Table S1. Global Proteomic Profile of Rats' Cerebellum Exposed Or Not To
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Supplementary Data
Figure 2S 4 7 A - C 080125 CSCs 080418 CSCs - + IFN-a 48 h + IFN-a 48 h + IFN-a 72 h 6 + IFN-a 72 h 3 5 MRFI 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 7 B 13 080125 FBS - D 080418 FBS - + IFN-a 48 h 12 + IFN-a 48 h + IFN-a 72 h + IFN-a 72 h 6 080125 FBS 11 10 5 9 8 4 7 6 3 MRFI 5 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 Molecule Molecule FIGURE 4S FIGURE 5S Panel A Panel B FIGURE 6S A B C D Supplemental Results Table 1S. Modulation by IFN-α of APM in GBM CSC and FBS tumor cell lines. Molecule * Cell line IFN-α‡ HLA β2-m# HLA LMP TAP1 TAP2 class II A A HC§ 2 7 10 080125 CSCs - 1∞ (1) 3 (65) 2 (91) 1 (2) 6 (47) 2 (61) 1 (3) 1 (2) 1 (3) + 2 (81) 11 (80) 13 (99) 1 (3) 8 (88) 4 (91) 1 (2) 1 (3) 2 (68) 080125 FBS - 2 (81) 4 (63) 4 (83) 1 (3) 6 (80) 3 (67) 2 (86) 1 (3) 2 (75) + 2 (99) 14 (90) 7 (97) 5 (75) 7 (100) 6 (98) 2 (90) 1 (4) 3 (87) 080418 CSCs - 2 (51) 1 (1) 1 (3) 2 (47) 2 (83) 2 (54) 1 (4) 1 (2) 1 (3) + 2 (81) 3 (76) 5 (75) 2 (50) 2 (83) 3 (71) 1 (3) 2 (87) 1 (2) 080418 FBS - 1 (3) 3 (70) 2 (88) 1 (4) 3 (87) 2 (76) 1 (3) 1 (3) 1 (2) + 2 (78) 7 (98) 5 (99) 2 (94) 5 (100) 3 (100) 1 (4) 2 (100) 1 (2) 070104 CSCs - 1 (2) 1 (3) 1 (3) 2 (78) 1 (3) 1 (2) 1 (3) 1 (3) 1 (2) + 2 (98) 8 (100) 10 (88) 4 (89) 3 (98) 3 (94) 1 (4) 2 (86) 2 (79) * expression of APM molecules was evaluated by intracellular staining and cytofluorimetric analysis; ‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α; # β-2 microglobulin; § β-2 microglobulin-free HLA-A heavy chain; ∞ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2). -
Fluorinated Mannosides Inhibit Cellular Fucosylation
Fluorinated mannosides inhibit cellular fucosylation. Johan F.A. Pijnenborg[a],†, Emiel Rossing[a],†, Marek Noga[b], Willem Titulaer[a], Raisa Veizaj[c], Dirk J. Lefeber[b,c] and Thomas J. Boltje*[a] [a] J.F.A. Pijnenborg, E. Rossing, W. Titulaer, Dr. T.J. Boltje Department of Synthetic Organic Chemistry Institute for Molecules and Materials, Radboud University Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands [email protected] [b] Dr. M. Noga, Prof. D.J. Lefeber Department of Laboratory Medicine, Translational Metabolic Laboratory Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands [c] R. Veizaj, Prof. D.J. Lefeber Department of Neurology Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands [†] These authors contributed equally to this work. Supporting information for this article is given via a link at the end of the document. Abstract: Fucose sugars are expressed on mammalian cell L-Fucose (Fuc) is a 6-deoxyhexose expressed at the termini of glycan membranes as part of glycoconjugates and mediates essential chains that decorate cell surface proteins and lipids.1 The fucose physiological processes. The aberrant expression of fucosylated residues on glycoconjugates are essential mediators of physiological glycans has been linked to pathologies such as cancer, inflammation, processes. For example, the fucose moiety in the tetrasaccharide infection, and genetic disorders. Tools to modulate fucose expression sialyl Lewisx (sLex) expressed on leukocytes is recognized by selectin on living cells are needed to elucidate the biological role of fucose receptors that regulate leukocyte recruitment and extravasation. -
An Atpase Domain Common to Prokaryotic Cell Cycle Proteins
Proc. Natl. Acad. Sci. USA Vol. 89, pp. 7290-7294, August 1992 Biochemistry An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp7O heat shock proteins (structural comparison/property pattern/remote homology) PEER BORK, CHRIS SANDER, AND ALFONSO VALENCIA European Molecular Biology Laboratory, D-6900 Heidelberg, Federal Republic of Germany Communicated by Russell F. Doolittle, March 6, 1992 ABSTRACT The functionally diverse actin, hexokinase, and hsp7O protein families have in common an ATPase domain of known three-dimensional structure. Optimal superposition ofthe three structures and alignment ofmany sequences in each of the three families has revealed a set of common conserved residues, distributed in five sequence motifs, which are in- volved in ATP binding and in a putative interdomain hinge. From the multiple sequence aliment in these motifs a pattern of amino acid properties required at each position is defined. The discriminatory power of the pattern is in part due to the use of several known three-dimensional structures and many sequences and in part to the "property" method ofgeneralizing from observed amino acid frequencies to amino acid fitness at each sequence position. A sequence data base search with the pattern significantly matches sugar kinases, such as fuco-, glucono-, xylulo-, ribulo-, and glycerokinase, as well as the prokaryotic cell cycle proteins MreB, FtsA, and StbA. These are predicted to have subdomains with the same tertiary structure as the ATPase subdomains Ia and Ha of hexokinase, actin, and Hsc7O, a very similar ATP binding pocket, and the capacity for interdomain hinge motion accompanying func- tional state changes. -
Dysregulated Hepatic Methionine
Virginia Commonwealth University VCU Scholars Compass Internal Medicine Publications Dept. of Internal Medicine 2015 Dysregulated Hepatic Methionine Metabolism Drives Homocysteine Elevation in Diet-Induced Nonalcoholic Fatty Liver Disease Tommy Pacana Virginia Commonwealth University, [email protected] Sophie Cazanave Virginia Commonwealth University Aurora Verdianelli Virginia Commonwealth University See next page for additional authors Follow this and additional works at: http://scholarscompass.vcu.edu/intmed_pubs Part of the Medicine and Health Sciences Commons Copyright: © 2015 Pacana et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Downloaded from http://scholarscompass.vcu.edu/intmed_pubs/98 This Article is brought to you for free and open access by the Dept. of Internal Medicine at VCU Scholars Compass. It has been accepted for inclusion in Internal Medicine Publications by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Authors Tommy Pacana, Sophie Cazanave, Aurora Verdianelli, Viashali Patel, Hae-Ki Min, Faridoddin Mirshahi, Eoin Quinlavin, and Arun J. Sanyal This article is available at VCU Scholars Compass: http://scholarscompass.vcu.edu/intmed_pubs/98 RESEARCH ARTICLE Dysregulated Hepatic Methionine Metabolism Drives Homocysteine Elevation in Diet-Induced Nonalcoholic Fatty -
Differential Physiological Role of BIN1 Isoforms in Skeletal Muscle Development, Function and Regeneration
bioRxiv preprint doi: https://doi.org/10.1101/477950; this version posted December 11, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Differential physiological role of BIN1 isoforms in skeletal muscle development, function and regeneration Ivana Prokic1,2,3,4, Belinda Cowling1,2,3,4, Candice Kutchukian5, Christine Kretz1,2,3,4, Hichem Tasfaout1,2,3,4, Josiane Hergueux1,2,3,4, Olivia Wendling1,2,3,4, Arnaud Ferry10, Anne Toussaint1,2,3,4, Christos Gavriilidis1,2,3,4, Vasugi Nattarayan1,2,3,4, Catherine Koch1,2,3,4, Jeanne Lainné6,7, Roy Combe2,3,4,8, Laurent Tiret9, Vincent Jacquemond5, Fanny Pilot-Storck9, Jocelyn Laporte1,2,3,4 1Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France 2Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France 3Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France 4Université de Strasbourg, Illkirch, France 5Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, 8 avenue Rockefeller, 69373 Lyon, France 6Sorbonne Université, INSERM, Institute of Myology, Centre of Research in Myology, UMRS 974, F- 75013, Paris, France 7Sorbonne Université, Department of Physiology, UPMC Univ Paris 06, Pitié-Salpêtrière Hospital, F- 75013, Paris, France 8CELPHEDIA-PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France 9U955 – IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, Ecole nationale vétérinaire d’Alfort, Maisons-Alfort, 94700, France 10Sorbonne Université, INSERM, Institute of Myology, Centre of Research in Myology, UMRS 794, F- 75013, Paris, France Correspondence to: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/477950; this version posted December 11, 2018. -
Table 1. Identified Proteins with Expression Significantly Altered in the Hippocampus of Rats of Exposed Group (Pb) Vs
Table 1. Identified proteins with expression significantly altered in the hippocampus of rats of exposed group (Pb) vs. Control. Fold Change Accession Id a Protein Description Score Pb P35213 14-3-3 protein beta/alpha 85420 −0.835 P62260 14-3-3 protein epsilon 96570 −0.878 P68511 14-3-3 protein eta 85420 −0.844 P68255 14-3-3 protein theta 85420 −0.835 P63102 14-3-3 protein zeta/delta 105051 −0.803 P13233 2',3'-cyclic-nucleotide 3'-phosphodiesterase 151400 1.405 P68035 Actin, alpha cardiac muscle 1 442584 −0.942 P68136 Actin, alpha skeletal muscle 441060 −0.970 P62738 Actin, aortic smooth muscle 438270 −0.970 P60711 Actin, cytoplasmic 1 630104 −0.942 P63259 Actin, cytoplasmic 2 630104 −0.942 P63269 Actin, gamma-enteric smooth muscle 438270 −0.951 Q05962 ADP/ATP translocase 1 60100 −0.554 Q09073 ADP/ATP translocase 2 49102 −0.482 P84079 ADP-ribosylation factor 1 34675 −0.644 P84082 ADP-ribosylation factor 2 22412 −0.644 P61206 ADP-ribosylation factor 3 34675 −0.619 P61751 ADP-ribosylation factor 4 22412 −0.670 P84083 ADP-ribosylation factor 5 22412 −0.625 P04764 Alpha-enolase 46219 −0.951 P23565 Alpha-internexin 9478 1.062 P37377 Alpha-synuclein 89619 −0.771 P13221 Aspartate aminotransferase, cytoplasmic 23661 1.083 P00507 Aspartate aminotransferase, mitochondrial 46049 1.116 P10719 ATP synthase subunit beta, mitochondrial 232442 −0.835 P85969 Beta-soluble NSF attachment protein 9638 1.419 Q63754 Beta-synuclein 66842 −0.779 P11275 Calcium/calmodulin-dependent protein kinase type II subunit alpha 181954 1.105 P08413 Calcium/calmodulin-dependent protein kinase type II subunit beta 80840 1.127 P15791 Calcium/calmodulin-dependent protein kinase type II subunit delta 62682 1.105 Int. -
Eradication of ENO1-Deleted Glioblastoma Through Collateral Lethality
bioRxiv preprint doi: https://doi.org/10.1101/331538; this version posted May 25, 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. Eradication of ENO1-deleted Glioblastoma through Collateral Lethality Yu-Hsi Lin1, Nikunj Satani1,2, Naima Hammoudi1, Jeffrey J. Ackroyd1, Sunada Khadka1, Victoria C. Yan1, Dimitra K. Georgiou1, Yuting Sun3, Rafal Zielinski4, Theresa Tran1, Susana Castro Pando1, Xiaobo Wang1, David Maxwell5, Zhenghong Peng6, Federica Pisaneschi1, Pijus Mandal7, Paul G. Leonard8, Quanyu Xu,9 Qi Wu9, Yongying Jiang9, Barbara Czako10, Zhijun Kang10, John M. Asara11, Waldemar Priebe4, William Bornmann12, Joseph R. Marszalek3, Ronald A. DePinho13 and Florian L. Muller#1 1) Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 2) Institute of Stroke and Cerebrovascular Disease, The University of Texas Health Science Center at Houston, TX 77030 3) Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 4) Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 5) Institutional Analytics & Informatics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 6) Cardtronics, Inc., Houston, TX 77042 7) Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 bioRxiv preprint doi: https://doi.org/10.1101/331538; this version posted May 25, 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. -
35 Disorders of Purine and Pyrimidine Metabolism
35 Disorders of Purine and Pyrimidine Metabolism Georges van den Berghe, M.- Françoise Vincent, Sandrine Marie 35.1 Inborn Errors of Purine Metabolism – 435 35.1.1 Phosphoribosyl Pyrophosphate Synthetase Superactivity – 435 35.1.2 Adenylosuccinase Deficiency – 436 35.1.3 AICA-Ribosiduria – 437 35.1.4 Muscle AMP Deaminase Deficiency – 437 35.1.5 Adenosine Deaminase Deficiency – 438 35.1.6 Adenosine Deaminase Superactivity – 439 35.1.7 Purine Nucleoside Phosphorylase Deficiency – 440 35.1.8 Xanthine Oxidase Deficiency – 440 35.1.9 Hypoxanthine-Guanine Phosphoribosyltransferase Deficiency – 441 35.1.10 Adenine Phosphoribosyltransferase Deficiency – 442 35.1.11 Deoxyguanosine Kinase Deficiency – 442 35.2 Inborn Errors of Pyrimidine Metabolism – 445 35.2.1 UMP Synthase Deficiency (Hereditary Orotic Aciduria) – 445 35.2.2 Dihydropyrimidine Dehydrogenase Deficiency – 445 35.2.3 Dihydropyrimidinase Deficiency – 446 35.2.4 Ureidopropionase Deficiency – 446 35.2.5 Pyrimidine 5’-Nucleotidase Deficiency – 446 35.2.6 Cytosolic 5’-Nucleotidase Superactivity – 447 35.2.7 Thymidine Phosphorylase Deficiency – 447 35.2.8 Thymidine Kinase Deficiency – 447 References – 447 434 Chapter 35 · Disorders of Purine and Pyrimidine Metabolism Purine Metabolism Purine nucleotides are essential cellular constituents 4 The catabolic pathway starts from GMP, IMP and which intervene in energy transfer, metabolic regula- AMP, and produces uric acid, a poorly soluble tion, and synthesis of DNA and RNA. Purine metabo- compound, which tends to crystallize once its lism can be divided into three pathways: plasma concentration surpasses 6.5–7 mg/dl (0.38– 4 The biosynthetic pathway, often termed de novo, 0.47 mmol/l). starts with the formation of phosphoribosyl pyro- 4 The salvage pathway utilizes the purine bases, gua- phosphate (PRPP) and leads to the synthesis of nine, hypoxanthine and adenine, which are pro- inosine monophosphate (IMP). -
Contig Protein Description Symbol Anterior Posterior Ratio
Table S2. List of proteins detected in anterior and posterior intestine pooled samples. Data on protein expression are mean ± SEM of 4 pools fed the experimental diets. The number of the contig in the Sea Bream Database (http://nutrigroup-iats.org/seabreamdb) is indicated. Contig Protein Description Symbol Anterior Posterior Ratio Ant/Pos C2_6629 1,4-alpha-glucan-branching enzyme GBE1 0.88±0.1 0.91±0.03 0.98 C2_4764 116 kDa U5 small nuclear ribonucleoprotein component EFTUD2 0.74±0.09 0.71±0.05 1.03 C2_299 14-3-3 protein beta/alpha-1 YWHAB 1.45±0.23 2.18±0.09 0.67 C2_268 14-3-3 protein epsilon YWHAE 1.28±0.2 2.01±0.13 0.63 C2_2474 14-3-3 protein gamma-1 YWHAG 1.8±0.41 2.72±0.09 0.66 C2_1017 14-3-3 protein zeta YWHAZ 1.33±0.14 4.41±0.38 0.30 C2_34474 14-3-3-like protein 2 YWHAQ 1.3±0.11 1.85±0.13 0.70 C2_4902 17-beta-hydroxysteroid dehydrogenase 14 HSD17B14 0.93±0.05 2.33±0.09 0.40 C2_3100 1-acylglycerol-3-phosphate O-acyltransferase ABHD5 ABHD5 0.85±0.07 0.78±0.13 1.10 C2_15440 1-phosphatidylinositol phosphodiesterase PLCD1 0.65±0.12 0.4±0.06 1.65 C2_12986 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-1 PLCD1 0.76±0.08 1.15±0.16 0.66 C2_4412 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 PLCG2 1.13±0.08 2.08±0.27 0.54 C2_3170 2,4-dienoyl-CoA reductase, mitochondrial DECR1 1.16±0.1 0.83±0.03 1.39 C2_1520 26S protease regulatory subunit 10B PSMC6 1.37±0.21 1.43±0.04 0.96 C2_4264 26S protease regulatory subunit 4 PSMC1 1.2±0.2 1.78±0.08 0.68 C2_1666 26S protease regulatory subunit 6A PSMC3 1.44±0.24 1.61±0.08 -
Generated by SRI International Pathway Tools Version 25.0, Authors S
An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility. -
Metabolism of Purines and Pyrimidines in Health and Disease
39th Meeting of the Polish Biochemical Society Gdañsk 16–20 September 2003 SESSION 6 Metabolism of purines and pyrimidines in health and disease Organized by A. C. Sk³adanowski, A. Guranowski 182 Session 6. Metabolism of purines and pyrimidines in health and disease 2003 323 Lecture The role of DNA methylation in cytotoxicity mechanism of adenosine analogues in treatment of leukemia Krystyna Fabianowska-Majewska Zak³ad Chemii Medycznej IFiB, Uniwersytet Medyczny, ul. Mazowiecka 6/8, 92 215 £ódŸ Changes in DNA methylation have been recognized tory effects of cladribine and fludarabine on DNA as one of the most common molecular alterations in hu- methylation, after 48 hr growth of K562 cells with the man neoplastic diseases and hypermethylation of drugs, are non-random and affect mainly CpG rich is- gene-promoter regions is one of the most frequent lands or CCGG sequences but do not affect sepa- mechanisms of the loss of gene functions. For this rea- rately-located CpG sequences. The analysis showed son, DNA methylation may be a tool for detection of that cladribine (0.1 mM) reduced the methylated early cell transformations as well as predisposition to cytosines in CpG islands and CCGG sequences to a sim- metastasis process. Moreover, DNA methylation seems ilar degree. The inhibition of cytosine methylation by to be a promissing target for new preventive and thera- fludarabine (3 mM) was observed mainly in CCGG se- peutic strategies. quences, sensitive to HpaII, but the decline in the meth- Our studies on DNA methylation and cytotoxicity ylated cytosine, located in CpG island was 2-fold lower mechanism of antileukemic drugs, cladribine and than that with cladribine. -
Liver Glucose Metabolism in Humans
Biosci. Rep. (2016) / 36 / art:e00416 / doi 10.1042/BSR20160385 Liver glucose metabolism in humans Mar´ıa M. Adeva-Andany*1, Noemi Perez-Felpete*,´ Carlos Fernandez-Fern´ andez*,´ Cristobal´ Donapetry-Garc´ıa* and Cristina Pazos-Garc´ıa* *Nephrology Division, Hospital General Juan Cardona, c/ Pardo Bazan´ s/n, 15406 Ferrol, Spain Synopsis Information about normal hepatic glucose metabolism may help to understand pathogenic mechanisms underlying obesity and diabetes mellitus. In addition, liver glucose metabolism is involved in glycosylation reactions and con- nected with fatty acid metabolism. The liver receives dietary carbohydrates directly from the intestine via the portal vein. Glucokinase phosphorylates glucose to glucose 6-phosphate inside the hepatocyte, ensuring that an adequate flow of glucose enters the cell to be metabolized. Glucose 6-phosphate may proceed to several metabolic path- ways. During the post-prandial period, most glucose 6-phosphate is used to synthesize glycogen via the formation of glucose 1-phosphate and UDP–glucose. Minor amounts of UDP–glucose are used to form UDP–glucuronate and UDP– galactose, which are donors of monosaccharide units used in glycosylation. A second pathway of glucose 6-phosphate metabolism is the formation of fructose 6-phosphate, which may either start the hexosamine pathway to produce UDP-N-acetylglucosamine or follow the glycolytic pathway to generate pyruvate and then acetyl-CoA. Acetyl-CoA may enter the tricarboxylic acid (TCA) cycle to be oxidized or may be exported to the cytosol to synthesize fatty acids, when excess glucose is present within the hepatocyte. Finally, glucose 6-phosphate may produce NADPH and ribose 5-phosphate through the pentose phosphate pathway.