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Omics metabolism

Fangzhou Shen, Jian Li, Ying Zhu, Zhuo Wang
Cancer cells have different metabolism in contrast to normal cells. The advancement in omics measurement technology enables the genome-wide characterization of altered cellular processes in cancers, but the metabolic flux landscape of cancer is still far from understood. In this study, we compared the well-reconstructed tissue-specific models of five cancers, including breast, liver, lung, renal, and urothelial cancer, and their corresponding normal cells. There are similar patterns in majority of significantly regulated pathways and enriched pathways in correlated reaction sets...
August 29, 2016: Journal of Bioinformatics and Computational Biology
Ajit Dash, Robert A Figler, Arun J Sanyal, B R Wamhoff
Drug induced steatohepatitis (DISH), a form of drug induced liver injury (DILI) is characterized by intracellular accumulation of lipids in hepatocytes and subsequent inflammatory events, in some ways similar to the pathology seen with other metabolic, viral and genetic causes of non alcoholic fatty liver disease and steatohepatitis (NAFLD and NASH). Areas covered: This paper provides a comprehensive review of the main underlying mechanisms by which various drugs cause DISH, and outlines existing preclinical tools to predict it and study underlying pathways involved...
October 19, 2016: Expert Opinion on Drug Metabolism & Toxicology
Stefano Papazian, Eliezer Khaling, Christelle Bonnet, Steve Lassueur, Philippe Reymond, Thomas Moritz, James Blande, Benedicte Riber Albrectsen
Plants have evolved adaptive mechanisms that allow them to tolerate a continuous range of abiotic and biotic stressors. Tropospheric ozone (O3), a global anthropogenic pollutant, directly affects living organisms and ecosystems, including plant-herbivore interactions. In this study, we investigate the stress responses of wild black mustard (Brassica nigra) exposed consecutively to O3 and the specialist herbivore Pieris brassicae. Transcriptomics and metabolomics data were evaluated using multivariate, correlation, and network analyses for the O3 and herbivory responses...
October 6, 2016: Plant Physiology
Xuelin Zhang, Yang Wang, Pingsheng Liu
Non-alcoholic fatty liver disease (NAFLD) is an epidemic metabolic condition driven by an underlying lipid homeostasis disorder. The lipid droplet (LD), the main organelle involved in neutral lipid storage and hydrolysis, is a potential target for NAFLD therapeutic treatment. In this review, we summarize recent progress elucidating the connections between LD-associated proteins and NAFLD found by genome-wide association studies (GWAS), genomic and proteomic studies. Finally, we discuss a possible mechanism by which the protein 17β-hydroxysteroid dehydrogenase 13 (17β-HSD13) may promote the development of NAFLD...
October 18, 2016: Protein & Cell
Radka Saldova
Many pathogens exist in metabolically inactive, non-culturable, cell-wall-deficient (CWD) forms that allow them to survive in conditions not conducive for growth. These forms were found in both cancer and chronic inflammatory autoimmune diseases. This review presents several novel concepts about how chronic inflammatory response and cancer develops from CWD infection, involvement and role of the immune system and other 'omics' systems and how to better diagnose, treat and even cure these conditions. This concept shows that CWD forms of intracellular microbes could also be evolutionary advantageous spreading through the host without using the classical replication route...
September 2016: Discovery Medicine
Jeong Wook Lee, Jongho Yi, Tae Yong Kim, Sol Choi, Jung Ho Ahn, Hyohak Song, Moon-Hee Lee, Sang Yup Lee
Succinic acid (SA) is a four carbon dicarboxylic acid of great industrial interest that can be produced by microbial fermentation. Here we report development of a high-yield homo-SA producing Mannheimia succiniciproducens strain by metabolic engineering. The PALFK strain (ldhA(-), pta(-), ackA(-), fruA(-)) was developed based on optimization of carbon flux towards SA production while minimizing byproducts formation through the integrated application of in silico genome-scale metabolic flux analysis, omics analyses, and reconstruction of central carbon metabolism...
October 13, 2016: Metabolic Engineering
P Zhang, L Tao, X Zeng, C Qin, S Y Chen, F Zhu, S Y Yang, Z R Li, W P Chen, Y Z Chen
The studies of biological, disease and pharmacological networks are facilitated by the systems-level investigations using computational tools. In particular, the network descriptors developed in other disciplines have found increasing applications in the study of the protein, gene regulatory, metabolic, disease, and drug-targeted networks. Facilities are provided by the public web-servers for computing network descriptors, but many descriptors are not covered including those used or useful for biological studies...
October 11, 2016: Journal of Molecular Biology
Meng Yang, Jinshao Ye, Huaming Qin, Yan Long, Yi Li
Perfluorooctanoic acid (PFOA) has received an increasing attention in the agricultural and food industries due to its risk to human health. To facilitate the development of novel biomarkers of Escherichia coli against PFOA through multi-omics technologies, and to reveal the resistance mechanism of E. coli against PFOA at protein levels, the interactions among pollutant stress, protein expression and cell metabolism was investigated by using iTRAQ-based quantitative proteomic analysis. The results revealed that the 63 up-regulated proteins mainly involved in tricarboxylic acid cycle, glyoxylate and dicarboxylate metabolism and fatty acid biosynthesis, whereas, the 69 down-regulated proteins related to oxidative phosphorylation, pyruvate metabolism and the cell cycle-caulobacter pathway, were also associated with the increase of membrane permeability, excessive expenditure of ATP, disruption of fatty acid biosynthesis under PFOA stress...
October 11, 2016: Environmental Pollution
Dong Ik Park, Carine Dournes, Inge Sillaber, Manfred Uhr, John M Asara, Nils C Gassen, Theo Rein, Marcus Ising, Christian Webhofer, Michaela D Filiou, Marianne B Müller, Christoph W Turck
Selective Serotonin Reuptake Inhibitors (SSRIs) are commonly used drugs for the treatment of psychiatric diseases including major depressive disorder (MDD). For unknown reasons a substantial number of patients do not show any improvement during or after SSRI treatment. We treated DBA/2J mice for 28 days with paroxetine and assessed their behavioral response with the forced swim test (FST). Paroxetine-treated long-time floating (PLF) and paroxetine-treated short-time floating (PSF) groups were stratified as proxies for drug non-responder and responder mice, respectively...
October 12, 2016: Scientific Reports
Anca Macovei, Andrea Pagano, Paola Leonetti, Daniela Carbonera, Alma Balestrazzi, Susana S Araújo
The pre-germinative metabolism is among the most fascinating aspects of seed biology. The early seed germination phase, or pre-germination, is characterized by rapid water uptake (imbibition), which directs a series of dynamic biochemical events. Among those are enzyme activation, DNA damage and repair, and use of reserve storage compounds, such as lipids, carbohydrates and proteins. Industrial seedling production and intensive agricultural production systems require seed stocks with high rate of synchronized germination and low dormancy...
October 11, 2016: Plant Cell Reports
Bruno S Dos Santos, Luís C N da Silva, Túlio D da Silva, João F S Rodrigues, Marcos A G Grisotto, Maria T Dos Santos Correia, Thiago H Napoleão, Márcia V da Silva, Patrícia M G Paiva
In the face of increasing bacterial resistance to antibiotics currently in use, the search for new antimicrobial agents has received a boost in recent years, with natural products playing an important role in this field. In fact, several methods have been proposed to investigate the antibacterial activities of natural products. However, given that the ultimate aim is future therapeutic use as novel drugs, it is extremely necessary to elucidate their modes of action, stating the molecular effects in detail, and identifying their targets in the bacterial cell...
2016: Frontiers in Microbiology
Jahangir Imam, Puneet K Singh, Pratyoosh Shukla
Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement...
2016: Frontiers in Microbiology
Anna Heintz-Buschart, Patrick May, Cédric C Laczny, Laura A Lebrun, Camille Bellora, Abhimanyu Krishna, Linda Wampach, Jochen G Schneider, Angela Hogan, Carine de Beaufort, Paul Wilmes
The gastrointestinal microbiome is a complex ecosystem with functions that shape human health. Studying the relationship between taxonomic alterations and functional repercussions linked to disease remains challenging. Here, we present an integrative approach to resolve the taxonomic and functional attributes of gastrointestinal microbiota at the metagenomic, metatranscriptomic and metaproteomic levels. We apply our methods to samples from four families with multiple cases of type 1 diabetes mellitus (T1DM)...
October 10, 2016: Nature Microbiology
Lu Yan, Chenxue Gong, Xiaofeng Zhang, Quan Zhang, Meirong Zhao, Cui Wang
The escalating demand for fipronil by the increasing insects' resistance to synthetic pyrethroids placed a burden on aquatic vertebrates. Although awareness regarding the toxicity of fipronil to fish is arising, the integral alteration caused by fipronil remains unexplored. Here, we investigated on the development toxicity of fipronil and the metabolic physiology perturbation at 120h post fertilization through GC-MS metabolomics on zebrafish embryo. We observed that fipronil dose-dependently induced malformations including uninflated swim bladder and bent spine...
October 5, 2016: Environmental Toxicology and Pharmacology
Lorenzo Vergani, Francesca Mapelli, Elisabetta Zanardini, Elisa Terzaghi, Antonio Di Guardo, Cristiana Morosini, Giuseppe Raspa, Sara Borin
Polychlorinated biphenyls (PCBs) are toxic chemicals, recalcitrant to degradation, bioaccumulative and persistent in the environment, causing adverse effects on ecosystems and human health. For this reason, the remediation of PCB-contaminated soils is a primary issue to be addressed. Phytoremediation represents a promising tool for in situ soil remediation, since the available physico-chemical technologies have strong environmental and economic impacts. Plants can extract and metabolize several xenobiotics present in the soil, but their ability to uptake and mineralize PCBs is limited due to the recalcitrance and low bioavailability of these molecules that in turn impedes an efficient remediation of PCB-contaminated soils...
October 5, 2016: Science of the Total Environment
Laura Mourino-Alvarez, Montserrat Baldan-Martin, Laura Gonzalez-Calero, Carlos Martinez-Laborde, Tamara Sastre-Oliva, Rafael Moreno-Luna, Luis F Lopez-Almodovar, Pedro L Sanchez, Francisco Fernandez-Aviles, Fernando Vivanco, Luis R Padial, Finn Akerstrom, Gloria Alvarez-Llamas, Fernando de la Cuesta, María G Barderas
BACKGROUND: The most common valve diseases are calcific aortic stenosis (AS) and aortic regurgitation (AR). The former is characterized by thickening of valve leaflets followed by progressive calcification, which produces progressive aortic valve (AV) narrowing, increased pressure afterload on the left ventricle (LV) and subsequent LV hypertrophy. On the other hand, AR is due to malcoaptation of the valve leaflets with resultant diastolic reflux of blood from aorta back to the LV producing volume and pressure overload and progressive LV dilatation...
September 26, 2016: International Journal of Cardiology
Xinrong Pan, Huanhuan Liu, Jiao Liu, Cheng Wang, Jianping Wen
In order to relieve the toxicity of furfural on Rhizopus oryzae fermentation, the molecular mechanism of R. oryzae responding to furfural stress for fumaric acid-production was investigated by omics-based approaches. In metabolomics analysis, 29 metabolites including amino acid, sugars, polyols and fatty acids showed significant changes for maintaining the basic cell metabolism at the cost of lowering fumaric acid production. To further uncover the survival mechanism, lipidomics was carried out, revealing that phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and polyunsaturated acyl chains might be closely correlated with R...
September 30, 2016: Bioresource Technology
Robert Häsler, Raheleh Sheibani-Tezerji, Anupam Sinha, Matthias Barann, Ateequr Rehman, Daniela Esser, Konrad Aden, Carolin Knecht, Berenice Brandt, Susanna Nikolaus, Sascha Schäuble, Christoph Kaleta, Andre Franke, Christoph Fretter, Werner Müller, Marc-Thorsten Hütt, Michael Krawczak, Stefan Schreiber, Philip Rosenstiel
OBJECTIVE: An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD...
September 30, 2016: Gut
Yan Qiao, Jinjin Zhang, Jinwen Zhang, Zhiwei Wang, An Ran, Haixia Guo, Di Wang, Junlian Zhang
Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus...
September 27, 2016: Molecular Genetics and Genomics: MGG
Jaeyun Sung, Vanessa Hale, Annette C Merkel, Pan-Jun Kim, Nicholas Chia
The recent advances in high-throughput omics technologies have enabled researchers to explore the intricacies of the human microbiome. On the clinical front, the gut microbial community has been the focus of many biomarker-discovery studies. While the recent deluge of high-throughput data in microbiome research has been vastly informative and groundbreaking, we have yet to capture the full potential of omics-based approaches. Realizing the promise of multi-omics data will require integration of disparate omics data, as well as a biologically relevant, mechanistic framework - or metabolic model - on which to overlay these data...
September 2016: Applied & Translational Genomics
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