Glucocerebrosidase Mutations and Synucleinopathies. Potential Role of Sterylglucosides and Relevance of Studying Both GBA1 and GBA2 Genes
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Bacteria Belonging to Pseudomonas Typographi Sp. Nov. from the Bark Beetle Ips Typographus Have Genomic Potential to Aid in the Host Ecology
insects Article Bacteria Belonging to Pseudomonas typographi sp. nov. from the Bark Beetle Ips typographus Have Genomic Potential to Aid in the Host Ecology Ezequiel Peral-Aranega 1,2 , Zaki Saati-Santamaría 1,2 , Miroslav Kolaˇrik 3,4, Raúl Rivas 1,2,5 and Paula García-Fraile 1,2,4,5,* 1 Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; [email protected] (E.P.-A.); [email protected] (Z.S.-S.); [email protected] (R.R.) 2 Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain 3 Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague, Czech Republic; [email protected] 4 Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic 5 Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain * Correspondence: [email protected] Received: 4 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Simple Summary: European Bark Beetle (Ips typographus) is a pest that affects dead and weakened spruce trees. Under certain environmental conditions, it has massive outbreaks, resulting in attacks of healthy trees, becoming a forest pest. It has been proposed that the bark beetle’s microbiome plays a key role in the insect’s ecology, providing nutrients, inhibiting pathogens, and degrading tree defense compounds, among other probable traits. During a study of bacterial associates from I. typographus, we isolated three strains identified as Pseudomonas from different beetle life stages. In this work, we aimed to reveal the taxonomic status of these bacterial strains and to sequence and annotate their genomes to mine possible traits related to a role within the bark beetle holobiont. -
The Rise and Fall of the Bovine Corpus Luteum
University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Spring 5-6-2017 The Rise and Fall of the Bovine Corpus Luteum Heather Talbott University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Biochemistry Commons, Molecular Biology Commons, and the Obstetrics and Gynecology Commons Recommended Citation Talbott, Heather, "The Rise and Fall of the Bovine Corpus Luteum" (2017). Theses & Dissertations. 207. https://digitalcommons.unmc.edu/etd/207 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. THE RISE AND FALL OF THE BOVINE CORPUS LUTEUM by Heather Talbott A DISSERTATION Presented to the Faculty of the University of Nebraska Graduate College in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biochemistry and Molecular Biology Graduate Program Under the Supervision of Professor John S. Davis University of Nebraska Medical Center Omaha, Nebraska May, 2017 Supervisory Committee: Carol A. Casey, Ph.D. Andrea S. Cupp, Ph.D. Parmender P. Mehta, Ph.D. Justin L. Mott, Ph.D. i ACKNOWLEDGEMENTS This dissertation was supported by the Agriculture and Food Research Initiative from the USDA National Institute of Food and Agriculture (NIFA) Pre-doctoral award; University of Nebraska Medical Center Graduate Student Assistantship; University of Nebraska Medical Center Exceptional Incoming Graduate Student Award; the VA Nebraska-Western Iowa Health Care System Department of Veterans Affairs; and The Olson Center for Women’s Health, Department of Obstetrics and Gynecology, Nebraska Medical Center. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
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. -
Molecular Reprogramming in Tomato Pollen During Development And
Molecular reprogramming in tomato pollen during development and heat stress Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften vorgelegt beim Fachbereich Biowissenschaften (FB15) der Goethe-Universität Frankfurt am Main von Mario Keller geboren in Frankfurt am Main (Hessen) Frankfurt am Main 2018 (D30) Vom Fachbereich Biowissenschaften (FB15) der Goethe-Universität als Dissertation angenommen. Dekan: Prof. Dr. Sven Klimpel Gutachter: Prof. Dr. Enrico Schleiff, Jun. Prof. Dr. Michaela Müller-McNicoll Datum der Disputation: 25.03.2019 Index of contents Index of contents Index of contents ....................................................................................................................................... i Index of figures ........................................................................................................................................ iii Index of tables ......................................................................................................................................... iv Index of supplemental material ................................................................................................................ v Index of supplemental figures ............................................................................................................... v Index of supplemental tables ................................................................................................................ v Abbreviations .......................................................................................................................................... -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Are Glucosylceramide-Related Sphingolipids Involved in the Increased Risk for Cancer in Gaucher Disease Patients? Review and Hypotheses
cancers Review Are Glucosylceramide-Related Sphingolipids Involved in the Increased Risk for Cancer in Gaucher Disease Patients? Review and Hypotheses 1,2, 1,3, 1 1,2 Patricia Dubot y , Leonardo Astudillo y, Nicole Therville , Frédérique Sabourdy , Jérôme Stirnemann 4 , Thierry Levade 1,2,* and Nathalie Andrieu-Abadie 1,* 1 INSERM UMR1037, CRCT (Cancer Research Center of Toulouse), and Université Paul Sabatier, 31037 Toulouse, France; [email protected] (P.D.); [email protected] (L.A.); [email protected] (N.T.); [email protected] (F.S.) 2 Laboratoire de Biochimie Métabolique, Centre de Référence en Maladies Héréditaires du Métabolisme, Institut Fédératif de Biologie, CHU de Toulouse, 31059 Toulouse, France 3 Service de Médecine Interne, CHU de Toulouse, 31059 Toulouse, France 4 Service de Médecine Interne Générale, Hôpitaux Universitaires de Genève, CH-1211 Geneva, Switzerland; [email protected] * Correspondence: [email protected] (T.L.); [email protected] (N.A.-A.) These authors contributed equally to this work. y Received: 28 November 2019; Accepted: 14 February 2020; Published: 18 February 2020 Abstract: The roles of ceramide and its catabolites, i.e., sphingosine and sphingosine 1-phosphate, in the development of malignancies and the response to anticancer regimens have been extensively described. Moreover, an abundant literature points to the effects of glucosylceramide synthase, the mammalian enzyme that converts ceramide to β-glucosylceramide, in protecting tumor cells from chemotherapy. Much less is known about the contribution of β-glucosylceramide and its breakdown products in cancer progression. In this chapter, we first review published and personal clinical observations that report on the increased risk of developing cancers in patients affected with Gaucher disease, an inborn disorder characterized by defective lysosomal degradation of β-glucosylceramide. -
Draft Genome of Thermomonospora Sp. CIT 1 (Thermomonosporaceae) and in Silico Evidence of Its Functional Role in Filter Cake Biomass Deconstruction
1 Genetics and Molecular Biology Suplementary material to: Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction Table S3 - Identifications of enzymes with activity on carbohydrate structures present in the draft genome CIT 1 recovered from metagenomic sequencing of filter cake. Predictions were performed with dbCAN online, following for blastp confirmation against the non-redundant NCBI protein database of the occurrence of predicted protein-like sequence deposition. Search results for dbCAN conserved domains BLASTP RESULTS ORF CAZy QUERY E- IDENTIT LENGTH ID CAZy ENZYME NAME (NCBI) ACCESSION FAMILY COVER VALUE Y 747 AA2.hmm peroxidase (EC 1.11.1.-) catalase/peroxidase HPI 100 0.00E+00 100 WP_012852289 glucose-methanol-choline 786 AA3.hmm glucose-methanol-choline (GMC) 100 0.00E+00 100 ACY97563 oxidoreductase mycofactocin system GMC family 520 AA3.hmm glucose-methanol-choline (GMC) 99 0.00E+00 99 WP_012852714 oxidoreductase MftG 582 AA3.hmm glucose-methanol-choline (GMC) GMC family oxidoreductase 100 0.00E+00 99 WP_012854558 531 AA3_2.hmm glucose-methanol-choline (GMC) choline dehydrogenase 100 0.00E+00 100 WP_012854223 533 AA4.hmm vanillyl-alcohol oxidase (EC 1.1.3.38) FAD-binding oxidoreductase 99 0.00E+00 99 WP_012852156 NAD(P)H:quinone oxidoreductase 4.00E- 209 AA6.hmm 1,4-benzoquinone reductase (EC. 1.6.5.6) 100 100 WP_012850533 type IV 152 187 AA6.hmm 1,4-benzoquinone reductase (EC. 1.6.5.6) NAD(P)H-dependent oxidoreductase 100 9.00E-86 69 WP_067443322 6.00E- 152 AA6.hmm 1,4-benzoquinone reductase (EC. -
ZHOU-THESIS-2018.Pdf (2.307Mb)
PHYLOGENY AND PREDICTED FUNCTIONAL CAPABILITIES OF A SULFUR- OXIDIZING AND DENITRIFYING CLADE OF BACTEROIDETES FROM SULFIDIC ENVIRONMENTS A Thesis by KECEN ZHOU Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Chair of Committee, Jason B. Sylvan Co-Chair of Committee, Lisa Campbell Committee Member, Brendan E. Roark Head of Department, Shari Yvon-Lewis August 2018 Major Subject: Oceanography Copyright 2018 Kecen Zhou ABSTRACT Environments rich in sulfur compounds (sulfidic) are common in the ocean, and the ability to gain energy (dissimilatory) from sulfur redox reactions is widespread in bacteria. The Sulfiphilic Bacteroidetes (SB), have been found exclusively in sulfidic environments, but little is known about their metabolic potential and membership. The ability to perform dissimilatory sulfur redox would make them unique among Bacteroidetes, which are primarily known as heterotrophs that specialize in degrading complex organic molecules. Using 16S rRNA phylogeny and analysis of single amplified genomes (SAGs) from Saanich Inlet, a seasonally hypoxic basin, we elucidate the global distribution and potential metabolic capabilities of the SB clade. Phylogenetic analysis revealed that this clade was monophyletic and had a global distribution. It is hypothesized this clade combines heterotrophic amino acid and sugar uptake with denitrification and respiratory sulfur oxidation/polysulfide reduction. Putative genes for sulfur oxidation via polysulfide reductase (psr) were found in the combined genome, and phylogenetic analysis confirmed these genes were likely to be psrABC. A denitrification pathway was present and complete save for the absence of a gene catalyzing reduction of NO to N2O. -
Isolation and Characterization of Cellulase-Producing Microorganisms in The
Isolation and Characterization of Cellulase-Producing Microorganisms in the Red Sea Dissertation by Siham Kamal Fatani In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia September, 2019 2 Examination Committee Page The Dissertation of Siham Fatani is Examined by the Committee Members Committee Chairperson: Prof. Takashi Gojobori Committee Members: Prof. Vladimir Bajic, Prof. Susana Agusti, Prof. Shugo Watabe 3 © September, 2019 Siham Kamal Fatani All Rights Reserved 4 ACKNOWLEDGMENTS This work is a consequence of great help and guidance from many people; faculty, family and friends. I am really happy to have these people by my side while undertaking my PhD Dissertation. First, I would like to express my profound gratitude and respect to my supervisor, Prof. Takashi Gojobori, Distinguished Professor of Bioscience and Associate Director of Computational Bioscience Research Center for his professional guidance, and regular encouragement and motivation at various stages of this work. I would also like to thank Dr. Katsuhiko Mineta for his support and advice during my research. Moreover, I would like to express my deepest appreciation to Dr. Yoshimoto Saito for his assistance and suggestions throughout my project. I also appreciate Mr. Mohammad Al-Arawi for his support and technical advice and without them this work would not have been possible for me to complete. In addition, I would like to thank my committee members, Prof. Vladimir Bajic, Prof. Susana Agusti and Prof. Shugo Watabe for giving their time to review my Ph.D. thesis and for offering their insight and suggestions. -
Lucerastat, an Iminosugar with Potential As Substrate Reduction Therapy for Glycolipid Storage Disorders: Safety, Tolerability
Guérard et al. Orphanet Journal of Rare Diseases (2017) 12:9 DOI 10.1186/s13023-017-0565-9 RESEARCH Open Access Lucerastat, an iminosugar with potential as substrate reduction therapy for glycolipid storage disorders: safety, tolerability, and pharmacokinetics in healthy subjects N. Guérard1*, O. Morand2 and J. Dingemanse1 Abstract Background: Lucerastat, an inhibitor of glucosylceramide synthase, has the potential to restore the balance between synthesis and degradation of glycosphingolipids in glycolipid storage disorders such as Gaucher disease and Fabry disease. The safety, tolerability, and pharmacokinetics of oral lucerastat were evaluated in two separate randomized, double-blind, placebo-controlled, single- and multiple-ascending dose studies (SAD and MAD, respectively) in healthy male subjects. Methods: In the SAD study, 31 subjects received placebo or a single oral dose of 100, 300, 500, or 1000 mg lucerastat. Eight additional subjects received two doses of 1000 mg lucerastat or placebo separated by 12 h. In the MAD study, 37 subjects received placebo or 200, 500, or 1000 mg b.i.d. lucerastat for 7 consecutive days. Six subjects in the 500 mg cohort received lucerastat in both absence and presence of food. Results: In the SAD study, 15 adverse events (AEs) were reported in ten subjects. Eighteen AEs were reported in 15 subjects in the MAD study, in which the 500 mg dose cohort was repeated because of elevated alanine aminotransferase (ALT) values in 4 subjects, not observed in other dose cohorts. No severe or serious AE was observed. No clinically relevant abnormalities regarding vital signs and 12–lead electrocardiograms were observed. Lucerastat Cmax values were comparable between studies, with geometric mean Cmax 10.5 (95% CI: 7.5, 14.7) and 11.1 (95% CI: 8.7, 14.2) μg/mL in the SAD and MAD study, respectively, after 1000 mg lucerastat b.i.d. -
The Design, Synthesis and Enzymatic Evaluation of Aminocyclitol Inhibitors of Glucocerebrosidase
Lakehead University Knowledge Commons,http://knowledgecommons.lakeheadu.ca Electronic Theses and Dissertations Electronic Theses and Dissertations from 2009 2014-01-22 The design, synthesis and enzymatic evaluation of aminocyclitol inhibitors of glucocerebrosidase Adams, Benjamin Tyler http://knowledgecommons.lakeheadu.ca/handle/2453/478 Downloaded from Lakehead University, KnowledgeCommons THE DESIGN, SYNTHESIS AND ENZYMATIC EVALUATION OF AMINOCYCLITOL INHIBITORS OF GLUCOCEREBROSIDASE By Benjamin Tyler Adams A Thesis submitted to The Department of Chemistry Faculty of Science and Environmental Studies Lakehead University In partial fulfillment of the requirements for the degree of Master of Science August 2013 © Benjamin Tyler Adams, 2013 i Abstract Gaucher disease, the most common lysosomal storage disorder, is caused by mutations in the GBA gene which codes for the enzyme glucocerebrosidase (GCase) resulting in its deficiency. GCase deficiency results in the accumulation of its substrate glucosylceramide (GlcCer) within the lysosomes leading to various severities of hepatosplenomegaly, bone disease and neurodegeneration. For most forms of Gaucher disease, the mutations in the GBA gene cause the enzyme to misfold but retain catalytic activity. However, the misfolded mutant enzyme is recognized and degraded by the endoplasmic reticulum-associated degradation (ERAD) pathway prior to delivery into the lysosome. Symptoms begin to show in patients when the function of the defective enzyme drops below 10-20% residual enzyme activity. There are currently three therapeutic approaches to treat Gaucher disease: enzyme replacement therapy (ERT), substrate reduction therapy (SRT), and a relatively recent addition, enzyme enhancement therapy (EET) through the use of pharmacological chaperones. Many pharmacological chaperones are competitive inhibitors that are capable of enhancing lysosomal GCase activity by stabilizing the folded conformation of GCase enabling it to bypass the ERAD pathway.