PubMed

Anti-phytopathogenic activity of sporothriolide, a metabolite from endophyte Nodulisporium sp. A21 in Ginkgo biloba. Pestic Biochem Physiol. 2016 May;129:7-13 Authors: Cao LL, Zhang YY, Liu YJ, Yang TT, Zhang JL, Zhang ZG, Shen L, Liu JY, Ye YH Abstract Phytopathogenic fungi such as Rhizoctonia solani and Sclerotinia sclerotiorum caused multiple plant diseases resulting in severe loss of crop production. Increasing documents endorsed that endophytes are a striking resource pool for numerous metabolites with various bioactivities such as anti-fungal. Here we reported the characterization and anti-phytopathogenic activity of sporothriolide, a metabolite produced by Nodulisporium sp. A21-an endophytic fungus in the leaves of Ginkgo biloba. Among the total twenty-five endophytic fungi isolated from the healthy leaves of G. biloba, the fermentation broth (FB) of the strain A21 was found potently inhibitory activity against R. solani and S. sclerotiorum using mycelia growth inhibition method. A21 was then identified as Nodulisporium sp., the asexual stage of Hypoxylon sp., by microscopic examination and ITS rDNA sequence data comparison. Under the bioassay-guided fractionation, sporothriolide was isolated from the petroleum ether extract of the FB of A21, whose structure was established by integrated interpretation of HR-ESI-MS and (1)H- and (13)C-NMR. Furthermore, the crystal structure of sporothriolide was first reported. In addition, sporothriolide was validated to be potently antifungal against R. solani, S. sclerotiorum and inhibit conidium germination of Magnaporthe oryzae in vitro and in vivo, indicating that it could be used as a lead compound for new fungicide development. PMID: 27017876 [PubMed - in process]

Related Articles Evolution in miniaturized column liquid chromatography instrumentation and applications: An overview. J Chromatogr A. 2015 Nov 20;1421:18-37 Authors: Nazario CE, Silva MR, Franco MS, Lanças FM Abstract The purpose of this article is to underline the miniaturized LC instrumental system and describe the evolution of commercially available systems by discussing their advantages and drawbacks. Nowadays, there are already many miniaturized LC systems available with a great variety of pump design, interface and detectors as well as efficient columns technologies and reduced connections devices. The solvent delivery systems are able to drive the mobile phase without flow splitters and promote gradient elution using either dual piston reciprocating or syringe-type pumps. The mass spectrometry as detection system is the most widely used detection system; among many alternative ionization sources direct-EI LC-MS is a promising alternative to APCI. In addition, capillary columns are now available showing many possibilities of stationary phases, inner diameters and hardware materials. This review provides a discussion about miniaturized LC demonstrating fundamentals and instrumentals' aspects of the commercially available miniaturized LC instrumental system mainly nano and micro LC formats. This review also covers the recent developments and trends in instrumentation, capillary and nano columns, and several applications of this very important and promising field. PMID: 26381569 [PubMed - indexed for MEDLINE]

Related Articles Moderate alcohol consumption in chronic form enhances the synthesis of cholesterol and C-21 steroid hormones, while treatment with Tinospora cordifolia modulate these events in men. Steroids. 2016 Mar 22; Authors: Kumari S, Mittal A, Dabur R Abstract Chronic and heavy alcohol consumption disrupts lipid metabolism and hormonal balance including testosterone levels. However, studies doubt the relationship between moderate alcohol intake and sex hormone levels. Therefore, the aim of the present investigation was to establish the direct impact of chronic and moderate alcohol intake on cholesterol homeostasis and steroid hormone synthesis. Asymptomatic chronic and moderate alcoholics (n=12) without chronic liver disease and healthy volunteers (n=14) were selected for the study. Furthermore, effects of standardized water extract of Tinospora cordifolia (Willd) Mier. (Menispermaceae) (TCJ), a well reported anti-alcoholic herbal drug, on urinary steroids was studied. This study included four groups, i.e. a) healthy; b) healthy+TCJ; c) alcoholic; d) alcoholic+TCJ. The blood and urine samples from each group were collected on day 0 and 14 of the post-treatment with TCJ and analyzed. Alcoholic blood samples showed the significantly higher values of traditional biomarkers γ-GT and MCV along with cholesterol, LDL, TGL and urinary methylglucuronide compared to healthy. Qualitative analysis of steroids showed that moderate alcohol intake in a chronic manner increased the cholesterol synthesis and directed its flow toward C-21 steroids; shown by increased levels of corticosterone (2.456 fold) and cortisol (3.7 fold). Moreover, alcohol intake also increased the synthesis of estradiol and clearance rate of other steroids through the formation of glucuronides. Therefore, it decreased the synthesis and increased the clearance rate of testosterone (T) and androstenedione (A). Quantitative analysis confirmed decreased T/A ratio from 2.31 to 1.59 in plasma and 2.47 to 1.51 in urine samples of alcoholics. TCJ intervention normalized the levels of steroids and significantly improved the T: A ratio to 2.0 and 2.12 in plasma and urine. The study revealed that TCJ modulated lipid metabolism by inhibiting cholesterol and glucuronides synthesis. PMID: 27016128 [PubMed - as supplied by publisher]

19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/03/26PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Evaluation of Cancer Metabolomics Using ex vivo High Resolution Magic Angle Spinning (HRMAS) Magnetic Resonance Spectroscopy (MRS). Metabolites. 2016;6(1) Authors: Fuss TL, Cheng LL Abstract According to World Health Organization (WHO) estimates, cancer is responsible for more deaths than all coronary heart disease or stroke worldwide, serving as a major public health threat around the world. High resolution magic angle spinning (HRMAS) magnetic resonance spectroscopy (MRS) has demonstrated its usefulness in the identification of cancer metabolic markers with the potential to improve diagnosis and prognosis for the oncology clinic, due partially to its ability to preserve tissue architecture for subsequent histological and molecular pathology analysis. Capable of the quantification of individual metabolites, ratios of metabolites, and entire metabolomic profiles, HRMAS MRS is one of the major techniques now used in cancer metabolomic research. This article reviews and discusses literature reports of HRMAS MRS studies of cancer metabolomics published between 2010 and 2015 according to anatomical origins, including brain, breast, prostate, lung, gastrointestinal, and neuroendocrine cancers. These studies focused on improving diagnosis and understanding patient prognostication, monitoring treatment effects, as well as correlating with the use of in vivo MRS in cancer clinics. PMID: 27011205 [PubMed - as supplied by publisher]

A Double-Clicking Bis-Azide Fluorogenic Dye for Bioorthogonal Self-Labeling Peptide Tags. Chemistry. 2016 Mar 24; Authors: Demeter O, Fodor EA, Kállay M, Mező G, Németh K, Szabó PT, Kele P Abstract Herein, we give the very first example for the development of a fluorogenic molecular probe that combines the two-point binding specificity of biarsenical-based dyes with the robustness of bioorthogonal click-chemistry. This proof-of-principle study reports on the synthesis and fluorogenic characterization of a new, double-quenched, bis-azide fluorogenic probe suitable for bioorthogonal two-point tagging of small peptide tags by double strain-promoted azide-alkyne cycloaddition. The presented probe exhibits remarkable increase in fluorescence intensity when reacted with bis-cyclooctynylated peptide sequences, which could also serve as possible self-labeling small peptide tag motifs. PMID: 27010966 [PubMed - as supplied by publisher]

Metabolomics reveals positive acceleration(+Gz)-induced metabolic perturbations and the protective effect of Ginkgo biloba extract in a rat model based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. J Pharm Biomed Anal. 2016 Mar 8;125:77-84 Authors: Yang Z, Zhao A, Li Z, Ge H, Li T, Zhang F, Zhan H, Wang J Abstract Positive acceleration (+Gz) in the head-to-foot direction generated by modern high-performance fighter jets during flight maneuvers is characterized by high G values and a rapid rate of acceleration, and is often long in duration and a repeated occurrence. The acceleration overload far exceeds the pilot's physiological tolerance limits and causes considerable strain on several organ systems. Despite the importance of monitoring pathophysiological alterations related to +Gz exposure, we lack a complete explanation of the pathophysiology of +Gz exposure. Ginkgo biloba extract (GBE) is a classic traditional Chinese medicine (TCM) that might exert a protective effect against +Gz exposure. However, its mechanism remains unclear. Here, a metabolomics approach based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOFMS) was used to characterize +Gz-induced metabolic fluctuations in a rat model and to evaluate the protective effect of GBE. Using partial least-squares discriminant analysis for the classification and selection of biomarkers, eighteen serum metabolites related to +Gz exposure were identified, and were found to primarily involve the fatty acid β-oxidation pathway, glycerophospholipid metabolism, phospholipid metabolism, bile acid metabolism, purine metabolism and lysine metabolism. Taking these potential biomarkers as screening indexes, we found that GBE could reverse the pathological process of +Gz exposure by partially regulating the perturbed fatty acid β-oxidation pathway, glycerophospholipid metabolism, purine metabolism and lysine metabolism. This indicates that UHPLC-Q-TOFMS-based metabolomics provides a powerful tool to reveal serum metabolic fluctuations in response to +Gz exposure and to study the mechanism underlying TCM. PMID: 27010354 [PubMed - as supplied by publisher]

MetaboLights: An Open-Access Database Repository for Metabolomics Data. Curr Protoc Bioinformatics. 2016;53:14.13.1-14.13.18 Authors: Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C Abstract MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. © 2016 by John Wiley & Sons, Inc. PMID: 27010336 [PubMed - as supplied by publisher]

Introduction to Cheminformatics. Curr Protoc Bioinformatics. 2016;53:14.1.1-14.1.21 Authors: Wishart DS Abstract Cheminformatics is a field of information technology that focuses on the collection, storage, analysis, and manipulation of chemical data. The chemical data of interest typically includes information on small molecule formulas, structures, properties, spectra, and activities (biological or industrial). Cheminformatics originally emerged as a vehicle to help the drug discovery and development process, however cheminformatics now plays an increasingly important role in many areas of biology, chemistry, and biochemistry. The intent of this unit is to give readers some introduction into the field of cheminformatics and to show how cheminformatics not only shares many similarities with the field of bioinformatics, but also enhances much of what is currently done in bioinformatics, molecular biology, and biochemistry. © 2016 by John Wiley & Sons, Inc. PMID: 27010335 [PubMed - as supplied by publisher]

Related Articles Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis. Sci Rep. 2015;5:10604 Authors: He B, Nohara K, Ajami NJ, Michalek RD, Tian X, Wong M, Losee-Olson SH, Petrosino JF, Yoo SH, Shimomura K, Chen Z Abstract Dietary fibers are increasingly appreciated as beneficial nutritional components. However, a requisite role of gut microbiota in fiber function and the overall impact of fibers on metabolomic flux remain unclear. We herein showed enhancing effects of a soluble resistant maltodextrin (RM) on glucose homeostasis in mouse metabolic disease models. Remarkably, fecal microbiota transplantation (FMT) caused pronounced and time-dependent improvement in glucose tolerance in RM recipient mice, indicating a causal relationship between microbial remodeling and metabolic efficacy. Microbial 16S sequencing revealed transmissible taxonomic changes correlated with improved metabolism, notably enrichment of probiotics and reduction of Alistipes and Bacteroides known to associate with high fat/protein diets. Metabolomic profiling further illustrated broad changes, including enrichment of phenylpropionates and decreases in key intermediates of glucose utilization, cholesterol biosynthesis and amino acid fermentation. These studies elucidate beneficial roles of RM-dependent microbial remodeling in metabolic homeostasis, and showcase prevalent health-promoting potentials of dietary fibers. PMID: 26040234 [PubMed - indexed for MEDLINE]

Related Articles Cell-derived extracellular vesicles as a platform to identify low-invasive disease biomarkers. Expert Rev Mol Diagn. 2015;15(7):907-23 Authors: González E, Falcón-Pérez JM Abstract Biomarkers are of great importance for prediction, diagnosis and monitoring the progression and therapeutic success of a disease. Whole body fluids, such as blood or urine, constitute the main desired biological source to identify these markers, mostly due to the minimally invasive procedures used to collect them. An additional benefit of studying these biological fluids that has been demonstrated by many different groups is that they contain cell-released extracellular vesicles, carrying a cargo of lipids, proteins and nucleic acids that reflects cell/tissue origin and, remarkably, cellular status. In this review, the information obtained from the characterization of this body fluid compartment in human samples is discussed in the context of its usefulness as diagnostic resource for several pathologies, including cancer, inflammatory, vascular and metabolic diseases. The review shows the great variety of methods used for this purpose as well as the different types of molecules that could serve as specific or common disease markers. PMID: 25948243 [PubMed - indexed for MEDLINE]

Related Articles Ketone body production is differentially altered in steatosis and non-alcoholic steatohepatitis in obese humans. Liver Int. 2015 Jul;35(7):1853-61 Authors: Männistö VT, Simonen M, Hyysalo J, Soininen P, Kangas AJ, Kaminska D, Matte AK, Venesmaa S, Käkelä P, Kärjä V, Arola J, Gylling H, Cederberg H, Kuusisto J, Laakso M, Yki-Järvinen H, Ala-Korpela M, Pihlajamäki J Abstract BACKGROUND & AIMS: Levels of ketone bodies have been reported to be both increased and decreased in individuals with non-alcoholic fatty liver disease. We investigated whether the metabolism of ketone bodies is different in simple steatosis and in non-alcoholic steatohepatitis (NASH). METHODS: Serum low molecular weight molecules including ketone bodies were measured using high-throughput proton (1H) nuclear magnetic resonance in 116 (76 categorized unequivocally to those with normal liver, simple steatosis or NASH) morbidly obese individuals [age 47.3 ± 8.7 (mean ± SD) years, body mass index 45.1 ± 6.1 kg/m(2) , 39 men and 77 women] with histological assessment of NASH and analysis of gene expression in the liver. Finally, we correlated β-hydroxybutyrate (β-OHB) levels with NASH predicting score in Metabolic Syndrome in Men Study (METSIM) population study (n = 8749 non-diabetic men). RESULTS: Levels of ketone bodies were lower in individuals with NASH compared to individuals with simple steatosis (P = 0.004 and P = 0.018 for β-OHB and acetoacetate respectively). Lower levels of β-OHB were associated with the NASH predicting score in the METSIM study (P = 0.001). Liver inflammation correlated with mRNA expression of genes regulating ketolysis in the liver (Spearman correlation 0.379-0.388, P < 0.0006 for ACAT1, ACSS2 and BDH1). CONCLUSION: Lower levels of ketone bodies in individuals with NASH compared to individuals with simple steatosis suggest a decrease in ketone body metabolism in NASH. PMID: 25533197 [PubMed - indexed for MEDLINE]

Related Articles Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals. Mucosal Immunol. 2015 Jul;8(4):760-72 Authors: Vázquez-Castellanos JF, Serrano-Villar S, Latorre A, Artacho A, Ferrús ML, Madrid N, Vallejo A, Sainz T, Martínez-Botas J, Ferrando-Martínez S, Vera M, Dronda F, Leal M, Del Romero J, Moreno S, Estrada V, Gosalbes MJ, Moya A Abstract Altered interplay between gut mucosa and microbiota during treated HIV infection may possibly contribute to increased bacterial translocation and chronic immune activation, both of which are predictors of morbidity and mortality. Although a dysbiotic gut microbiota has recently been reported in HIV+ individuals, the metagenome gene pool associated with HIV infection remains unknown. The aim of this study is to characterize the functional gene content of gut microbiota in HIV+ patients and to define the metabolic pathways of this bacterial community, which is potentially associated with immune dysfunction. We determined systemic markers of innate and adaptive immunity in a cohort of HIV-infected individuals on successful antiretroviral therapy without comorbidities and in healthy non-HIV-infected subjects. Metagenome sequencing revealed an altered functional profile, with enrichment of the genes involved in various pathogenic processes, lipopolysaccharide biosynthesis, bacterial translocation, and other inflammatory pathways. In contrast, we observed depletion of genes involved in amino acid metabolism and energy processes. Bayesian networks showed significant interactions between the bacterial community, their altered metabolic pathways, and systemic markers of immune dysfunction. This study reveals altered metabolic activity of microbiota and provides novel insight into the potential host-microbiota interactions driving the sustained inflammatory state in successfully treated HIV-infected patients. PMID: 25407519 [PubMed - indexed for MEDLINE]

Related Articles The analysis of volatile organic compounds in exhaled breath and biomarkers in exhaled breath condensate in children - clinical tools or scientific toys? Clin Exp Allergy. 2015 Jul;45(7):1170-88 Authors: van Mastrigt E, de Jongste JC, Pijnenburg MW Abstract Current monitoring strategies for respiratory diseases are mainly based on clinical features, lung function and imaging. As airway inflammation is the hallmark of many respiratory diseases in childhood, noninvasive methods to assess the presence and severity of airway inflammation might be helpful in both diagnosing and monitoring paediatric respiratory diseases. At present, the measurement of fractional exhaled nitric oxide is the only noninvasive method available to assess eosinophilic airway inflammation in clinical practice. We aimed to evaluate whether the analysis of volatile organic compounds (VOCs) in exhaled breath (EB) and biomarkers in exhaled breath condensate (EBC) is helpful in diagnosing and monitoring respiratory diseases in children. An extensive literature search was conducted in Medline, Embase and PubMed on the analysis and applications of VOCs in EB and EBC in children. We retrieved 1165 papers, of which nine contained original data on VOCs in EB and 84 on biomarkers in EBC. These were included in this review. We give an overview of the clinical applications in childhood and summarize the methodological issues. Several VOCs in EB and biomarkers in EBC have the potential to distinguish patients from healthy controls and to monitor treatment responses. Lack of standardization of collection methods and analysis techniques hampers the introduction in clinical practice. The measurement of metabolomic profiles may have important advantages over detecting single markers. There is a lack of longitudinal studies and external validation to reveal whether EB and EBC analysis have added value in the diagnostic process and follow-up of children with respiratory diseases. In conclusion, the use of VOCs in EB and biomarkers in EBC as markers of inflammatory airway diseases in children is still a research tool and not validated for clinical use. PMID: 25394891 [PubMed - indexed for MEDLINE]

22 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/03/24PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2016/03/22PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Matrix removal in state of the art sample preparation methods for serum by charged aerosol detection and metabolomics-based LC-MS. Anal Chim Acta. 2016 Apr 7;915:56-63 Authors: Schimek D, Francesconi KA, Mautner A, Libiseller G, Raml R, Magnes C Abstract Investigations into sample preparation procedures usually focus on analyte recovery with no information provided about the fate of other components of the sample (matrix). For many analyses, however, and particularly those using liquid chromatography-mass spectrometry (LC-MS), quantitative measurements are greatly influenced by sample matrix. Using the example of the drug amitriptyline and three of its metabolites in serum, we performed a comprehensive investigation of nine commonly used sample clean-up procedures in terms of their suitability for preparing serum samples. We were monitoring the undesired matrix compounds using a combination of charged aerosol detection (CAD), LC-CAD, and a metabolomics-based LC-MS/MS approach. In this way, we compared analyte recovery of protein precipitation-, liquid-liquid-, solid-phase- and hybrid solid-phase extraction methods. Although all methods provided acceptable recoveries, the highest recovery was obtained by protein precipitation with acetonitrile/formic acid (amitriptyline 113%, nortriptyline 92%, 10-hydroxyamitriptyline 89%, and amitriptyline N-oxide 96%). The quantification of matrix removal by LC-CAD showed that the solid phase extraction method (SPE) provided the lowest remaining matrix load (48-123 μg mL(-1)), which is a 10-40 fold better matrix clean-up than the precipitation- or hybrid solid phase extraction methods. The metabolomics profiles of eleven compound classes, comprising 70 matrix compounds showed the trends of compound class removal for each sample preparation strategy. The collective data set of analyte recovery, matrix removal and matrix compound profile was used to assess the effectiveness of each sample preparation method. The best performance in matrix clean-up and practical handling of small sample volumes was showed by the SPE techniques, particularly HLB SPE. CAD proved to be an effective tool for revealing the considerable differences between the sample preparation methods. This detector can be used to follow matrix compound elution during chromatographic separations, and the facile monitoring of matrix signal can assist in avoiding unfavourable matrix effects on analyte quantification. PMID: 26995640 [PubMed - as supplied by publisher]

A review on emerging frontiers of house dust mite and cockroach allergy research. Allergol Immunopathol (Madr). 2016 Mar 16; Authors: Patel S, Meher BR Abstract Currently, mankind is afflicted with diversified health issues, allergies being a common, yet little understood malady. Allergies, the outcome of a baffled immune system encompasses myriad allergens and causes an array of health consequences, ranging from transient to recurrent and mild to fatal. Indoor allergy is a serious hypersensitivity in genetically-predisposed people, triggered by ingestion, inhalation or mere contact of allergens, of which mite and cockroaches are one of the most-represented constituents. Arduous to eliminate, these aeroallergens pose constant health challenges, mostly manifested as respiratory and dermatological inflammations, leading to further aggravations if unrestrained. Recent times have seen an unprecedented endeavour to understand the conformation of these allergens, their immune manipulative ploys and other underlying causes of pathogenesis, most importantly therapies. Yet a large section of vulnerable people is ignorant of these innocuous-looking immune irritants, prevailing around them, and continues to suffer. This review aims to expedite this field by a concise, informative account of seminal findings in the past few years, with particular emphasis on leading frontiers like genome-wide association studies (GWAS), epitope mapping, metabolomics etc. Drawbacks linked to current approaches and solutions to overcome them have been proposed. PMID: 26994963 [PubMed - as supplied by publisher]

Tailored sensitivity reduction improves pattern recognition and information recovery with a higher tolerance to varied sample concentration for targeted urinary metabolomics. J Chromatogr A. 2016 Mar 11; Authors: Yan Z, Yan R Abstract Variation in total metabolite concentration among different samples has been a major challenge for urinary metabolomics. Here we investigated the potential of tailored sensitivity reduction of high abundance metabolites for improved targeted urinary metabolomics. Two levels of sensitivity reduction of the 21 predominant urinary metabolites were assessed by employing less sensitive transition or collision energy with level 1 (reduced 1) and 2 (reduced 2) exhibiting 30-90% and 2-20% of the optimal sensitivity, respectively. Five postacquisition normalization methods were compared including no normalization, probabilistic quotient normalization, and normalization to sample median, creatinine intensity, and total intensity. Normalization to total intensity with reduced 2 gave the best pattern recognition and information recovery with a higher tolerance to varied sample concentration. Pareto scaling could improve the performance of tailored sensitivity reduction (reduced 2) for targeted urinary metabolomics while data transformation and autoscaling were susceptible to varied sample concentration. Using controlled spike-in experiments, we demonstrated that tailored sensitivity reduction revealed more differentially expressed markers with higher accuracy than did the conventional optimal sensitivity. This was particularly true when the differences between the sample groups are small. This work also served as an introductory guideline for handling targeted metabolomics data using the open-source software MetaboAnalyst. PMID: 26994924 [PubMed - as supplied by publisher]

Activation of the transcription factor EB rescues lysosomal abnormalities in cystinotic kidney cells. Kidney Int. 2016 Apr;89(4):862-873 Authors: Rega LR, Polishchuk E, Montefusco S, Napolitano G, Tozzi G, Zhang J, Bellomo F, Taranta A, Pastore A, Polishchuk R, Piemonte F, Medina DL, Catz SD, Ballabio A, Emma F Abstract Nephropathic cystinosis is a rare autosomal recessive lysosomal storage disease characterized by accumulation of cystine into lysosomes secondary to mutations in the cystine lysosomal transporter, cystinosin. The defect initially causes proximal tubular dysfunction (Fanconi syndrome) which in time progresses to end-stage renal disease. Cystinotic patients treated with the cystine-depleting agent, cysteamine, have improved life expectancy, delayed progression to chronic renal failure, but persistence of Fanconi syndrome. Here, we have investigated the role of the transcription factor EB (TFEB), a master regulator of the autophagy-lysosomal pathway, in conditionally immortalized proximal tubular epithelial cells derived from the urine of a healthy volunteer or a cystinotic patient. Lack of cystinosin reduced TFEB expression and induced TFEB nuclear translocation. Stimulation of endogenous TFEB activity by genistein, or overexpression of exogenous TFEB lowered cystine levels within 24 hours in cystinotic cells. Overexpression of TFEB also stimulated delayed endocytic cargo processing within 24 hours. Rescue of other abnormalities of the lysosomal compartment was observed but required prolonged expression of TFEB. These abnormalities could not be corrected with cysteamine. Thus, these data show that the consequences of cystinosin deficiency are not restricted to cystine accumulation and support the role of TFEB as a therapeutic target for the treatment of lysosomal storage diseases, in particular of cystinosis. PMID: 26994576 [PubMed - as supplied by publisher]