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https://www.readbyqxmd.com/read/29156542/computational-approaches-for-integrative-analysis-of-the-metabolome-and-microbiome
#1
REVIEW
Jasmine Chong, Jianguo Xia
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies...
November 18, 2017: Metabolites
https://www.readbyqxmd.com/read/29154799/integrative-omics-data-analyses-of-repeated-dose-toxicity-of-valproic-acid-in-vitro-reveal-new-mechanisms-of-steatosis-induction
#2
Simone G J van Breda, Sandra M H Claessen, Marcel van Herwijnen, Daniël H J Theunissen, Danyel G J Jennen, Theo M C M de Kok, Jos C S Kleinjans
Valproic acid (VPA) is a very potent anti-cancer and neuro-protective drug probably by its HDAC inhibiting properties, which may cause steatosis in the liver. The present study investigates the effect of repetitive VPA treatment of primary human hepatocytes (PHH) on whole genome gene expression-, DNA methylation-, and miRNA changes, using microarrays and integrated data analyses. PHH were exposed to a non-cytotoxic dose of VPA for 5days daily which induced lipid accumulation. Part of the PHH was left untreated for 3days for studying the persistence of 'omics' changes...
November 14, 2017: Toxicology
https://www.readbyqxmd.com/read/29151691/parallel-mrna-proteomics-and-mirna-expression-analysis-in-cell-line-models-of-the-intestine
#3
Finbarr O'Sullivan, Joanne Keenan, Sinead Aherne, Fiona O'Neill, Colin Clarke, Michael Henry, Paula Meleady, Laura Breen, Niall Barron, Martin Clynes, Karina Horgan, Padraig Doolan, Richard Murphy
AIM: To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. METHODS: Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array...
November 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#4
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29138271/addressing-the-perfect-storm-biomarkers-in-obesity-and-pathophysiology-of-cardiometabolic-risk
#5
REVIEW
Krasimira Aleksandrova, Dariush Mozaffarian, Tobias Pischon
BACKGROUND: The worldwide rise of obesity has provoked intensified research to better understand its pathophysiology as a means for disease prevention. Several biomarkers that may reflect various pathophysiological pathways that link obesity and cardiometabolic diseases have been identified over the past decades. CONTENT: We summarize research evidence regarding the role of established and novel obesity-related biomarkers, focusing on recent epidemiological evidence for detrimental associations with cardiometabolic diseases including obesity-related cancer...
November 14, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/29137180/metabolomic-modularity-analysis-mma-to-quantify-human-liver-perfusion-dynamics
#6
Gautham Vivek Sridharan, Bote Bruinsma, Shyam Sundhar Bale, Anandh Swaminathan, Nima Saeidi, Martin L Yarmush, Korkut Uygun
Large-scale -omics data are now ubiquitously utilized to capture and interpret global responses to perturbations in biological systems, such as the impact of disease states on cells, tissues, and whole organs. Metabolomics data, in particular, are difficult to interpret for providing physiological insight because predefined biochemical pathways used for analysis are inherently biased and fail to capture more complex network interactions that span multiple canonical pathways. In this study, we introduce a nov-el approach coined Metabolomic Modularity Analysis (MMA) as a graph-based algorithm to systematically identify metabolic modules of reactions enriched with metabolites flagged to be statistically significant...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29136241/wikipathways-a-multifaceted-pathway-database-bridging-metabolomics-to-other-omics-research
#7
Denise N Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L Coort, Daniela Digles, Friederike Ehrhart, Pieter Giesbertz, Marianthi Kalafati, Marvin Martens, Ryan Miller, Kozo Nishida, Linda Rieswijk, Andra Waagmeester, Lars M T Eijssen, Chris T Evelo, Alexander R Pico, Egon L Willighagen
WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation...
November 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29134060/modelling-pyruvate-dehydrogenase-under-hypoxia-and-its-role-in-cancer-metabolism
#8
Filmon Eyassu, Claudio Angione
Metabolism is the only biological system that can be fully modelled at genome scale. As a result, metabolic models have been increasingly used to study the molecular mechanisms of various diseases. Hypoxia, a low-oxygen tension, is a well-known characteristic of many cancer cells. Pyruvate dehydrogenase (PDH) controls the flux of metabolites between glycolysis and the tricarboxylic acid cycle and is a key enzyme in metabolic reprogramming in cancer metabolism. Here, we develop and manually curate a constraint-based metabolic model to investigate the mechanism of pyruvate dehydrogenase under hypoxia...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29123532/food-legumes-and-rising-temperatures-effects-adaptive-functional-mechanisms-specific-to-reproductive-growth-stage-and-strategies-to-improve-heat-tolerance
#9
REVIEW
Kumari Sita, Akanksha Sehgal, Bindumadhava HanumanthaRao, Ramakrishnan M Nair, P V Vara Prasad, Shiv Kumar, Pooran M Gaur, Muhammad Farooq, Kadambot H M Siddique, Rajeev K Varshney, Harsh Nayyar
Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29123506/challenges-and-advances-for-genetic-engineering-of-non-model-bacteria-and-uses-in-consolidated-bioprocessing
#10
REVIEW
Qiang Yan, Stephen S Fong
Metabolic diversity in microorganisms can provide the basis for creating novel biochemical products. However, most metabolic engineering projects utilize a handful of established model organisms and thus, a challenge for harnessing the potential of novel microbial functions is the ability to either heterologously express novel genes or directly utilize non-model organisms. Genetic manipulation of non-model microorganisms is still challenging due to organism-specific nuances that hinder universal molecular genetic tools and translatable knowledge of intracellular biochemical pathways and regulatory mechanisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29121773/systems-biology-approaches-to-redox-metabolism-in-stress-and-disease-states
#11
Rui-Sheng Wang, William M Oldham, Bradley A Maron, Joseph Loscalzo
Significance All cellular metabolic processes are tied to the cellular redox environment. Therefore, maintaining redox homeostasis is critically important for normal cell function. Indeed, redox stress contributes to the pathobiology of many human diseases. The cellular redox response system is composed of numerous interconnected components including free radicals, redox couples, protein thiols, enzymes, metabolites, and transcription factors. Moreover, interactions between and among these factors are regulated in time and space...
November 9, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29114021/imaging-of-cellular-oxidoreductase-activity-suggests-mixotrophic-metabolisms-in-thiomargarita-spp
#12
Jake V Bailey, Beverly E Flood, Elizabeth Ricci, Nathalie Delherbe
The largest known bacteria, Thiomargarita spp., have yet to be isolated in pure culture, but their large size allows for individual cells to be monitored in time course experiments or to be individually sorted for omics-based investigations. Here we investigated the metabolism of individual cells of Thiomargarita spp. by using a novel application of a tetrazolium-based dye that measures oxidoreductase activity. When coupled with microscopy, staining of the cells with a tetrazolium-formazan dye allows metabolic responses in Thiomargarita spp...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29113454/modulators-of-redox-metabolism-in-head-and-neck-cancer
#13
Xiaofei Chen, Jade Mims, Xiumei Huang, Naveen Singh, Edward A Motea, Sarah M Planchon, Muhammad Beg, Allen W Tsang, Mercedes Porosnicu, Melissa L Kemp, David A Boothman, Cristina Furdui
SIGNIFICANCE: Head and Neck Squamous Cell Cancer (HNSCC) is a complex disease characterized by high genetic and metabolic heterogeneity. Radiation therapy (RT) alone or combined with systemic chemotherapy is widely used for treatment of HNSCC as definitive treatment or as adjuvant treatment after surgery. Antibodies against Epidermal Growth Factor Receptor (EGFR) are used in definitive or palliative treatment. Recent Advances. Emerging targeted therapies against other proteins of interest as well as programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1) immunotherapies are being explored in clinical trials...
November 7, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29113067/omics-approaches-for-identifying-physiological-adaptations-to-genome-instability-in-aging
#14
REVIEW
Diletta Edifizi, Björn Schumacher
DNA damage causally contributes to aging and age-related diseases. The declining functioning of tissues and organs during aging can lead to the increased risk of succumbing to aging-associated diseases. Congenital syndromes that are caused by heritable mutations in DNA repair pathways lead to cancer susceptibility and accelerated aging, thus underlining the importance of genome maintenance for withstanding aging. High-throughput mass-spectrometry-based approaches have recently contributed to identifying signalling response networks and gaining a more comprehensive understanding of the physiological adaptations occurring upon unrepaired DNA damage...
November 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29111762/metabolomics-and-lipidomics-profiling-of-a-combined-mitochondrial-plus-endoplasmic-reticulum-fraction-of-human-fibroblasts-a-robust-tool-for-clinical-studies
#15
Charlotte Veyrat-Durebex, Cinzia Bocca, Stéphanie Chupin, Judith Kouassi Nzoughet, Gilles Simard, Guy Lenaers, Pascal Reynier, Hélène Blasco
Mitochondria and endoplasmic reticulum (ER) are physically and functionally connected. This close interaction, via mitochondria-associated membranes, is increasingly explored and supports the importance of studying these two organelles as a whole. Metabolomics and lipidomics are powerful approaches for the exploration of metabolic pathways that may be useful to provide deeper information on these organelles' functions, dysfunctions, and interactions. We developed a quick and simple experimental procedure for the purification of a mitochondria-ER fraction from human fibroblasts...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29107462/each-meal-matters-in-the-exposome-biological-and-community-considerations-in-fast-food-socioeconomic-associations
#16
Susan L Prescott, Alan C Logan
Advances in omics and microbiome technology have transformed the ways in which the biological consequences of life in the 'ecological theatre' can be visualized. Exposome science examines the total accumulated environmental exposures (both detrimental and beneficial) as a means to understand the response of the 'total organism to the total environment' over time. The repetitive stimulation of compensatory physiological responses (immune, cardiovascular, neuroendocrine) in response to stress - including sources of stress highly relevant to socioeconomic disadvantage - may lead to metabolic dysregulation and cellular damage, ultimately influencing behavior and disease...
September 27, 2017: Economics and Human Biology
https://www.readbyqxmd.com/read/29106965/unravelling-the-effects-of-multiple-experimental-factors-in-metabolomics-analysis-of-human-neural-cells-with-hydrophilic-interaction-liquid-chromatography-hyphenated-to-high-resolution-mass-spectrometry
#17
Víctor González-Ruiz, Julian Pezzatti, Adrien Roux, Luc Stoppini, Julien Boccard, Serge Rudaz
This work introduces a strategy for decomposing variable contributions within the data obtained from structured metabolomic studies. This approach was applied in the context of an in vitro human neural model to investigate biochemical changes related to neuroinflammation. Neural cells were exposed to the neuroinflammatory toxicant trimethyltin at different doses and exposure times. In the frame of an untargeted approach, cell contents were analysed using HILIC hyphenated with HRMS. Detected features were annotated at level 1 by comparison against a library of standards, and the 126 identified metabolites were analysed using a recently proposed chemometric tool dedicated to multifactorial Omics datasets, namely, ANOVA multiblock OPLS (AMOPLS)...
October 25, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29106651/target-pathogen-a-structural-bioinformatic-approach-to-prioritize-drug-targets-in-pathogens
#18
Ezequiel J Sosa, Germán Burguener, Esteban Lanzarotti, Lucas Defelipe, Leandro Radusky, Agustín M Pardo, Marcelo Marti, Adrián G Turjanski, Darío Fernández Do Porto
Available genomic data for pathogens has created new opportunities for drug discovery and development to fight them, including new resistant and multiresistant strains. In particular structural data must be integrated with both, gene information and experimental results. In this sense, there is a lack of an online resource that allows genome wide-based data consolidation from diverse sources together with thorough bioinformatic analysis that allows easy filtering and scoring for fast target selection for drug discovery...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29106475/quantitative-serum-nuclear-magnetic-resonance-metabolomics-in-large-scale-epidemiology-a-primer-on-omic-technologies
#19
Peter Würtz, Antti J Kangas, Pasi Soininen, Debbie A Lawlor, George Davey Smith, Mika Ala-Korpela
Detailed metabolic profiling in large-scale epidemiologic studies has uncovered novel biomarkers for cardiometabolic diseases and clarified the molecular associations of established risk factors. A quantitative metabolomics platform based on nuclear magnetic resonance spectroscopy has found widespread use, already profiling over 400,000 blood samples. Over 200 metabolic measures are quantified per sample; in addition to many biomarkers routinely used in epidemiology, the method simultaneously provides fine-grained lipoprotein subclass profiling and quantification of circulating fatty acids, amino acids, gluconeogenesis-related metabolites, and many other molecules from multiple metabolic pathways...
November 1, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29104519/metabolite-profiling-of-yam-dioscorea-spp-accessions-for-use-in-crop-improvement-programmes
#20
Elliott J Price, Ranjana Bhattacharjee, Antonio Lopez-Montes, Paul D Fraser
Introduction: Ninety-seven percent of yam (Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs...
2017: Metabolomics: Official Journal of the Metabolomic Society
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