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https://www.readbyqxmd.com/read/29339647/proceedings-of-the-11th-congress-of-the-international-society-of-nutrigenetics-and-nutrigenomics-isnn-2017
#1
William T Barrington, Anna C Salvador, Jaana A Hartiala, Raffaele De Caterina, Martin Kohlmeier, J Alfredo Martinez, Carin B Kreutzer, David Heber, Aldons J Lusis, Zhaoping Li, Hooman Allayee
The International Society of Nutrigenetics and Nutrigenomics (ISNN) held its 11th annual Congress in Los Angeles, California, between September 16 and 19, 2017. In addition to 2 keynote lectures, 4 plenary sessions included presentations by internationally renowned speakers on cutting-edge areas of research and new discoveries in genetics/genomics, the microbiome, and nutrition. Scientific topics included multi-omics approaches; diet and the microbiome; cancer, longevity, and metabolism; moving the field forward; and translational/educational aspects and the future of medicine...
January 17, 2018: Journal of Nutrigenetics and Nutrigenomics
https://www.readbyqxmd.com/read/29335637/expression-profiling-of-host-and-virus-during-a-coccolithophore-bloom-provides-insights-into-the-role-of-viral-infection-in-promoting-carbon-export
#2
Uri Sheyn, Shilo Rosenwasser, Yoav Lehahn, Noa Barak-Gavish, Ron Rotkopf, Kay D Bidle, Ilan Koren, Daniella Schatz, Assaf Vardi
The cosmopolitan coccolithophore Emiliania huxleyi is a unicellular eukaryotic alga that forms vast blooms in the oceans impacting large biogeochemical cycles. These blooms are often terminated due to infection by the large dsDNA virus, E. huxleyi virus (EhV). It was recently established that EhV-induced modulation of E. huxleyi metabolism is a key factor for optimal viral infection cycle. Despite the huge ecological importance of this host-virus interaction, the ability to assess its spatial and temporal dynamics and its possible impact on nutrient fluxes is limited by current approaches that focus on quantification of viral abundance and biodiversity...
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29335535/a-multi-omics-study-of-the-grapevine-downy-mildew-plasmopara-viticola-pathosystem-unveils-a-complex-protein-coding-and-noncoding-based-arms-race-during-infection
#3
Matteo Brilli, Elisa Asquini, Mirko Moser, Pier Luigi Bianchedi, Michele Perazzolli, Azeddine Si-Ammour
Fungicides are applied intensively to prevent downy mildew infections of grapevines (Vitis vinifera) with high impact on the environment. In order to develop alternative strategies we sequenced the genome of the oomycete pathogen Plasmopara viticola causing this disease. We show that it derives from a Phytophthora-like ancestor that switched to obligate biotrophy by losing genes involved in nitrogen metabolism and γ-Aminobutyric acid catabolism. By combining multiple omics approaches we characterized the pathosystem and identified a RxLR effector that trigger an immune response in the wild species V...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29328914/rewiring-of-the-fruit-metabolome-in-tomato-breeding
#4
Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Mao Qin, Meng Peng, Chenkun Yang, Xue Cao, Xu Han, Xiaoxuan Wang, Esther van der Knaap, Zhonghua Zhang, Xia Cui, Harry Klee, Alisdair R Fernie, Jie Luo, Sanwen Huang
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29325019/deep-molecular-phenotypes-link-complex-disorders-and-physiological-insult-to-cpg-methylation
#5
Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Maija Pezer, Gordan Lauc, Johannes Graumann, Joel A Malek, Karsten Suhre
Epigenetic regulation of cellular function provides a mechanism for rapid organismal adaptation to changes in health, lifestyle, and environment. Associations of cytosine-guanine di-nucleotide (CpG) methylation with clinical endpoints that overlap with metabolic phenotypes suggest a regulatory role for these CpG sites in the body's response to disease or environmental stress. We previously identified 20 CpG sites in an epigenome-wide association study (EWAS) with metabolomics that were also associated in recent EWASs with diabetes-, obesity-, and smoking-related endpoints...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29317475/omics-assisted-n-terminal-proteoform-and-protein-expression-profiling-upon-methionine-aminopeptidase-1-metap1-deletion
#6
Veronique Jonckheere, Daria Fijałkowska, Petra Van Damme
Excision of the N-terminal initiator methionine (iMet) residue from nascent peptide chains is an essential and omnipresent protein modification carried out by methionine aminopeptidases (MetAPs) that accounts for a major source of N-terminal proteoform diversity. While MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of human MetAP1 deletion and general MetAP inhibition...
January 9, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29317273/mitochondrial-network-responses-in-oxidative-physiology-and-disease
#7
REVIEW
Young-Mi Go, Jolyn Fernandes, Xin Hu, Karan Uppal, Dean P Jones
Mitochondrial activities are linked directly or indirectly to all cellular functions in aerobic eukaryotes. Omics methods enable new approaches to study functional organization of mitochondria and their adaptive and maladaptive network responses to bioenergetic fuels, physiologic demands, environmental challenges and aging. In this review, we consider mitochondria collectively within a multicellular organism as a macroscale "mitochondriome", functioning to organize bioenergetics and metabolism as an organism utilizes environmental resources and protects against environmental threats...
January 6, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29312565/dissect-new-mechanistic-insights-for-geniposide-efficacy-on-the-hepatoprotection-using-multiomics-approach
#8
Shi Qiu, Aihua Zhang, Tianlei Zhang, Hui Sun, Yu Guan, Guangli Yan, Xijun Wang
A multi-omics approach could yield in-depth mechanistic insights. Here, we performed an integrated analysis of miRNAome, proteome and metabolome, aimed to investigate the underlying mechanism of active product geniposide in ethanol-induced apoptosis. We found that integrative meta-analysis identified 28 miRNAs, 20 proteins and 7 metabolites significantly differentially expressed, respectively. Further analysis identified geniposide extensively regulated multiple metabolism pathways and the most important related pathway was citrate cycle (TCA cycle)...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29306676/improving-the-success-and-impact-of-the-metabolic-engineering-design-build-test-learn-cycle-by-addressing-proteins-of-unknown-function
#9
REVIEW
Laura R Jarboe
Rational, predictive metabolic engineering of organisms requires an ability to associate biological activity to the corresponding gene(s). Despite extensive advances in the 20 years since the Escherichia coli genome was published, there are still gaps in our knowledge of protein function. The substantial amount of data that has been published, such as: omics-level characterization in a myriad of conditions; genome-scale libraries; and evolution and genome sequencing, provide means of identifying and prioritizing proteins for characterization...
January 4, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29304189/metabolomics-technology-and-bioinformatics-for-precision-medicine
#10
Rajeev K Azad, Vladimir Shulaev
Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment...
January 3, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29289672/a-multi-omics-analysis-reveals-metabolic-reprogramming-in-thp-1-cells-upon-treatment-with-the-contact-allergen-dncb
#11
Franz Mussotter, Sarah Potratz, Jan Budczies, Andreas Luch, Andrea Haase
Dendritic cell (DC) activation by contact allergens is one of the key steps in the development of allergic contact dermatitis (ACD). Recent evidence suggests that metabolic reprogramming is a prerequisite for the activation of DCs, macrophages and monocytes. Therefore, we used an integrated approach by combining proteomics and metabolomics to investigate the metabolism of human THP-1 cells in response to the strong contact allergen, 2,4-dinitrochlorobenzene (DNCB). Cells were treated with 5, 10 and 20μM DNCB for 4, 8, and 24h, respectively...
December 28, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29285398/combination-of-itraq-proteomics-and-rna-seq-transcriptomics-reveals-multiple-levels-of-regulation-in-phytoplasma-infected-ziziphus-jujuba-mill
#12
Xia Ye, Huiyu Wang, Peng Chen, Bing Fu, Mengyang Zhang, Jidong Li, Xianbo Zheng, Bin Tan, Jiancan Feng
Jujube witches' broom (JWB) is caused by infection with a phytoplasma. A multi-omics approach was taken during graft infection of jujube by JWB-infected scion through the analysis of the plant transcriptome, proteome and phytohormone levels. A high number of differentially expressed genes (DEGs) were identified 37 weeks after grafting (WAG), followed by observation of typical symptoms of JWB at 48 WAG. At 37 WAG, the majority of the upregulated DEGs and differentially expressed proteins (DEPs) were related to flavonoid biosynthesis, phenylalanine metabolism and phenylpropanoid biosynthesis...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29285300/renal-oncocytoma-characterized-by-the-defective-complex-i-of-the-respiratory-chain-boosts-the-synthesis-of-the-ros-scavenger-glutathione
#13
Gerrit Kürschner, Qingzhou Zhang, Rosanna Clima, Yi Xiao, Jonas Felix Busch, Ergin Kilic, Klaus Jung, Nikolaus Berndt, Sascha Bulik, Hermann-Georg Holzhütter, Giuseppe Gasparre, Marcella Attimonelli, Mohan Babu, David Meierhofer
Renal oncocytomas are rare benign tumors of the kidney and characterized by a deficient complex I (CI) enzyme activity of the oxidative phosphorylation (OXPHOS) system caused by mitochondrial DNA (mtDNA) mutations. Yet, little is known about the underlying molecular mechanisms and alterations of metabolic pathways in this tumor. We compared renal oncocytomas with adjacent matched normal kidney tissues on a global scale by multi-omics approaches, including whole exome sequencing (WES), proteomics, metabolomics, and metabolic pathway simulation...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29258228/multi-omic-biogeography-of-the-gastrointestinal-microbiota-of-a-pre-weaned-lamb
#14
Antonio Palomba, Alessandro Tanca, Cristina Fraumene, Marcello Abbondio, Francesco Fancello, Alberto Stanislao Atzori, Sergio Uzzau
The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composition and metabolic functions, although low amounts of microbial proteins could be identified in the small intestinal and mucosal samples...
December 18, 2017: Proteomes
https://www.readbyqxmd.com/read/29245896/metabolomic-mapping-of-cancer-stem-cells-for-reducing-and-exploiting-tumor-heterogeneity
#15
Elisabet Cuyàs, Sara Verdura, Salvador Fernández-Arroyo, Joaquim Bosch-Barrera, Begoña Martin-Castillo, Jorge Joven, Javier A Menendez
Personalized cancer medicine based on the analysis of tumors en masse is limited by tumor heterogeneity, which has become a major obstacle to effective cancer treatment. Cancer stem cells (CSC) are emerging as key drivers of inter- and intratumoral heterogeneity. CSC have unique metabolic dependencies that are required not only for specific bioenergetic/biosynthetic demands but also for sustaining their operational epigenetic traits, i.e. self-renewal, tumor-initiation, and plasticity. Given that the metabolome is the final downstream product of all the -omic layers and, therefore, most representative of the biological phenotype, we here propose that a novel approach to better understand the complexity of tumor heterogeneity is by mapping and cataloging small numbers of CSC metabolomic phenotypes...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29241556/hepatic-dysfunction-caused-by-consumption-of-a-high-fat-diet
#16
Anthony R Soltis, Norman J Kennedy, Xiaofeng Xin, Feng Zhou, Scott B Ficarro, Yoon Sing Yap, Bryan J Matthews, Douglas A Lauffenburger, Forest M White, Jarrod A Marto, Roger J Davis, Ernest Fraenkel
Obesity is a major human health crisis that promotes insulin resistance and, ultimately, type 2 diabetes. The molecular mechanisms that mediate this response occur across many highly complex biological regulatory levels that are incompletely understood. Here, we present a comprehensive molecular systems biology study of hepatic responses to high-fat feeding in mice. We interrogated diet-induced epigenomic, transcriptomic, proteomic, and metabolomic alterations using high-throughput omic methods and used a network modeling approach to integrate these diverse molecular signals...
December 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/29237567/integrated-metabolomics-and-proteomics-analysis-of-hippocampus-in-a-rat-model-of-depression
#17
Yuqing Zhang, Shuai Yuan, Juncai Pu, Lining Yang, Xinyu Zhou, Lanxiang Liu, Xiaofeng Jiang, Hanping Zhang, Teng Teng, Lu Tian, Peng Xie
Major depressive disorder (MDD) is a prevalent and serious mental disorder with high rates of suicide and disability. However, the underlying pathogenesis of MDD is complicated and remains largely unclear. An integrated analysis of multiple types of omics data may improve comprehensive understanding of the entire molecular mechanism of MDD. In this study, we applied an integrated analysis of gas chromatography/mass spectrometry (GC-MS)-based metabolomics and isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics to investigate changes in the hippocampus in the chronic unpredictable mild stress (CUMS) rat model of depression...
December 10, 2017: Neuroscience
https://www.readbyqxmd.com/read/29233025/ralstonia-eutropha-h16-in-progress-applications-beside-phas-and-establishment-as-production-platform-by-advanced-genetic-tools
#18
Matthias Raberg, Elena Volodina, Kaichien Lin, Alexander Steinbüchel
Ralstonia eutropha strain H16 is a Gram-negative non-pathogenic betaproteobacterium ubiquitously found in soils and has been the subject of intensive research for more than 50 years. Due to its remarkable metabolically versatility, it utilizes a broad range of renewable heterotrophic resources. The substrate utilization range can be further extended by metabolic engineering as genetic tools are available. It has become the best studied "Knallgas" bacterium capable of chemolithoautotrophic growth with hydrogen as the electron donor and carbon dioxide as the carbon source...
December 12, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29227475/an-alox12-12-hete-gpr31-signaling-axis-is-a-key-mediator-of-hepatic-ischemia-reperfusion-injury
#19
Xiao-Jing Zhang, Xu Cheng, Zhen-Zhen Yan, Jing Fang, Xiaozhan Wang, Weijun Wang, Zhen-Yu Liu, Li-Jun Shen, Peng Zhang, Pi-Xiao Wang, Rufang Liao, Yan-Xiao Ji, Jun-Yong Wang, Song Tian, Xue-Yong Zhu, Yan Zhang, Rui-Feng Tian, Lin Wang, Xin-Liang Ma, Zan Huang, Zhi-Gang She, Hongliang Li
Hepatic ischemia-reperfusion (IR) injury is a common clinical issue lacking effective therapy and validated pharmacological targets. Here, using integrative 'omics' analysis, we identified an arachidonate 12-lipoxygenase (ALOX12)-12-hydroxyeicosatetraenoic acid (12-HETE)-G-protein-coupled receptor 31 (GPR31) signaling axis as a key determinant of the hepatic IR process. We found that ALOX12 was markedly upregulated in hepatocytes during ischemia to promote 12-HETE accumulation and that 12-HETE then directly binds to GPR31, triggering an inflammatory response that exacerbates liver damage...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29222764/optimization-of-multi-omic-genome-scale-models-methodologies-hands-on-tutorial-and-perspectives
#20
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models...
2018: Methods in Molecular Biology
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