PubMed

Related Articles Quiescent Endothelial Cells Upregulate Fatty Acid β-Oxidation for Vasculoprotection via Redox Homeostasis. Cell Metab. 2018 Aug 20;: Authors: Kalucka J, Bierhansl L, Conchinha NV, Missiaen R, Elia I, Brüning U, Scheinok S, Treps L, Cantelmo AR, Dubois C, de Zeeuw P, Goveia J, Zecchin A, Taverna F, Morales-Rodriguez F, Brajic A, Conradi LC, Schoors S, Harjes U, Vriens K, Pilz GA, Chen R, Cubbon R, Thienpont B, Cruys B, Wong BW, Ghesquière B, Dewerchin M, De Bock K, Sagaert X, Jessberger S, Jones EAV, Gallez B, Lambrechts D, Mazzone M, Eelen G, Li X, Fendt SM, Carmeliet P Abstract Little is known about the metabolism of quiescent endothelial cells (QECs). Nonetheless, when dysfunctional, QECs contribute to multiple diseases. Previously, we demonstrated that proliferating endothelial cells (PECs) use fatty acid β-oxidation (FAO) for de novo dNTP synthesis. We report now that QECs are not hypometabolic, but upregulate FAO >3-fold higher than PECs, not to support biomass or energy production but to sustain the tricarboxylic acid cycle for redox homeostasis through NADPH regeneration. Hence, endothelial loss of FAO-controlling CPT1A in CPT1AΔEC mice promotes EC dysfunction (leukocyte infiltration, barrier disruption) by increasing endothelial oxidative stress, rendering CPT1AΔEC mice more susceptible to LPS and inflammatory bowel disease. Mechanistically, Notch1 orchestrates the use of FAO for redox balance in QECs. Supplementation of acetate (metabolized to acetyl-coenzyme A) restores endothelial quiescence and counters oxidative stress-mediated EC dysfunction in CPT1AΔEC mice, offering therapeutic opportunities. Thus, QECs use FAO for vasculoprotection against oxidative stress-prone exposure. PMID: 30146488 [PubMed - as supplied by publisher]

Related Articles Impairment of Angiogenesis by Fatty Acid Synthase Inhibition Involves mTOR Malonylation. Cell Metab. 2018 Aug 21;: Authors: Bruning U, Morales-Rodriguez F, Kalucka J, Goveia J, Taverna F, Queiroz KCS, Dubois C, Cantelmo AR, Chen R, Loroch S, Timmerman E, Caixeta V, Bloch K, Conradi LC, Treps L, Staes A, Gevaert K, Tee A, Dewerchin M, Semenkovich CF, Impens F, Schilling B, Verdin E, Swinnen JV, Meier JL, Kulkarni RA, Sickmann A, Ghesquière B, Schoonjans L, Li X, Mazzone M, Carmeliet P Abstract The role of fatty acid synthesis in endothelial cells (ECs) remains incompletely characterized. We report that fatty acid synthase knockdown (FASNKD) in ECs impedes vessel sprouting by reducing proliferation. Endothelial loss of FASN impaired angiogenesis in vivo, while FASN blockade reduced pathological ocular neovascularization, at >10-fold lower doses than used for anti-cancer treatment. Impaired angiogenesis was not due to energy stress, redox imbalance, or palmitate depletion. Rather, FASNKD elevated malonyl-CoA levels, causing malonylation (a post-translational modification) of mTOR at lysine 1218 (K1218). mTOR K-1218 malonylation impaired mTOR complex 1 (mTORC1) kinase activity, thereby reducing phosphorylation of downstream targets (p70S6K/4EBP1). Silencing acetyl-CoA carboxylase 1 (an enzyme producing malonyl-CoA) normalized malonyl-CoA levels and reactivated mTOR in FASNKD ECs. Mutagenesis unveiled the importance of mTOR K1218 malonylation for angiogenesis. This study unveils a novel role of FASN in metabolite signaling that contributes to explaining the anti-angiogenic effect of FASN blockade. PMID: 30146486 [PubMed - as supplied by publisher]

Related Articles Direct screening of malonylginsenosides from nine Ginseng extracts by an untargeted profiling strategy incorporating in-source collision-induced dissociation, mass tag, and neutral loss scan on a hybrid linear ion-trap/Orbitrap mass spectrometer coupled to ultra-high performance liquid chromatography. J Chromatogr A. 2018 Aug 11;: Authors: Shi X, Yang W, Huang Y, Hou J, Qiu S, Yao C, Feng Z, Wei W, Wu W, Guo D Abstract Specific analytical approaches that enable untargeted profiling of modified metabolites are in great need. An untargeted profiling strategy, by integrating in-source collision-induced dissociation (ISCID)-MS1, mass tag-MS2, and neutral loss scan-MS3, is established on a linear ion-trap/Orbitrap mass spectrometer coupled to ultra-high performance liquid chromatography. This strategy is applied to screen malonylginsenosides from three reputable Panax species (P. ginseng, P. quinquefolius, and P. notoginseng). In light of the preferred neutral elimination of CO2 and entire malonyl substituent (C3H2O3) in the negative electrospray ionization mode, a pseudo-neutral loss scan (PNL) method was established by applying ISCID energy 40 V in MS1, mass tag 43.9898 Da oriented CID-MS2 at normalized collision energy (NCE) 30%, and neutral loss 43.9898 Da-triggered high-energy C-trap dissociation-MS3 at NCE 70%. The PNL approach achieved a high coverage of targeted malonylginsenosides but introduced less false positives. It displayed comparable performance to a precursor ions list-driven targeted approach we have reported in the profiling and characterization of malonylginsenosides, but could avoid complex data processing. Totally 178 malonylginsenosides were characterized from the roots, leaves, and flower buds of P. ginseng, P. quinquefolius, and P. notoginseng, and most of them possess potentially new structures. The compositions of malonylginsenosides identified from these three Panax species are similar, and only malonylginsenoside Rb2 and some minor may have potential chemotaxonomic significance. In conclusion, we provide a potent analytical strategy for the direct and efficient screening of modified metabolites, which may have broad applications in the fields of metabolomics, drug metabolism, and natural product research. PMID: 30146372 [PubMed - as supplied by publisher]

Related Articles Are we closer to the vision? A proposed framework for incorporating omics into environmental assessments. Environ Toxicol Pharmacol. 2018 Apr;59:87-93 Authors: Martyniuk CJ Abstract Environmental science has benefited a great deal from omics-based technologies. High-throughput toxicology has defined adverse outcome pathways (AOPs), prioritized chemicals of concern, and identified novel actions of environmental chemicals. While many of these approaches are conducted under rigorous laboratory conditions, a significant challenge has been the interpretation of omics data in "real-world" exposure scenarios. Clarity in the interpretation of these data limits their use in environmental monitoring programs. In recent years, one overarching objective of many has been to address fundamental questions concerning experimental design and the robustness of data collected under the broad umbrella of environmental genomics. These questions include: (1) the likelihood that molecular profiles return to a predefined baseline level following remediation efforts, (2) how reference site selection in an urban environment influences interpretation of omics data and (3) what is the most appropriate species to monitor in the environment from an omics point of view. In addition, inter-genomics studies have been conducted to assess transcriptome reproducibility in toxicology studies. One lesson learned from inter-genomics studies is that there are core molecular networks that can be identified by multiple laboratories using the same platform. This supports the idea that "omics-networks" defined a priori may be a viable approach moving forward for evaluating environmental impacts over time. Both spatial and temporal variability in ecosystem structure is expected to influence molecular responses to environmental stressors, and it is important to recognize how these variables, as well as individual factor (i.e. sex, age, maturation), may confound interpretation of network responses to chemicals. This mini-review synthesizes the progress made towards adopting these tools into environmental monitoring and identifies future challenges to be addressed, as we move into the next era of high throughput sequencing. A conceptual framework for validating and incorporating molecular networks into environmental monitoring programs is proposed. As AOPs become more defined and their potential in environmental monitoring assessments becomes more recognized, the AOP framework may prove to be the conduit between omics and penultimate ecological responses for environmental risk assessments. PMID: 29549817 [PubMed - indexed for MEDLINE]

Related Articles Energy-Protein Supplementation and Lactation Affect Fatty Acid Profile of Liver and Adipose Tissue of Dairy Cows. Molecules. 2018 Mar 09;23(3): Authors: Brzozowska AM, Lukaszewicz M, Oprzadek JM Abstract This article addresses the hypothesis that lactation stage, parity and energy-protein feed additive affect fatty acid composition of blood, liver and adipose tissue of cows. The experiment was conducted on 24 Polish Holstein-Friesian cows divided into two feeding groups. One group of cows was fed solely a total mixed ration, while the other group was fed a ration with the addition of 2 kg of energy-protein supplement per cow/day. During the experiment, the samples of liver, adipose tissue and blood were taken and their fatty acid compositions were determined. Analysis of variance was applied to fatty acid relative weight percentage to determine the effect of the stage of lactation, parity, and energy-protein supplement on the fatty acid composition of the tissues. Stage of lactation had a significant impact on the content of many fatty acids in all examined tissues. We found that parity had no effect on fatty acid composition of blood, whereas it significantly affected C16:1 c9 in liver, and C16:1 c9 and C18:0 in adipose tissue. Energy-protein supplement significantly affected the content of most fatty acids in blood (e.g., C18:1 t11 and C18:3 n-3) and liver (C18:3 n-3, both isomers of conjugated linolenic acid and n-3 fatty acids derived from fish oil), but it did not affect the profile of the adipose tissue of cows. According to our best knowledge, this is the first study showing the relationship between parity, stage of lactation and the composition of fatty acids in blood, liver and adipose tissue of cows. PMID: 29522430 [PubMed - indexed for MEDLINE]

Related Articles Calycophyllum spruceanum (Benth.), the Amazonian "Tree of Youth" Prolongs Longevity and Enhances Stress Resistance in Caenorhabditis elegans. Molecules. 2018 Feb 27;23(3): Authors: Peixoto H, Roxo M, Koolen H, da Silva F, Silva E, Braun MS, Wang X, Wink M Abstract The tree popularly known in Brazil as mulateiro or pau-mulato (Calycophyllum spruceanum (Benth.) K. Schum.) is deeply embedded in the herbal medicine of the Amazon region. Different preparations of the bark are claimed to have anti-aging, antioxidant, antimicrobial, emollient, wound healing, hemostatic, contraceptive, stimulant, and anti-diabetic properties. The current study aims to provide the first step towards a science-based evidence of the beneficial effects of C. spruceanum in the promotion of longevity and in the modulation of age-related markers. For this investigation, we used the model system Caenorhabditis elegans to evaluate in vivo antioxidant and anti-aging activity of a water extract from C. spruceanum. To chemically characterize the extract, HPLC MS (High Performance Liquid Chromatography Mass Spectrometry)/MS analyses were performed. Five secondary metabolites were identified in the extract, namely gardenoside, 5-hydroxymorin, cyanidin, taxifolin, and 5-hydroxy-6-methoxycoumarin-7-glucoside. C. spruceanum extract was able to enhance stress resistance and to extend lifespan along with attenuation of aging-associated markers in C. elegans. The demonstrated bioactivities apparently depend on the DAF-16/FOXO pathway. The data might support the popular claims of mulateiro as the "tree of youth", however more studies are needed to clarify its putative benefits to human health. PMID: 29495517 [PubMed - indexed for MEDLINE]

Related Articles Black Tea Samples Origin Discrimination Using Analytical Investigations of Secondary Metabolites, Antiradical Scavenging Activity and Chemometric Approach. Molecules. 2018 Feb 26;23(3): Authors: Koch W, Kukula-Koch W, Komsta Ł Abstract A comprehensive study on the composition and antioxidant properties of black tea samples with a chemometric approach was performed via LC-ESI-Q-TOF-MS, DPPH radical scavenging assay, and Folin-Ciocalteu assay (TPC). Marked differences between the teas from seven different countries (China, India, Iran, Japan, Kenya, Nepal, Sri Lanka) were shown. The Indian samples demonstrated the highest total catechin content (184.8 mg/100 mL), the largest TPC and DPPH scavenging potential (58.2 mg/100 mL and 84.5%, respectively). The applied principal component analysis (PCA) and ANOVA revealed several correlations between the level of catechins in tea infusions. EC (epicatechin), ECG (epicatechin gallate), EGC (epigallocatechin), and EGCG (epigallocatechin-3-gallate) content was not correlated with DPPH, gallic acid, and TPC; however, a strong correlation of EC and ECG between themselves and a negative correlation of these two catechins with EGCG and EGC was noted. Interestingly, simple catechins were not found to be responsible for antioxidant properties of the black teas. The samples collected in the higher altitudes were similar. PMID: 29495365 [PubMed - indexed for MEDLINE]

Related Articles Six genes of ompA family shuffling for development of polyvalent vaccines against Vibrio alginolyticus and Edwardsiella tarda. Fish Shellfish Immunol. 2018 Apr;75:308-315 Authors: Cheng ZX, Chu X, Wang SN, Peng XX, Li H Abstract Polyvalent vaccines against more than one species of pathogens are especially important due to the complex ecosystem in aquaculture. We have previously shown that the development of polyvalent vaccines by shuffling six ompA genes from different bacteria with V. parahaemolyticus VP0764 primers. Here, we used the same 6 genes, V. alginolyticus VA0764 and VA1186, V. parahaemolyticus VP0764 and VP1186, E. tarda ompA and E. coli ompA, but with E. tarda ompA primers to develop new polyvalent vaccines. By this approach, we identified 7 potential polyvalent vaccines that were effective against both V. alginolyticus and E. tarda infections. Furthermore, the innate immunity triggered by the vaccines were also explored in three groups, no protection (group I), protection against V. alginolyticus (group II), and protection against both V. alginolyticus and E. tarda (group III). The transcription of IL-1β, IL-6, IL-8, C3b and NF-kB were significantly increased in group II and group III but not group I, where the expression level of group III was higher than group II. In addition, differential activities of succinate dehydrogenase were detected among the three groups. These results indicate the expansion of polyvalent vaccine reservoir with the same shuffling genes but different primers, and promote the understanding of the mechanisms of polyvalent vaccines based on vaccine-induced innate immunity. PMID: 29438846 [PubMed - indexed for MEDLINE]

Related Articles Associations Between CagA, VacA, and the Clinical Outcomes of Helicobacter Pylori Infections in Okinawa, Japan. Kobe J Med Sci. 2017 Nov 22;63(2):E58-E67 Authors: Inagaki T, Nishiumi S, Ito Y, Yamakawa A, Yamazaki Y, Yoshida M, Azuma T Abstract Helicobacter pylori, which is involved in the pathogenesis of gastroduodenal disease, produces CagA and VacA as major virulence factors. CagA is classified into East Asian and Western types based on the number and sequences of its Glu-Pro-Ile-Tyr-Ala motifs. The vacA gene has three polymorphic regions: the signal (s), intermediate (i), and middle (m) regions. The lowest gastric cancer mortality rate is seen in Okinawa. On the Japanese mainland (Honshu), most H. pylori produce s1/m1-VacA, which exhibits strong toxicity, and East Asian-type CagA. However, the H. pylori detected in Okinawa produces s1/m2-VacA, which exhibits weak toxicity, or s2/m2-VacA, which is non-toxic, and Western-type CagA. Studies about the i-region of vacA have been performed around the world, but there have been few such studies in Japan. Therefore, the aim of this study was to assess the relationships between the clinical outcomes of H. pylori infections in Okinawa, vacA (especially the i-region genotype), and cagA. H. pylori strains that were collected from patients with gastric cancer or gastric ulcers in Okinawa only produced the i1-type VacA virulence factor. The vacuolating cytotoxin activity of i1-type VacA was stronger than that of i2-type VacA, suggesting that the i-region genotype of vacA is closely associated with vacuolating cytotoxin activity. These results indicate that the i-region genotype of vacA is a useful marker of both H. pylori virulence and the clinical outcomes of H. pylori infections in Okinawa, Japan. PMID: 29434176 [PubMed - indexed for MEDLINE]

Related Articles Effects of perinatal exposure to BPA and its alternatives (BPS, BPF and BPAF) on hepatic lipid and glucose homeostasis in female mice adolescent offspring. Chemosphere. 2018 Aug 17;212:297-306 Authors: Meng Z, Wang D, Yan S, Li R, Yan J, Teng M, Zhou Z, Zhu W Abstract The widespread application of bisphenols (BPs) makes them ubiquitous in the natural environment and poses many potential risks. In this study, we examined the effects of perinatal exposure to BPA and its 3 alternatives (BPS, BPF, and BPAF) on lipid and glucose homeostasis in female mice adolescent offspring. Specifically, BPA exposure promoted the expression of hepatic lipid synthesis and fatty acid accumulation genes, resulting in a significant increase in 2 free fatty acids contents. BPS exposure caused an increase in 6 free fatty acids and triglyceride contents through promoting the expression of fatty acid synthesis, triglyceride synthesis and fatty acid accumulation genes and inhibiting the expression of fatty acid β-oxidation genes. Interestingly, BPAF exposure showed completely opposite effects on hepatic lipid metabolism compared to BPS exposure. 9 free fatty acids and triglycerides contents in the liver were significantly reduced. In particular, BPF exposure caused decreases in 2 free fatty acids contents, but no significant changes were found in the genes for lipid metabolism. In addition, unlike BPA and BPF exposure, BPS and BPAF exposure also resulted in significant increases in glucose and glycogen contents in the liver by activation of Fxr-Shp pathway and glycolysis, and inhibition of gluconeogenesis. The results showed that compared to BPA and BPF exposure, BPS and BPAF exposure significantly regulated the expression of genes related to glucose and lipid metabolism and severely interfered with hepatic lipid and glucose homeostasis. This suggested that we should thoroughly evaluate the potential health risks of BPA and its alternatives. PMID: 30145421 [PubMed - as supplied by publisher]

Related Articles Comprehensive improvement of sample preparation methodologies facilitates dynamic metabolomics of Aspergillus niger. Biotechnol J. 2018 Aug 25;:e1800315 Authors: Zheng X, Yu J, Cairns TC, Zhang L, Zhang Z, Zhang Q, Zheng P, Sun J, Ma Y Abstract Metabolomics is an essential discipline in industrial biotechnology. Sample preparation approaches dramatically influence data quality and, ultimately, interpretation and conclusions from metabolomic experiments. However, standardized protocols for highly reproducible metabolic datasets are limited, especially for the fungal cell factory Aspergillus niger. Here, we developed an improved liquid chromatography-tandem mass spectrometry-based pipeline for A. niger metabolomics. It was found that fast filtration with liquid nitrogen was more suitable for cell quenching, causing minimal disruption to cell integrity, and improved intracellular metabolite recovery when compared to cold methanol quenching approaches. We evaluated seven solutions for intracellular metabolite extraction, and found acetonitrile/water (1:1, v/v) at -20°C, combined with boiling ethanol extraction protocols, showed unbiased metabolite profiling. We applied this improved methodology to unveil the dynamic metabolite profile of one citrate over-producing A. niger isolate under citrate fermentation. Citrate precursors, especially pyruvate, oxaloacetate, and malate, were maintained at a relatively high intracellular level, which could be necessary for high citrate synthesis flux. Glutamine showed a similar trend compared to citrate production, suggesting glutamine may be involved in intracellular pH homeostasis. Taken together, our study delivers a highly standardized and improved metabolomics methodology and paves the way for systems metabolic engineering in biotechnologically important fungi. PMID: 30144348 [PubMed - as supplied by publisher]

Related Articles Acid Stress Induces Differential Accumulation of Metabolites in Escherichia coli O26:H11. J Appl Microbiol. 2018 Aug 24;: Authors: Shayanfar S, Baroumand A, Pillai SD Abstract AIMS: Acid exposure induces expression of certain metabolites in bacteria. The experimental objective was to identify the primary metabolites accumulating in E.coli O26:H11 as a function of acid (pH 3.6) exposure. METHODS AND RESULTS: Different buffers of pH 7.5 and pH 3.6 were used to study the metabolites accumulating in E.coli O26:H11 cells during such pH exposure. After 24 hours of acid exposure, there was over 7-log decline in E.coli colonies populations on Trypticase soy agar (TSA) plates. Untargeted metabolomic analysis identified 293 primary metabolites of which, 145 metabolites were differentially (P < 0.01) expressed between pH 7.5 and pH 3.6 in E.coli O26:H11. CONCLUSIONS: After 24 hours of acid exposure 21 different metabolic pathways appeared to be still functional, suggesting that the cells were still metabolically active. Among the identifiable pathways, the key differentially expressed pathways were associated with peptidoglycan biosynthesis, purine metabolism, D-Glutamine/D-glutamate metabolism, nitrogen metabolism, unsaturated fatty acid biosynthesis, and inositol phosphate metabolism. SIGNIFICANCE AND IMPACT OF STUDY: Shiga toxin producing non-O157 E.coli strains such as E.coli O26 are responsible for a growing number of food-related illnesses in the US and around the world. From food production to consumption, microorganisms in food experience dramatic pH fluctuations by organic acids introduced either during food processing or by inorganic acids in the stomach. Acid exposure induces certain metabolites expression in bacteria. Understanding the resistance mechanism of pathogenic microorganisms though studying the metabolome would be helpful to introduce more effective hurdles and thus ensure food safety to a higher degree. This article is protected by copyright. All rights reserved. PMID: 30144243 [PubMed - as supplied by publisher]

Related Articles Synthesis versus degradation: directions of amino acid metabolism during Arabidopsis abiotic stress response. Plant Mol Biol. 2018 Aug 24;: Authors: Hildebrandt TM Abstract KEY MESSAGE: During abiotic stress low abundant amino acids are not synthesized but they accumulate due to increased protein turnover under conditions inducing carbohydrate starvation (dehydration, salt stress, darkness) and are degraded. Metabolic adaptation is crucial for abiotic stress resistance in plants, and accumulation of specific amino acids as well as secondary metabolites derived from amino acid metabolism has been implicated in increased tolerance to adverse environmental conditions. The role of proline, which is synthesized during Arabidopsis stress response to act as a compatible osmolyte, has been well established. However, conclusions drawn about potential functions of other amino acids such as leucine, valine, and isoleucine are not entirely consistent. This study reevaluates published datasets with a special emphasis on changes in the free amino acid pool and transcriptional regulation of the associated anabolic and catabolic pathways. In order to gain a comprehensive overview about the general direction of amino acid metabolism under abiotic stress conditions a complete map of all currently known enzymatic steps involved in amino acid synthesis and degradation was assembled including also the initial steps leading to the synthesis of secondary metabolites. Microarray datasets and amino acid profiles of Arabidopsis plants exposed to dehydration, high salinity, extended darkness, cold, and heat were systematically analyzed to identify trends in fluxes of amino acid metabolism. Some high abundant amino acids such as proline, arginine, asparagine, glutamine, and GABA are synthesized during abiotic stress to act as compatible osmolytes, precursors for secondary metabolites, or storage forms of organic nitrogen. In contrast, most of the low abundant amino acids are not synthesized but they accumulate due to increased protein turnover under conditions inducing carbohydrate starvation (dehydration, salt stress, extended darkness) and are degraded. PMID: 30143990 [PubMed - as supplied by publisher]

Related Articles JunB defines functional and structural integrity of the epidermo-pilosebaceous unit in the skin. Nat Commun. 2018 Aug 24;9(1):3425 Authors: Singh K, Camera E, Krug L, Basu A, Pandey RK, Munir S, Wlaschek M, Kochanek S, Schorpp-Kistner M, Picardo M, Angel P, Niemann C, Maity P, Scharffetter-Kochanek K Abstract Transcription factors ensure skin homeostasis via tight regulation of distinct resident stem cells. Here we report that JunB, a member of the AP-1 transcription factor family, regulates epidermal stem cells and sebaceous glands through balancing proliferation and differentiation of progenitors and by suppressing lineage infidelity. JunB deficiency in basal progenitors results in a dermatitis-like syndrome resembling seborrheic dermatitis harboring structurally and functionally impaired sebaceous glands with a globally altered lipid profile. A fate switch occurs in a subset of JunB deficient epidermal progenitors during wound healing resulting in de novo formation of sebaceous glands. Dysregulated Notch signaling is identified to be causal for this phenotype. In fact, pharmacological inhibition of Notch signaling can efficiently restore the lineage drift, impaired epidermal differentiation and disrupted barrier function in JunB conditional knockout mice. These findings define an unprecedented role for JunB in epidermal-pilosebaceous stem cell homeostasis and its pathology. PMID: 30143626 [PubMed - in process]

Related Articles Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2018 Aug 24;: Authors: Tiwari S, van Tonder AJ, Vilchèze C, Mendes V, Thomas SE, Malek A, Chen B, Chen M, Kim J, Blundell TL, Parkhill J, Weinrick B, Berney M, Jacobs WR Abstract Reactive oxygen species (ROS)-mediated oxidative stress and DNA damage have recently been recognized as contributing to the efficacy of most bactericidal antibiotics, irrespective of their primary macromolecular targets. Inhibitors of targets involved in both combating oxidative stress as well as being required for in vivo survival may exhibit powerful synergistic action. This study demonstrates that the de novo arginine biosynthetic pathway in Mycobacterium tuberculosis (Mtb) is up-regulated in the early response to the oxidative stress-elevating agent isoniazid or vitamin C. Arginine deprivation rapidly sterilizes the Mtb de novo arginine biosynthesis pathway mutants ΔargB and ΔargF without the emergence of suppressor mutants in vitro as well as in vivo. Transcriptomic and flow cytometry studies of arginine-deprived Mtb have indicated accumulation of ROS and extensive DNA damage. Metabolomics studies following arginine deprivation have revealed that these cells experienced depletion of antioxidant thiols and accumulation of the upstream metabolite substrate of ArgB or ArgF enzymes. ΔargB and ΔargF were unable to scavenge host arginine and were quickly cleared from both immunocompetent and immunocompromised mice. In summary, our investigation revealed in vivo essentiality of the de novo arginine biosynthesis pathway for Mtb and a promising drug target space for combating tuberculosis. PMID: 30143580 [PubMed - as supplied by publisher]

Related Articles Differential effects of restrictive and malabsorptive bariatric surgery procedures on the serum lipidome in obese subjects. J Clin Lipidol. 2018 Jul 25;: Authors: Ramos-Molina B, Castellano-Castillo D, Alcaide-Torres J, Pastor Ó, de Luna Díaz R, Salas-Salvadó J, López-Moreno J, Fernández-García JC, Macías-González M, Cardona F, Tinahones FJ Abstract BACKGROUND: Bariatric surgery (BS) is the most effective treatment for severe obesity. Our group and others have previously reported that the type of BS (restrictive vs malabsorptive) can lead to different effects on the lipid profile and glucose homeostasis in morbidly obese patients. Furthermore, BS exerts significant changes in lipid metabolism, which are not yet fully understood and that might be dependent of surgical technique. OBJECTIVE: The objective of this study was to evaluate the differential changes in the serum lipidomic profile of morbidly obese subjects who underwent two different BS techniques: sleeve gastrectomy (SG) (restrictive) and biliopancreatic diversion (BPD) (malabsorptive). METHODS: This study included 37 morbidly obese patients (body mass index ≥ 40 kg/m2) who underwent either SG (n = 25) or BPD (n = 12). Serum lipid extracts were assessed at baseline and 6 months after BS and were analyzed in a ultra-high performance liquid chromatography time-of-flight mass spectrometry-based platform. RESULTS: SG not only restores the circulating levels of fatty acids and glycerolipids to similar levels to those observed in nonobese subjects but also results in a consistent increase of phospholipid and sphingolipid species, ranging from antioxidant plasmalogens to lipotoxic ceramides. BPD, however, leads to an overall reduction in circulating fatty acids, glycerolipids, phospholipids and sphingolipids, and a substantial increase of bile acids. CONCLUSION: Our lipidomic analysis suggests that the differential metabolic effects typically observed after restrictive vs malabsorptive BS procedures could be explained, at least partially, to BS-specific lipid changes and provides novel aspects of lipid remodeling in obesity during weight loss. PMID: 30143432 [PubMed - as supplied by publisher]

Related Articles Dilution correction for dynamically influenced urinary analyte data. Anal Chim Acta. 2018 Nov 22;1032:18-31 Authors: Hertel J, Rotter M, Frenzel S, Zacharias HU, Krumsiek J, Rathkolb B, Hrabe de Angelis M, Rabstein S, Pallapies D, Brüning T, Grabe HJ, Wang-Sattler R Abstract Urinary analyte data has to be corrected for the sample specific dilution as the dilution varies intra- and interpersonally dramatically, leading to non-comparable concentration measures. Most methods of dilution correction utilized nowadays like probabilistic quotient normalization or total spectra normalization result in a division of the raw data by a dilution correction factor. Here, however, we show that the implicit assumption behind the application of division, log-linearity between the urinary flow rate and the raw urinary concentration, does not hold for analytes which are not in steady state in blood. We explicate the physiological reason for this short-coming in mathematical terms and demonstrate the empirical consequences via simulations and on multiple time-point metabolomic data, showing the insufficiency of division-based normalization procedures to account for the complex non-linear analyte specific dependencies on the urinary flow rate. By reformulating normalization as a regression problem, we propose an analyte specific way to remove the dilution variance via a flexible non-linear regression methodology which then was shown to be more effective in comparison to division-based normalization procedures. In the progress, we developed several, easily applicable methods of normalization diagnostics to decide on the method of dilution correction in a given sample. On the way, we identified furthermore the time-span since last urination as an important variance factor in urinary metabolome data which is until now completely neglected. In conclusion, we present strong theoretical and empirical evidence that normalization has to be analyte specific in dynamically influenced data. Accordingly, we developed a normalization methodology for removing the dilution variance in urinary data respecting the single analyte kinetics. PMID: 30143216 [PubMed - in process]

Related Articles Effective mobility as a robust criterion for compound annotation and identification in metabolomics: Toward a mobility-based library. Anal Chim Acta. 2018 Nov 22;1032:178-187 Authors: Drouin N, Pezzatti J, Gagnebin Y, González-Ruiz V, Schappler J, Rudaz S Abstract Capillary electrophoresis (CE) presents many advantageous features as an analytical technique in metabolomics, such as very low consumption of a sample or the possibility to easily detect very polar and ionizable compounds. However, CE remains an approach only used by a few research groups due to a relatively lower sensitivity and, higher analysis time compared to liquid chromatography. To circumvent these drawbacks, herein we propose a generic CE-mass spectrometry (MS) approach using positive electrospray ionization mode and performing normal- and reverse-polarity CE separations to analyze anionic and acidic compounds. Preliminary experiments showed better sensitivity using the ESI positive mode compared to the ESI negative mode on a set of representative anionic compounds from different biochemical families. This approach was applied to the investigation of an available library of metabolites. More than 450 compounds out of the 596 in the library were detected, with the possibility to monitor negatively ionizable compounds through their ammonium adducts. Migration time of each data point was converted to an effective mobility (μeff) scale and used for peak alignment in data pre-processing; μeff features were used as a robust migration index for peak annotation and identification criterion. For the first time, a large database based on experimental μeff was built, allowing for the straightforward annotation of detected features in biological samples and demonstrating how CE-MS can complement other analytical techniques commonly used in metabolomics. PMID: 30143215 [PubMed - in process]

Related Articles Assessing the impact of wastewater treatment plant effluent on downstream drinking water-source quality using a zebrafish (Danio Rerio) liver cell-based metabolomics approach. Water Res. 2018 Aug 14;145:198-209 Authors: Zhen H, Ekman DR, Collette TW, Glassmeyer ST, Mills MA, Furlong ET, Kolpin DW, Teng Q Abstract Cell-based metabolomics was used in a proof-of-concept fashion to investigate the biological effects of contaminants as they traveled from a wastewater treatment plant (WWTP) discharge to a drinking water treatment plant (DWTP) intake in a surface-water usage cycle. Zebrafish liver (ZFL) cells were exposed to water samples collected along a surface-water flowpath, where a WWTP was located ∼14.5 km upstream of a DWTP. The sampling sites included: 1) upstream of the WWTP, 2) the WWTP effluent discharging point, 3) a proximal location downstream of the WWTP outfall, 4) a distal location downstream of the WWTP outfall, 5) the drinking water intake, and 6) the treated drinking water collected prior to discharge to the distribution system. After a 48-h laboratory exposure, the hydrophilic and lipophilic metabolites in ZFL cell extracts were analyzed by proton nuclear magnetic resonance (1H NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS), respectively. Multivariate statistical analysis revealed distinct changes in metabolite profiles in response to WWTP effluent exposure. These effects on the hydrophilic metabolome gradually diminished downstream of the WWTP, becoming non-significant at the drinking water intake (comparable to upstream of the WWTP, p = 0.98). However, effects on the lipophilic metabolome increased significantly as the river flowed from the distal location downstream of the WWTP to the drinking water intake (p < 0.001), suggesting a source of bioactive compounds in this watershed other than the WWTP. ZFL cells exposed to treated drinking water did not exhibit significant changes in either the hydrophilic (p = 0.15) or lipophilic metabolome (p = 0.83) compared to the upstream site, suggesting that constituents in the WWTP effluent were efficiently removed by the drinking water treatment process. Impacts on ZFL cells from the WWTP effluent included disrupted energy metabolism, a global decrease in amino acids, and altered lipid metabolism pathways. Overall, this study demonstrated the utility of cell-based metabolomics as an effective tool for assessing the biological effects of complex pollutant mixtures, particularly when used as a complement to conventional chemical monitoring. PMID: 30142518 [PubMed - as supplied by publisher]

Related Articles The therapeutic effect of Ilex pubescens extract on blood stasis model rats according to serum metabolomics. J Ethnopharmacol. 2018 Aug 21;: Authors: Cao D, Xu C, Xue Y, Ruan Q, Yang B, Liu Z, Cui H, Zhang L, Zhao Z, Jin J Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Ilex pubescens Hook. et Arn (MDQ), a traditional Chinese herb, is used in the treatment of cardiovascular diseases. However, the mechanisms underlying the preventive effect of MDQ on blood stasis remain unclear. AIM OF THE STUDY: In this study, serum metabolomics integrated with a biochemical assay strategy were established to evaluate the preventive effect and mechanism of action of MDQ on rats with acute blood stasis. MATERIALS AND METHODS: Forty-nine rats were divided into seven groups: the control group, model group, aspirin treatment group (30mg/kg), clopidogrel treatment group (8mg/kg) and three MDQ treatment groups (250, 500 and 1000mg/kg). A hybrid quadrupole time of flight mass spectrometry (QTOF/MS) coupled to ultra-high-performance liquid chromatography (UPLC) was applied for profiling the serum metabolites. The multivariate data analysis techniques using unsupervised principal component analysis (PCA) and supervised orthogonal projections to latent structures discriminant analysis (OPLS-DA) were used for pattern recognition and distinguishing variabilities among groups. RESULTS: MDQ protected the rats against blood stasis, as evidenced by the restoration of the anti-platelet aggregation activity, fibrinogen concentration, prothrombin time, thrombin time, activated partial thromboplastin time, endothelial nitric oxide synthase, endothelin, thromboxane B2 and 6-keto-prostaglandin F1α. The combination of PCA and OPLS-DA revealed deviations in eighteen differential biomarkers in serum. The identified biomarkers were primarily engaged in the metabolic pathways including arachidonic acid metabolism, glycerophospholipid metabolism, phospholipid biosynthesis and bile acid biosynthesis. The levels of eleven biomarkers showed significant alterations and a tendency to be restored to normal values in MDQ-treated blood stasis rats. Moreover, a correlation network diagram was constructed to show the serum biomarkers perturbed by MDQ. CONCLUSIONS: These results suggested that MDQ had preventive effects on blood stasis in rats via arachidonic acid metabolism and glycerophospholipid metabolism. PMID: 30142425 [PubMed - as supplied by publisher]