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www.nature.com/scientificreports OPEN Comprehensive polar metabolomics and lipidomics profling discriminates the transformed from the non‑transformed state in colon tissue and cell lines Caroline Rombouts1,2,3, Margot De Spiegeleer1, Lieven Van Meulebroek1, Lynn Vanhaecke1,4,5* & Winnok H. De Vos3,5* Colorectal cancer (CRC) is the fourth most lethal disease worldwide. Despite an urgent need for therapeutic advance, selective target identifcation in a preclinical phase is hampered by molecular and metabolic variations between cellular models. To foster optimal model selection from a translational perspective, we performed untargeted ultra‑high performance liquid chromatography coupled to high‑resolution mass spectrometry‑based polar metabolomics and lipidomics to non‑ transformed (CCD841‑CON and FHC) and transformed (HCT116, HT29, Caco2, SW480 and SW948) colon cell lines as well as tissue samples from ten colorectal cancer patients. This unveiled metabolic signatures discriminating the transformed from the non‑transformed state. Metabolites involved in glutaminolysis, tryptophan catabolism, pyrimidine, lipid and carnitine synthesis were elevated in transformed cells and cancerous tissue, whereas those involved in the glycerol‑3‑phosphate shuttle, urea cycle and redox reactions were lowered. The degree of glutaminolysis and lipid synthesis was specifc to the colon cancer cell line at hand. Thus, our study exposed pathways that are specifcally associated with the transformation state and revealed diferences between colon cancer cell lines that should be considered when targeting cancer‑associated pathways. Colorectal cancer (CRC) is the second and third most diagnosed cancer in females and males, respectively, and the fourth leading cause of cancer-related mortality worldwide. Te incidence rates are strongly variable throughout the world, whereby developed regions have more CRC patients than less developed countries. -
Liquid Chromatography with Electrospray Ionization And
Hindawi Publishing Corporation International Journal of Analytical Chemistry Volume 2016, Article ID 9269357, 8 pages http://dx.doi.org/10.1155/2016/9269357 Research Article Liquid Chromatography with Electrospray Ionization and Tandem Mass Spectrometry Applied in the Quantitative Analysis of Chitin-Derived Glucosamine for a Rapid Estimation of Fungal Biomass in Soil Madelen A. Olofsson and Dan Bylund DepartmentofNaturalSciences,MidSwedenUniversity,85170Sundsvall,Sweden Correspondence should be addressed to Madelen A. Olofsson; [email protected] Received 2 September 2015; Accepted 12 January 2016 Academic Editor: Frantisek Foret Copyright © 2016 M. A. Olofsson and D. Bylund. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This method employs liquid chromatography-tandem mass spectrometry to rapidly quantify chitin-derived glucosamine for estimating fungal biomass. Analyte retention was achieved using hydrophilic interaction liquid chromatography, with a zwitter- ionic stationary phase (ZIC-HILIC), and isocratic elution using 60% 5 mM ammonium formate buffer (pH 3.0) and 40% ACN. Inclusion of muramic acid and its chromatographic separation from glucosamine enabled calculation of the bacterial contribution to the latter. Galactosamine, an isobaric isomer to glucosamine, found in significant amounts in soil samples, was also investigated. Thetwoisomersformthesameprecursorandproductionsandcouldnotbechromatographicallyseparatedusingthisrapid method. Instead, glucosamine and galactosamine were distinguished mathematically, using the linear relationships describing the differences in product ion intensities for the two analytes. The m/z transitions of 180 → 72 and 180 → 84 were applied for the detection of glucosamine and galactosamine and that of 252 → 126 for muramic acid. -
Chapter 12 Slides
11/15/17 CHAPTER 12: Carbohydrates: Structure and Function OUTLINE • 12.1 Role of Carbohydrates • 12.2 Monosaccharides • 12.3 Complex Carbohydrates • 12.4 Carbohydrate Catabolism • 12.5 Oligosaccharides as Cell Markers CHAPTER 12: Carbohydrates: Structure and Function WHAT ARE CARBOHYDRATES? • Glucose and its derivatives are carbohydrates: Ø Carbohydrates are simple organic molecules that have a shared basic chemical Formula: Cn(H2O)n Ø The name “carbo + hydrate” represents that Fact that they are made from CO2 and H2O by photosynthesis • About halF oF all earth’s solid carbon is Found in two polymers of glucose found in plants: Ø Starch = major energy storage molecule Ø Cellulose = major structural component oF the plant cell wall (aka. “fiber”) CHAPTER 12: Carbohydrates: Structure and Function THE SIMPLEST CARBOHYDRATES • Monosaccharides are carbohydrates that cannot be hydrolyZed into simpler carbohydrates: Ø These are the Fundamental building blocks For all other carbohydrates (oFten called “simple sugars”) Ø All have Formulas of based on the basic pattern: Cn(H2O)n • Monosaccharides have speciFic Functional groups: 1. An aldehyde OR a ketone (not both!) 2. Several (two or more) alcohol (-OH) groups 1 11/15/17 CHAPTER 12: Carbohydrates: Structure and Function STRUCTURE & NOMENCLATURE OF MONOSACCHARIDES • Monosaccharides are classiFied by two features: 1. Length of their main carbon chain (utilize standard IUPAC naming For # oF carbons) 2. Whether they contain an aldehyde or ketone group • Names always end with –ose • Two common hexoses: -
Amino Sugars and Muramic Acid—Biomarkers for Soil Microbial Community Structure Analysis
Soil Biology & Biochemistry 36 (2004) 399–407 www.elsevier.com/locate/soilbio Amino sugars and muramic acid—biomarkers for soil microbial community structure analysis Bruno Glasera,*, Marı´a-Bele´n Turrio´nb, Kassem Alefc aInstitute of Soil Science and Soil Geography, University of Bayreuth, Bayreuth D-95440, Germany bArea of Soil Science and Soil Chemistry, ETSIIAA, University of Valladolid, Palencia 34004, Spain cUmwelt und Technologie Consulting, Bayreuth D-95448, Germany Received 13 December 2002; received in revised form 22 July 2003; accepted 7 October 2003 Abstract Characterizing functional and phylogenetic microbial community structure in soil is important for understanding the fate of microbially- derived compounds during the decomposition and turn-over of soil organic matter. This study was conducted to test whether amino sugars and muramic acid are suitable biomarkers to trace bacterial, fungal, and actinomycetal residues in soil. For this aim, we investigated the pattern, amounts, and dynamics of three amino sugars (glucosamine, mannosamine and galactosamine) and muramic acid in the total microbial biomass and selectively cultivated bacteria, fungi, and actinomycetes offive different soils amended with and without glucose. Our results revealed that total amino sugar and muramic acid concentrations in microbial biomass, extracted from soil after chloroform fumigation varied between 1 and 27 mg kg21 soil. In all soils investigated, glucose addition resulted in a 50–360% increase of these values. In reference to soil microbial biomass-C, the total amino sugar- and muramic acid-C concentrations ranged from 1–71 g C kg21 biomass-C. After an initial lag phase, the cultivated microbes revealed similar amino sugar concentrations of about 35, 27 and 17 g glucosamine-C kg21 TOC in bacteria, fungi, and actinomycetes, respectively. -
Cysteine Dioxygenase 1 Is a Metabolic Liability for Non-Small Cell Lung Cancer Authors: Yun Pyo Kang1, Laura Torrente1, Min Liu2, John M
bioRxiv preprint doi: https://doi.org/10.1101/459602; this version posted November 1, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Cysteine dioxygenase 1 is a metabolic liability for non-small cell lung cancer Authors: Yun Pyo Kang1, Laura Torrente1, Min Liu2, John M. Asara3,4, Christian C. Dibble5,6 and Gina M. DeNicola1,* Affiliations: 1 Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA 2 Proteomics and Metabolomics Core Facility, Moffitt Cancer Center and Research Institute, Tampa, FL, USA 3 Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA 4 Department of Medicine, Harvard Medical School, Boston, MA, USA 5 Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA, USA 6 Department of Pathology, Harvard Medical School, Boston, MA, USA *Correspondence to: [email protected]. Keywords: KEAP1, NRF2, cysteine, CDO1, sulfite Summary NRF2 is emerging as a major regulator of cellular metabolism. However, most studies have been performed in cancer cells, where co-occurring mutations and tumor selective pressures complicate the influence of NRF2 on metabolism. Here we use genetically engineered, non-transformed primary cells to isolate the most immediate effects of NRF2 on cellular metabolism. We find that NRF2 promotes the accumulation of intracellular cysteine and engages the cysteine homeostatic control mechanism mediated by cysteine dioxygenase 1 (CDO1), which catalyzes the irreversible metabolism of cysteine to cysteine sulfinic acid (CSA). Notably, CDO1 is preferentially silenced by promoter methylation in non-small cell lung cancers (NSCLC) harboring mutations in KEAP1, the negative regulator of NRF2. -
Methionine + Cystine Levels and Vitamin B6 Supplementation on Performance and Enzyme Expression of Methionine Metabolism of Gilts from 75 to 100 Kg
Revista Brasileira de Zootecnia Brazilian Journal of Animal Science © 2017 Sociedade Brasileira de Zootecnia ISSN 1806-9290 R. Bras. Zootec., 46(3):223-230, 2017 www.sbz.org.br Methionine + cystine levels and vitamin B6 supplementation on performance and enzyme expression of methionine metabolism of gilts from 75 to 100 kg Cleiton Pagliari Sangali1*, Eliane Gasparino2, Ricardo Souza Vasconcellos2, Marcelise Regina Fachinello1, Alessandra Nardina Trícia Rigo Monteiro1, Lucas Antonio Costa Esteves1, Lucas Pimentel Bonagurio1, Paulo Cesar Pozza2 1 Universidade Estadual de Maringá, Programa de Pós-graduação em Zootecnia, Maringá, PR, Brazil. 2 Universidade Estadual de Maringá, Departamento de Zootecnia, Maringá, PR, Brazil. ABSTRACT - This study was carried out to evaluate the effect of different levels of standardized ileal digestible (SID) methionine + cystine (Met+Cys) and vitamin B6 supplementation on the performance, blood variables, and gene expression of enzymes involved in methionine metabolism in female pigs between 75 and 100 kg. Fifty six female pigs were used (Talent × Topigs 20), averaging 75.06±1.68 kg in initial weight, allotted in a completely randomized block design arranged in a 2 × 4 factorial scheme, composed of two vitamin B6 supplementation levels (1.58 and 3.58 mg/kg) and four levels of SID Met+Cys (0.370, 0.470, 0.570, and 0.670%), with seven replicates and one animal per experimental unit. No interactions between vitamin B6 supplementation and SID Met+Cys levels were observed. The levels of SID Met+Cys and vitamin B6 supplementation did not affect animal performance. Triacylglycerols showed a quadratic response to the SID Met+Cys levels, in which the lowest plasma concentration was estimated as 0.575%. -
Xorox Univerelty Microfilms
INFORMATION TO USERS This material was producad from a microfilm copy of the original document. While the moit advanced technological meant to photograph and reproduce thii document have been used, the quality it heavily dependent upon the quality of the original submitted. The following explanation of techniques is provided to help ou understand markings or patterns which may appear on this reproduction. 1. The sign or "target" for pages apparently lacking from the document photographed is "Missing Page(s)". If it was possible to ob tain the mining page(s) or section, they are spliced into the film along w ith: adjacent pages, This may have necessitated cutting thru an image and dupli eating adjacent pages to insure you complete continuity. 2. When an image on the film is obliterated with a large round black mark, it is an indication that the photographer suspected that the copy may have moved during exposure and thus cause a blurred image, fou will find a good image of the page in the adjacent frame. 3. When a map, drawing or chart, etc., was part of the material being photographed the photographer followed a definite method in "sectioning” the material. It is customary to begin photoi ig at the upper left hand comer of a large dieet and to continue photoi ig from left to right in equal sections with a small overlap. If necessary, sectioning is continued agein — beginning below the first row and continuing on until complete. 4. The majority of users indicate that the textual content is of greatest value, however, a somewhat higher quality reproduction could be made from "photographs" if essential to the understanding of the dissertation. -
Serum Metabolite Profiles As Potential Biochemical Markers in Young
www.nature.com/scientificreports OPEN Serum metabolite profles as potential biochemical markers in young adults with community- acquired pneumonia cured by moxifoxacin therapy Bo Zhou1, Bowen Lou2,4, Junhui Liu3* & Jianqing She2,4* Despite the utilization of various biochemical markers and probability calculation algorithms based on clinical studies of community-acquired pneumonia (CAP), more specifc and practical biochemical markers remain to be found for improved diagnosis and prognosis. In this study, we aimed to detect the alteration of metabolite profles, explore the correlation between serum metabolites and infammatory markers, and seek potential biomarkers for young adults with CAP. 13 Eligible young mild CAP patients between the ages of 18 and 30 years old with CURB65 = 0 admitted to the respiratory medical department were enrolled, along with 36 healthy participants as control. Untargeted metabolomics profling was performed and metabolites including alcohols, amino acids, carbohydrates, fatty acids, etc. were detected. A total of 227 serum metabolites were detected. L-Alanine, 2-Hydroxybutyric acid, Methylcysteine, L-Phenylalanine, Aminoadipic acid, L-Tryptophan, Rhamnose, Palmitoleic acid, Decanoylcarnitine, 2-Hydroxy-3-methylbutyric acid and Oxoglutaric acid were found to be signifcantly altered, which were enriched mainly in propanoate and tryptophan metabolism, as well as antibiotic-associated pathways. Aminoadipic acid was found to be signifcantly correlated with CRP levels and 2-Hydroxy-3-methylbutyric acid and Palmitoleic acid with PCT levels. The top 3 metabolites of diagnostic values are 2-Hydroxybutyric acid(AUC = 0.90), Methylcysteine(AUC = 0.85), and L-Alanine(AUC = 0.84). The AUC for CRP and PCT are 0.93 and 0.91 respectively. -
Analysis of Proteomic Responses of Freeze-Dried Oenococcus Oeni to Access the Molecular Mechanism of Acid Acclimation on Cell Freeze-Drying Resistance
Accepted Manuscript Analysis of proteomic responses of freeze-dried Oenococcus oeni to access the molecular mechanism of acid acclimation on cell freeze-drying resistance Kun Yang, Yang Zhu, Yiman Qi, Tingjing Zhang, Miaomiao Liu, Jie Zhang, Xinyuan Wei, Mingtao Fan, Guoqiang Zhang PII: S0308-8146(19)30188-8 DOI: https://doi.org/10.1016/j.foodchem.2019.01.120 Reference: FOCH 24215 To appear in: Food Chemistry Received Date: 2 October 2018 Revised Date: 24 December 2018 Accepted Date: 17 January 2019 Please cite this article as: Yang, K., Zhu, Y., Qi, Y., Zhang, T., Liu, M., Zhang, J., Wei, X., Fan, M., Zhang, G., Analysis of proteomic responses of freeze-dried Oenococcus oeni to access the molecular mechanism of acid acclimation on cell freeze-drying resistance, Food Chemistry (2019), doi: https://doi.org/10.1016/j.foodchem. 2019.01.120 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Analysis of proteomic responses of freeze-dried Oenococcus oeni to access the molecular mechanism of acid acclimation on cell freeze-drying resistance Kun Yang1,2, Yang Zhu3, Yiman Qi2,Tingjing Zhang4, Miaomiao Liu2, Jie Zhang2, Xinyuan Wei2, Mingtao Fan2,*, Guoqiang Zhang1,* 1 College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, 241000, China 2 College of Food Science and Engineering, Northwest A ＆ F University, Yangling, 712100, China 3 School of Agriculture and Food Sciences, University of Queensland, QLD, 4046, Australia 4 College of Food Science and Technology, Henan University of Technology, Zhenzhou, 450001, China * Corresponding author: 1. -
The Metabolic Building Blocks of a Minimal Cell Supplementary
The metabolic building blocks of a minimal cell Mariana Reyes-Prieto, Rosario Gil, Mercè Llabrés, Pere Palmer and Andrés Moya Supplementary material. Table S1. List of enzymes and reactions modified from Gabaldon et. al. (2007). n.i.: non identified. E.C. Name Reaction Gil et. al. 2004 Glass et. al. 2006 number 2.7.1.69 phosphotransferase system glc + pep → g6p + pyr PTS MG041, 069, 429 5.3.1.9 glucose-6-phosphate isomerase g6p ↔ f6p PGI MG111 2.7.1.11 6-phosphofructokinase f6p + atp → fbp + adp PFK MG215 4.1.2.13 fructose-1,6-bisphosphate aldolase fbp ↔ gdp + dhp FBA MG023 5.3.1.1 triose-phosphate isomerase gdp ↔ dhp TPI MG431 glyceraldehyde-3-phosphate gdp + nad + p ↔ bpg + 1.2.1.12 GAP MG301 dehydrogenase nadh 2.7.2.3 phosphoglycerate kinase bpg + adp ↔ 3pg + atp PGK MG300 5.4.2.1 phosphoglycerate mutase 3pg ↔ 2pg GPM MG430 4.2.1.11 enolase 2pg ↔ pep ENO MG407 2.7.1.40 pyruvate kinase pep + adp → pyr + atp PYK MG216 1.1.1.27 lactate dehydrogenase pyr + nadh ↔ lac + nad LDH MG460 1.1.1.94 sn-glycerol-3-phosphate dehydrogenase dhp + nadh → g3p + nad GPS n.i. 2.3.1.15 sn-glycerol-3-phosphate acyltransferase g3p + pal → mag PLSb n.i. 2.3.1.51 1-acyl-sn-glycerol-3-phosphate mag + pal → dag PLSc MG212 acyltransferase 2.7.7.41 phosphatidate cytidyltransferase dag + ctp → cdp-dag + pp CDS MG437 cdp-dag + ser → pser + 2.7.8.8 phosphatidylserine synthase PSS n.i. cmp 4.1.1.65 phosphatidylserine decarboxylase pser → peta PSD n.i. -
REVIEW J Am Soc Nephrol 12: 2181–2189, 2001
REVIEW J Am Soc Nephrol 12: 2181–2189, 2001 The Kidney and Homocysteine Metabolism ALLON N. FRIEDMAN,*† ANDREW G. BOSTOM,*‡ JACOB SELHUB,* ANDREW S. LEVEY,† and IRWIN H. ROSENBERG* *Vitamin Metabolism and Aging, Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts; †Division of Nephrology, Tufts University-New England Medical Center, Boston, Massachusetts; and ‡Division of General Internal Medicine, Memorial Hospital of Rhode Island, Pawtucket, Rhode Island. Abstract. Homocysteine (Hcy) is an intermediate of methio- renal Hcy handling and should be considered when measuring nine metabolism that, at elevated levels, is an independent risk Hcy plasma flux and renal clearance. The underlying cause of factor for vascular disease and atherothrombosis. Patients with hyperhomocysteinemia in renal disease is not entirely under- renal disease, who exhibit unusually high rates of cardiovas- stood but seems to involve reduced clearance of plasma Hcy. cular morbidity and death, tend to be hyperhomocysteinemic, This reduction may be attributable to defective renal clearance particularly as renal function declines. This observation and the and/or extrarenal clearance and metabolism, the latter possibly inverse relationship between Hcy levels and GFR implicate the resulting from retained uremic inhibitory substances. Although kidney as an important participant in Hcy handling. The nor- the currently available evidence is not conclusive, it seems mal kidney plays a major role in plasma amino acid clearance more likely that a reduction in renal Hcy clearance and me- and metabolism. The existence in the kidney of specific Hcy tabolism is the cause of the hyperhomocysteinemic state. Ef- uptake mechanisms and Hcy-metabolizing enzymes suggests forts to resolve this important issue will advance the search for that this role extends to Hcy. -
NMR Spectroscopy and MD Simulations of Carbohydrates
NMR spectroscopy and MD simul ations of carbohydrates Elin Säwén © Elin Säwén, Stockholm 2011 Cover picture: Five repeating units of the exopolysaccharide produced by Streptococcus thermophilus ST1 and a 1H NMR spectrum of the same exopolysaccharide. ISSN XXXX-XXXX ISBN XXX-XX-XXXXX-XX-X Printed in Sweden by US-AB, Stockholm 2011 Distributor: Department of Organic Chemistry, Stockholm University Till Ingrid Abstract Knowledge about the structure, conformation and dynamics of carbohydrates is important in our understanding of the way carbohydrates function in bio- logical systems, for example in intermolecular signaling and recognition. This thesis is a summary of five papers studying these properties in carbohy- drate-containing molecules with NMR spectroscopy and molecular dynamics simulations. In paper I, the ring-conformations of the six-membered rings of two car- baiduronic analogs were investigated. These carbasugars could potentially be used as hydrolytically stable mimics of iduronic acid in drugs. The study 4 showed that the equilibrium is entirely shifted towards the C1 conformation. Paper II is an investigation of the conformational flexibility and dynamics of two (1 →6)-linked disaccharides related to an oligosaccharide epitope expressed on malignant tumor cells. In paper III, the conformational space of the glycosidic linkage of the di- saccharide α-D-Man p-(1 →2)-α-D-Man p-OMe, which is present in N- and O- linked glycoproteins, was studied. A maximum entropy analysis using dif- ferent priors as background information was used and four new Karplus 3 3 equations for JC,C and JC,H coupling constants, related to the glycosidic linkage, were presented.