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1.
Nadia Lamari Vanessa Zhendre Maria Urrutia Stéphane Bernillon Mickaël Maucourt Catherine Deborde Duyen Prodhomme Daniel Jacob Patricia Ballias Dominique Rolin Hélène Sellier Dominique Rabier Yves Gibon Catherine Giauffret Annick Moing 《Metabolomics : Official journal of the Metabolomic Society》2018,14(10):132
Introduction
In Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context.Objectives
Using an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass.Methods
Thirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping.Results
NMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance.Conclusion
After validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.2.
Renato de Souza Pinto Lemgruber Kaspar Valgepea Mark P. Hodson Ryan Tappel Sean D. Simpson Michael Köpke Lars K. Nielsen Esteban Marcellin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):35
Introduction
Quantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.Objective
To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.Methods
Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC–MS/MS was used for quantification.Results
Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.Conclusion
Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.3.
Leonie Venter Du Toit Loots Lodewyk Japie Mienie Peet J. Jansen van Rensburg Shayne Mason Andre Vosloo Jeremie Zander Lindeque 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):49
Introduction
Oxygen is essential for metabolic processes and in the absence thereof alternative metabolic pathways are required for energy production, as seen in marine invertebrates like abalone. Even though hypoxia has been responsible for significant losses to the aquaculture industry, the overall metabolic adaptations of abalone in response to environmental hypoxia are as yet, not fully elucidated.Objective
To use a multiplatform metabolomics approach to characterize the metabolic changes associated with energy production in abalone (Haliotis midae) when exposed to environmental hypoxia.Methods
Metabolomics analysis of abalone adductor and foot muscle, left and right gill, hemolymph, and epipodial tissue samples were conducted using a multiplatform approach, which included untargeted NMR spectroscopy, untargeted and targeted LC–MS spectrometry, and untargeted and semi-targeted GC-MS spectrometric analyses.Results
Increased levels of anaerobic end-products specific to marine animals were found which include alanopine, strombine, tauropine and octopine. These were accompanied by elevated lactate, succinate and arginine, of which the latter is a product of phosphoarginine breakdown in abalone. Primarily amino acid metabolism was affected, with carbohydrate and lipid metabolism assisting with anaerobic energy production to a lesser extent. Different tissues showed varied metabolic responses to hypoxia, with the largest metabolic changes in the adductor muscle.Conclusions
From this investigation, it becomes evident that abalone have well-developed (yet understudied) metabolic mechanisms for surviving hypoxic periods. Furthermore, metabolomics serves as a powerful tool for investigating the altered metabolic processes in abalone.4.
Cyril Jousse Céline Dalle Isabelle Canet Marie Lagrée Mounir Traïkia Bernard Lyan Cédric Mendes Martine Sancelme Pierre Amato Anne-Marie Delort 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):11
Introduction
Active microorganisms have been recently discovered in clouds, thus demonstrating the capacity of microorganisms to exist in harsh environments, including exposure to UV and oxidants, osmotic and cold shocks, etc. It is important to understand how microorganisms respond to and survive such stresses at the metabolic level.Objectives
The objective of this work is to assess metabolome modulation in a strain of Pseudomonas syringae isolated from cloud water and facing temperature downshift from 17 to 5 °C by identifying key molecules and pathways of the response/adaptation to cold shock.Methods
Bacterial extracts from suspensions of cells grown at 17 °C and further incubated in microcosms at 5 and 17 °C to mimic cloud conditions were analysed by combining LC-MS and NMR; the results were evaluated in comparison to similar suspensions kept at constant temperature. The differences in the metabolome profiles were deciphered using multivariate statistics (PLS-DA).Results
Key cold shock biomarkers were observed, including cryoprotectants (trehalose, glucose, glycerol, carnitine, glutamate), antioxidants (glutathione and carnitine) and their precursors, alkaloids (bellendine and slaframine) and metabolites involved in energy metabolism (ATP, carbohydrates). Furthermore, new short peptides (nine dipeptides and a tetrapeptide) were found that have no known function.Conclusions
This study shows that in response to cold temperatures, Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures.5.
Background
Clinical statement alone is not enough to predict the progression of disease. Instead, the gene expression profiles have been widely used to forecast clinical outcomes. Many genes related to survival have been identified, and recently miRNA expression signatures predicting patient survival have been also investigated for several cancers. However, miRNAs and their target genes associated with clinical outcomes have remained largely unexplored.Methods
Here, we demonstrate a survival analysis based on the regulatory relationships of miRNAs and their target genes. The patient survivals for the two major cancers, ovarian cancer and glioblastoma multiforme (GBM), are investigated through the integrated analysis of miRNA-mRNA interaction pairs.Results
We found that there is a larger survival difference between two patient groups with an inversely correlated expression profile of miRNA and mRNA. It supports the idea that signatures of miRNAs and their targets related to cancer progression can be detected via this approach.Conclusions
This integrated analysis can help to discover coordinated expression signatures of miRNAs and their target mRNAs that can be employed for therapeutics in human cancers.6.
Karimeh Haghani Pouyan Asadi Gholamreza Taheripak Ali Noori-Zadeh Shahram Darabi Salar Bakhtiyari 《生物学前沿》2018,13(6):406-417
Background
Diabetes mellitus (DM) is one of the most prevalent chronic diseases, and its prevalence continues to increase globally. The impact of mitochondrial dysfunction and lipid metabolism on diabetes mellitus and insulin resistance (IR) has been implicated in several previous reports; however, the results of studies are confusing despite four decades of study.Methods/Results
This review has evaluated updated understanding of the role of mitochondrial dysfunction and lipid metabolism on type 2 diabetes, and found that mitochondrial dysfunction and lipid metabolism disorder induce the dysregulation of liver and pancreatic beta cells, insulin resistance, and type 2 diabetes.Conclusion
Mitochondrial dysfunction and lipid metabolism induce metabolic dysregulation and finally increasing the possibility of diabetes.7.
Lia Bally Cédric Bovet Christos T. Nakas Thomas Zueger Jean-Christophe Prost Jean-Marc Nuoffer Alexander B. Leichtle Georg Martin Fiedler Christoph Stettler 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):78
Introduction
Exercise-associated metabolism in type 1 diabetes (T1D) remains under-studied due to the complex interplay between exogenous insulin, counter-regulatory hormones and insulin-sensitivity.Objective
To identify the metabolic differences induced by two exercise modalities in T1D using ultra high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) based metabolomics.Methods
Twelve T1D adults performed intermittent high-intensity (IHE) and continuous-moderate-intensity (CONT) exercise. Serum samples were analysed by UHPLC–HRMS.Results
Metabolic profiling of IHE and CONT highlighted exercise-induced changes in purine and acylcarnitine metabolism.Conclusion
IHE may increase beta-oxidation through higher ATP-turnover. UHPLC–HRMS based metabolomics as a data-driven approach without an a priori hypothesis may help uncover distinctive metabolic effects during exercise in T1D.Clinical trial registration number is www.clinicaltrials.gov: NCT02068638.8.
Objective
To reveal the shifts of microbial communities along ammonium gradients, and the relationship between microbial community composition and the anaerobic digestion performance using a high throughput sequencing technique.Results
Methane production declined with increasing ammonium concentration, and was inhibited above 4 g l?1. The volatile fatty acids, especially acetate, accumulated with elevated ammonium. Prokaryotic populations showed different responses to the ammonium concentration: Clostridium, Tepidimicrobium, Sporanaerobacter, Peptostreptococcus, Sarcina and Peptoniphilus showed good tolerance to ammonium ions. However, Syntrophomonas with poor tolerance to ammonium may be inhibited during anaerobic digestion. During methanogenesis, Methanosarcina was the dominant methanogen.Conclusion
Excessive ammonium inhibited methane production probably by decoupling the linkage between acidification process and methanogenesis, and finally resulted in different performance in anaerobic digestion.9.
Background
The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.Results
The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid.Conclusion
The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.10.
Dimitrios Botsios Emmanouil Zacharakis Ioannis Lambrou Kostas Tsalis Emmanouil Christoforidis Stavros Kalfadis Evangelos Zacharakis Dimitrios Betsis Ioannis Dadoukis 《International Seminars in Surgical Oncology : ISSO》2005,2(1):16
Background
The aim of this study is to report the outcome after surgical treatment of 32 patients with ampullary cancers from 1990 to 1999.Methods
Twenty-one of them underwent pancreaticoduodenectomy and 9 local excision of the ampullary lesion. The remaining 2 patients underwent palliative surgery.Results
When the final histological diagnosis was compared with the preoperative histological finding on biopsy, accurate diagnosis was preoperatively established in 24 patients. The hospital morbidity was 18.8% as 9 complications occurred in 6 patients. Following local excision of the ampullary cancer, the survival rate at 3 and 5 years was 77.7% and 33.3% respectively. Among the patients that underwent Whipple's procedure, the 3-year survival rate was 76.2% and the 5-year survival rate 62%.Conclusion
In this series, local resection was a safe option in patients with significant co-morbidity or small ampullary tumors less than 2 cm in size, and was associated with satisfactory long-term survival rates.11.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
Introduction
Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.Objectives
In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.Methods
The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.Results
A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.Conclusion
The workflow generated repeatable and informative fingerprints for robust metabolome characterization.12.
Neha Dhami Drupad K. Trivedi Royston Goodacre David Mainwaring David P. Humphreys 《Metabolomics : Official journal of the Metabolomic Society》2018,14(10):136
Introduction
Mammalian cells like Chinese hamster ovary (CHO) cells are routinely used for production of recombinant therapeutic proteins. Cells require a continuous supply of energy and nutrients to sustain high cell densities whilst expressing high titres of recombinant proteins. Cultured mammalian cells are primarily dependent on glucose and glutamine metabolism for energy production.Objectives
The TCA cycle is the main source of energy production and its continuous flow is essential for cell survival. Modulated regulation of TCA cycle can affect ATP production and influence CHO cell productivity.Methods
To determine the key metabolic reactions of the cycle associated with cell growth in CHO cells, we transiently silenced each gene of the TCA cycle using RNAi.Results
Silencing of at least four TCA cycle genes was detrimental to CHO cell growth. With an exception of mitochondrial aconitase (or Aco2), all other genes were associated with ATP production reactions of the TCA cycle and their resulting substrates can be supplied by other anaplerotic and cataplerotic reactions. This study is the first of its kind to have established key role of aconitase gene in CHO cells. We further investigated the temporal effects of aconitase silencing on energy production, CHO cell metabolism, oxidative stress and recombinant protein production.Conclusion
Transient silencing of mitochondrial aconitase inhibited cell growth, reduced ATP production, increased production of reactive oxygen species and reduced cell specific productivity of a recombinant CHO cell line by at least twofold.13.
Background
Recently, growing attention has been directed toward stem cell metabolism, with the key observation that metabolism not only fuels the proper functioning of stem cells but also regulates the fate of these cells. There seems to be a clear link between the self-renewal of pluripotent stem cells (PSCs), in which cells proliferate indefinitely without differentiation, and the activity of specific metabolic pathways. The unique metabolism in PSCs plays an important role in maintaining pluripotency by regulating signaling pathways and resetting the epigenome.Objective
To review the most recent publications concerning the metabolism of pluripotent stem cells and the role of metabolism in PSC self-renewal and differentiation.Methods
A systematic literature search related to the metabolism of PSCs was conducted in databases including Medline, Embase, and Web of Science. The search was performed without language restrictions on all papers published before May 2016. The following keywords were used: “metabolism” combined with either “embryonic stem cell” or “epiblast stem cell.”Results
Hundreds of papers focusing specifically on the metabolism of pluripotent stem cells were uncovered and summarized.Conclusion
Identifying the specific metabolic pathways involved in pluripotency maintenance is crucial for progress in the field of developmental biology and regenerative medicine. Additionally, better understanding of the metabolism in PSCs will facilitate the derivation and maintenance of authentic PSCs from species other than mouse, rat, and human.14.
Background and aims
Serpentine soils impose limits on plant growth and survival and thus provide an ideal model for studying plant adaptation under environmental stress. Despite the increasing amount of data on serpentine ecotypic differentiation, no study has assessed the potential role of polyploidy. We tested for links between polyploidy and the response to serpentine stress in Knautia arvensis, a diploid-tetraploid, edaphically differentiated complex.Methods
Variation in growth, biomass yield and tissue Mg and Ni accumulation in response to high Mg and Ni concentrations were experimentally tested using hydroponic cultivation of seedlings from eight populations of different ploidy and edaphic origin.Results
Regardless of ploidy level, serpentine populations exhibited higher tolerance to both Mg and Ni stress than their non-serpentine counterparts, suggesting an adaptive character of these traits in K. arvensis. The effect of ploidy was rather weak and confined to a slightly better response of serpentine tetraploids to Mg stress and to higher biomass yields in tetraploids from both soil types.Conclusions
The similar response of diploid and tetraploid serpentine populations to edaphic stress corresponded with their previously described genetic proximity. This suggests that serpentine tolerance might have been transmitted during the local autopolyploid origin of serpentine tetraploids.15.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
Introduction
Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.Objectives
(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.Methods
A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.Results
Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.Conclusion
Further efforts are required to improve data sharing in metabolomics.16.
Objectives
To compare the degradation performance and biodiversity of a polyvinyl alcohol-degrading microbial community under aerobic and anaerobic conditions.Results
An anaerobic–aerobic bioreactor was operated to degrade polyvinyl alcohol (PVA) in simulated wastewater. The degradation performance of the bioreactor during sludge cultivation and the microbial communities in each reactor were compared. Both anaerobic and aerobic bioreactors demonstrated high chemical oxygen demand removal efficiencies of 87.5 and 83.6 %, respectively. Results of 16S rDNA sequencing indicated that Proteobacteria dominated in both reactors and that the microbial community structures varied significantly under different operating conditions. Both reactors obviously differed in bacterial diversity from the phyla Planctomycetes, Chlamydiae, Bacteroidetes, and Chloroflexi. Betaproteobacteria and Alphaproteobacteria dominated, respectively, in the anaerobic and aerobic reactors.Conclusions
The anaerobic–aerobic system is suitable for PVA wastewater treatment, and the microbial genetic analysis may serve as a reference for PVA biodegradation.17.
Bing-Qian Su Ying-Qian Han Shuang-Shuang Fan Sheng-Li Ming Bo Wan Wei-Fei Lu Bei-Bei Chu Guo-Yu Yang Jiang Wang 《Biotechnology letters》2018,40(4):641-648
Objective
The purpose of the article is to evaluate the changes in lipid metabolism in bovine mammary-gland epithelial MAC-T cells after PKM2 knockdown.Results
MAC-T cells stably expressing low levels of PKM2 were established with lentivirus-mediated small hairpin RNA. Although the knockdown of PKM2 had no effect on MAC-T cell growth, the reduced expression of PKM2 attenuated the mRNA and protein expression of key enzymes involved in sterol synthesis through the SREBP pathway.Conclusions
The downregulation of PKM2 significantly influenced lipid synthesis in bovine mammary-gland epithelial MAC-T cells. These findings extend our understanding of the crosstalk between glycolysis and lipid metabolism in bovine mammary-gland epithelial cells.18.
Background
In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.Methods
The physical basis of these intuitive maps is clarified by means of analytically solvable problems.Results
Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.Conclusion
Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.19.
Kayoko Yoshida Chiyo K. Imamura Kanako Hara Mayumi Mochizuki Yusuke Tanigawara 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):98
Introduction
Everolimus selectively inhibits mammalian target of rapamycin complex 1 (mTORC1) and exerts an antineoplastic effect. Metabolic disturbance has emerged as a common and unique side effect of everolimus.Objectives
We used targeted metabolomic analysis to investigate the effects of everolimus on the intracellular glycometabolic pathway.Methods
Mouse skeletal muscle cells (C2C12) were exposed to everolimus for 48 h, and changes in intracellular metabolites were determined by capillary electrophoresis time-of-flight mass spectrometry. mRNA abundance, protein expression and activity were measured for enzymes involved in glycometabolism and related pathways.Results
Both extracellular and intracellular glucose levels increased with exposure to everolimus. Most intracellular glycometabolites were decreased by everolimus, including those involved in glycolysis and the pentose phosphate pathway, whereas no changes were observed in the tricarboxylic acid cycle. Everolimus suppressed mRNA expression of enzymes related to glycolysis, downstream of mTOR signaling enzymes and adenosine 5′-monophosphate protein kinases. The activity of key enzymes involved in glycolysis and the pentose phosphate pathway were decreased by everolimus. These results show that everolimus impairs glucose utilization in intracellular metabolism.Conclusions
The present metabolomic analysis indicates that everolimus impairs glucose metabolism in muscle cells by lowering the activities of glycolysis and the pentose phosphate pathway.20.