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One carbon metabolism

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https://www.readbyqxmd.com/read/29917330/microbial-methylotrophic-metabolism-recent-metabolic-modeling-efforts-and-their-applications-in-industrial-biotechnology
#1
REVIEW
Christian Lieven, Markus J Herrgård, Nikolaus Sonnenschein
Developing methylotrophic bacteria into cell factories that meet the chemical demand of the future could be both economical and environmentally friendly. Methane is not only an abundant, low-cost resource but also a potent greenhouse gas, the capture of which could help to reduce greenhouse gas emissions. Rational strain design workflows rely on the availability of carefully combined knowledge often in the form of genome-scale metabolic models to construct high-producer organisms. In this review, we present the most recent genome-scale metabolic models in aerobic methylotrophy and their applications...
June 19, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29915106/proteome-response-of-a-metabolically-flexible-anoxygenic-phototroph-to-fe-ii-oxidation
#2
Casey Bryce, Mirita Franz-Wachtel, Nicolas Nalpas, Jennyfer Miot, Karim Benzerara, James M Byrne, Sara Kleindienst, Boris Macek, Andreas Kappler
The oxidation of Fe(II) by anoxygenic photosynthetic bacteria was likely a key contributor to Earth's biosphere prior to the evolution of oxygenic photosynthesis and is still found in a diverse range of modern environments. All known phototrophic Fe(II)-oxidizers can utilize a wide range of substrates thus making them very metabolically flexible. However, the underlying adaptations required to oxidize Fe(II), a potential stressor, are not completely understood. We used a combination of quantitative proteomics and cryogenic transmission electron microscopy (cryo-TEM) to compare cells of Rhodopseudomonas palustris TIE-1 grown photoautotrophically with Fe(II) or H2 , and photoheterotrophically with acetate...
June 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29911072/inhibiting-glycine-decarboxylase-suppresses-pyruvate-to-lactate-metabolism-in-lung-cancer-cells
#3
Chern Chiuh Woo, Kavita Kaur, Wei Xin Chan, Xing Qi Teo, Teck Hock Philip Lee
Glycine decarboxylase (GLDC) gene is frequently upregulated in various types of cancer including lung, prostate and brain. It catabolizes glycine to yield 5,10-methylenetetrahydrofolate, an important substrate in one-carbon metabolism for nucleotide synthesis. In this study, we used exon splicing modulating steric hindrance antisense oligonucleotide (shAON) to suppress GLDC expression and investigated its effect on pyruvate metabolism via hyperpolarized carbon-13 magnetic resonance spectroscopy (MRS). The MRS technique allows us to study in vivo metabolic flux in tumor tissues with/without GLDC-shAON intervention...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29907311/daring-metabolic-designs-for-enhanced-plant-carbon-fixation
#4
Arren Bar-Even
Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., "low hanging fruit". Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco's catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon...
August 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29898540/characterization-and-toxicity-of-nanoscale-fragments-in-wastewater-treatment-plant-effluent
#5
Xiangang Hu, Chaoxiu Ren, Weilu Kang, Li Mu, Xiaowei Liu, Xiaokang Li, Tong Wang, Qixing Zhou
Much attention has been paid to extracting and isolating specific and well-known nanoparticles (especially for engineered nanomaterials) from complex environmental matrices. However, such research may not provide global information on actual contamination because nanoscale fragments exist as mixtures of various elements and matrices in the real environment. The present work first isolated and characterized nanoscale fragments in effluents from municipal wastewater treatment plants (WWTPs). The nanoscale fragments were found to be composed of 70-85% carbon and low amounts of oxygen, heavy metals and other elements and exhibited nanosheet topographies (approximately 0...
June 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29895827/oxidized-phospholipids-regulate-amino-acid-metabolism-through-mthfd2-to-facilitate-nucleotide-release-in-endothelial-cells
#6
Juliane Hitzel, Eunjee Lee, Yi Zhang, Sofia Iris Bibli, Xiaogang Li, Sven Zukunft, Beatrice Pflüger, Jiong Hu, Christoph Schürmann, Andrea Estefania Vasconez, James A Oo, Adelheid Kratzer, Sandeep Kumar, Flávia Rezende, Ivana Josipovic, Dominique Thomas, Hector Giral, Yannick Schreiber, Gerd Geisslinger, Christian Fork, Xia Yang, Fragiska Sigala, Casey E Romanoski, Jens Kroll, Hanjoong Jo, Ulf Landmesser, Aldons J Lusis, Dmitry Namgaladze, Ingrid Fleming, Matthias S Leisegang, Jun Zhu, Ralf P Brandes
Oxidized phospholipids (oxPAPC) induce endothelial dysfunction and atherosclerosis. Here we show that oxPAPC induce a gene network regulating serine-glycine metabolism with the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) as a causal regulator using integrative network modeling and Bayesian network analysis in human aortic endothelial cells. The cluster is activated in human plaque material and by atherogenic lipoproteins isolated from plasma of patients with coronary artery disease (CAD)...
June 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29894955/bright-carbon-dots-via-inner-filter-effect-for-the-sensitive-determination-of-the-purine-metabolic-disorder-in-human-fluids
#7
Ju Qin, Qian Nan, Jing Yang, Rui Yang
In this paper, the high performance fluorescent carbon dots were synthesized with maleic acid, tris and benzoic acid as raw materials by one-step hydrothermal method. The obtained carbon dots with uniform size emitted strong blue fluorescence, which the maximum excitation and emission wavelengths at 250 nm and 415 nm, respectively. Under the optimum condition, it was meaningfully founded that the reaction between the carbon dots and uric acid resulting in the fluorescence quenching of the carbon dots at the emission spectrum of 415 nm...
May 26, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29893878/non-structural-carbohydrate-dynamics-associated-with-drought-induced-die-off-in-woody-species-of-a-shrubland-community
#8
Francisco Lloret, Gerard Sapes, Teresa Rosas, Lucía Galiano, Sandra Saura-Mas, Anna Sala, Jordi Martínez-Vilalta
Background and Aims: The relationship between plant carbon economy and drought responses of co-occurring woody species can be assessed by comparing carbohydrate (C) dynamics following drought and rain periods, relating these dynamics to species' functional traits. We studied nine woody species coexisting in a continental Mediterranean shrubland that experienced severe drought effects followed by rain. Methods: We measured total non-structural carbohydrates (NSC) and soluble sugars (SS) in roots and stems during drought and after an autumn rain pulse in plants exhibiting leaf loss and in undefoliated ones...
June 8, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29892275/hydrogen-fueled-microbial-pathways-in-biogas-upgrading-systems-revealed-by-genome-centric-metagenomics
#9
Laura Treu, Stefano Campanaro, Panagiotis G Kougias, Cristina Sartori, Ilaria Bassani, Irini Angelidaki
Biogas upgrading via carbon dioxide hydrogenation is an emerging technology for electrofuel production. The biomethanation efficiency is strongly dependent on a balanced microbial consortium, whose high- resolution characterization along with their functional potential and interactions are pivotal for process optimization. The present work is the first genome-centric metagenomic study on mesophilic and thermophilic biogas upgrading reactors aiming to define the metabolic profile of more than 200 uncultivated microbes involved in hydrogen assisted methanogenesis...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29891211/effective-thiafentanil-immobilization-and-physiological-responses-of-free-ranging-moose-alces-alces-in-northern-sweden
#10
Daniela Sb Barros, Alina L Evans, Jon M Arnemo, Fredrik Stenbacka, Göran Ericsson
OBJECTIVE: To evaluate clinical and physiological responses in moose to thiafentanil administration for immobilization. STUDY DESIGN: Cross-sectional clinical study. ANIMALS: Eleven (six males and five females) free-ranging adult moose (Alces alces). METHODS: Each moose was darted from a helicopter with 7.5 mg thiafentanil during March 2014 in northern Sweden. Physiological evaluation included vital signs and blood gases...
March 31, 2018: Veterinary Anaesthesia and Analgesia
https://www.readbyqxmd.com/read/29889360/cell-cycle-regulation-of-folate-mediated-one-carbon-metabolism
#11
REVIEW
Xu Lan, Martha S Field, Patrick J Stover
Folate-mediated one-carbon metabolism (FOCM) comprises a network of interconnected folate-dependent metabolic pathways responsible for serine and glycine interconversion, de novo purine synthesis, de novo thymidylate synthesis and homocysteine remethylation to methionine. These pathways are compartmentalized in the cytosol, nucleus and mitochondria. Individual enzymes within the FOCM network compete for folate cofactors because intracellular folate concentrations are limiting. Although there are feedback mechanisms that regulate the partitioning of folate cofactors among the folate-dependent pathways, less recognized is the impact of cell cycle regulation on FOCM...
June 11, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29888958/the-effect-of-inflammation-related-lifestyle-exposures-and-interactions-with-gene-variants-on-long-interspersed-nuclear-element-1-dna-methylation
#12
Priyanka Gogna, Dylan E O'Sullivan, Will D King
AIM: To examine the relationship between inflammation-related lifestyle factors and long interspersed nuclear element-1 (LINE-1) DNA methylation, and test for interaction by gene variants involved in one-carbon metabolism. PATIENTS & METHODS: The study population consisted of 280 individuals undergoing colonoscopy screening. Multivariable linear regression was employed to examine associations of physical activity, BMI and NSAID use with LINE-1 DNA methylation and interactions with MTR and MTHFR gene variants...
June 11, 2018: Epigenomics
https://www.readbyqxmd.com/read/29887684/b-l-basal-ganglia-lesions-in-a-child-leading-to-a-diagnosis-of-glucose-6-phosphate-dehydrogenase-deficiency
#13
Nidhi Prabhakar, Chirag K Ahuja, Niranjan Khandelwal
Bilateral basal ganglia lesions are a common non-specific finding seen in many diseases. One of the differential diagnoses for it, in a child, is kernicterus occurring due to hyperbilirubinemia. Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common cause of severe hyperbilirubinemia. A 1-year old child presented to the hospital with history of generalized dystonia in the previous 3 days. MRI showed evidence of symmetrical lesions in bilateral globus pallidus, which were hyperintense on T2/FLAIR and isointense on T1...
April 2018: Annals of Neurosciences
https://www.readbyqxmd.com/read/29883540/thiazolidine-peracetates-carbohydrate-derivatives-that-readily-assign-cis-trans-2-3-monosaccharides-by-gc-ms-analysis
#14
Neil P J Price, Trina M Hartman, Karl E Vermillion
A novel group of carbohydrate derivatives is described that uniquely assign cis/trans-2,3 aldose stereoisomers at low nanomolar concentrations. Aldopentoses or aldohexoses, or component aldoses from hydrolysis of polysaccharides or oligosaccharides, react with cysteamine in pyridine to give quantitative formation of thiazolidines, which are subsequently peracetylated in a one-pot reaction. The non-polar thiazolidines peracetate (TPA) derivatives are analyzed by GC/EI-MS, each aldose giving rise to two TPA geometric isomers...
June 8, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29883100/the-biochemical-basis-of-vitamin-a-production-from-asymmetric-carotenoid-%C3%AE-cryptoxanthin
#15
Mary E Kelly, Srinivasagan Ramkumar, Weizhong Sun, Crystal Colon Ortiz, Philip D Kiser, Marcin Golczak, Johannes von Lintig
Vitamin A serves essential functions in mammalian biology as a signaling molecule and chromophore. This lipid can be synthesized from more than 50 putative dietary provitamin A precursor molecules which contain at least one unsubstituted β-ionone ring. We here scrutinized the enzymatic properties and substrate specificities of the two structurally related carotenoid cleavage dioxygenases (CCDs) which catalyze this synthesis. Recombinant BCO1 split substrates across the C15,C15' double bond adjacent to a canonical β-ionone ring site to vitamin A aldehyde...
June 8, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29879670/analysis-of-pharmaceutical-biodegradation-of-wwtp-sludge-using-composting-and-identification-of-certain-microorganisms-involved-in-the-process
#16
María Iranzo, Miguel Gamón, Rafael Boluda, Salvador Mormeneo
Pharmaceuticals (PhCs) are organic contaminants that have been detected in wastewater, surface water, and soils throughout the world. The presence of 10 commonly used PhCs in Spain (azithromycin, benzylpenicillin, citalopram, fluconazole, fluoxetine, ibuprofen, irbesartan, olanzapine, telmisartan, and venlafaxine) was analysed at four wastewater treatment plants, and the changes in their concentrations during treatment were assessed. Although certain some PhCs were degraded in the treated water, their presence in sewage sludge increased in all cases...
June 4, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29879172/using-genome-scale-metabolic-models-to-compare-serovars-of-the-foodborne-pathogen-listeria-monocytogenes
#17
Zachary P Metz, Tong Ding, David J Baumler
Listeria monocytogenes is a microorganism of great concern for the food industry and the cause of human foodborne disease. Therefore, novel methods of control are needed, and systems biology is one such approach to identify them. Using a combination of computational techniques and laboratory methods, genome-scale metabolic models (GEMs) can be created, validated, and used to simulate growth environments and discern metabolic capabilities of microbes of interest, including L. monocytogenes. The objective of the work presented here was to generate GEMs for six different strains of L...
2018: PloS One
https://www.readbyqxmd.com/read/29876016/meta-analysis-of-homocysteine-related-factors-on-the-risk-of-colorectal-cancer
#18
S Pamela K Shiao, Amanda Lie, Chong Ho Yu
The major objective of this meta-analysis was to examine the association between homocysteine and related measurements with the risk of colorectal cancer (CRC) and adenomatous polyps (AP). Many studies presented an association between methyltetrahydrofolate reductase (MTHFR) gene polymorphisms and risk of CRC. Yet, there have been variances on what homocysteine-related and dietary factors play on the risk of CRC or AP, in association with folate-related one carbon metabolism pathways. We pooled analyses to examine comprehensively all homocysteine related factors including blood tests measurements, dietary, and lifestyle factors for their associations with the risk of CRC and AP...
May 22, 2018: Oncotarget
https://www.readbyqxmd.com/read/29874574/cross-talk-between-one-carbon-metabolism-eph-signaling-and-histone-methylation-promotes-neural-stem-cell-differentiation
#19
Mohamad-Ali Fawal, Thomas Jungas, Anthony Kischel, Christophe Audouard, Jason S Iacovoni, Alice Davy
Metabolic pathways, once seen as a mere consequence of cell states, have emerged as active players in dictating different cellular events such as proliferation, self-renewal, and differentiation. Several studies have reported a role for folate-dependent one-carbon (1C) metabolism in stem cells; however, its exact mode of action and how it interacts with other cues are largely unknown. Here, we report a link between the Eph:ephrin cell-cell communication pathway and 1C metabolism in controlling neural stem cell differentiation...
June 5, 2018: Cell Reports
https://www.readbyqxmd.com/read/29873416/ews-fli1-reprograms-the-metabolism-of-ewing-sarcoma-cells-via-positive-regulation-of-glutamine-import-and-serine-glycine-biosynthesis
#20
Nirmalya Sen, Allison M Cross, Philip L Lorenzi, Javed Khan, Berkley E Gryder, Suntae Kim, Natasha J Caplen
Ewing sarcoma (EWS) is a soft tissue and bone tumor that occurs primarily in adolescents and young adults. In most cases of EWS, the chimeric transcription factor, EWS-FLI1 is the primary oncogenic driver. The epigenome of EWS cells reflects EWS-FLI1 binding and activation or repression of transcription. Here, we demonstrate that EWS-FLI1 positively regulates the expression of proteins required for serine-glycine biosynthesis and uptake of the alternative nutrient source glutamine. Specifically, we show that EWS-FLI1 activates expression of PHGDH, PSAT1, PSPH, and SHMT2...
June 6, 2018: Molecular Carcinogenesis
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