Characterization of Α-L-Fucosidase and Other Digestive Hydrolases From
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Glycoproteomics-Based Signatures for Tumor Subtyping and Clinical Outcome Prediction of High-Grade Serous Ovarian Cancer
ARTICLE https://doi.org/10.1038/s41467-020-19976-3 OPEN Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer Jianbo Pan 1,2,3, Yingwei Hu1,3, Shisheng Sun 1,3, Lijun Chen1, Michael Schnaubelt1, David Clark1, ✉ Minghui Ao1, Zhen Zhang1, Daniel Chan1, Jiang Qian2 & Hui Zhang 1 1234567890():,; Inter-tumor heterogeneity is a result of genomic, transcriptional, translational, and post- translational molecular features. To investigate the roles of protein glycosylation in the heterogeneity of high-grade serous ovarian carcinoma (HGSC), we perform mass spectrometry-based glycoproteomic characterization of 119 TCGA HGSC tissues. Cluster analysis of intact glycoproteomic profiles delineates 3 major tumor clusters and 5 groups of intact glycopeptides. It also shows a strong relationship between N-glycan structures and tumor molecular subtypes, one example of which being the association of fucosylation with mesenchymal subtype. Further survival analysis reveals that intact glycopeptide signatures of mesenchymal subtype are associated with a poor clinical outcome of HGSC. In addition, we study the expression of mRNAs, proteins, glycosites, and intact glycopeptides, as well as the expression levels of glycosylation enzymes involved in glycoprotein biosynthesis pathways in each tumor. The results show that glycoprotein levels are mainly controlled by the expression of their individual proteins, and, furthermore, that the glycoprotein-modifying glycans cor- respond to the protein levels of glycosylation enzymes. The variation in glycan types further shows coordination to the tumor heterogeneity. Deeper understanding of the glycosylation process and glycosylation production in different subtypes of HGSC may provide important clues for precision medicine and tumor-targeted therapy. -
United States Patent (19) 11 Patent Number: 5,981,835 Austin-Phillips Et Al
USOO598.1835A United States Patent (19) 11 Patent Number: 5,981,835 Austin-Phillips et al. (45) Date of Patent: Nov. 9, 1999 54) TRANSGENIC PLANTS AS AN Brown and Atanassov (1985), Role of genetic background in ALTERNATIVE SOURCE OF Somatic embryogenesis in Medicago. Plant Cell Tissue LIGNOCELLULOSC-DEGRADING Organ Culture 4:107-114. ENZYMES Carrer et al. (1993), Kanamycin resistance as a Selectable marker for plastid transformation in tobacco. Mol. Gen. 75 Inventors: Sandra Austin-Phillips; Richard R. Genet. 241:49-56. Burgess, both of Madison; Thomas L. Castillo et al. (1994), Rapid production of fertile transgenic German, Hollandale; Thomas plants of Rye. Bio/Technology 12:1366–1371. Ziegelhoffer, Madison, all of Wis. Comai et al. (1990), Novel and useful properties of a chimeric plant promoter combining CaMV 35S and MAS 73 Assignee: Wisconsin Alumni Research elements. Plant Mol. Biol. 15:373-381. Foundation, Madison, Wis. Coughlan, M.P. (1988), Staining Techniques for the Detec tion of the Individual Components of Cellulolytic Enzyme 21 Appl. No.: 08/883,495 Systems. Methods in Enzymology 160:135-144. de Castro Silva Filho et al. (1996), Mitochondrial and 22 Filed: Jun. 26, 1997 chloroplast targeting Sequences in tandem modify protein import specificity in plant organelles. Plant Mol. Biol. Related U.S. Application Data 30:769-78O. 60 Provisional application No. 60/028,718, Oct. 17, 1996. Divne et al. (1994), The three-dimensional crystal structure 51 Int. Cl. ............................. C12N 15/82; C12N 5/04; of the catalytic core of cellobiohydrolase I from Tricho AO1H 5/00 derma reesei. Science 265:524-528. -
(10) Patent No.: US 8119385 B2
US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
(12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall Et Al
USOO9689046B2 (12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall et al. (45) Date of Patent: Jun. 27, 2017 (54) SYSTEM AND METHODS FOR THE FOREIGN PATENT DOCUMENTS DETECTION OF MULTIPLE CHEMICAL WO O125472 A1 4/2001 COMPOUNDS WO O169245 A2 9, 2001 (71) Applicants: Robert Matthew Mayall, Calgary (CA); Emily Candice Hicks, Calgary OTHER PUBLICATIONS (CA); Margaret Mary-Flora Bebeselea, A. et al., “Electrochemical Degradation and Determina Renaud-Young, Calgary (CA); David tion of 4-Nitrophenol Using Multiple Pulsed Amperometry at Christopher Lloyd, Calgary (CA); Lisa Graphite Based Electrodes', Chem. Bull. “Politehnica” Univ. Kara Oberding, Calgary (CA); Iain (Timisoara), vol. 53(67), 1-2, 2008. Fraser Scotney George, Calgary (CA) Ben-Yoav. H. et al., “A whole cell electrochemical biosensor for water genotoxicity bio-detection”. Electrochimica Acta, 2009, 54(25), 6113-6118. (72) Inventors: Robert Matthew Mayall, Calgary Biran, I. et al., “On-line monitoring of gene expression'. Microbi (CA); Emily Candice Hicks, Calgary ology (Reading, England), 1999, 145 (Pt 8), 2129-2133. (CA); Margaret Mary-Flora Da Silva, P.S. et al., “Electrochemical Behavior of Hydroquinone Renaud-Young, Calgary (CA); David and Catechol at a Silsesquioxane-Modified Carbon Paste Elec trode'. J. Braz. Chem. Soc., vol. 24, No. 4, 695-699, 2013. Christopher Lloyd, Calgary (CA); Lisa Enache, T. A. & Oliveira-Brett, A. M., "Phenol and Para-Substituted Kara Oberding, Calgary (CA); Iain Phenols Electrochemical Oxidation Pathways”, Journal of Fraser Scotney George, Calgary (CA) Electroanalytical Chemistry, 2011, 1-35. Etesami, M. et al., “Electrooxidation of hydroquinone on simply prepared Au-Pt bimetallic nanoparticles'. Science China, Chem (73) Assignee: FREDSENSE TECHNOLOGIES istry, vol. -
Supplementary Table 2
Supplementary Table 2. Differentially Expressed Genes following Sham treatment relative to Untreated Controls Fold Change Accession Name Symbol 3 h 12 h NM_013121 CD28 antigen Cd28 12.82 BG665360 FMS-like tyrosine kinase 1 Flt1 9.63 NM_012701 Adrenergic receptor, beta 1 Adrb1 8.24 0.46 U20796 Nuclear receptor subfamily 1, group D, member 2 Nr1d2 7.22 NM_017116 Calpain 2 Capn2 6.41 BE097282 Guanine nucleotide binding protein, alpha 12 Gna12 6.21 NM_053328 Basic helix-loop-helix domain containing, class B2 Bhlhb2 5.79 NM_053831 Guanylate cyclase 2f Gucy2f 5.71 AW251703 Tumor necrosis factor receptor superfamily, member 12a Tnfrsf12a 5.57 NM_021691 Twist homolog 2 (Drosophila) Twist2 5.42 NM_133550 Fc receptor, IgE, low affinity II, alpha polypeptide Fcer2a 4.93 NM_031120 Signal sequence receptor, gamma Ssr3 4.84 NM_053544 Secreted frizzled-related protein 4 Sfrp4 4.73 NM_053910 Pleckstrin homology, Sec7 and coiled/coil domains 1 Pscd1 4.69 BE113233 Suppressor of cytokine signaling 2 Socs2 4.68 NM_053949 Potassium voltage-gated channel, subfamily H (eag- Kcnh2 4.60 related), member 2 NM_017305 Glutamate cysteine ligase, modifier subunit Gclm 4.59 NM_017309 Protein phospatase 3, regulatory subunit B, alpha Ppp3r1 4.54 isoform,type 1 NM_012765 5-hydroxytryptamine (serotonin) receptor 2C Htr2c 4.46 NM_017218 V-erb-b2 erythroblastic leukemia viral oncogene homolog Erbb3 4.42 3 (avian) AW918369 Zinc finger protein 191 Zfp191 4.38 NM_031034 Guanine nucleotide binding protein, alpha 12 Gna12 4.38 NM_017020 Interleukin 6 receptor Il6r 4.37 AJ002942 -
Bacterial Symbioses and the Innate Immune Response of the Model Host: Euprymna Scolopes Andrew J
University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 8-14-2014 Bacterial Symbioses and the Innate Immune Response of the Model Host: Euprymna scolopes Andrew J. Collins University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Collins, Andrew J., "Bacterial Symbioses and the Innate Immune Response of the Model Host: Euprymna scolopes" (2014). Doctoral Dissertations. 516. https://opencommons.uconn.edu/dissertations/516 Bacterial Symbioses and the Innate Immune Response of the Model Host: Euprymna scolopes Andrew Collins University of Connecticut, 2014 All animals enter into beneficial relationships with bacteria. The light organ of the Hawaiian Bobtail squid, Euprymna scolopes, is a unique model for studying the establishment and maintenance of a symbiosis between a host and a single bacterial species, Vibrio fischeri. This bacterium inhabits a specialized structure known as the light organ and provides counter-illumination to mask the silhouette of the predator as it hunts for food during the night. Hemocytes, the primary innate immune cells, preferentially bind and phagocytose non-symbiotic at higher rates than their symbiont, but this can change with the colonization state of the animal. A goal of this work was to use high-throughput sequencing to identify genes expressed within hemocytes of adult animals. Of the many genes identified was a novel peptidoglycan recognition protein, EsPGRP5, which is one of the most abundant transcripts in circulating hemocytes. In addition to the light organ, female squid have an accessory nidamental gland (ANG) which contributes to making the jelly coat that covers the squid’s eggs. -
Selective Loss of Glucocerebrosidase Activity in Sporadic Parkinsonłs
Chiasserini et al. Molecular Neurodegeneration (2015) 10:15 DOI 10.1186/s13024-015-0010-2 SHORT REPORT Open Access Selective loss of glucocerebrosidase activity in sporadic Parkinson’s disease and dementia with Lewy bodies Davide Chiasserini1†, Silvia Paciotti2†, Paolo Eusebi1,3, Emanuele Persichetti2, Anna Tasegian2, Marzena Kurzawa-Akanbi4,5, Patrick F Chinnery4,5, Christopher M Morris6, Paolo Calabresi1,7, Lucilla Parnetti1* and Tommaso Beccari2* Abstract Background: Lysosomal dysfunction is thought to be a prominent feature in the pathogenetic events leading to Parkinson’s disease (PD). This view is supported by the evidence that mutations in GBA gene, coding the lysosomal hydrolase β-glucocerebrosidase (GCase), are a common genetic risk factor for PD. Recently, GCase activity has been shown to be decreased in substantia nigra and in cerebrospinal fluid of patients diagnosed with PD or dementia with Lewy Bodies (DLB). Here we measured the activity of GCase and other endo-lysosomal enzymes in different brain regions (frontal cortex, caudate, hippocampus, substantia nigra, cerebellum) from PD (n = 26), DLB (n = 16) and age-matched control (n = 13) subjects, screened for GBA mutations. The relative changes in GCase gene expression in substantia nigra were also quantified by real-time PCR. The role of potential confounders (age, sex and post-mortem delay) was also determined. Findings: Substantia nigra showed a high activity level for almost all the lysosomal enzymes assessed. GCase activity was significantly decreased in the caudate (−23%) and substantia nigra (−12%) of the PD group; the same trend was observed in DLB. In both groups, a decrease in GCase mRNA was documented in substantia nigra. -
A Study of the Molecular Basis of the Lysosomal Storage Disorder
P\ ■Studies of the Molecular Basis of the Lysosomal Storage Disorder Fucosidosis by Helen Marie Cragg Thesis submitted for the degree of Doctor of Philosophy University of London Division of Biochemistry and Genetics Institute of Child Health ProQuest Number: U541539 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U541539 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Abstract Fucosidosis is a rare, autosomal recessive, lysosomal storage disorder resulting from a deficiency of the enzyme a-fucosidase. This defect leads to the accumulation in the lysosomes of tissues and excretion in urine of fucose-containing oligosaccharides, glycoasparagines, and glycolipids. The gene encoding lysosomal a-fucosidase has been mapped to the short arm of chromosome 1 at position lp34.1-36.1 and consists of eight exons spanning 23kb ofDNA. In this thesis the molecular basis of the enzyme defect has been investigated in thirteen fucosidosis patients. The residual a-fucosidase activity in extracts of fibroblasts, leukocytes and plasma has been characterised and the urinary oligosaccharides investigated by thin layer chromatography. -
Characterization of Aspartylglucosaminidase Activation and Aspartylglucosaminuria Mutations
Arto Pennanen Publications of the National Public Health Institute A 1 / 2004 — INDOOR AIR POLLUTION AND HEALTH RISKS IN FINNISH ICE ARENAS RISKSINFINNISHICE AND HEALTH AIR POLLUTION INDOOR Jani Saarela CHARACTERIZATION OF ASPARTYLGLUCOSAMINIDASE ACTIVATION AND ASPARTYLGLUCOSAMINURIA MUTATIONS ISBN 951-740-485-9 ISSN 0359-3584 ISBN 951-740-486-7 (pdf) Department of Molecular Medicine, ISSN 1458-6290 (pdf) National Public Health Institute, Helsinki, Finland and http://www.ktl.fi /portal/suomi/julkaisut/julkaisusarjat/ Department of Medical Genetics, kansanterveyslaitoksen_julkaisuja_a/ University of Helsinki, Finland Kopijyvä Kuopio 2005 Helsinki 2004 PPennanen_kansi.inddennanen_kansi.indd 1 117.2.20057.2.2005 115:26:195:26:19 CHARACTERIZATION OF ASPARTYLGLUCOSAMINIDASE ACTIVATION AND ASPARTYLGLUCOSAMINURIA MUTATIONS Jani Saarela Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland and Department of Medical Genetics, University of Helsinki, Finland Academic Dissertation To be publicly discussed with the permission of the Medical Faculty of the University of Helsinki, in the lecture room 3 of Biomedicum Helsinki, Haartmaninkatu 8, Helsinki, on January 30th, 2004, at 12 o’clock noon. Helsinki 2004 Supervised by Professor Leena Peltonen-Palotie National Public Health Institute and Department of Medical Genetics University of Helsinki, Helsinki, Finland Reviewed by Professor Ole Kristian Tollersrud and Docent Marc Baumann Department of Medical Biochemistry Protein Chemistry/Proteomics Unit University of Tromsoe and Neuroscience Research Program Tromsoe, Norway University of Helsinki, Helsinki, Finland To be publicly discussed with Professor Marja Makarow Institute of Biotechnology and Department of Applied Biochemistry and Molecular Biology University of Helsinki, Helsinki, Finland Julkaisija-Utgivare-Publisher Kansanterveyslaitos (KTL) Mannerheimintie 166 00300 Helsinki puh. vaihde 09-47441, felefax 09-4744 8408 Folkhälsoinstitutet Mannerheimvägen 166 00300, Helsinki tel. -
Substrate Specificity and Transfucosylation Activity of GH29 Α-L-Fucosidases for Enzymatic Production of Human Milk Oligosaccharides
Downloaded from orbit.dtu.dk on: Oct 01, 2021 Substrate specificity and transfucosylation activity of GH29 -l-fucosidases for enzymatic production of human milk oligosaccharides Zeuner, Birgitte; Muschiol, Jan; Holck, Jesper; Lezyk, Mateusz; Gedde, Mattias Raae; Jers, Carsten; Mikkelsen, Jørn Dalgaard; Meyer, Anne S. Published in: New Biotechnology Link to article, DOI: 10.1016/j.nbt.2017.12.002 Publication date: 2018 Document Version Peer reviewed version Link back to DTU Orbit Citation (APA): Zeuner, B., Muschiol, J., Holck, J., Lezyk, M., Gedde, M. R., Jers, C., Mikkelsen, J. D., & Meyer, A. S. (2018). Substrate specificity and transfucosylation activity of GH29 -l-fucosidases for enzymatic production of human milk oligosaccharides. New Biotechnology, 41, 34-45. https://doi.org/10.1016/j.nbt.2017.12.002 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Accepted Manuscript Title: Substrate specificity and transfucosylation activity of GH29 ␣-L-fucosidases for enzymatic production of human milk oligosaccharides Authors: Birgitte Zeuner, Jan Muschiol, Jesper Holck, Mateusz Lezyk, Mattias Raae Gedde, Carsten Jers, Jørn Dalgaard Mikkelsen, Anne S. -
“Algae's Sulfated Polysaccharides Modifications: Potential Use Of
Process Biochemistry 51 (2016) 989–998 Contents lists available at ScienceDirect Process Biochemistry jo urnal homepage: www.elsevier.com/locate/procbio Review “Algae’s sulfated polysaccharides modifications: Potential use of microbial enzymes” a,∗ a a Daniela de Borba Gurpilhares , Tatiane Rodrigues Moreira , Julia da Luz Bueno , a,b c e d Leonardo Paes Cinelli , Priscila Gava Mazzola , Adalberto Pessoa , Lara Durães Sette a Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Av. Aluizio da Silva Gomes, 50, Granja dos Cavaleiros, 27930-560, Macaé, RJ, Brazil b Grupo de Glicofármacos—Laboratório Integrado de Prospecc¸ ão em Produtos Bioativos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Av. Aluizio da Silva Gomes, 50, Granja dos Cavaleiros, 27930-560, Macaé, RJ, Brazil c Faculdade de Ciências Farmacêuticas, Universidade de Campinas—UNICAMP, Sérgio Buarque de Holanda, 250, Piso II, E06, 13083-859 Campinas, SP, Brazil/Departamento de Patologia Clinica, Faculdade de Ciências Médicas, Universidade de Campinas—UNICAMP, R. Alexander Fleming, 105, Bloco FCM 12, 13083-881, Campinas, SP, Brazil d Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho—UNESP, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP, Brazil e Departamento de Tecnologia Bioquímico-Farmacêutica, Escola de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, Bloco 16, 05508-900, São Paulo, SP, Brazil a r t i c l e i n f o a b s t r a c t Article history: Marine algae are valuable sources of structurally diverse bioactive compounds, among them, the group Received 10 December 2015 of sulfated polysaccharides (SPs).