PubMed

Related Articles Identification of urinary metabolites that correlate with clinical improvements in children with autism treated with sulforaphane from broccoli. Mol Autism. 2018;9:35 Authors: Bent S, Lawton B, Warren T, Widjaja F, Dang K, Fahey JW, Cornblatt B, Kinchen JM, Delucchi K, Hendren RL Abstract Background: Children with autism spectrum disorder (ASD) have urinary metabolites suggesting impairments in several pathways, including oxidative stress, inflammation, mitochondrial dysfunction, and gut microbiome alterations. Sulforaphane, a supplement with indirect antioxidant effects that are derived from broccoli sprouts and seeds, was recently shown to lead to improvements in behavior and social responsiveness in children with ASD. We conducted the current open-label study to determine if we could identify changes in urinary metabolites that were associated with clinical improvements with the goal of identifying a potential mechanism of action. Methods: Children and young adults enrolled in a school for children with ASD and related neurodevelopmental disorders were recruited to participate in a 12-week, open-label study of sulforaphane. Fasting urinary metabolites and measures of behavior (Aberrant Behavior Checklist-ABC) and social responsiveness (Social Responsiveness Scale-SRS) were measured at baseline and at the end of the study. Pearson's correlation coefficient was calculated for the pre- to post-intervention change in each of the two clinical scales (ABS and SRS) versus the change in each metabolite. Results: Fifteen children completed the 12-week study. Mean scores on both symptom measures showed improvements (decreases) over the study period, but only the change in the SRS was significant. The ABC improved - 7.1 points (95% CI - 17.4 to 3.2), and the SRS improved - 9.7 points (95% CI - 18.7 to - 0.8). We identified 77 urinary metabolites that were correlated with changes in symptoms, and they clustered into pathways of oxidative stress, amino acid/gut microbiome, neurotransmitters, hormones, and sphingomyelin metabolism. Conclusions: Urinary metabolomics analysis is a useful tool to identify pathways that may be involved in the mechanism of action of treatments targeting abnormal physiology in ASD. Trial registration: This study was prospectively registered at clinicaltrials.gov (NCT02654743) on January 11, 2016. PMID: 29854372 [PubMed - in process]

Related Articles Combining mechanism-based prediction with patient-based profiling for psoriasis metabolomics biomarker discovery. AMIA Annu Symp Proc. 2017;2017:1734-1743 Authors: Wang Q, McCormick TS, Ward NL, Cooper KD, Conic R, Xu R Abstract Psoriasis is a chronic, debilitating skin condition that affects approximately 125 million individuals worldwide. The cause of psoriasis appears multifactorial, and no unified mitigating signal or single antigenic target has been identified to date. Metabolomic studies hold great potential for explaining disease mechanism, facilitating early diagnosis, and identifying potential therapeutic areas. Here, we present an integrated disease metabolomic biomarker discovery strategy that combines mechanism-based biomarker discovery with clinical sample-based metabolomic profiling. We applied this strategy in identifying and understanding metabolite biomarkers for psoriasis. The key innovation of our strategy is a novel mechanism-based metabolite prediction system, mmPredict, which assimilates vast amounts of existing knowledge of diseases and metabolites. mmPredict first constructed a psoriasis-specific mouse mutational phenotype profile. It then constructed phenotype profiles for a total of 259,170 chemicals/metabolites using known chemical genetics and human metabolomic data. Metabolites were then prioritized based on the phenotypic similarities between disease- and metabolites. We evaluated mmPredict using 150 metabolites identified using our in-house metabolome profiling study of psoriasis patient samples. mmPredict found 96 of the 150 metabolites and ranked them highly (recall: 0.64, mean ranking: 8.73%, median ranking: 2.33%, p-value: 4.75E-44). These results show that mmPredict is consistent with, as well as a complement to, traditional human metabolomic profiling studies. We then developed a strategy to combine outputs from both systems and found that the oxidative product of linoleic acid, 13(S)-hydroxy-9Z,11E-octadecadienoic acid (13- HODE), ranked highly by both mmPredict and our in-house experiments. Our integrated analysis indicates that 13- HODE may be a mechanistic link between psoriasis and cardiovascular comorbidities associated with psoriasis. In summary, we developed an integrated metabolomic prediction system that combines both human metabolomic studies and mechanism-based prediction and demonstrated its application in the skin disease psoriasis. Our system is highly general and can be applied to other diseases when patient-based metabolomic profiling data becomes more increasingly available. Data is publicly available at: http://nlp. CASE: edu/public/data/mmPredict_PSO. PMID: 29854244 [PubMed - in process]

Related Articles PROMIS, global analysis of PROtein-Metabolite Interactions using Size separation in Arabidopsis thaliana. J Biol Chem. 2018 May 31;: Authors: Veyel D, Sokolowska EM, Moreno JC, Kierszniowska S, Cichon J, Wojciechowska I, Luzarowski M, Kosmacz M, Szlachetko J, Gorka M, Méret M, Graf A, Meyer EH, Willmitzer L, Skirycz A Abstract Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we describe a method, dubbed PROtein-Metabolite Interactions using Size separation (PROMIS) that allows simultaneous, global analysis of endogenous protein-small molecule and of protein‒protein complexes. To this end, a cell-free native lysate from Arabidopsis thaliana cell cultures was fractionated by size-exclusion chromatography, followed by quantitative metabolomic and proteomic analyses. Proteins and small molecules showing similar elution behavior, across protein containing fractions, constituted putative interactors. Applying PROMIS to an A. thaliana extract, we ascertained known protein‒protein (PPIs) and protein-metabolite (PMIs) interactions and reproduced binding between small-molecule protease inhibitors and their respective proteases. More importantly, we present examples of two experimental strategies that exploit the PROMIS dataset to identify novel PMIs. By looking for similar elution behavior of metabolites and enzymes belonging to the same biochemical pathways, we identified putative feedback and feed-forward regulations in pantothenate biosynthesis and the methionine salvage cycle, respectively. By combining PROMIS with an orthogonal affinity purification approach, we identified an interaction between the dipeptide Tyr-Asp and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase. In summary, we present proof of concept for a powerful experimental tool that enables system-wide analysis of PMIs and PPIs across all biological systems. The dataset obtained here comprises nearly 140 metabolites and 5000 proteins, which can be mined for putative interactors. PMID: 29853640 [PubMed - as supplied by publisher]

Related Articles Striking changes in tea metabolites due to elevational effects. Food Chem. 2018 Oct 30;264:334-341 Authors: Kfoury N, Morimoto J, Kern A, Scott ER, Orians CM, Ahmed S, Griffin T, Cash SB, Stepp JR, Xue D, Long C, Robbat A Abstract Climate effects on crop quality at the molecular level are not well-understood. Gas and liquid chromatography-mass spectrometry were used to measure changes of hundreds of compounds in tea at different elevations in Yunnan Province, China. Some increased in concentration while others decreased by 100's of percent. Orthogonal projection to latent structures-discriminant analysis revealed compounds exhibiting analgesic, antianxiety, antibacterial, anticancer, antidepressant, antifungal, anti-inflammatory, antioxidant, anti-stress, and cardioprotective properties statistically (p = 0.003) differentiated high from low elevation tea. Also, sweet, floral, honey-like notes were higher in concentration in the former while the latter displayed grassy, hay-like aroma. In addition, multivariate analysis of variance showed low elevation tea had statistically (p = 0.0062) higher concentrations of caffeine, epicatechin gallate, gallocatechin, and catechin; all bitter compounds. Although volatiles represent a small fraction of the total mass, this is the first comprehensive report illustrating how normal variations in temperature, 5 °C, due to elevational effects impact tea quality. PMID: 29853384 [PubMed - in process]

Related Articles A high-resolution HPLC-QqTOF platform using parallel reaction monitoring for in-depth lipid discovery and rapid profiling. Anal Chim Acta. 2018 Oct 05;1026:87-100 Authors: Yu D, Rupasinghe TWT, Boughton BA, Natera SHA, Hill CB, Tarazona P, Feussner I, Roessner U Abstract Here, we developed a robust lipidomics workflow merging both targeted and untargeted approaches on a single liquid chromatography coupled to quadrupole-time of flight (LC-QqTOF) mass spectrometry platform with parallel reaction monitoring (PRM). PRM assays integrate both untargeted profiling from MS1 scans and targeted profiling obtained from MS/MS data. This workflow enabled the discovery of more than 2300 unidentified features and identification of more than 600 lipid species from 23 lipid classes at the level of fatty acid/long chain base/sterol composition in a barley root extracts. We detected the presence of 142 glycosyl inositol phosphorylceramides (GIPC) with HN(Ac)-HA as the core structure of the polar head, 12 cardiolipins and 17 glucuronosyl diacylglycerols (GlcADG) which have been rarely reported previously for cereal crops. Using a scheduled algorithm with up to 100 precursors multiplexed per duty cycle, the PRM assay was able to achieve a rapid profiling of 291 species based on MS/MS data by a single injection. We used this novel approach to demonstrate the applicability and efficiency of the workflow to study salt stress induced changes in the barley root lipidome. Results show that 221 targeted lipids and 888 unknown features were found to have changed significantly in response to salt stress. This combined targeted and untargeted single workflow approach provides novel applications of lipidomics addressing biological questions. PMID: 29852998 [PubMed - in process]

Related Articles Model selection for within-batch effect correction in UPLC-MS metabolomics using quality control - Support vector regression. Anal Chim Acta. 2018 Oct 05;1026:62-68 Authors: Sánchez-Illana Á, Pérez-Guaita D, Cuesta-García D, Sanjuan-Herráez JD, Vento M, Ruiz-Cerdá JL, Quintás G, Kuligowski J Abstract Ultra performance liquid chromatography - mass spectrometry (UPLC-MS) is increasingly being used for untargeted metabolomics in biomedical research. Complex matrices and a large number of samples per analytical batch lead to gradual changes in the instrumental response (i.e. within-batch effects) that reduce the repeatability and reproducibility and limit the power to detect biological responses. A strategy for within-batch effect correction based on the use of quality control (QC) samples and Support Vector Regression (QC-SVRC) with a radial basis function kernel was recently proposed. QC-SVRC requires the optimization of three hyperparameters that determine the accuracy of the within-batch effects elimination: the tolerance threshold (ε), the penalty term (C) and the kernel width (γ). This work compares three widely used strategies for QC-SVRC hyperparameter optimization (grid search, random search and particle swarm optimization) using a UPLC-MS data set containing 193 urine injections as model example. Results show that QC-SVRC is robust to hyperparameter selection and that a pre-selection of C and ε, followed by optimization of γ is competitive in terms of accuracy, precision and number of function evaluations with full grid analysis, random search and particle swarm optimization. The QC-SVRC optimization procedure can be regarded as a useful non-parametric tool for efficiently complementing alternative approaches such as QC-robust splines correction (RSC). PMID: 29852994 [PubMed - in process]

Related Articles The α-melanocyte stimulating hormone/peroxisome proliferator activated receptor-γ pathway down-regulates proliferation in melanoma cell lines. J Exp Clin Cancer Res. 2017 Oct 11;36(1):142 Authors: Flori E, Rosati E, Cardinali G, Kovacs D, Bellei B, Picardo M, Maresca V Abstract BACKGROUND: The α-Melanocyte Stimulating Hormone (αMSH)/Melanocortin-1 receptor (MC1R) interaction promotes melanogenesis through the cAMP/PKA pathway. The direct induction of this pathway by Forskolin (FSK) is also known to enhance melanocyte proliferation. αMSH acts as a mitogenic agent in melanocytes and its effect on proliferation of melanoma cells is less known. We previously identified the αMSH/Peroxisome Proliferator Activated Receptor (PPARγ) pathway as a new pathway on the B16-F10 mouse melanoma cell line. αMSH induced the translocation of PPARγ into the nucleus as an active transcription factor. This effect was independent of the cAMP/PKA pathway and was mediated by the activation of the PI(4,5)P2/PLC pathway, a pathway which we have described to be triggered by the αMSH-dependent MC1R stimulation. Moreover, in the same study, preliminary experiments showed that mouse melanoma cells responded to αMSH by reducing proliferation and that PPARγ was involved in this effect. Due to its key role in the control of cell proliferation, PPARγ agonists are used in therapeutic models for different forms of cancer, including melanoma. The purpose of this study was: (a) to confirm the different proliferative behavior in response to αMSH in healthy and in melanoma condition; (b) to verify whether the cAMP/PKA pathway and the PLC/PPARγ pathway could exert an antagonistic function in the control of proliferation; (c) to deepen the knowledge of the molecular basis responsible for the down-proliferative response of melanoma cells after exposure to αMSH. METHODS: We employed B16-F10 cell line, a human melanoma cell line (Mel 13) and two primary cultures of human melanocytes (NHM 1 and NHM 2, respectively), all expressing a wild type MC1R and responding to the αMSH in terms of pigmentation. We evaluated cell proliferation through: a) cell counting, b) cell cycle analysis c) protein expression of proliferation modulators (p27, p21, cyclin D1 and cyclin E). RESULTS: The αMSH acted as a mitogenic agent in primary cultures of human melanocytes, whereas it determined a slow down of proliferation in melanoma cell lines. FSK, as an inducer of the cAMP/PKA pathway, reproduced the αMSH mediated effect on proliferation in NHMs but it did not mimic the αMSH effect on proliferation in B16-F10 and Mel 13 melanoma cell lines. Meanwhile, 3 M3-FBS (3 M3), as an inducer of PI(4,5)P2/PLC pathway, reproduced the αMSH proliferative effect. Further experiments, treating melanoma cell lines with αMSH in the presence/absence of GW9662, as an inhibitor of PPARγ, confirmed the key role of this transcription factor in decreasing cell proliferation in response to the hormone exposure. CONCLUSIONS: In both melanoma cell lines, αMSH determined the reduction of proliferation through the PI(4,5)P2/PLC pathway, employing PPARγ as an effector element. These evidence could offer perspectives for new therapeutic approaches for melanoma. PMID: 29020973 [PubMed - indexed for MEDLINE]

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 2018/06/01PubMed comprises more than millions of 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.

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 2018/06/01PubMed comprises more than millions of 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.

25 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 2018/05/31PubMed comprises more than millions of 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.

25 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 2018/05/31PubMed comprises more than millions of 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.

31 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 2018/05/29PubMed comprises more than millions of 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.

Related Articles Plasma N-Glycan Signatures Associate With Features of Inflammatory Bowel Diseases. Gastroenterology. 2018 May 21;: Authors: Clerc F, Novokmet M, Dotz V, Reiding KR, de Haan N, Kammeijer GSM, Dalebout H, Bladergroen MR, Vukovic F, Rapp E, IBD-BIOM consortium, Targan SR, Barron G, Manetti N, Latiano A, McGovern DPB, Annese V, Lauc G, Wuhrer M Abstract BACKGROUND & AIMS: Biomarkers are needed for early detection of Crohn's disease (CD) and ulcerative colitis (UC) or to predict patient outcomes. Glycosylation is a common and complex post-translational modification of proteins that affects their structure and activity. We compared plasma N-glycosylation profiles between patients with CD or UC and healthy individuals (controls). METHODS: We analyzed the total plasma N-glycomes of 2635 patients with inflammatory bowel diseases and 996 controls by mass spectrometry with a linkage-specific sialic acid derivatization technique. Plasma samples were acquired from 2 hospitals in Italy (discovery cohort, 1989 patients with IBD and 570 controls) and 1 medical center in the United States (validation cohort, 646 cases of IBD and 426 controls). Sixty-three glycoforms met our criteria for relative quantification and were extracted from the raw data with the software MassyTools. Common features shared by the glycan compositions were combined in 78 derived traits, including the number of antennae of complex-type glycans and levels of fucosylation, bisection, galactosylation, and sialylation. Associations of plasma N-glycomes with age, sex, CD, UC and IBD-related parameters such as disease location, surgery and medication, level of C-reactive protein, and sedimentation rate were tested by linear and logistic regression. RESULTS: Plasma samples from patients with IBD had a higher abundance of large-size glycans compared with controls, a decreased relative abundance of hybrid and high-mannose structures, lower fucosylation, lower galactosylation, and higher sialylation (alpha2,3- and alpha2,6-linked). We could discriminate plasma from patients with CD from that of patients with UC based on higher bisection, lower galactosylation and higher sialylation (alpha2,3-linked). Glycosylation patterns associated with disease location and progression, the need for a more potent medication, and surgery. These results were replicated in a large independent cohort. CONCLUSIONS: We performed high-throughput analysis to compare total plasma N-glycomes of individuals with vs. without IBD and to identify patterns associated with disease features and the need for treatment. These profiles might be used in diagnosis and for predicting patients' response to treatment. PMID: 29792883 [PubMed - as supplied by publisher]

Related Articles Metabolomics Reveals the Molecular Mechanisms of Copper Induced Cucumber Leaf (Cucumis sativus) Senescence. Environ Sci Technol. 2018 May 24;: Authors: Zhao L, Huang Y, Paglia K, Vaniya A, Wancewicz B, Keller AA Abstract Excess copper may disturb plant photosynthesis and induce leaf senescence. The underlying toxicity mechanism is not well understood. Here, 3-week-old cucumber plants were foliar exposed to different copper concentrations (10, 100 and 500 mg/L) for a final dose of 0.21, 2.1 and 10 mg/plant, using CuSO4 as the Cu ion source for seven days, three times per day. Metabolomics quantified 149 primary and 79 secondary metabolites. A number of intermediates of the tricarboxylic acid (TCA) cycle were significantly down-regulated 1.4-2.4 fold, indicating a perturbed carbohydrate metabolism. Ascorbate and aldarate metabolism and shikimate-phenylpropanoid biosynthesis (antioxidant and defense related pathways) were perturbed by excess copper. These metabolic responses occur even at the lowest copper dose considered although no phenotype changes were observed at this dose. High copper dose resulted in a 2-fold increase in phytol, a degradation product of chlorophyll. Polyphenol metabolomics revealed that some flavonoids were down-regulated, while the nonflavonoid 4-hydroxycinnamic acid and trans-2-hydroxycinnamic acid were significantly up-regulated 4- and 26-fold compared to the control. This study enhances current understanding of copper toxicity to plants, and demonstrates that metabolomics profiling provides a more comprehensive view of plant responses to stressors, which can be applied to other plant species and contaminants. PMID: 29792813 [PubMed - as supplied by publisher]

Related Articles Potential biotechnological capabilities of cultivable mycobiota from carwash effluents. Microbiologyopen. 2017 Oct;6(5): Authors: Sibanda T, Selvarajan R, Tekere M, Nyoni H, Meddows-Taylor S Abstract Urban life has created man-made extreme environments like carwashes. These environments have, however, not been sufficiently explored for mycobiota that can be sources of biotechnologically useful products, as has been the case with natural extreme environments. Using a combination of culture and molecular techniques, fungi from carwash effluents was characterized for production of lipase and cellulase enzymes, nonpolar and polar biotechnologically relevant secondary metabolites and hydrocarbon utilization. The isolated fungal strains belonged to the genera Alternaria, Cladosporium, Penicillium, Peyronellaea, Rhizopus, Spegazzinia, Trichoderma, Ulocladium and Yarrowia. Sixty-six percent (66%) of the fungal isolates were found to be able to metabolize naphthalene and benzanthracene, showing potential for application in bioremediation of hydrocarbon polluted sites. Lipase production by the isolates Penicillium sp. BPS3 (2.61 U/ml), Trichoderma sp. BPS9 (2.01 U/ml), Rhizopus sp. CAL1 (2.05 U/ml), Penicillium sp. PCW1 (2.99 U/ml) and Penicillium sp. SAS1 (2.16 U/ml) compared well with previously recorded lipase production levels by other fungi. The highest producers of cellulase were Penicillium sp. SAS1 (12.10 U/ml), Peyronella sp. CAW5 (4.49 U/ml) and Cladosporium sp. SAS3 (4.07 U/ml), although these activities were lower than previously reported levels. GC-MS analysis of the fungal secondary metabolites resulted in identification of 572 compounds, including azulene, methanamine, N-pentylidene, metoclopramide, and mepivacaine while compounds determined by UHPLC-MS included 10-undecen-1-ol, piquerol A, 10-undecyn-1-ol, cyclo(leucylprolyl) and rac-etomidate. These compounds were previously determined to have various activities including anticancer, antibacterial, antifungal, antihypertensive, antidiabetic and anti-inflammatory properties. The study demonstrated that fungi from carwash effluents are natural sources of some biotechnologically important products. PMID: 28714266 [PubMed - indexed for MEDLINE]

Related Articles Brachiaria Grasses (Brachiaria spp.) harbor a diverse bacterial community with multiple attributes beneficial to plant growth and development. Microbiologyopen. 2017 Oct;6(5): Authors: Mutai C, Njuguna J, Ghimire S Abstract Endophytic and plant-associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty-four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole-3-acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production. The 16S rDNA-based identification grouped these 84 bacterial strains into 3 phyla, 5 classes, 8 orders, 12 families, 16 genera, and 50 unique taxa. The four most frequently isolated genera were Pseudomonas (23), Pantoea (17), Acinetobacter (9), and Enterobacter (8). The functional characterization of these strains revealed that 41 of 84 strains had a minimum of three plant beneficial properties. Inoculation of maize seedlings with Acinetobacter spp., Microbacterium spp., Pectobacterium spp., Pseudomonas spp., and Enterobacter spp. showed positive effects on seedling biomass production. The ability of Brachiaria grasses to host genetically diverse bacteria, many of them with multiple plant growth-promoting attributes, might have contributed to high biomass production and adaptation of Brachiaria grasses to drought and low fertility soils. PMID: 28639414 [PubMed - indexed for MEDLINE]

Related Articles Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE). Proteomics. 2018 May 23;:e1800110 Authors: Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias J, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M Abstract Minimal Information about an Immuno-Peptidomics Experiment (MIAIPE) is an initiative of the members of the Human Immuno-Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement and associated mass spectrometry (MS)-related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (Minimal Information About a Proteomics Experiment) guidelines. This article is protected by copyright. All rights reserved. PMID: 29791771 [PubMed - as supplied by publisher]

Related Articles SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy. PLoS Pathog. 2018 May 23;14(5):e1007071 Authors: Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR, Jones KA Abstract HIV-1 Tat is a key regulator of viral transcription, however little is known about the mechanisms that control its turnover in T cells. Here we use a novel proteomics technique, called DiffPOP, to identify the molecular target of JIB-04, a small molecule compound that potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines. Mass-spectrometry analysis of whole-cell extracts from 2D10 Jurkat T cells revealed that JIB-04 targets Serine Hydroxymethyltransferase 2 (SHMT2), a regulator of glycine biosynthesis and an adaptor for the BRCC36 K63Ub-specific deubiquitinase in the BRISC complex. Importantly, knockdown of SHMT1,2 or BRCC36, or exposure of cells to JIB-04, strongly increased Tat K63Ub-dependent destruction via autophagy. Moreover, point mutation of multiple lysines in Tat, or knockdown of BRCC36 or SHMT1,2, was sufficient to prevent destruction of Tat by JIB-04. We conclude that HIV-1 Tat levels are regulated through K63Ub-selective autophagy mediated through SHMT1,2 and the BRCC36 deubiquitinase. PMID: 29791506 [PubMed - as supplied by publisher]

Related Articles The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018 May 22;: Authors: Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D Abstract Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially. PMID: 29790989 [PubMed - as supplied by publisher]

Related Articles Target-decoy Based False Discovery Rate Estimation for Large-scale Metabolite Identification. J Proteome Res. 2018 May 23;: Authors: Wang X, Jones DR, Shaw TI, Cho JH, Wang Y, Tan H, Xie B, Zhou S, Li Y, Peng J Abstract Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However, it is still challenging to assess the confidence of assigned metabolites. In this study, we report a novel method for estimating false discovery rate (FDR) of metabolite assignment with a target-decoy strategy, in which the decoys are generated through violating the octet rule of chemistry by adding small odd numbers of hydrogen atoms. The target-decoy strategy was integrated into JUMPm, an automated metabolite identification pipeline for large-scale MS analysis, and was also evaluated with two other metabolomics tools, mzMatch and mzMine 2. The reliability of FDR calculation was examined by false datasets, which were simulated by altering MS1 or MS2 spectra. Finally, we used the JUMPm pipeline coupled with the target-decoy strategy to process unlabeled and stable-isotope labeled metabolomic datasets. The results demonstrate that the target-decoy strategy is a simple and effective method for evaluating the confidence of high-throughput metabolite identification. PMID: 29790753 [PubMed - as supplied by publisher]