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One carbon metabolism

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https://www.readbyqxmd.com/read/28220994/positional-enrichment-by-proton-analysis-pepa-a-one-dimensional-1-h-nmr-approach-for-13-c-stable-isotope-tracer-studies-in-metabolomics
#1
Maria Vinaixa, Miguel A Rodríguez, Suvi Aivio, Jordi Capellades, Josep Gómez, Nicolau Canyellas, Travis H Stracker, Oscar Yanes
A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of (13) C-satellite peaks using 1D-(1) H-NMR spectra. In comparison with (13) C-NMR, TOCSY and HSQC, PEPA improves sensitivity, accelerates the elucidation of (13) C positions in labeled metabolites and the quantification of the percentage of stable isotope enrichment...
February 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28220590/biosynthesis-and-mass-spectral-fragmentation-pathways-of-13-c-and-15-n-labeled-cytochalasin-d-produced-by-xylaria-arbuscula
#2
Luciana da Silva Amaral, Taicia Pacheco Fill, Luiz Fernando Arruda Santos, Edson Rodrigues-Filho
The fungus Xylaria arbuscula was isolated as an endophyte from Cupressus lusitanica and has shown to be a prominent producer of cytochalasans, mainly cytochalasin C, D and Q. Cytochalasans comprise an important class of fungal secondary metabolites that have aroused attention due to their uncommon molecular structures and pronounced biological activities. Due to the few published studies on the ESI-MS/MS fragmentation of this important class of secondary metabolites, in the first part of our work we studied the cytochalasin D fragmentation pathways using an ESI-Q-ToF mass spectrometer coupled with liquid chromatography...
February 21, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28219798/integrative-hepatoprotective-efficacy-comparison-of-raw-and-vinegar-baked-radix-bupleuri-using-nuclear-magnetic-resonance-based-metabolomics
#3
Jie Xing, Hui-Min Sun, Jin-Ping Jia, Xue-Mei Qin, Zhen-Yu Li
Radix Bupleuri (RB), with a Chinese name Chaihu, is one of the most popular Traditional Chinese herbal drug. It can be baked with vinegar to afford vinegar-baked Radix Bupleuri (VBRB), which is used in Traditional Chinese Medicine (TCM) for liver diseases treatment. In the present study, nuclear magnetic resonance-based metabolomic approach was used to compare the liver protective effect of RB and two types of VBRBs, which were prepared by two kinds of vinegar. The contents of 14 metabolites in the liver of carbon tetrachloride (CCl4) treated mice were significantly altered in comparison with control group, and VBRB prepared by Shanxi vinegar showed best effect as revealed by the amount and regulatory degree of the perturbed metabolites...
February 7, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28214879/thiamine-deprivation-produces-a-liver-atp-deficit-and-metabolic-and-genomic-effects-in-mice-findings-are-parallel-to-those-of-biotin-deficiency-and-have-implications-for-energy-disorders
#4
Alain de J Hernandez-Vazquez, Josue Andres Garcia-Sanchez, Elizabeth Moreno-Arriola, Ana Salvador-Adriano, Daniel Ortega-Cuellar, Antonio Velazquez-Arellano
Thiamine is one of several essential cofactors for ATP generation. Its deficiency, like in beriberi and in the Wernicke-Korsakoff syndrome, has been studied for many decades. However, its mechanism of action is still not completely understood at the cellular and molecular levels. Since it acts as a coenzyme for dehydrogenases of pyruvate, branched-chain keto acids, and ketoglutarate, its nutritional privation is partly a phenocopy of inborn errors of metabolism, among them maple syrup urine disease. In the present paper, we report metabolic and genomic findings in mice deprived of thiamine...
February 18, 2017: Journal of Nutrigenetics and Nutrigenomics
https://www.readbyqxmd.com/read/28212441/depressive-disorder-and-gastrointestinal-dysfunction-after-myocardial-infarct-are-associated-with-abnormal-tryptophan-5-hydroxytryptamine-metabolism-in-rats
#5
Xiaofang Lu, Yuefen Wang, Chunyan Liu, Yangang Wang
In this study, we investigated the relationship between tryptophan-5-hydroxytryptamine metabolism, depressive disorder, and gastrointestinal dysfunction in rats after myocardial infarction. Our goal was to elucidate the physiopathologic bases of somatic/psychiatric depression symptoms after myocardial infarction. A myocardial infarction model was established by permanent occlusion of the left anterior descending coronary artery. Depression-like behavior was evaluated using the sucrose preference test, open field test, and forced swim test...
2017: PloS One
https://www.readbyqxmd.com/read/28211874/datf4-regulation-of-mitochondrial-folate-mediated-one-carbon-metabolism-is-neuroprotective
#6
Ivana Celardo, Susann Lehmann, Ana C Costa, Samantha Hy Loh, L Miguel Martins
Neurons rely on mitochondria as their preferred source of energy. Mutations in PINK1 and PARKIN cause neuronal death in early-onset Parkinson's disease (PD), thought to be due to mitochondrial dysfunction. In Drosophila pink1 and parkin mutants, mitochondrial defects lead to the compensatory upregulation of the mitochondrial one-carbon cycle metabolism genes by an unknown mechanism. Here we uncover that this branch is triggered by the activating transcription factor 4 (ATF4). We show that ATF4 regulates the expression of one-carbon metabolism genes SHMT2 and NMDMC as a protective response to mitochondrial toxicity...
February 17, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28208582/nutrients-in-energy-and-one-carbon-metabolism-learning-from-metformin-users
#7
REVIEW
Fedra Luciano-Mateo, Anna Hernández-Aguilera, Noemi Cabre, Jordi Camps, Salvador Fernández-Arroyo, Jose Lopez-Miranda, Javier A Menendez, Jorge Joven
Metabolic vulnerability is associated with age-related diseases and concomitant co-morbidities, which include obesity, diabetes, atherosclerosis and cancer. Most of the health problems we face today come from excessive intake of nutrients and drugs mimicking dietary effects and dietary restriction are the most successful manipulations targeting age-related pathways. Phenotypic heterogeneity and individual response to metabolic stressors are closely related food intake. Understanding the complexity of the relationship between dietary provision and metabolic consequences in the long term might provide clinical strategies to improve healthspan...
February 10, 2017: Nutrients
https://www.readbyqxmd.com/read/28197141/metabolomic-and-metagenomic-analysis-of-two-crude-oil-production-pipelines-experiencing-differential-rates-of-corrosion
#8
Vincent Bonifay, Boris Wawrik, Jan Sunner, Emily C Snodgrass, Egemen Aydin, Kathleen E Duncan, Amy V Callaghan, Athenia Oldham, Turid Liengen, Iwona Beech
Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28188804/metabolite-profiling-of-infection-associated-metabolic-markers-of-onchocerciasis
#9
Sasisekhar Bennuru, Sara Lustigman, David Abraham, Thomas B Nutman
The global efforts for onchocerciasis elimination may require additional tools (safe micro and macrofilaricidal drugs, vaccines and biomarkers) as elimination efforts move toward the "end game". Efforts toward the identification of suitable biomarkers have focused on specific protein(s) and/or nucleic acids, but metabolites present an alternative option as they have limited half-lives and are the result of combinatorial effects. In comparison to previously used methodology of LC-MS for metabolomic approaches, we used a non-targeted capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) to analyze the serum metabolic profiles of Ov-infected and -uninfected individuals (n=20)...
February 8, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28187917/oxygen-and-placental-development-parallels-and-differences-with-tumour-biology
#10
Graham J Burton, Eric Jauniaux, Andrew J Murray
Human placentation involves the invasion of the conceptus into the wall of the uterus, and establishment of a blood supply from the maternal spiral arteries. The placenta has therefore been likened to a malignant tumour, albeit a highly regulated one. Oxygen plays an important role in controlling both placental development and tumour behaviour. In the placenta, early development takes place in a physiological low oxygen environment, which undergoes a transition with onset of the full maternal arterial circulation towards the end of the first trimester...
February 1, 2017: Placenta
https://www.readbyqxmd.com/read/28186720/cuprizone-intoxication-induces-cell-intrinsic-alterations-in-oligodendrocyte-metabolism-independent-of-copper-chelation
#11
Alexandra Taraboletti, Tia Louise Walker, Robin Avila, He Huang, Joel Caporoso, Erendra Manandhar, Thomas C Leeper, David A Modarelli, Satish Medicetty, Leah P Shriver
Cuprizone intoxication is a common animal model used to test myelin regenerative therapies to treat diseases such as multiple sclerosis. Mice fed this copper chelator develop reversible, region-specific oligodendrocyte loss and demyelination. While the cellular changes influencing the demyelinating process have been explored in this model, there is no consensus on the biochemical mechanisms of toxicity in oligodendrocytes and if this damage arises from the chelation of copper in vivo. Here we have identified an oligodendroglial cell line that displays sensitivity to cuprizone toxicity and performed global metabolomic profiling to determine biochemical pathways altered by this treatment...
February 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28181409/metabolic-diversity-of-the-emerging-pathogenic-lineages-of-klebsiella-pneumoniae
#12
Camille Blin, Virginie Passet, Marie Touchon, Eduardo P C Rocha, Sylvain Brisse
Multidrug resistant and hypervirulent clones of Klebsiella pneumoniae are emerging pathogens. To understand the association between genotypic and phenotypic diversity in this process, we combined genomic, phylogenomic, and phenotypic analysis of a diverse set of K. pneumoniae and closely related species. These species were able to use an unusually large panel of metabolic substrates for growth, many of which were shared between all strains. We analysed the substrates used by only a fraction of the strains, identified some of their genetic basis, and found that many could not be explained by the phylogeny of the strains...
February 9, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28177894/one-carbon-metabolism-and-nucleotide-biosynthesis-as-attractive-targets-for-anticancer-therapy
#13
Oleg Shuvalov, Alexey Petukhov, Alexandra Daks, Olga Fedorova, Elena Vasileva, Nickolai A Barlev
Cancer-related metabolism has recently emerged as one of the "hallmarks of cancer". It has several important features, including altered metabolism of glucose and glutamine. Importantly, altered cancer metabolism connects different biochemical pathways into the one fine-tuned metabolic network, which stimulates high proliferation rates and plasticity to malignant cells. Among the keystones of cancer metabolism are one-carbon metabolism and nucleotide biosynthesis, which provide building blocks to anabolic reactions...
February 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28175958/metabolic-and-co-metabolic-transformation-of-diclofenac-by-enterobacter-hormaechei-d15-isolated-from-activated-sludge
#14
Salima Aissaoui, Houria Ouled-Haddar, Mohamed Sifour, Kamel Harrouche, Haitham Sghaier
The presence of non-steroidal anti-inflammatory drugs, such as diclofenac (DCF), in the environment, is an emerging problem due to their harmful effects on non-target organisms, even at low concentrations. We studied the biodegradation of DCF by the strain D15 of Enterobacter hormaechei. The strain was isolated from an activated sludge, and identified as E. hormaechei based on its physiological characteristics and its 16 S RNA sequence. Using HPTLC and GC-MS methods, we demonstrated that this strain metabolized DCF at an elimination rate of 52...
March 2017: Current Microbiology
https://www.readbyqxmd.com/read/28174563/metabolic-flexibility-of-yarrowia-lipolytica-growing-on-glycerol
#15
Michael Egermeier, Hannes Russmayer, Michael Sauer, Hans Marx
The yeast Yarrowia lipolytica is a fascinating microorganism with an amazing metabolic flexibility. This yeast grows very well on a wide variety of carbon sources from alkanes over lipids, to sugars and glycerol. Y. lipolytica accumulates a wide array of industrially relevant metabolites. It is very tolerant to many environmental factors, above all the pH value. It grows perfectly well over a wide pH range, but it has been described, that the pH has a decisive influence on the metabolite pattern accumulated by this yeast...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28167519/regulation-of-polyhydroxybutyrate-accumulation-in-sinorhizobium-meliloti-by-the-trans-encoded-small-rna-mmgr
#16
Antonio Lagares, Germán Ceizel Borella, Uwe Linne, Anke Becker, Claudio Valverde
Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans-encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti, over 400 sRNAs are expressed under different stimuli. The sRNA MmgR-standing for Makes more granules Regulator-has been of particular interest to us since its sequence and structure are highly conserved among the α-proteobacteria, and its expression is regulated by the amount and quality of the bacterium's available nitrogen source...
February 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28161958/comprehensive-metaboproteomics-of-burkitt-s-and-diffuse-large-b-cell-lymphoma-cell-lines-and-primary-tumor-tissues-reveals-distinct-differences-in-pyruvate-content-and-metabolism
#17
Philipp Schwarzfischer, Joerg Reinders, Katja Dettmer, Karsten Kleo, Lora Dimitrova, Michael Hummel, Maren Feist, Dieter Kube, Monika Szczepanowski, Wolfram Klapper, Franziska Taruttis, Julia C Engelmann, Rainer Spang, Wolfram Gronwald, Peter J Oefner
Burkitt's lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL) are pathologically and clinically distinct subtypes of aggressive non-Hodgkin B-cell lymphoma. To learn more about their biology, we employed metabolomic and proteomic methods to study both established cell lines as well as cryopreserved and formalin-fixed paraffin-embedded (FFPE) tissue sections of BL and DLBCL. Strikingly, NMR analyses revealed DLBCL cell lines to produce and secrete significantly (padj=1.72 x 10-22) more pyruvic acid than BL cell lines...
February 6, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28161091/associations-between-genetic-variation-in-one-carbon-metabolism-and-leukocyte-dna-methylation-in-valproate-treated-patients-with-epilepsy
#18
Guanzhong Ni, Jiaming Qin, Ziyi Chen, Hongliang Li, Jueqian Zhou, Min Huang, Liemin Zhou
BACKGROUND: Valproate (VPA) as a first-line antiepileptic drug is useful for the most types of epileptic seizure treatment. Previous studies observed that VPA influenced one-carbon metabolism (OCM), consequently, DNA methylation. However, other individual genetic variations, as well as VPA, modify DNA methylation. OBJECTIVE: In this study, we investigated associations between genetic variations in OCM and leukocyte DNA methylation in VPA-treated patients with epilepsy...
January 20, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/28152017/genetic-toolbox-for-controlled-expression-of-functional-proteins-in-geobacillus-spp
#19
Ivan Pogrebnyakov, Christian Bille Jendresen, Alex Toftgaard Nielsen
Species of genus Geobacillus are thermophilic bacteria and play an ever increasing role as hosts for biotechnological applications both in academia and industry. Here we screened a number of Geobacillus strains to determine which industrially relevant carbon sources they can utilize. One of the strains, G. thermoglucosidasius C56-YS93, was then chosen to develop a toolbox for controlled gene expression over a wide range of levels. It includes a library of semi-synthetic constitutive promoters (76-fold difference in expression levels) and an inducible promoter from the xylA gene...
2017: PloS One
https://www.readbyqxmd.com/read/28139919/genome-resolved-meta-omics-ties-microbial-dynamics-to-process-performance-in-biotechnology-for-thiocyanate-degradation
#20
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
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