronide was reported as a biomarker after a dietary intake, however its origins have to be examined by future hypothesis driven experiments using a more targeted approach. This metabolomic analysis has identified a number of dose dependent urinary biomarkers (i.e. proline betaine or iberin-N-acetyl cysteine), which can be used in future observation and intervention studies to assess flavonoids and nonflavonoid phenolic intakes and compliance to fruit and vegetable intervention.