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https://www.readbyqxmd.com/read/29792918/translational-omics-future-potential-and-current-challenges-in-precision-medicine
#1
Arsalan Wafi, Reza Mirnezami
Rapid advances in computational science and biotechnology are paving the way for precision medicine - a vision in next-generation healthcare that promises to provide a care package uniquely tailored to each individual's molecular make-up. Until relatively recently, the focus has been firmly centred around the genome; however, over the past two decades there has been a surge in the study of molecular activity within other biological domains (proteome/transcriptome/metabolome) involved in health and pathogenesis...
May 21, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29792813/metabolomics-reveals-the-molecular-mechanisms-of-copper-induced-cucumber-leaf-cucumis-sativus-senescence
#2
Lijuan Zhao, Yuxiong Huang, Kelly Paglia, Arpana Vaniya, Benjamin Wancewicz, Arturo A Keller
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...
May 24, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29790989/the-galaxy-platform-for-accessible-reproducible-and-collaborative-biomedical-analyses-2018-update
#3
Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel Blankenberg
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...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790936/simextargid-a-comprehensive-package-for-real-time-lc-ms-data-acquisition-and-analysis
#4
William M B Edmands, Josie Hayes, Stephen M Rappaport
Summary: Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790753/target-decoy-based-false-discovery-rate-estimation-for-large-scale-metabolite-identification
#5
Xusheng Wang, Drew R Jones, Timothy I Shaw, Ji-Hoon Cho, Yuanyuan Wang, Haiyan Tan, Boer Xie, Suiping Zhou, Yuxin Li, Junmin Peng
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...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29790270/metabolomics-reveals-the-key-role-of-oxygen-metabolism-in-the-heat-susceptibility-of-an-alpine-dwelling-ghost-moth-thitarodes-xiaojinensis-lepidoptera-hepialidae
#6
Wei Zhu, Qian Meng, Huan Zhang, Meng-Long Wang, Xuan Li, Hong-Tuo Wang, Gui-Ling Zhou, Lin Miao, Qi-Lian Qin, Ji-Hong Zhang
Ghost moths inhabiting the alpine meadows of the Tibetan Plateau are cold-adapted stenothermal organisms that are susceptible to heat (dead within 7 days of 27 °C exposure). Exploring the metabolic basis of their heat susceptibility would extend our understanding of the thermal biology of alpine dwelling invertebrates. Here, gas chromatography-mass spectrometry-based metabolomics was combined with physiological and transcriptional approaches to determine the metabolic mechanisms of heat susceptibility in Thitarodes xiaojinensis larvae...
May 23, 2018: Insect Science
https://www.readbyqxmd.com/read/29790096/metabolomic-and-proteomic-analyses-of-mouse-primordial-germ-cells
#7
Yohei Hayashi, Yasuhisa Matsui
Primordial germ cells (PGCs), the precursors of gametes, are the only cells capable of acquiring totipotency upon fertilization, but the molecular mechanisms regulating germ cell characteristics have not been fully elucidated. Although intracellular metabolic status and regulation are responsible for the control of cell function and differentiation, little is known about the metabolic features of PGCs. Here, we describe use of an integrated metabolomic, proteomic, and energy metabolic analysis method to comprehensively elucidate the metabolic characteristics of PGCs using mass spectrometry...
May 23, 2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29789980/metabolic-remodeling-of-substrate-utilization-during-heart-failure-progression
#8
REVIEW
Liang Chen, Jiangping Song, Shengshou Hu
Heart failure (HF) is a clinical syndrome caused by a decline in cardiac systolic or diastolic function, which leaves the heart unable to pump enough blood to meet the normal physiological requirements of the human body. It is a serious disease burden worldwide affecting nearly 23 million patients. The concept that heart failure is "an engine out of fuel" has been generally accepted and metabolic remodeling has been recognized as an important aspect of this condition; it is characterized by defects in energy production and changes in metabolic pathways involved in the regulation of essential cellular functions such as the process of substrate utilization, the tricarboxylic acid cycle, oxidative phosphorylation, and high-energy phosphate metabolism...
May 23, 2018: Heart Failure Reviews
https://www.readbyqxmd.com/read/29789708/combined-genotyping-microbial-diversity-and-metabolite-profiling-studies-on-farmed-mytilus-spp-from-kiel-fjord
#9
Caroline Utermann, Delphine Parrot, Corinna Breusing, Heiko Stuckas, Tim Staufenberger, Martina Blümel, Antje Labes, Deniz Tasdemir
The blue mussel Mytilus is a popular food source with high economical value. Species of the M. edulis complex (M. edulis, M. galloprovincialis and M. trossulus) hybridise whenever their geographic ranges overlap posing difficulties to species discrimination, which is important for blue mussel aquaculture. The aim of this study was to determine the genetic structure of farmed blue mussels in Kiel Fjord. Microbial and metabolic profile patterns were studied to investigate a possible dependency on the genotype of the bivalves...
May 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29789665/existing-and-novel-biomarkers-for-precision-medicine-in-systemic-sclerosis
#10
REVIEW
Peter J Wermuth, Sonsoles Piera-Velazquez, Joel Rosenbloom, Sergio A Jimenez
The discovery and validation of biomarkers resulting from technological advances in the analysis of genomic, transcriptomic, lipidomic and metabolomic pathways involved in the pathogenesis of complex human diseases have led to the development of personalized and rationally designed approaches for the clinical management of such disorders. Although some of these approaches have been applied to systemic sclerosis (SSc), an unmet need remains for validated, non-invasive biomarkers to aid in the diagnosis of SSc, as well as in the assessment of disease progression and response to therapeutic interventions...
May 22, 2018: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/29789485/association-of-plasma-lipids-and-polar-metabolites-with-low-bone-mineral-density-in-singaporean-chinese-menopausal-women-a-pilot-study
#11
Diana Cabrera, Marlena Kruger, Frances M Wolber, Nicole C Roy, John J Totman, Christiani Jeyakumar Henry, David Cameron-Smith, Karl Fraser
The diagnosis of osteoporosis is mainly based on clinical examination and bone mineral density assessments. The present pilot study compares the plasma lipid and polar metabolite profiles in blood plasma of 95 Singaporean-Chinese (SC) menopausal women with normal and low bone mineral density (BMD) using an untargeted metabolomic approach. The primary finding of this study was the association between lipids and femoral neck BMD in SC menopausal women. Twelve lipids were identified to be associated with low BMD by the orthogonal partial least squares (OPLS) model...
May 22, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29789481/concepts-and-methods-to-access-novel-antibiotics-from-actinomycetes
#12
REVIEW
Joachim J Hug, Chantal D Bader, Maja Remškar, Katarina Cirnski, Rolf Müller
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics...
May 22, 2018: Antibiotics
https://www.readbyqxmd.com/read/29789170/method-selectivity-evaluation-using-the-co-feature-ratio-in-lc-ms-metabolomics-comparison-of-hilic-stationary-phase-performance-for-the-analysis-of-plasma-urine-and-cell-extracts
#13
Albert Elmsjö, Jakob Haglöf, Mikael K R Engskog, Ida Erngren, Marika Nestor, Torbjörn Arvidsson, Curt Pettersson
Evaluation of the chromatographic separation in metabolomics studies has primarily been done using preselected sets of standards or by counting the number of detected features. An alternative approach is to calculate each feature's co-feature ratio, which is a combined selectivity measurement for the separation (i.e. extent of co-elution) and the MS-signal (i.e. adduct formation and in-source fragmentation). The aim of this study was to demonstrate how the selectivity of different HILIC stationary phases can be evaluated using the co-feature ratio approach...
May 4, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29788433/metabolic-footprinting-of-fermented-milk-consumption-in-serum-of-healthy-men
#14
Grégory Pimentel, Kathryn J Burton, Ueli von Ah, Ueli Bütikofer, François P Pralong, Nathalie Vionnet, Reto Portmann, Guy Vergères
Background: Fermentation is a widely used method of natural food preservation that has consequences on the nutritional value of the transformed food. Fermented dairy products are increasingly investigated in view of their ability to exert health benefits beyond their nutritional qualities. Objective: To explore the mechanisms underpinning the health benefits of fermented dairy intake, the present study followed the effects of milk fermentation, from changes in the product metabolome to consequences on the human serum metabolome after its ingestion...
May 21, 2018: Journal of Nutrition
https://www.readbyqxmd.com/read/29788292/biological-processes-modulating-longevity-across-primates-a-phylogenetic-genome-phenome-analysis
#15
Gerard Muntané, Xavier Farré, Juan Antonio Rodríguez, Cinta Pegueroles, David A Hughes, João Pedro de Magalhães, Toni Gabaldón, Arcadi Navarro
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan (MLS) across primate species...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788285/altered-asparagine-and-glutamate-homeostasis-precede-coronary-artery-disease-and-type-2-diabetes
#16
Filip Ottosson, Einar Smith, Olle Melander, Céline Fernandez
Context: Type 2 diabetes (T2DM) is accompanied by an increased risk of coronary artery disease (CAD), but the overlapping metabolic disturbances preceding both diseases are insufficiently described. Objective: We hypothesized that alterations in metabolism occur years before clinical manifestation of T2DM and CAD and that these alterations are reflected in the plasma metabolome. We thus aimed to identify plasma metabolites that predict future T2DM and CAD. Design: Using targeted liquid chromatography-mass spectrometry (LC-MS), 35 plasma metabolites (amino acid metabolites and acylcarnitines) were quantified in 1049 individuals, free from CAD and diabetes, drawn from a population sample of 5386 in the Malmö Preventive Project (mean age 69...
May 16, 2018: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29788224/iron-sequestration-in-microbiota-biofilms-as-a-novel-strategy-for-treating-inflammatory-bowel-disease
#17
Jean-Paul Motta, Thibault Allain, Luke E Green-Harrison, Ryan A Groves, Troy Feener, Hena Ramay, Paul L Beck, Ian A Lewis, John L Wallace, Andre G Buret
Significant alterations of intestinal microbiota and anemia are hallmarks of inflammatory bowel disease (IBD). It is widely accepted that iron is a key nutrient for pathogenic bacteria, but little is known about its impact on microbiota associated with IBD. We used a model device to grow human mucosa-associated microbiota in its physiological anaerobic biofilm phenotype. Compared to microbiota from healthy donors, microbiota from IBD patients generate biofilms ex vivo that were larger in size and cell numbers, contained higher intracellular iron concentrations, and exhibited heightened virulence in a model of human intestinal epithelia in vitro and in the nematode Caenorhabditis elegans...
May 17, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29788121/targeted-metabolomics-shows-low-plasma-lysophosphatidylcholine-18-2-predicts-greater-decline-of-gait-speed-in-older-adults-the-baltimore-longitudinal-study-of-aging
#18
Marta Gonzalez-Freire, Ruin Moaddel, Kai Sun, Elisa Fabbri, Pingbo Zhang, Mohammed Khadeer, Norman Salem, Luigi Ferrucci, Richard D Semba
Background: Gait speed is an important measure of lower extremity physical performance in older adults and is predictive of disability and mortality. The biological pathways involved in the decline of lower extremity physical performance are not well understood. We used a targeted metabolomics approach to identify plasma metabolites predictive of change in gait speed over time. Methods: Gait speed was measured at baseline and over median follow-up of 50.5 months in 504 adults, aged ≥50 years, who had two or more study visits in the Baltimore Longitudinal Study of Aging (BLSA)...
May 17, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29787870/oral-hydroxysafflor-yellow-a-reduces-obesity-in-mice-by-modulating-the-gut-microbiota-and-serum-metabolism
#19
Juan Liu, Shijun Yue, Zhirui Yan, Wuwen Feng, Xintong Meng, Aiting Wang, Cheng Peng, Changyun Wang, Dan Yan
Given the high and increasing prevalence of obesity, the safe and effective treatment of obesity would be beneficial. Here, we examined whether oral hydroxysafflor yellow A (HSYA), an active compound from the dried florets of Carthamus tinctorius L., can reduce high-fat (HF) diet-induced obesity in C57BL/6 J mice. Our results showed that the average body weight of HF group treated by HSYA was significantly lower than that of the HF group (P < 0.01). HSYA also reduced fat accumulation, ameliorated insulin resistance, restored glucose homeostasis, reduced inflammation, enhanced intestinal integrity, and increased short-chain fatty acids ((SCFAs)) production in HF diet-fed mice...
May 19, 2018: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29787425/a-metabolomic-serum-signature-from-nonhuman-primates-treated-with-a-radiation-countermeasure-gamma-tocotrienol-and-exposed-to-ionizing-radiation
#20
Evan L Pannkuk, Evagelia C Laiakis, Albert J Fornace, Oluseyi O Fatanmi, Vijay K Singh
The search for and development of radiation countermeasures to treat acute lethal radiation injury has been underway for the past six decades, resulting in the identification of multiple classes of radiation countermeasures. However, to date only granulocyte colony-stimulating factor (Neupogen) and PEGylated granulocyte colony-stimulating factor (Neulasta) have been approved by the U.S. Food and Drug Administration for the treatment of hematopoietic acute radiation syndrome. Gamma-tocotrienol has demonstrated radioprotective efficacy in murine and nonhuman primate models...
July 2018: Health Physics
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