De novo lipogenesis in the liver in health and disease: more than just a shunting yard for glucose

Hepatic de novo lipogenesis (DNL) is the biochemical process of synthesising fatty acids from acetyl-CoA subunits that are produced from a number of different pathways within the cell, most commonly carbohydrate catabolism. In addition to glucose which most commonly supplies carbon units for DNL, fructose is also a profoundly lipogenic substrate that can drive DNL, important when considering the increasing use of fructose in corn syrup as a sweetener. In the context of disease, DNL is thought to contribute to the pathogenesis of non-alcoholic fatty liver disease, a common condition often associated with the metabolic syndrome and consequent insulin resistance. Whether DNL plays a significant role in the pathogenesis of insulin resistance is yet to be fully elucidated, but it may be that the prevalent products of this synthetic process induce some aspect of hepatic insulin resistance

IonFlow: a galaxy tool for the analysis of ionomics data sets.

INTRODUCTION: Inductively coupled plasma mass spectrometry (ICP-MS) experiments generate complex multi-dimensional data sets that require specialist data analysis tools. OBJECTIVE: Here we describe tools to facilitate analysis of the ionome composed of high-throughput elemental profiling data. METHODS: IonFlow is a Galaxy tool written in R for ionomics data analysis and is freely accessible at https://github.com/wanchanglin/ionflow . It is designed as a pipeline that can process raw data to enable exploration and interpretation using multivariate statistical techniques and network-based algorithms, including principal components analysis, hierarchical clustering, relevance network extraction and analysis, and gene set enrichment analysis. RESULTS AND CONCLUSION: The pipeline is described and tested on two benchmark data sets of the haploid S. Cerevisiae ionome and of the human HeLa cell ionome

The effect of social preference on academic diligence in adolescence

In the current study, we were interested in whether adolescents show a preference for social stimuli compared with non-social stimuli in the context of academic diligence, that is, the ability to expend effort on tedious tasks that have long-term benefits. Forty-five female adolescents (aged 11–17) and 46 female adults (aged 23–33) carried out an adapted version of the Academic Diligence Task (ADT). We created two variations of the ADT: a social ADT and non-social ADT. Individuals were required to freely split their time between an easy, boring arithmetic task and looking at a show-reel of photographs of people (in the social ADT) or landscapes (in the non-social ADT). Individuals also provided enjoyment ratings for both the arithmetic task and the set of photographs they viewed. Adolescents reported enjoying the social photographs significantly more than the non-social photographs, with the converse being true for adults. There was no significant difference in the time spent looking at the social photographs between the adolescents and adults. However, adults spent significantly more time than adolescents looking at the non-social photographs, suggesting that adolescents were less motivated to look at the non-social stimuli. Further, the correlation between self-reported enjoyment of the pictures and choice behaviour in the ADT was stronger for adults than for adolescents in the non-social condition, revealing a greater discrepancy between self-reported enjoyment and ADT choice behaviour for adolescents. Our results are discussed within the context of the development of social cognition and introspective awareness between adolescence and adulthood

Ten years of Genome Medicine.

This year marks the 10th anniversary of Genome Medicine. The journal was launched to meet the need in the community for a platform to publish impactful and open science that advances basic and clinical research—using genetic, genomic, omic, and systems approaches—that has the potential to revolutionize the practice of medicine. We have seen the journal evolve along with the changing landscape of health and disease, including the increasing use of genome-scale approaches in medical research and clinical practice, the generation and analysis of patient- and population-level data, and the clinical implementation of these approaches in precision medicine and public health. Genome Medicine, guided by our renowned Section Editors, continues to serve an ever-growing community of interdisciplinary researchers. Here, our Section Editors discuss the major advances in the field and their applications in genomic medicine during the past decade

Metabolomic analysis in inflammatory bowel disease: a systematic review

BACKGROUND AND AIMS: The inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are chronic, idiopathic gastrointestinal (GI) diseases. Whilst their precise etiology is unknown, it is thought to involve a complex interaction between genetic predisposition and an abnormal host immune response to environmental exposures, likely microbial. Microbial dysbiosis has frequently been documented in IBD. Metabolomics (the study of small molecular intermediates and end products of metabolism in biological samples) provides a unique opportunity to characterize disease-associated metabolic changes and may be of particular use in quantifying gut microbial metabolism. Numerous metabolomic studies have been undertaken in inflammatory bowel disease populations, identifying consistent alterations in a range of molecules across several biological matrices. This systematic review aims to summarize these findings. METHODS: A comprehensive, systematic search was carried out using Medline and EMBASE. All studies were reviewed by two authors independently using predefined exclusion criteria. A total of sixty-four relevant papers were quality assessed and included in the review. RESULTS: Consistent metabolic perturbations were identified, including increases in levels of branched chain amino acids and lipid classes across stool, serum, plasma and tissue biopsy samples, and reduced levels of microbially modified metabolites in both urine (such as hippurate) and stool (such as secondary bile acids). CONCLUSIONS: This review provides a summary of metabolomic research in IBD to date, highlighting underlying themes of perturbed gut microbial metabolism and mammalian-microbial co-metabolism associated with disease status

Fungal microbiota from rain water and pathogenicity of Fusarium species isolated from atmospheric dust and rainfall dust

In order to determine the presence of Fusarium spp. in atmospheric dust and rainfall dust, samples were collected during September 2007, and July, August, and October 2008. The results reveal the prevalence of airborne Fusarium species coming from the atmosphere of the South East coast of Spain. Five different Fusarium species were isolated from the settling dust: Fusarium oxysporum, F. solani, F. equiseti, F. dimerum, and F. proliferatum. Moreover, rainwater samples were obtained during significant rainfall events in January and February 2009. Using the dilution-plate method, 12 fungal genera were identified from these rainwater samples. Specific analyses of the rainwater revealed the presence of three species of Fusarium: F. oxysporum, F. proliferatum and F. equiseti. A total of 57 isolates of Fusarium spp. obtained from both rainwater and atmospheric rainfall dust sampling were inoculated onto melon (Cucumis melo L.) cv. Piñonet and tomato (Lycopersicon esculentum Mill.) cv. San Pedro. These species were chosen because they are the main herbaceous crops in Almeria province. The results presented in this work indicate strongly that spores or propagules of Fusarium are able to cross the continental barrier carried by winds from the Sahara (Africa) to crop or coastal lands in Europe. Results show differences in the pathogenicity of the isolates tested. Both hosts showed root rot when inoculated with different species of Fusarium, although fresh weight measurements did not bring any information about the pathogenicity. The findings presented above are strong indications that long-distance transmission of Fusarium propagules may occur. Diseases caused by species of Fusarium are common in these areas. They were in the past, and are still today, a problem for greenhouses crops in Almería, and many species have been listed as pathogens on agricultural crops in this region. Saharan air masses dominate the Mediterranean regions. The evidence of long distance dispersal of Fusarium spp. by atmospheric dust and rainwater together with their proved pathogenicity must be taken into account in epidemiological studies

A combination of metabolites predicts adherence to the Mediterranean diet pattern and its associations with insulin sensitivity and lipid homeostasis in the general population: The Fenland Study, United Kingdom

BACKGROUND: Cardiometabolic benefits of the Mediterranean diet have been recognized, but underlying mechanisms are not fully understood. OBJECTIVES: We aimed to investigate how the Mediterranean diet could influence circulating metabolites and how the metabolites could mediate the associations of the diet with cardiometabolic risk factors. METHODS: Among 10,806 participants (58.9% women, mean age = 48.4 y) in the Fenland Study (2004-2015) in the United Kingdom, we assessed dietary consumption with FFQs and conducted a targeted metabolomics assay for 175 plasma metabolites (acylcarnitines, amines, sphingolipids, and phospholipids). We examined cross-sectional associations of the Mediterranean diet score (MDS) and its major components with each metabolite, modeling multivariable-adjusted linear regression. We used the regression estimates to summarize metabolites associated with the MDS into a metabolite score as a marker of the diet. Subsequently, we assessed how much metabolite subclasses and the metabolite score would mediate the associations of the MDS with circulating lipids, homeostasis model assessment of insulin resistance (HOMA-IR), and other metabolic factors by comparing regression estimates upon adjustment for the metabolites. RESULTS: Sixty-six metabolites were significantly associated with the MDS (P ≤ 0.003, corrected for false discovery rate) (Spearman correlations, r: -0.28 to +0.28). The metabolite score was moderately correlated with the MDS (r = 0.43). Of MDS components, consumption of nuts, cereals, and meats contributed to variations in acylcarnitines; fruits, to amino acids and amines; and fish, to phospholipids. The metabolite score was estimated to explain 37.2% of the inverse association of the MDS with HOMA-IR (P for mediation < 0.05). The associations of the MDS with cardiometabolic factors were estimated to be mediated by acylcarnitines, sphingolipids, and phospholipids. CONCLUSIONS: Multiple metabolites relate to the Mediterranean diet in a healthy general British population and highlight the potential to identify a set of biomarkers for an overall diet. The associations may involve pathways of phospholipid metabolism, carnitine metabolism, and development of insulin resistance and dyslipidemia

Correlations of genetic resistance of chickens to Marek's disease viruses with vaccination protection and in vivo response to phytohemaglutinin

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The potential of Ion Mobility Mass Spectrometry for high-throughput and high-resolution lipidomics

Lipids are a large and highly diverse family of biomolecules, which play essential structural, storage and signalling roles in cells and tissues. Although traditional mass spectrometry (MS) approaches used in lipidomics are highly sensitive and selective, lipid analysis remains challenging due to the chemical diversity of lipid structures, multiple isobaric species and incomplete separation using many forms of chromatography. Ion mobility (IM) separates ions in the gas phase based on their physicochemical properties. Addition of IM to the traditional lipidomic workflow both enhances separation of complex lipid mixtures, beneficial for lipid identification, and improves isomer resolution. Herein, we discuss the recent developments in IM-MS for lipidomics.This work was supported by Agilent Technologies, Santa Clara, USA; and the Medical Research Council, UK (MC UP A90 1006 & MC PC 13030)

Liquid Extraction Surface Analysis Mass Spectrometry Method for Identifying the Presence and Severity of Nonalcoholic Fatty Liver Disease

The early stages of nonalcoholic fatty liver disease (NAFLD) are characterized by the accumulation of fat in the liver (steatosis). This can lead to cell injury and inflammation resulting in nonalcoholic steatohepatitis (NASH). To determine whether lipid profiling of liver tissue can identify metabolic signatures associated with disease presence and severity, we explored liquid extraction surface analysis mass spectrometry (LESA-MS) as a novel sampling tool. Using LESA-MS, lipids were extracted directly from the surface of ultrathin slices of liver tissue prior to detection by high-resolution mass spectrometry (MS). An isotopically labeled internal standard mix was incorporated into the extraction solvent to attain semiquantitative data. Data mining and multivariate statistics were employed to evaluate the generated lipid profiles and abundances. With this approach, we were able to differentiate healthy and NAFLD liver in mouse and human tissue samples, finding several triacylglyceride (TAG) and free fatty acid (FFA) species to be significantly increased. Furthermore, LESA-MS was able to successfully differentiate between simple steatosis and more severe NASH, based on a set of short-chain TAGs and FFAs. We compared the data obtained by LESA-MS to that from liquid chromatography (LC)-MS and matrix-assisted laser desorption ionization MS. Advantages of LESA-MS include rapid analysis, minimal sample preparation, and high lipid coverage. Furthermore, since tissue slices are routinely used for diagnostics in clinical settings, LESA-MS is ideally placed to complement traditional histology. Overall LESA-MS is found to be a robust, fast, and discriminating approach for determining NAFLD presence and severity in clinical samples.J.L.G. and Z.H. are funded by the Medical Research Council (Lipid Profiling and Signalling, MC UP A90 1006 and Lipid Dynamics and Regulation, MC PC 13030). The Human Research Tissue Bank is supported by the NIHR Cambridge Biomedical Research Centre