Improved Cognition, Mild Anxiety-Like Behavior and Decreased Motor
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Single-Cell Expression Profiling Of
Edinburgh Research Explorer Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene Citation for published version: Elstner, M, Morris, CM, Heim, K, Lichtner, P, Bender, A, Mehta, D, Schulte, C, Sharma, M, Hudson, G, Goldwurm, S, Giovanetti, A, Zeviani, M, Burn, DJ, McKeith, IG, Perry, RH, Jaros, E, Krueger, R, Wichmann, H-E, Schreiber, S, Campbell, H, Wilson, JF, Wright, AF, Dunlop, M, Pistis, G, Toniolo, D, Chinnery, PF, Gasser, T, Klopstock, T, Meitinger, T, Prokisch, H & Turnbull, DM 2009, 'Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene', Annals of Neurology, vol. 66, no. 6, pp. 792-798. https://doi.org/10.1002/ana.21780 Digital Object Identifier (DOI): 10.1002/ana.21780 Link: Link to publication record in Edinburgh Research Explorer Document Version: Peer reviewed version Published In: Annals of Neurology Publisher Rights Statement: Published in final edited form as: Ann Neurol. 2009 December ; 66(6): 792–798. doi:10.1002/ana.21780. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Brain-Specific Knock-Out of Hypoxia-Inducible Factor-1Α
The Journal of Neuroscience, April 20, 2005 • 25(16):4099–4107 • 4099 Neurobiology of Disease Brain-Specific Knock-Out of Hypoxia-Inducible Factor-1␣ Reduces Rather Than Increases Hypoxic–Ischemic Damage Rob Helton,1* Jiankun Cui,2* John R. Scheel,1* Julie A. Ellison,1 Chris Ames,1 Claire Gibson,2 Barbara Blouw,3 Ling Ouyang,1 Ioannis Dragatsis,4 Scott Zeitlin,5 Randall S. Johnson,3 Stuart A. Lipton,2 and Carrolee Barlow1 1Laboratory of Genetics, The Salk Institute for Biological Studies, and 2Center for Neuroscience and Aging, The Burnham Institute, La Jolla, California 92037, 3Molecular Biology Section, Division of Biology, University of California, San Diego, La Jolla, California 92093, 4Department of Physiology, The University of Tennessee, Health Science Center, Memphis, Tennessee 38163, and 5Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, Virginia 22908 ␣ ␣ Hypoxia-inducible factor-1 (HIF-1 ) plays an essential role in cellular and systemic O2 homeostasis by regulating the expression of genes important in glycolysis, erythropoiesis, angiogenesis, and catecholamine metabolism. It is also believed to be a key component of the cellular response to hypoxia and ischemia under pathophysiological conditions, such as stroke. To clarify the function of HIF-1␣ in the brain, we exposed adult mice with late-stage brain deletion of HIF-1␣ to hypoxic injuries. Contrary to expectations, the brains from the HIF-1␣-deficient mice were protected from hypoxia-induced cell death. These surprising findings suggest that decreas- ing the level of HIF-1␣ can be neuroprotective. Gene chip expression analysis revealed that, contrary to expectations, the majority of hypoxia-dependent gene-expression changes were unaltered, whereas a specific downregulation of apoptotic genes was observed in the HIF-1␣-deficient mice. -
PDXK Is Differentially Expressed in the Brains of Patients With
1 Pyridoxal kinase, encoded by the PDXK gene, is differentially expressed in the brains of patients 2 with schizophrenia. 3 Shahan Mamoor, MS1 4 [email protected] East Islip, NY USA 5 6 Visual and auditory hallucinations are a cardinal feature of psychotic disorders1. We mined published and public microarray datasets2,3 to discover differentially expressed genes in 7 schizophrenia and schizoaffective disorder. We found significant differential expression of the 8 gene encoding pyridoxal kinase, PDXK in neurons of the dorsolateral pre-frontal cortex from 9 patients with schizophrenia and schizoaffective disorder. 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Keywords: schizophrenia, schizoaffective disorder, psychotic disorders, psychosis, systems biology of schizophrenia, PDXK. 28 PAGE 1 OF 12 1 Psychiatric diseases schizophrenia and schizoaffective disorder have in common the 2 existence of psychotic symptoms1,4,5, like visual and auditory hallucinations, that can plague 3 4 affected patients. Understanding the transcriptional profiles of cells and tissues from the brain of 5 patients diagnosed with schizophrenia or schizoaffective disorder has the potential to provide 6 insights into molecular mechanisms underlying disease initiation, progression and associated 7 8 symptoms like psychosis. We mined published and public microarray data from layer 3 and 9 layer 5 pyramidal neurons of the dorsolateral pre-frontal cortex from patients with schizophrenia 10 and schizoaffective disorder and from the layer 3 parvalbumin-positive neurons of the 11 12 dorsolateral prefrontal cortex of patients with schizoaffective disorder to discover genes whose 13 expression was most significantly different in the brains of patients with psychosis at the 14 15 systems-level. -
(PDXK) Human Variants in Drosophila Impacts on Genome Integrity
www.nature.com/scientificreports OPEN The expression of four pyridoxal kinase (PDXK) human variants in Drosophila impacts on genome Received: 11 July 2019 Accepted: 15 September 2019 integrity Published: xx xx xxxx Elisa Mascolo1, Anna Barile2, Lorenzo Stufera Mecarelli 1, Noemi Amoroso1, Chiara Merigliano3, Arianna Massimi4, Isabella Saggio1,5, Torben Hansen 6, Angela Tramonti7,2, Martino Luigi Di Salvo2, Fabrizio Barbetti4, Roberto Contestabile2 & Fiammetta Vernì 1 In eukaryotes, pyridoxal kinase (PDXK) acts in vitamin B6 salvage pathway to produce pyridoxal 5′-phosphate (PLP), the active form of the vitamin, which is implicated in numerous crucial metabolic reactions. In Drosophila, mutations in the dPdxk gene cause chromosome aberrations (CABs) and increase glucose content in larval hemolymph. Both phenotypes are rescued by the expression of the wild type human PDXK counterpart. Here we expressed, in dPdxk1 mutant fies, four PDXK human variants: three (D87H, V128I and H246Q) listed in databases, and one (A243G) found in a genetic screening in patients with diabetes. Diferently from human wild type PDXK, none of the variants was able to completely rescue CABs and glucose content elicited by dPdxk1 mutation. Biochemical analysis of D87H, V128I, H246Q and A243G proteins revealed reduced catalytic activity and/or reduced afnity for PLP precursors which justify this behavior. Although these variants are rare in population and carried in heterozygous condition, our fndings suggest that in certain metabolic contexts and diseases in which PLP levels are reduced, the presence of these PDXK variants could threaten genome integrity and increase cancer risk. Diferently from bacteria and plants which synthesize ex novo the active form of vitamin B6, pyridoxal 5′ phos- phate (PLP), in other organisms PLP production relies on the salvaging activity of two enzymes: pyridoxal 5′-phosphate kinase (PDXK) and pyridoxine 5′-phosphate oxidase (PNPO). -
(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. -
"The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. -
Paraneoplastic Neurological and Muscular Syndromes
Paraneoplastic neurological and muscular syndromes Short compendium Version 4.5, April 2016 By Finn E. Somnier, M.D., D.Sc. (Med.), copyright ® Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark 30/01/2016, Copyright, Finn E. Somnier, MD., D.S. (Med.) Table of contents PARANEOPLASTIC NEUROLOGICAL SYNDROMES .................................................... 4 DEFINITION, SPECIAL FEATURES, IMMUNE MECHANISMS ................................................................ 4 SHORT INTRODUCTION TO THE IMMUNE SYSTEM .................................................. 7 DIAGNOSTIC STRATEGY ..................................................................................................... 12 THERAPEUTIC CONSIDERATIONS .................................................................................. 18 SYNDROMES OF THE CENTRAL NERVOUS SYSTEM ................................................ 22 MORVAN’S FIBRILLARY CHOREA ................................................................................................ 22 PARANEOPLASTIC CEREBELLAR DEGENERATION (PCD) ...................................................... 24 Anti-Hu syndrome .................................................................................................................. 25 Anti-Yo syndrome ................................................................................................................... 26 Anti-CV2 / CRMP5 syndrome ............................................................................................ -
Chromosome 21 Leading Edge Gene Set
Chromosome 21 Leading Edge Gene Set Genes from chr21q22 that are part of the GSEA leading edge set identifying differences between trisomic and euploid samples. Multiple probe set IDs corresponding to a single gene symbol are combined as part of the GSEA analysis. Gene Symbol Probe Set IDs Gene Title 203865_s_at, 207999_s_at, 209979_at, adenosine deaminase, RNA-specific, B1 ADARB1 234539_at, 234799_at (RED1 homolog rat) UDP-Gal:betaGlcNAc beta 1,3- B3GALT5 206947_at galactosyltransferase, polypeptide 5 BACE2 217867_x_at, 222446_s_at beta-site APP-cleaving enzyme 2 1553227_s_at, 214820_at, 219280_at, 225446_at, 231860_at, 231960_at, bromodomain and WD repeat domain BRWD1 244622_at containing 1 C21orf121 240809_at chromosome 21 open reading frame 121 C21orf130 240068_at chromosome 21 open reading frame 130 C21orf22 1560881_a_at chromosome 21 open reading frame 22 C21orf29 1552570_at, 1555048_at_at, 1555049_at chromosome 21 open reading frame 29 C21orf33 202217_at, 210667_s_at chromosome 21 open reading frame 33 C21orf45 219004_s_at, 228597_at, 229671_s_at chromosome 21 open reading frame 45 C21orf51 1554430_at, 1554432_x_at, 228239_at chromosome 21 open reading frame 51 C21orf56 223360_at chromosome 21 open reading frame 56 C21orf59 218123_at, 244369_at chromosome 21 open reading frame 59 C21orf66 1555125_at, 218515_at, 221158_at chromosome 21 open reading frame 66 C21orf7 221211_s_at chromosome 21 open reading frame 7 C21orf77 220826_at chromosome 21 open reading frame 77 C21orf84 239968_at, 240589_at chromosome 21 open reading frame 84 -
Disorders Affecting Vitamin B6 Metabolism
Received: 8 October 2018 Accepted: 12 December 2018 DOI: 10.1002/jimd.12060 REVIEW Disorders affecting vitamin B6 metabolism Matthew P. Wilson1 | Barbara Plecko2 | Philippa B. Mills1 | Peter T. Clayton1 1Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK Abstract 0 2Department of Pediatrics and Adolescent Vitamin B6 is present in our diet in many forms, however, only pyridoxal 5 -phosphate Medicine, Division of General Pediatrics, (PLP) can function as a cofactor for enzymes. The intestine absorbs nonphosphorylated University Childrens' Hospital Graz, B vitamers, which are converted by specific enzymes to the active PLP form. The role Medical University Graz, Graz, Austria 6 of PLP is enabled by its reactive aldehyde group. Pathways reliant on PLP include Correspondence amino acid and neurotransmitter metabolism, folate and 1-carbon metabolism, protein Philippa B. Mills, Genetics and Genomic and polyamine synthesis, carbohydrate and lipid metabolism, mitochondrial function Medicine, UCL GOS Institute of Child Health, 30 Guilford Street, London WC1N and erythropoiesis. Besides the role of PLP as a cofactor B6 vitamers also play other 1EH, UK. cellular roles, for example, as antioxidants, modifying expression and action of steroid Email: [email protected] Communicating Editor: Slyvia Stockler- hormone receptors, affecting immune function, as chaperones and as an antagonist of Ipsiroglu Adenosine-5'-triphosphate (ATP) at P2 purinoceptors. Because of the vital role of PLP in neurotransmitter metabolism, particularly synthesis of the inhibitory transmitter Funding information γ Schweizerischer Nationalfonds zur -aminobutyric acid, it is not surprising that various inborn errors leading to PLP defi- Förderung der wissenschaftlichen Forschung ciency manifest as B6-responsive epilepsy, usually of early onset. -
Supplementary Informations SI2. Supplementary Table 1
Supplementary Informations SI2. Supplementary Table 1. M9, soil, and rhizosphere media composition. LB in Compound Name Exchange Reaction LB in soil LBin M9 rhizosphere H2O EX_cpd00001_e0 -15 -15 -10 O2 EX_cpd00007_e0 -15 -15 -10 Phosphate EX_cpd00009_e0 -15 -15 -10 CO2 EX_cpd00011_e0 -15 -15 0 Ammonia EX_cpd00013_e0 -7.5 -7.5 -10 L-glutamate EX_cpd00023_e0 0 -0.0283302 0 D-glucose EX_cpd00027_e0 -0.61972444 -0.04098397 0 Mn2 EX_cpd00030_e0 -15 -15 -10 Glycine EX_cpd00033_e0 -0.0068175 -0.00693094 0 Zn2 EX_cpd00034_e0 -15 -15 -10 L-alanine EX_cpd00035_e0 -0.02780553 -0.00823049 0 Succinate EX_cpd00036_e0 -0.0056245 -0.12240603 0 L-lysine EX_cpd00039_e0 0 -10 0 L-aspartate EX_cpd00041_e0 0 -0.03205557 0 Sulfate EX_cpd00048_e0 -15 -15 -10 L-arginine EX_cpd00051_e0 -0.0068175 -0.00948672 0 L-serine EX_cpd00054_e0 0 -0.01004986 0 Cu2+ EX_cpd00058_e0 -15 -15 -10 Ca2+ EX_cpd00063_e0 -15 -100 -10 L-ornithine EX_cpd00064_e0 -0.0068175 -0.00831712 0 H+ EX_cpd00067_e0 -15 -15 -10 L-tyrosine EX_cpd00069_e0 -0.0068175 -0.00233919 0 Sucrose EX_cpd00076_e0 0 -0.02049199 0 L-cysteine EX_cpd00084_e0 -0.0068175 0 0 Cl- EX_cpd00099_e0 -15 -15 -10 Glycerol EX_cpd00100_e0 0 0 -10 Biotin EX_cpd00104_e0 -15 -15 0 D-ribose EX_cpd00105_e0 -0.01862144 0 0 L-leucine EX_cpd00107_e0 -0.03596182 -0.00303228 0 D-galactose EX_cpd00108_e0 -0.25290619 -0.18317325 0 L-histidine EX_cpd00119_e0 -0.0068175 -0.00506825 0 L-proline EX_cpd00129_e0 -0.01102953 0 0 L-malate EX_cpd00130_e0 -0.03649016 -0.79413596 0 D-mannose EX_cpd00138_e0 -0.2540567 -0.05436649 0 Co2 EX_cpd00149_e0 -
S41598-021-85062-3.Pdf
www.nature.com/scientificreports OPEN Genetic dissection of down syndrome‑associated alterations in APP/amyloid‑β biology using mouse models Justin L. Tosh1,2, Elena R. Rhymes1, Paige Mumford3, Heather T. Whittaker1, Laura J. Pulford1, Sue J. Noy1, Karen Cleverley1, LonDownS Consortium*, Matthew C. Walker4, Victor L. J. Tybulewicz2,5, Rob C. Wykes4,6, Elizabeth M. C. Fisher1* & Frances K. Wiseman3* Individuals who have Down syndrome (caused by trisomy of chromosome 21), have a greatly elevated risk of early‑onset Alzheimer’s disease, in which amyloid‑β accumulates in the brain. Amyloid‑β is a product of the chromosome 21 gene APP (amyloid precursor protein) and the extra copy or ‘dose’ of APP is thought to be the cause of this early‑onset Alzheimer’s disease. However, other chromosome 21 genes likely modulate disease when in three‑copies in people with Down syndrome. Here we show that an extra copy of chromosome 21 genes, other than APP, infuences APP/Aβ biology. We crossed Down syndrome mouse models with partial trisomies, to an APP transgenic model and found that extra copies of subgroups of chromosome 21 gene(s) modulate amyloid‑β aggregation and APP transgene‑associated mortality, independently of changing amyloid precursor protein abundance. Thus, genes on chromosome 21, other than APP, likely modulate Alzheimer’s disease in people who have Down syndrome. Down syndrome (DS), which occurs in approximately 1 in 1000 births, is the most common cause of early-onset Alzheimer’s disease-dementia (AD-DS)1. Approximately 6 million people have DS world-wide and by the age of 65 two-thirds of these individuals will have a clinical dementia diagnosis.