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Journal articles on the topic 'Metabolome modification'

Author: Grafiati

Published: 11 March 2023

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1

Rieusset, Laura, Marjolaine Rey, Florence Wisniewski-Dyé, Claire Prigent-Combaret, and Gilles Comte. "Wheat Metabolite Interferences on Fluorescent Pseudomonas Physiology Modify Wheat Metabolome through an Ecological Feedback." Metabolites 12, no. 3 (2022): 236. http://dx.doi.org/10.3390/metabo12030236.

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Plant roots exude a wide variety of secondary metabolites able to attract and/or control a large diversity of microbial species. In return, among the root microbiota, some bacteria can promote plant development. Among these, Pseudomonas are known to produce a wide diversity of secondary metabolites that could have biological activity on the host plant and other soil microorganisms. We previously showed that wheat can interfere with Pseudomonas secondary metabolism production through its root metabolites. Interestingly, production of Pseudomonas bioactive metabolites, such as phloroglucinol, ph

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Zhang, Zhonghui, Feng Zhang, Yuan Deng, et al. "Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice." Metabolites 12, no. 5 (2022): 384. http://dx.doi.org/10.3390/metabo12050384.

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Rice (Oryza sativa L.) is one of the most globally important crops, nutritionally and economically. Therefore, analyzing the genetic basis of its nutritional quality is a paramount prerequisite for cultivating new varieties with increased nutritional health. To systematically compare the nutritional quality differences between landraces and cultivated rice, and to mine key genes that determine the specific nutritional traits of landraces, a seed metabolome database of 985 nutritional metabolites covering amino acids, flavonoids, anthocyanins, and vitamins by a widely targeted metabolomic appro

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Brindle, Kevin M. "Metabolomics: Pandora's Box or Aladdin's Cave?" Biochemist 25, no. 1 (2003): 15–17. http://dx.doi.org/10.1042/bio02501015.

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Functional genomics, the elucidation of gene function from studies of the effects of gene modification on cellular phenotype, has prompted the development of massively parallel and increasingly comprehensive screening tools for assessing the expression of mRNAs (transcriptomics) and proteins (proteomics). For a more complete description of the effects of changes in genotype or physiological conditions on cellular phenotype, we also need to define the status of a third class of biomolecules in the cell, the small-molecule metabolites. Study of the latter has been termed metabolomics and the met

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Creek, Darren J., Brunda Nijagal, Dong-Hyun Kim, Federico Rojas, Keith R. Matthews, and Michael P. Barrett. "Metabolomics Guides Rational Development of a Simplified Cell Culture Medium for Drug Screening against Trypanosoma brucei." Antimicrobial Agents and Chemotherapy 57, no. 6 (2013): 2768–79. http://dx.doi.org/10.1128/aac.00044-13.

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ABSTRACTIn vitroculture methods underpin many experimental approaches to biology and drug discovery. The modification of established cell culture methods to make them more biologically relevant or to optimize growth is traditionally a laborious task. Emerging metabolomic technology enables the rapid evaluation of intra- and extracellular metabolites and can be applied to the rational development of cell culture media. In this study, untargeted semiquantitative and targeted quantitative metabolomic analyses of fresh and spent media revealed the major nutritional requirements for the growth of b

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Saunier, Amélie, Stéphane Greff, James D. Blande, et al. "Amplified Drought and Seasonal Cycle Modulate Quercus pubescens Leaf Metabolome." Metabolites 12, no. 4 (2022): 307. http://dx.doi.org/10.3390/metabo12040307.

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The intensification of summer drought expected with climate change can induce metabolism modifications in plants to face such constraints. In this experiment, we used both a targeted approach focused on flavonoids, as well as an untargeted approach, to study a broader fraction of the leaf metabolome of Quercus pubescens exposed to amplified drought. A forest site equipped with a rainfall exclusion device allowed reduction of natural rainfall by ~30% over the tree canopy. Leaves of natural drought (ND) and amplified drought (AD) plots were collected over three seasonal cycles (spring, summer, a

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Balonov, Ilja, Max Kurlbaum, Ann-Cathrin Koschker, Christine Stier, Martin Fassnacht, and Ulrich Dischinger. "Changes in Plasma Metabolomic Profile Following Bariatric Surgery, Lifestyle Intervention or Diet Restriction—Insights from Human and Rat Studies." International Journal of Molecular Sciences 24, no. 3 (2023): 2354. http://dx.doi.org/10.3390/ijms24032354.

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Although bariatric surgery is known to change the metabolome, it is unclear if this is specific for the intervention or a consequence of the induced bodyweight loss. As the weight loss after Roux-en-Y Gastric Bypass (RYGB) can hardly be mimicked with an evenly effective diet in humans, translational research efforts might be helpful. A group of 188 plasma metabolites of 46 patients from the randomized controlled Würzburg Adipositas Study (WAS) and from RYGB-treated rats (n = 6) as well as body-weight-matched controls (n = 7) were measured using liquid chromatography tandem mass spectrometry. W

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Včelařová, Ludmila, Vladimír Skalický, Ivo Chamrád, et al. "Auxin Metabolome Profiling in the Arabidopsis Endoplasmic Reticulum Using an Optimised Organelle Isolation Protocol." International Journal of Molecular Sciences 22, no. 17 (2021): 9370. http://dx.doi.org/10.3390/ijms22179370.

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The endoplasmic reticulum (ER) is an extensive network of intracellular membranes. Its major functions include proteosynthesis, protein folding, post-transcriptional modification and sorting of proteins within the cell, and lipid anabolism. Moreover, several studies have suggested that it may be involved in regulating intracellular auxin homeostasis in plants by modulating its metabolism. Therefore, to study auxin metabolome in the ER, it is necessary to obtain a highly enriched (ideally, pure) ER fraction. Isolation of the ER is challenging because its biochemical properties are very similar

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Desmet, Sandrien, Kris Morreel, and Rebecca Dauwe. "Origin and Function of Structural Diversity in the Plant Specialized Metabolome." Plants 10, no. 11 (2021): 2393. http://dx.doi.org/10.3390/plants10112393.

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The plant specialized metabolome consists of a multitude of structurally and functionally diverse metabolites, variable from species to species. The specialized metabolites play roles in the response to environmental changes and abiotic or biotic stresses, as well as in plant growth and development. At its basis, the specialized metabolism is built of four major pathways, each starting from a few distinct primary metabolism precursors, and leading to distinct basic carbon skeleton core structures: polyketides and fatty acid derivatives, terpenoids, alkaloids, and phenolics. Structural diversit

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Wu, Si, Jun Zhang, Feifei Li, et al. "One-Carbon Metabolism Links Nutrition Intake to Embryonic Development via Epigenetic Mechanisms." Stem Cells International 2019 (March 10, 2019): 1–8. http://dx.doi.org/10.1155/2019/3894101.

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Beyond energy production, nutrient metabolism plays a crucial role in stem cell lineage determination. Changes in metabolism based on nutrient availability and dietary habits impact stem cell identity. Evidence suggests a strong link between metabolism and epigenetic mechanisms occurring during embryonic development and later life of offspring. Metabolism regulates epigenetic mechanisms such as modifications of DNA, histones, and microRNAs. In turn, these epigenetic mechanisms regulate metabolic pathways to modify the metabolome. One-carbon metabolism (OCM) is a crucial metabolic process invol

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Tong, Tong, Si Chen, Lianrong Wang, et al. "Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria." Proceedings of the National Academy of Sciences 115, no. 13 (2018): E2988—E2996. http://dx.doi.org/10.1073/pnas.1721916115.

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The chemical diversity of physiological DNA modifications has expanded with the identification of phosphorothioate (PT) modification in which the nonbridging oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together with DndFGH as cognate restriction enzymes, DNA PT modification, which is catalyzed by the DndABCDE proteins, functions as a bacterial restriction-modification (R-M) system that protects cells against invading foreign DNA. However, the occurrence of dnd systems across a large number of bacterial genomes and their functions other than R-M are poorly understood. H

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Shen, Ling, Catherine Roullier, François-Hugues Porée, et al. "Complementary Strategies to Unlock Biosynthesis Gene Clusters Encoding Secondary Metabolites in the Filamentous Fungus Podospora anserina." Journal of Fungi 9, no. 1 (2022): 9. http://dx.doi.org/10.3390/jof9010009.

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The coprophilous ascomycete Podospora anserina is known to have a high potential to synthesize a wide array of secondary metabolites (SMs). However, to date, the characterization of SMs in this species, as in other filamentous fungal species, is far less than expected by the functional prediction through genome mining, likely due to the inactivity of most SMs biosynthesis gene clusters (BGCs) under standard conditions. In this work, our main objective was to compare the global strategies usually used to deregulate SM gene clusters in P. anserina, including the variation of culture conditions a

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Sookaromdee, Pathum, and Viroj Wiwanitkit. "Tuberculous pleural effusion: Modification of metabolome by the effect of common metabolic disease, diabetes mellitus." Biomedical and Biotechnology Research Journal (BBRJ) 3, no. 1 (2019): 19. http://dx.doi.org/10.4103/bbrj.bbrj_34_19.

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Veach, Allison M., Daniel Yip, Nancy L. Engle, et al. "Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants." Plant and Soil 429, no. 1-2 (2018): 349–61. http://dx.doi.org/10.1007/s11104-018-3692-8.

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Bi, Xiaoyi, Ling Liao, Lijun Deng, et al. "Combined Transcriptome and Metabolome Analyses Reveal Candidate Genes Involved in Tangor (Citrus reticulata × Citrus sinensis) Fruit Development and Quality Formation." International Journal of Molecular Sciences 23, no. 10 (2022): 5457. http://dx.doi.org/10.3390/ijms23105457.

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Tangor, an important citrus type, is a hybrid of orange and mandarin and possesses their advantageous characteristics. Fruit quality is an important factor limiting the development of the citrus industry and highly depends on fruit development and ripening programs. However, fruit development and quality formation have not been completely explored in mandarin-orange hybrids. We sequenced the metabolome and transcriptome of three mandarin-orange hybrid cultivars at the early fruiting [90 days after full bloom (DAFB)], color change (180 DAFB), and ripening (270 DAFB) stages. Metabolome sequencin

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Rojas, Joselyn, Nailet Arraiz, Miguel Aguirre, Manuel Velasco, and Valmore Bermúdez. "AMPK as Target for Intervention in Childhood and Adolescent Obesity." Journal of Obesity 2011 (2011): 1–19. http://dx.doi.org/10.1155/2011/252817.

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Childhood obesity is a major worldwide health problem. Intervention programs to ameliorate the rate of obesity have been designed and implemented; yet the epidemic has no end near in sight. AMP-activated protein kinase (AMPK) has become one of the most important key elements in energy control, appetite regulation, myogenesis, adipocyte differentiation, and cellular stress management. Obesity is a multifactorial disease, which has a very strong genetic component, especially epigenetic factors. The intrauterine milieu has a determinant impact on adult life, since the measures taken for survival

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Hall, Madeline, and Natalia Krupenko. "Dietary Methionine Restriction Reverses Liver Cancer Driving Metabotype in GNMT KO Mice." Current Developments in Nutrition 6, Supplement_1 (2022): 241. http://dx.doi.org/10.1093/cdn/nzac052.008.

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Abstract Objectives Glycine N-methyltransferase (GNMT) is a major liver enzyme that catalyzes the S-adenosyl-methionine (SAM) dependent synthesis of sarcosine from glycine and regulates the availability of SAM for cellular methylation reactions, as well as for detoxification pathways in liver cells. The whole-body enzyme knockout in mice results in dysregulated methionine metabolism, including massive elevations of SAM. As a result, Gnmt−/− mice develop fatty livers and subsequently, hepatocellular carcinomas (HCC). We hypothesize that since the HCC development in Gnmt−/− mice is associated wi

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Zheng, Shanshan, Raquel Loreto, Philip Smith, Andrew Patterson, David Hughes, and Liande Wang. "Specialist and Generalist Fungal Parasites Induce Distinct Biochemical Changes in the Mandible Muscles of Their Host." International Journal of Molecular Sciences 20, no. 18 (2019): 4589. http://dx.doi.org/10.3390/ijms20184589.

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Some parasites have evolved the ability to adaptively manipulate host behavior. One notable example is the fungus Ophiocordyceps unilateralis sensu lato, which has evolved the ability to alter the behavior of ants in ways that enable fungal transmission and lifecycle completion. Because host mandibles are affected by the fungi, we focused on understanding changes in the metabolites of muscles during behavioral modification. We used High-Performance Liquid Chromatography-Mass/Mass (HPLC-MS/MS) to detect the metabolite difference between controls and O. unilateralis-infected ants. There was a si

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Mangeot-Peter, L., T. J. Tschaplinski, N. L. Engle, C. Veneault-Fourrey, F. Martin, and A. Deveau. "Impacts of Soil Microbiome Variations on Root Colonization by Fungi and Bacteria and on the Metabolome of Populus tremula × alba." Phytobiomes Journal 4, no. 2 (2020): 142–55. http://dx.doi.org/10.1094/pbiomes-08-19-0042-r.

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Trees depend on beneficial interactions between roots and soil microbes for their nutrition and protection against stresses. The soil microbiome provides the main reservoir of microbes for root colonization and is subject to natural variations that can affect its composition. It is not clear whether the tree’s root system is able to buffer the natural variations occurring in the soil microbiome to capture a stable and effective microbiome or whether these variations affect its microbiome to impact its physiology. To address this question, we planted cuttings of Gray Poplar (Populus tremula × a

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Reimer, Julia Jessica, Basel Shaaban, Noud Drummen, et al. "Capsicum Leaves under Stress: Using Multi-Omics Analysis to Detect Abiotic Stress Network of Secondary Metabolism in Two Species." Antioxidants 11, no. 4 (2022): 671. http://dx.doi.org/10.3390/antiox11040671.

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The plant kingdom contains an enormous diversity of bioactive compounds which regulate plant growth and defends against biotic and abiotic stress. Some of these compounds, like flavonoids, have properties which are health supporting and relevant for industrial use. Many of these valuable compounds are synthesized in various pepper (Capsicum sp.) tissues. Further, a huge amount of biomass residual remains from pepper production after harvest, which provides an important opportunity to extract these metabolites and optimize the utilization of crops. Moreover, abiotic stresses induce the synthesi

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Olivares-García, Carol A., Martín Mata-Rosas, Carolina Peña-Montes, et al. "Phenylpropanoids Are Connected to Cell Wall Fortification and Stress Tolerance in Avocado Somatic Embryogenesis." International Journal of Molecular Sciences 21, no. 16 (2020): 5679. http://dx.doi.org/10.3390/ijms21165679.

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Somatic embryogenesis (SE) is a valuable model for understanding the mechanism of plant embryogenesis and a tool for the mass production of plants. However, establishing SE in avocado has been complicated due to the very low efficiency of embryo induction and plant regeneration. To understand the molecular foundation of the SE induction and development in avocado, we compared embryogenic (EC) and non-embryogenic (NEC) cultures of two avocado varieties using proteomic and metabolomic approaches. Although Criollo and Hass EC exhibited similarities in the proteome and metabolome profile, in gener

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Mugume, Yosia, Geng Ding, Maria Emilia Dueñas, et al. "Complex Changes in Membrane Lipids Associated with the Modification of Autophagy in Arabidopsis." Metabolites 12, no. 2 (2022): 190. http://dx.doi.org/10.3390/metabo12020190.

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Autophagy is a conserved mechanism among eukaryotes that degrades and recycles cytoplasmic components. Autophagy is known to influence the plant metabolome, including lipid content; however, its impact on the plant lipidome is not fully understood, and most studies have analyzed a single or few mutants defective in autophagy. To gain more insight into the effect of autophagy on lipid concentrations and composition, we quantitatively profiled glycerolipids from multiple Arabidopsis thaliana mutants altered in autophagy and compared them with wild-type seedlings under nitrogen replete (+N; norma

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Puglisi, Fabrizio, Antonella Padella, Nunziatina Laura Parrinello, et al. "Dissecting the Adaptive Response to Arginine Deprivation in Hodgkin Lymphoma." Blood 138, Supplement 1 (2021): 4497. http://dx.doi.org/10.1182/blood-2021-151006.

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Abstract Background In Hodgkin Lymphoma (HL), neoplastic cells orchestrate an inflammatory microenvironment leading to sterile inflammation, T-cell anergy, and immune deficiency. Our group showed that in HL patients the aminoacid degrading enzyme Arginase-1 is increased, associated with poor outcome, and leads to arginine (Arg) deprivation. However, how the reduction of Arg in the extracellular milieu of the tumor microenvironment can contribute to neoplastic cell fitness is largely unknown. Aims To detect the adaptive response (via evaluation of global transcriptome and metabolome changes) in

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Lin, Shuang, Shaohua Zeng, Biao A, et al. "Integrative Analysis of Transcriptome and Metabolome Reveals Salt Stress Orchestrating the Accumulation of Specialized Metabolites in Lycium barbarum L. Fruit." International Journal of Molecular Sciences 22, no. 9 (2021): 4414. http://dx.doi.org/10.3390/ijms22094414.

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Salt stress seriously affects yield and quality of crops. The fruit of Lycium barbarum (LBF) is extensively used as functional food due to its rich nutrient components. It remains unclear how salt stress influences the quality of LBF. In this study, we identified 71 differentially accumulated metabolites (DAMs) and 1396 differentially expressed genes (DEGs) among ripe LBF with and without 300 mM of NaCl treatment. Pearson correlation analysis indicated that the metabolomic changes caused by salt stress were strongly related to oxidoreductases; hydrolases; and modifying enzymes, in particular,

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Rabbani, Naila, and Paul J. Thornalley. "Reading patterns of proteome damage by glycation, oxidation and nitration: quantitation by stable isotopic dilution analysis LC-MS/MS." Essays in Biochemistry 64, no. 1 (2020): 169–83. http://dx.doi.org/10.1042/ebc20190047.

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Abstract Liquid chromatography-tandem mass spectrometry (LC-MS/MS) provides a high sensitivity, high specificity multiplexed method for concurrent detection of adducts formed by protein glycation, oxidation and nitration, also called AGEomics. Combined with stable isotopic dilution analysis, it provides for robust quantitation of protein glycation, oxidation and nitration adduct analytes. It is the reference method for such measurements. LC-MS/MS has been used to measure glycated, oxidized and nitrated amino acids – also called glycation, oxidation and nitration free adducts, with a concurrent

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Ferreira, Maria João, Diana C. G. A. Pinto, Ângela Cunha, and Helena Silva. "Halophytes as Medicinal Plants against Human Infectious Diseases." Applied Sciences 12, no. 15 (2022): 7493. http://dx.doi.org/10.3390/app12157493.

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Halophytes have long been used for medicinal purposes. However, for many decades, their use was entirely empirical, with virtually no knowledge of the bioactive compounds underlying the different applications. In recent decades, the growing problem of antibiotic resistance triggered the research on alternative antimicrobial approaches, and halophytes, along with other medicinal plants, regained attention as an underexplored pharmacological vein. Furthermore, the high nutritional/nutraceutical/pharmacological value of some halophytic species may represent added value to the emerging activity of

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Lund, Peder, Sarah Smith, Johayra Simithy, et al. "P165 INFLUENCE OF THE GUT MICROBIOTA ON COLONIC HISTONE MODIFICATIONS THROUGH BUTYRATE METABOLISM UNDER HEALTHY AND INFLAMMATORY CONDITIONS." Inflammatory Bowel Diseases 26, Supplement_1 (2020): S40—S41. http://dx.doi.org/10.1093/ibd/zaa010.105.

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Abstract Inflammatory bowel disease (IBD) is often associated with a disruption in the composition and activity of the gut microbiota, referred to as dysbiosis. Since the microbiota has the potential to interact with host epithelial cells through small molecules generated from microbial metabolism, knowledge of how inflammation alters the microbial metabolome and how epithelial cells react is important for a better understanding of how IBD develops and persists. Butyrate, a short chain fatty acid produced through fermentation of dietary polysaccharides, has long been known to inhibit histone d

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Rebholz, Casey M., Aditya Surapaneni, Andrew S. Levey, et al. "The Serum Metabolome Identifies Biomarkers of Dietary Acid Load in 2 Studies of Adults with Chronic Kidney Disease." Journal of Nutrition 149, no. 4 (2019): 578–85. http://dx.doi.org/10.1093/jn/nxy311.

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ABSTRACT Background Dietary acid load is a clinically important aspect of the diet that reflects the balance between acid-producing foods, for example, meat and cheese, and base-producing foods, for example, fruits and vegetables. Methods We used metabolomics to identify blood biomarkers of dietary acid load in 2 independent studies of chronic kidney disease patients: the African American Study of Kidney Disease and Hypertension (AASK, n = 689) and the Modification of Diet in Renal Disease (MDRD, n = 356) study. Multivariable linear regression was used to assess the cross-sectional association

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Vitetta, Luis, Samantha Coulson, and Anthony W. Linnane. "Reactive oxygen species in disease: Rebuttal of a conventional concept." Journal of Controversies in Biomedical Research 1, no. 1 (2015): 23–27. http://dx.doi.org/10.15586/jcbmr.2015.7.

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 The production of intracellular reactive oxygen species and reactive nitrogen species has long been proposed as leading to the random deleterious modification of macromolecules (i.e., nucleic acids, proteins) with an associated progressive development of the age associated systemic diseases (e.g., diabetes, Parkinson’s disease) as well as contributing to the ageing process. Superoxide anion (hydrogen peroxide) and nitric oxide (peroxynitrite) comprise regulated intracellular second messenger pro-oxidant systems, with specific sub-cellular locales of production and are essential for the

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Mercado-Gómez, Maria, Fernando Lopitz-Otsoa, Mikel Azkargorta, et al. "Multi-Omics Integration Highlights the Role of Ubiquitination in CCl4-Induced Liver Fibrosis." International Journal of Molecular Sciences 21, no. 23 (2020): 9043. http://dx.doi.org/10.3390/ijms21239043.

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Liver fibrosis is the excessive accumulation of extracellular matrix proteins that occurs in chronic liver disease. Ubiquitination is a post-translational modification that is crucial for a plethora of physiological processes. Even though the ubiquitin system has been implicated in several human diseases, the role of ubiquitination in liver fibrosis remains poorly understood. Here, multi-omics approaches were used to address this. Untargeted metabolomics showed that carbon tetrachloride (CCl4)-induced liver fibrosis promotes changes in the hepatic metabolome, specifically in glycerophospholipi

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Quinlan, Zachary A., Irina Koester, Allegra T. Aron, et al. "ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction." Metabolites 12, no. 12 (2022): 1275. http://dx.doi.org/10.3390/metabo12121275.

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Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Sili

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Tandon, Sonia, Ines Gonzalez-Casanova, Albino Barraza-Villarreal, et al. "The Effect of Maternal Fatty Acid Desaturase Single Nucleotide Polymorphism rs174602 and Prenatal Supplementation with Docosahexaenoic Acid on the Offspring Metabolome." Current Developments in Nutrition 4, Supplement_2 (2020): 1276. http://dx.doi.org/10.1093/cdn/nzaa058_034.

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Abstract Objectives To assess if maternal fatty acid desaturase (FADS) single nucleotide polymorphism (SNP) rs174602 modifies the effect of prenatal DHA supplementation on the offspring metabolome at age 3 months. Methods Data were obtained from POSGRAD, a double-blind randomized controlled trial in Mexico in which 1094 women received 400 mg/day of algal DHA or a placebo (corn and soy oil) from mid-gestation until delivery. Genotyping was performed using maternal blood samples collected from women at baseline. Using liquid chromatography with high-resolution mass spectrometry, untargeted metab

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Riwes, Mary Mansour, Alexander Schmidt, Thomas Braun, et al. "Rational Modification of Intestinal Microbiome and Metabolites after Allogeneic Hematopoietic Stem Cell Transplantation with Resistant Starch: A Pilot Study." Blood 134, Supplement_1 (2019): 3276. http://dx.doi.org/10.1182/blood-2019-131216.

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Background Graft versus host disease (GVHD) is the principal cause of non-relapse mortality after allogeneic hematopoietic stem cell transplantation (allo HCT) and is associated with intestinal microbial dysbiosis. Administration of microbial metabolite butyrate or microbial cocktails of butyrogenic bacteria reduce the severity of acute GVHD in mice. Furthermore, this intestinal microbiome-metabolome axis can be manipulated via dietary intervention in healthy humans with supplementation by defined quantities of resistant potato starch (RPS), an indigestible carbohydrate that is metabolized by

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Alipour, Shirin, Karolina Bilska, Ewelina Stolarska, Natalia Wojciechowska, and Ewa Marzena Kalemba. "Nicotinamide adenine dinucleotides are associated with distinct redox control of germination in Acer seeds with contrasting physiology." PLOS ONE 16, no. 1 (2021): e0245635. http://dx.doi.org/10.1371/journal.pone.0245635.

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Seed germination is a complex process enabling plant reproduction. Germination was found to be regulated at the proteome, metabolome and hormonal levels as well as via discrete post-translational modification of proteins including phosphorylation and carbonylation. Redox balance is also involved but less studied. Acer seeds displaying orthodox and recalcitrant characteristics were investigated to determine the levels of redox couples of nicotinamide adenine dinucleotide (NAD) phosphate (NADP) and integrated with the levels of ascorbate and glutathione. NAD and NADP concentrations were higher i

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Li, Xiang, Yan Li, Minghui Zhao, et al. "Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Leaf Color Change in Chokecherry (Padus virginiana)." International Journal of Molecular Sciences 22, no. 19 (2021): 10697. http://dx.doi.org/10.3390/ijms221910697.

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Chokecherry (Padus virginiana L.) is an important landscaping tree with high ornamental value because of its colorful purplish-red leaves (PRL). The quantifications of anthocyanins and the mechanisms of leaf color change in this species remain unknown. The potential biosynthetic and regulatory mechanisms and the accumulation patterns of anthocyanins in P. virginiana that determine three leaf colors were investigated by combined analysis of the transcriptome and the metabolome. The difference of chlorophyll, carotenoid and anthocyanin content correlated with the formation of P. virginiana leaf

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Du, Lin, April L. Risinger, Carter A. Mitchell, et al. "Unique amalgamation of primary and secondary structural elements transform peptaibols into potent bioactive cell-penetrating peptides." Proceedings of the National Academy of Sciences 114, no. 43 (2017): E8957—E8966. http://dx.doi.org/10.1073/pnas.1707565114.

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Mass-spectrometry-based metabolomics and molecular phylogeny data were used to identify a metabolically prolific strain ofTolypocladiumthat was obtained from a deep-water Great Lakes sediment sample. An investigation of the isolate’s secondary metabolome resulted in the purification of a 22-mer peptaibol, gichigamin A (1). This peptidic natural product exhibited an amino acid sequence including several β-alanines that occurred in a repeatingααβmotif, causing the compound to adopt a unique right-handed 311helical structure. The unusual secondary structure of 1 was confirmed by spectroscopic app

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Kachroo, Priyadarshini, Joanne E. Sordillo, Sharon M. Lutz, et al. "Pharmaco-Metabolomics of Inhaled Corticosteroid Response in Individuals with Asthma." Journal of Personalized Medicine 11, no. 11 (2021): 1148. http://dx.doi.org/10.3390/jpm11111148.

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Metabolomic indicators of asthma treatment responses have yet to be identified. In this study, we aimed to uncover plasma metabolomic profiles associated with asthma exacerbations while on inhaled corticosteroid (ICS) treatment. We determined whether these profiles change with age from adolescence to adulthood. We utilized data from 170 individuals with asthma on ICS from the Mass General Brigham Biobank to identify plasma metabolites associated with asthma exacerbations while on ICS and examined potential effect modification of metabolite-exacerbation associations by age. We used liquid chrom

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Lau, Zhi Ch’ng, Barakatun Nisak Mohd Yusof, Faridah Abas, Norasyikin Abd Wahab, Wan Zul Haikal Wan Zukiman, and Amin Ismail. "Postprandial Metabolome Following a Low Glycaemic Index Meal-Challenge Test: A Narrative Review." Malaysian Journal of Medical Sciences 29, no. 5 (2022): 5–16. http://dx.doi.org/10.21315/mjms2022.29.5.2.

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The Identifying the dynamic metabolome of the individual in response to a particular stimulus using a metabolomic approach is an emerging research area. Measuring the postprandial metabolite response utilising a meal-challenge test (MCT) provides information beyond the fasting state, which is especially important since human beings spend most of their time in the postprandial state. This is pertinent as an excessive rise in postprandial glycaemia is common in individuals with type 2 diabetes mellitus (T2DM), which puts them at a high risk of developing cardiovascular disease (CVD). While a low

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Lee, Eunbi, Seo Yoon Choi, Jihye Park, Anders M. Lindroth, and Yoon Jung Park. "A Possible Role of Angiogenin in Intergenerational Transmission of Diet-Induced Metabolic Stress." Current Developments in Nutrition 5, Supplement_2 (2021): 508. http://dx.doi.org/10.1093/cdn/nzab041_023.

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Abstract Objectives Epigenetic is one of the possible mechanisms of transmit parental metabolic stress to offspring. tRNA modification or fragmentation is a promising candidate. We investigated the molecular mechanism of intergeneration transmission of diet-induced metabolic stress. Methods Male mice fed with control diet (CD) or high-fat diet (HFD) for 9 weeks. Body weight, amount of food intake and organ weights were measured. Metabolism-related proteins and gene expression were measured in testis and liver. tRNA methylation in sperm was investigated by bisulfite conversion-based sequencing.

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Lima, Ana Rita, Joana Pinto, Filipa Amaro, Maria de Lourdes Bastos, Márcia Carvalho, and Paula Guedes de Pinho. "Advances and Perspectives in Prostate Cancer Biomarker Discovery in the Last 5 Years through Tissue and Urine Metabolomics." Metabolites 11, no. 3 (2021): 181. http://dx.doi.org/10.3390/metabo11030181.

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Prostate cancer (PCa) is the second most diagnosed cancer in men worldwide. For its screening, serum prostate specific antigen (PSA) test has been largely performed over the past decade, despite its lack of accuracy and inability to distinguish indolent from aggressive disease. Metabolomics has been widely applied in cancer biomarker discovery due to the well-known metabolic reprogramming characteristic of cancer cells. Most of the metabolomic studies have reported alterations in urine of PCa patients due its noninvasive collection, but the analysis of prostate tissue metabolome is an ideal ap

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Shi, Lei, and Benjamin P. Tu. "Protein acetylation as a means to regulate protein function in tune with metabolic state." Biochemical Society Transactions 42, no. 4 (2014): 1037–42. http://dx.doi.org/10.1042/bst20140135.

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Protein acetylation has emerged as a prominent post-translational modification that can occur on a wide variety of proteins. The metabolite acetyl-CoA is a key intermediate in energy metabolism that also serves as the acetyl group donor in protein acetylation modifications. Therefore such acetylation modifications might be coupled to the intracellular availability of acetyl-CoA. In the present article, we summarize recent evidence suggesting that the particular protein acetylation modifications enable the regulation of protein function in tune with acetyl-CoA availability and thus the metaboli

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Donnellan, Leigh, Clifford Young, Bradley S. Simpson, et al. "Proteomic Analysis of Methylglyoxal Modifications Reveals Susceptibility of Glycolytic Enzymes to Dicarbonyl Stress." International Journal of Molecular Sciences 23, no. 7 (2022): 3689. http://dx.doi.org/10.3390/ijms23073689.

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Methylglyoxal (MGO) is a highly reactive cellular metabolite that glycates lysine and arginine residues to form post-translational modifications known as advanced glycation end products. Because of their low abundance and low stoichiometry, few studies have reported their occurrence and site-specific locations in proteins. Proteomic analysis of WIL2-NS B lymphoblastoid cells in the absence and presence of exogenous MGO was conducted to investigate the extent of MGO modifications. We found over 500 MGO modified proteins, revealing an over-representation of these modifications on many glycolytic

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Wesseler, Katharina, Florian Kraft, and Thomas Eggermann. "Molecular and Clinical Opposite Findings in 11p15.5 Associated Imprinting Disorders: Characterization of Basic Mechanisms to Improve Clinical Management." International Journal of Molecular Sciences 20, no. 17 (2019): 4219. http://dx.doi.org/10.3390/ijms20174219.

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Silver–Russell and Beckwith–Wiedemann syndromes (SRS, BWS) are rare congenital human disorders characterized by opposite growth disturbances. With the increasing knowledge on the molecular basis of SRS and BWS, it has become obvious that the disorders mirror opposite alterations at the same genomic loci in 11p15.5. In fact, these changes directly or indirectly affect the expression of IGF2 and CDKN1C and their associated pathways, and thereby, cause growth disturbances as key features of both diseases. The increase of knowledge has become possible with the development and implementation of new

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Rosa, Maria Francesca, Paola Scano, Antonio Noto, et al. "Monitoring the Modifications of the Vitreous Humor Metabolite Profile after Death: An Animal Model." BioMed Research International 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/627201.

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We applied a metabolomic approach to monitor the modifications occurring in goat vitreous humor (VH) metabolite composition at different times (0, 6, 12, 18, and 24 hours) after death. The1H-NMR analysis of the VH samples was performed for the simultaneous determination of several metabolites (i.e., the metabolite profile) representative of the VHstatusat different times. Spectral data were analyzed by Principal Component Analysis (PCA) and by Orthogonal Projection to Latent Structures (OPLS) regression technique. PCA and OPLS suggested that different spectral regions were involved in time-rel

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García-Chávez, J. Noé, Verónica R. Vásquez-Garzón, Mercedes G. López, Saúl Villa-Treviño, and Rafael Montiel. "Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma." PLOS ONE 16, no. 8 (2021): e0256016. http://dx.doi.org/10.1371/journal.pone.0256016.

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Mitochondria participate in multiple functions in eukaryotic cells. Although disruption of mitochondrial function has been associated with energetic deregulation in cancer, the chronological changes in mitochondria during cancer development remain unclear. With the aim to assess the role of mitochondria throughout cancer development, we analyzed samples chronologically obtained from induced hepatocellular carcinoma (HCC) in rats. In our analyses, we integrated mitochondrial proteomic data, mitochondrial metabolomic data and nuclear genome transcriptomic data. We used pathway over-representatio

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Thompson, Sharon, Ziyang Pan, Caitlyn Edwards, Ginger Reeser, Naiman Khan, and Hannah Holscher. "The Impact of Fresh Hass Avocado on the Fecal Metabolome Among Adults with Overweight and Obesity: A Randomized, Controlled Trial." Current Developments in Nutrition 4, Supplement_2 (2020): 1593. http://dx.doi.org/10.1093/cdn/nzaa062_050.

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Abstract Objectives Avocados are nutrient-rich fruits that have been recently linked to beneficial alterations to the gastrointestinal microbiota. However, previous research on shifts in the fecal metabolome with avocado intake has largely been conducted in in vitro or preclinical models and little is known about their metabolomic impact in human subjects. Methods Adult participants (n = 109) 25–45 years of age with BMI ≥ 25.0 kg/m2 were enrolled in an investigator-blinded, parallel arm, randomized, controlled trial. Participants consumed isocaloric meals with or without fresh Hass avocado onc

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Kikushige, Yoshikane, Toshihiro Miyamoto, Takahiro Maeda, and Koichi Akashi. "Human Acute Leukemia Is Addicted to Branched-Chain Amino Acid Metabolism to Maintain Leukemia Stemness." Blood 134, Supplement_1 (2019): 2516. http://dx.doi.org/10.1182/blood-2019-129372.

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Hematopoietic stem cells (HSCs) have capabilities to self-renew, maintaining an undifferentiated status, as well as to proliferate and mature into blood cells. Similarly, cancer stem cells (CSCs) self-renew and propagate to form cancer tissues. In human acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), CSC-like populations that can reconstitute human leukemia in immuno-deficient mice have been found, and are called leukemic stem cells or leukemia-initiating cells (LICs). In order to obtain "cure" by eradicating LICs, it should be critical to understand molecular machineries

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Brehin, Camille, Damien Dubois, Odile Dicky, Sophie Breinig, Eric Oswald, and Matteo Serino. "Evolution of Gut Microbiome and Metabolome in Suspected Necrotizing Enterocolitis: A Case-Control Study." Journal of Clinical Medicine 9, no. 7 (2020): 2278. http://dx.doi.org/10.3390/jcm9072278.

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Background: Necrotizing enterocolitis (NEC) is a devastating condition in preterm infants due to multiple factors, including gut microbiota dysbiosis. NEC development is poorly understood, due to the focus on severe NEC (NEC-2/3). Methods: We studied the gut microbiota, microbiome and metabolome of children with suspected NEC (NEC-1). Results: NEC-1 gut microbiota had a higher abundance of the Streptococcus (second 10-days of life) and Staphylococcus (third 10-days of life) species. NEC-1 children showed a microbiome evolution in the third 10-days of life being the most divergent, and were ass

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Thomas, Daniel, Yusuke Nakauchi, Manhong Wu, et al. "IDH1 Mutant AML Is Susceptible to Targeting De Novo Lipid Synthesis Independent of 2-Hydroxyglutarate and Has a Distinct Metabolic Profile from IDH2 Mutant AML." Blood 132, Supplement 1 (2018): 440. http://dx.doi.org/10.1182/blood-2018-99-115040.

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Abstract Introduction: Mutations in IDH1 and IDH2 are recurrent in AML and several other cancers, resulting in the aberrant production of the onco-metabolite, R-2-hydroxyglutarate (2-HG), as well as an inability of mutant IDH1 to convert cytoplasmic alpha-ketoglutarate to isocitrate via reductive carboxylation. Currently, inhibitors of the neomorphic enzymes that abrogate the production of 2-HG, such as AG-120, are FDA-approved, but are not curative. Using a novel computational method (MiSL), we identified acetyl CoA carboxylase (ACACA) as a potential druggable target specifically in IDH1-muta

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Boullaud, Luc, Hélène Blasco, Eliott Caillaud, Patrick Emond, and David Bakhos. "Immediate-Early Modifications to the Metabolomic Profile of the Perilymph Following an Acoustic Trauma in a Sheep Model." Journal of Clinical Medicine 11, no. 16 (2022): 4668. http://dx.doi.org/10.3390/jcm11164668.

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The pathophysiological mechanisms of noise-induced hearing loss remain unknown. Identifying biomarkers of noise-induced hearing loss may increase the understanding of pathophysiological mechanisms of deafness, allow for a more precise diagnosis, and inform personalized treatment. Emerging techniques such as metabolomics can help to identify these biomarkers. The objective of the present study was to investigate immediate-early changes in the perilymph metabolome following acoustic trauma. Metabolomic analysis was performed using liquid chromatography coupled to mass spectrophotometry to analyz

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Harjivan, Shrika G., Catarina Charneira, Inês L. Martins, et al. "Covalent Histone Modification by an Electrophilic Derivative of the Anti-HIV Drug Nevirapine." Molecules 26, no. 5 (2021): 1349. http://dx.doi.org/10.3390/molecules26051349.

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Nevirapine (NVP), a non-nucleoside reverse transcriptase inhibitor widely used in combined antiretroviral therapy and to prevent mother-to-child transmission of the human immunodeficiency virus type 1, is associated with several adverse side effects. Using 12-mesyloxy-nevirapine, a model electrophile of the reactive metabolites derived from the NVP Phase I metabolite, 12-hydroxy-NVP, we demonstrate that the nucleophilic core and C-terminal residues of histones are targets for covalent adduct formation. We identified multiple NVP-modification sites at lysine (e.g., H2BK47, H4K32), histidine (e.

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