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Omics metabolism

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https://www.readbyqxmd.com/read/28215528/a-systematic-evaluation-of-methods-for-tailoring-genome-scale-metabolic-models
#1
Sjoerd Opdam, Anne Richelle, Benjamin Kellman, Shanzhong Li, Daniel C Zielinski, Nathan E Lewis
Genome-scale models of metabolism can illuminate the molecular basis of cell phenotypes. Since some enzymes are only active in specific cell types, several algorithms use omics data to construct cell-line- and tissue-specific metabolic models from genome-scale models. However, these methods are often not rigorously benchmarked, and it is unclear how algorithm and parameter selection (e.g., gene expression thresholds, metabolic constraints) affects model content and predictive accuracy. To investigate this, we built hundreds of models of four different cancer cell lines using six algorithms, four gene expression thresholds, and three sets of metabolic constraints...
February 14, 2017: Cell Systems
https://www.readbyqxmd.com/read/28201992/high-flavonoid-accompanied-with-high-starch-accumulation-triggered-by-nutrient-starvation-in-bioenergy-crop-duckweed-landoltia-punctata
#2
Xiang Tao, Yang Fang, Meng-Jun Huang, Yao Xiao, Yang Liu, Xin-Rong Ma, Hai Zhao
BACKGROUND: As the fastest growing plant, duckweed can thrive on anthropogenic wastewater. The purple-backed duckweed, Landoltia punctata, is rich in starch and flavonoids. However, the molecular biological basis of high flavonoid and low lignin content remains largely unknown, as does the best method to combine nutrients removed from sewage and the utilization value improvement of duckweed biomass. RESULTS: A combined omics study was performed to investigate the biosynthesis of flavonoid and the metabolic flux changes in L...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28187207/a-multi-objective-constraint-based-approach-for-modeling-genome-scale-microbial-ecosystems
#3
Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard
Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients...
2017: PloS One
https://www.readbyqxmd.com/read/28174585/the-understanding-of-the-plant-iron-deficiency-responses-in-strategy-i-plants-and-the-role-of-ethylene-in-this-process-by-omic-approaches
#4
REVIEW
Wenfeng Li, Ping Lan
Iron (Fe) is an essential plant micronutrient but is toxic in excess. Fe deficiency chlorosis is a major constraint for plant growth and causes severe losses of crop yields and quality. Under Fe deficiency conditions, plants have developed sophisticated mechanisms to keep cellular Fe homeostasis via various physiological, morphological, metabolic, and gene expression changes to facilitate the availability of Fe. Ethylene has been found to be involved in the Fe deficiency responses of plants through pharmacological studies or by the use of ethylene mutants...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28170342/linking-childhood-allergic-asthma-phenotypes-with-endotype-through-integrated-systems-biology-current-evidence-and-research-needs
#5
Hyunok Choi, Won-Min Song, Bin Zhang
Asthma and other complex diseases results from a complex web of interactions involving inflammation, immunity, cell cycle, apoptosis, and metabolic perturbations across multiple organ systems. The extent to which various degrees of the age at onset, symptom severity, and the natural progression of the disease reflect multiple disease subtypes, influenced by unique process of development remains unknown. One of the most critical challenges to our understanding stems from incomplete understanding of the mechanisms...
February 7, 2017: Reviews on Environmental Health
https://www.readbyqxmd.com/read/28165194/diversity-and-functions-of-the-sheep-faecal-microbiota-a-multi-omic-characterization
#6
Alessandro Tanca, Cristina Fraumene, Valeria Manghina, Antonio Palomba, Marcello Abbondio, Massimo Deligios, Daniela Pagnozzi, Maria Filippa Addis, Sergio Uzzau
Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi-omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and shotgun metaproteomics were applied to unravel taxonomy, genetic potential and actively expressed functions and pathways respectively...
February 6, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28162022/proteomic-analysis-of-red-blood-cells-and-the-potential-for-the-clinic-what-have-we-learned-so-far
#7
Angelo D'Alessandro, Lello Zolla
Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating "bags of hemoglobin". The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology...
February 4, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28152593/combining-deep-sequencing-proteomics-phosphoproteomics-and-functional-screens-to-discover-novel-regulators-of-sphingolipid-homeostasis
#8
Nicolas Lebesgue, Márton Megyeri, Alba Cristobal, Arjen Scholten, Silvia G Chuartzman, Yoav Voichek, Richard A Scheltema, Shabaz Mohammed, Anthony H Futerman, Maya Schuldiner, Albert J R Heck, Simone Lemeer
Sphingolipids (SLs) are essential components of cell membranes and are broad-range bioactive signaling molecules. SL levels must be tightly regulated as imbalances affect cellular function and contribute to pathologies ranging from neurodegenerative and metabolic disorders to cancer and aging. Deciphering how SL homeostasis is maintained and uncovering new regulators is required for understanding lipid biology and for identifying new targets for therapeutic interventions. Here we combine omics technologies to identify the changes of the transcriptome, proteome, and phosphoproteome in the yeast Saccharomyces cerevisiae upon SL depletion induced by myriocin...
February 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28148918/mixing-omics-combining-genetics-and-metabolomics-to-study-rheumatic-diseases
#9
REVIEW
Cristina Menni, Jonas Zierer, Ana M Valdes, Tim D Spector
Metabolomics is an exciting field in systems biology that provides a direct readout of the biochemical activities taking place within an individual at a particular point in time. Metabolite levels are influenced by many factors, including disease status, environment, medications, diet and, importantly, genetics. Thanks to their dynamic nature, metabolites are useful for diagnosis and prognosis, as well as for predicting and monitoring the efficacy of treatments. At the same time, the strong links between an individual's metabolic and genetic profiles enable the investigation of pathways that underlie changes in metabolite levels...
February 2, 2017: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/28140518/metabonomics-by-proton-nuclear-magnetic-resonance-in-human-pleural-effusions-a-route-to-discriminate-between-benign-and-malignant-pleural-effusions-and-to-target-small-molecules-as-potential-cancer-biomarkers
#10
Lucio Zennaro, Paola Vanzani, Lorenzo Nicolè, Rocco Cappellesso, Ambrogio Fassina
BACKGROUND: Cytopathology is a noninvasive and cost-effective method for detecting cancer cells in pleural effusions (PEs), although in many cases, the diagnostic performance is hindered by the paucity of significant cells or the lack of clear morphological criteria. This study presents the results of an omics approach to improving the diagnostic performance of PE cytology. METHODS: Metabolic profiling with proton nuclear magnetic resonance ((1) H-NMR) was performed for 92 PEs (44 malignant cases of 8 different cancers and 48 benign cases of 7 nonneoplastic conditions)...
January 31, 2017: Cancer
https://www.readbyqxmd.com/read/28139919/genome-resolved-meta-omics-ties-microbial-dynamics-to-process-performance-in-biotechnology-for-thiocyanate-degradation
#11
Rose S Kantor, Robert J Huddy, Ramsunder Iyer, Brian C Thomas, Christopher T Brown, Karthik Anantharaman, Susannah Tringe, Robert L Hettich, Susan T L Harrison, Jillian F Banfield
Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN(-)), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN(-) loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN(-). A second reactor was fed ammonium sulfate to mimic breakdown products of SCN(-)...
February 13, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28131859/systems-biology-of-robustness-and-flexibility-lactobacillus-buchneri-a-show-case
#12
REVIEW
Stefan Heinl, Reingard Grabherr
Lactobacillus buchneri is a lactic acid bacterium that naturally inhabits very different ecological niches and plays an ambivalent role in many food and feed fermentation processes, where it can act as useful starter or as spoilage organism. Due to its vicinity to important biotechnological processes like silage making, ethanol production, baking, fermenting vegetables or brewing, L. buchneri was subject of extensive research and is now a quite well studied microorganism. Recently, next generation 'OMICS'-methods were applied to investigate L...
January 25, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28126921/integrative-fourd-omics-approach-profiles-the-target-network-of-the-carbon-storage-regulatory-system
#13
Steven W Sowa, Grant Gelderman, Abigail N Leistra, Aishwarya Buvanendiran, Sarah Lipp, Areen Pitaktong, Christopher A Vakulskas, Tony Romeo, Michael Baldea, Lydia M Contreras
Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network...
January 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28125790/metabolism-centric-trans-omics
#14
Katsuyuki Yugi, Shinya Kuroda
Two recent studies in Cell and Science demonstrate the reconstruction of global mechanistic networks and identification of regulatory principles from multi-omics data.
January 25, 2017: Cell Systems
https://www.readbyqxmd.com/read/28121076/targeting-a-metabolic-pathway-to-fight-the-flu
#15
Yvonne Boergeling, Stephan Ludwig
Our antiviral arsenal to fight influenza viruses is limited and we need novel anti-flu drugs. Recently, cellular drug targets came into focus and omics analysis were instrumental to suggest candidate factors. In this issue of The FEBS Journal, Kainov and colleagues used transcriptome data to investigate virus-induced changes in tryptophan metabolism that may serve as immunomodulatory approach against viruses.
January 2017: FEBS Journal
https://www.readbyqxmd.com/read/28117091/metabolizing-data-in-the-cloud
#16
Benedikt Warth, Nadine Levin, Duane Rinehart, John Teijaro, H Paul Benton, Gary Siuzdak
Cloud-based bioinformatic platforms address the fundamental demands of creating a flexible scientific environment, facilitating data processing and general accessibility independent of a countries' affluence. These platforms have a multitude of advantages as demonstrated by omics technologies, helping to support both government and scientific mandates of a more open environment.
January 20, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28112229/multi-omics-analyses-reveal-metabolic-alterations-regulated-by-hepatitis-b-virus-core-protein-in-hepatocellular-carcinoma-cells
#17
Qi Xie, Fengxu Fan, Wei Wei, Yang Liu, Zhongwei Xu, Linhui Zhai, Yingzi Qi, Bingyu Ye, Yao Zhang, Sumit Basu, Zhihu Zhao, Junzhu Wu, Ping Xu
Chronic hepatitis B virus (HBV) infection is partly responsible for hepatitis, fatty liver disease and hepatocellular carcinoma (HCC). HBV core protein (HBc), encoded by the HBV genome, may play a significant role in HBV life cycle. However, the function of HBc in the occurrence and development of liver disease is still unclear. To investigate the underlying mechanisms, HBc-transfected HCC cells were characterized by multi-omics analyses. Combining proteomics and metabolomics analyses, our results showed that HBc promoted the expression of metabolic enzymes and the secretion of metabolites in HCC cells...
January 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28109438/proteomic-analysis-of-metabolic-responses-to-biofuels-and-chemicals-in-photosynthetic-cyanobacteria
#18
T Sun, L Chen, W Zhang
Recent progresses in various "omics" technologies have enabled quantitative measurements of biological molecules in a high-throughput manner. Among them, high-throughput proteomics is a rapidly advancing field that offers a new means to quantify metabolic changes at protein level, which has significantly facilitated our understanding of cellular process, such as protein synthesis, posttranslational modifications, and degradation in responding to environmental perturbations. Cyanobacteria are autotrophic prokaryotes that can perform oxygenic photosynthesis and have recently attracted significant attentions as one promising alternative to traditionally biomass-based "microbial cell factories" to produce green fuels and chemicals...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109168/integrated-omics-analysis-of-specialized-metabolism-in-medicinal-plants
#19
Amit Rai, Kazuki Saito, Mami Yamazaki
Medicinal plants are the rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their approach to explore biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. Recent advancements in the high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. Reduced cost to generate omics datasets, and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several plant origin bio-active metabolites...
January 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#20
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
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