Different Effects on Fast Exocytosis Induced by Synaptotagmin 1 and 2 Isoforms and Abundance but Not by Phosphorylation
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Targeted Genes and Methodology Details for Neuromuscular Genetic Panels
Targeted Genes and Methodology Details for Neuromuscular Genetic Panels Reference transcripts based on build GRCh37 (hg19) interrogated by Neuromuscular Genetic Panels Next-generation sequencing (NGS) and/or Sanger sequencing is performed Motor Neuron Disease Panel to test for the presence of a mutation in these genes. Gene GenBank Accession Number Regions of homology, high GC-rich content, and repetitive sequences may ALS2 NM_020919 not provide accurate sequence. Therefore, all reported alterations detected ANG NM_001145 by NGS are confirmed by an independent reference method based on laboratory developed criteria. However, this does not rule out the possibility CHMP2B NM_014043 of a false-negative result in these regions. ERBB4 NM_005235 Sanger sequencing is used to confirm alterations detected by NGS when FIG4 NM_014845 appropriate.(Unpublished Mayo method) FUS NM_004960 HNRNPA1 NM_031157 OPTN NM_021980 PFN1 NM_005022 SETX NM_015046 SIGMAR1 NM_005866 SOD1 NM_000454 SQSTM1 NM_003900 TARDBP NM_007375 UBQLN2 NM_013444 VAPB NM_004738 VCP NM_007126 ©2018 Mayo Foundation for Medical Education and Research Page 1 of 14 MC4091-83rev1018 Muscular Dystrophy Panel Muscular Dystrophy Panel Gene GenBank Accession Number Gene GenBank Accession Number ACTA1 NM_001100 LMNA NM_170707 ANO5 NM_213599 LPIN1 NM_145693 B3GALNT2 NM_152490 MATR3 NM_199189 B4GAT1 NM_006876 MYH2 NM_017534 BAG3 NM_004281 MYH7 NM_000257 BIN1 NM_139343 MYOT NM_006790 BVES NM_007073 NEB NM_004543 CAPN3 NM_000070 PLEC NM_000445 CAV3 NM_033337 POMGNT1 NM_017739 CAVIN1 NM_012232 POMGNT2 -
Supplementary Table 4
Li et al. mir-30d in human cancer Table S4. The probe list down-regulated in MDA-MB-231 cells by mir-30d mimic transfection Gene Probe Gene symbol Description Row set 27758 8119801 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 15497 8101675 ABCG2 ATP-binding cassette, sub-family G (WHITE), member 2 18536 8158725 ABL1 c-abl oncogene 1, receptor tyrosine kinase 21232 8058591 ACADL acyl-Coenzyme A dehydrogenase, long chain 12466 7936028 ACTR1A ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) 18102 8056005 ACVR1 activin A receptor, type I 20790 8115490 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 15688 7979904 ADAM21 ADAM metallopeptidase domain 21 14937 8054254 AFF3 AF4/FMR2 family, member 3 23560 8121277 AIM1 absent in melanoma 1 20209 7921434 AIM2 absent in melanoma 2 19272 8136336 AKR1B10 aldo-keto reductase family 1, member B10 (aldose reductase) 18013 7954777 ALG10 asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog (S. pombe) 30049 7954789 ALG10B asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast) 28807 7962579 AMIGO2 adhesion molecule with Ig-like domain 2 5576 8112596 ANKRA2 ankyrin repeat, family A (RFXANK-like), 2 23414 7922121 ANKRD36BL1 ankyrin repeat domain 36B-like 1 (pseudogene) 29782 8098246 ANXA10 annexin A10 22609 8030470 AP2A1 adaptor-related protein complex 2, alpha 1 subunit 14426 8107421 AP3S1 adaptor-related protein complex 3, sigma 1 subunit 12042 8099760 ARAP2 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2 30227 8059854 ARL4C ADP-ribosylation factor-like 4C 32785 8143766 ARP11 actin-related Arp11 6497 8052125 ASB3 ankyrin repeat and SOCS box-containing 3 24269 8128592 ATG5 ATG5 autophagy related 5 homolog (S. -
Mechanisms of Synaptic Plasticity Mediated by Clathrin Adaptor-Protein Complexes 1 and 2 in Mice
Mechanisms of synaptic plasticity mediated by Clathrin Adaptor-protein complexes 1 and 2 in mice Dissertation for the award of the degree “Doctor rerum naturalium” at the Georg-August-University Göttingen within the doctoral program “Molecular Biology of Cells” of the Georg-August University School of Science (GAUSS) Submitted by Ratnakar Mishra Born in Birpur, Bihar, India Göttingen, Germany 2019 1 Members of the Thesis Committee Prof. Dr. Peter Schu Institute for Cellular Biochemistry, (Supervisor and first referee) University Medical Center Göttingen, Germany Dr. Hans Dieter Schmitt Neurobiology, Max Planck Institute (Second referee) for Biophysical Chemistry, Göttingen, Germany Prof. Dr. med. Thomas A. Bayer Division of Molecular Psychiatry, University Medical Center, Göttingen, Germany Additional Members of the Examination Board Prof. Dr. Silvio O. Rizzoli Department of Neuro-and Sensory Physiology, University Medical Center Göttingen, Germany Dr. Roland Dosch Institute of Developmental Biochemistry, University Medical Center Göttingen, Germany Prof. Dr. med. Martin Oppermann Institute of Cellular and Molecular Immunology, University Medical Center, Göttingen, Germany Date of oral examination: 14th may 2019 2 Table of Contents List of abbreviations ................................................................................. 5 Abstract ................................................................................................... 7 Chapter 1: Introduction ............................................................................ -
Mapping Protein Interactions of Sodium Channel Nav1.7 Using 2 Epitope-Tagged Gene Targeted Mice
bioRxiv preprint doi: https://doi.org/10.1101/118497; this version posted March 20, 2017. 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. 1 Mapping protein interactions of sodium channel NaV1.7 using 2 epitope-tagged gene targeted mice 3 Alexandros H. Kanellopoulos1†, Jennifer Koenig1, Honglei Huang2, Martina Pyrski3, 4 Queensta Millet1, Stephane Lolignier1, Toru Morohashi1, Samuel J. Gossage1, Maude 5 Jay1, John Linley1, Georgios Baskozos4, Benedikt Kessler2, James J. Cox1, Frank 6 Zufall3, John N. Wood1* and Jing Zhao1†** 7 1Molecular Nociception Group, WIBR, University College London, Gower Street, 8 London WC1E 6BT, UK. 9 2Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, The 10 Old Road Campus, Oxford, OX3 7FZ, UK. 11 3Center for Integrative Physiology and Molecular Medicine, Saarland University, 12 Kirrbergerstrasse, Bldg. 48, 66421 Homburg, Germany. 13 4Division of Bioscience, University College London, Gower Street, London WC1E 6BT, UK.14 15 †These authors contributed equally to directing this work. 16 *Correspondence author. Tel: +44 207 6796 954; E-mail: [email protected] 17 **Corresponding author: Tel: +44 207 6790 959; E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/118497; this version posted March 20, 2017. 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. 18 Abstract 19 The voltage-gated sodium channel NaV1.7 plays a critical role in pain pathways. 20 Besides action potential propagation, NaV1.7 regulates neurotransmitter release, 21 integrates depolarizing inputs over long periods and regulates transcription. -
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 -
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. -
Familial Hyperkalemic Hypertension
Disease of the Month Familial Hyperkalemic Hypertension Juliette Hadchouel,* Ce´line Delaloy,* Se´bastien Faure´,† Jean-Michel Achard,† and Xavier Jeunemaitre* *Colle`ge de France, Paris; INSERM U36, Paris; AP-HP, Department of Genetics, Hoˆpital Europe´en Georges Pompidou; University Paris-Descartes, Faculty of Medicine, Paris, France; and †Division of Nephrology and Department of Physiology, Limoges University Hospital, Limoges, France J Am Soc Nephrol 17: 208–217, 2006. doi: 10.1681/ASN.2005030314 amilial hyperkalemic hypertension (FHHt) syndrome biochemical abnormalities and age or BP, which seemed to (1,2), also known as Gordon syndrome (3) or pseudohy- depend primarily on age in affected individuals (11). This F poaldosteronism type 2 (4), is a rare inherited form of phenotypic variability, associated with sensitivity to thia- low-renin hypertension associated with hyperkalemia and hy- zides—which are widely used in hypertension—and with a low perchloremic metabolic acidosis in patients with a normal GFR probability of this rare disease’s being recognized by most (OMIM no. 145260). This monogenic form of arterial hyperten- doctors may have led to an underestimation of its frequency. sion has excited new interest since the discovery of a new, The mode of inheritance of the disease is consistent with unsuspected molecular pathway that is responsible for both the autosomal dominant transmission in most, if not all, of the biochemical abnormalities and the increase in BP observed. pedigrees reported. However, we have identified two families Genetic analysis has led to the identification of mutations in in which the parents of the affected individuals were first two genes that belong to a new family of kinases, the WNK cousins, suggesting possible autosomal recessive transmission. -
Integrating Protein Copy Numbers with Interaction Networks to Quantify Stoichiometry in Mammalian Endocytosis
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 2020. 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-ND 4.0 International license. Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis Daisy Duan1, Meretta Hanson1, David O. Holland2, Margaret E Johnson1* 1TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218. 2NIH, Bethesda, MD, 20892. *Corresponding Author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 2020. 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-ND 4.0 International license. Abstract Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at various copy numbers within a cell, from hundreds (e.g. auxilin) to millions (e.g. clathrin). Between cell types with identical genomes, copy numbers further vary significantly both in absolute and relative abundance. These variations contain essential information about each protein’s function, but how significant are these variations and how can they be quantified to infer useful functional behavior? Here, we address this by quantifying the stoichiometry of proteins involved in the CME network. We find robust trends across three cell types in proteins that are sub- vs super-stoichiometric in terms of protein function, network topology (e.g. -
Mapping Protein Interactions of Sodium Channel
Published online: January 15, 2018 Resource Mapping protein interactions of sodium channel NaV1.7 using epitope-tagged gene-targeted mice Alexandros H Kanellopoulos1,†, Jennifer Koenig1,†, Honglei Huang2, Martina Pyrski3 , Queensta Millet1, Stéphane Lolignier1,4, Toru Morohashi1, Samuel J Gossage1, Maude Jay1, John E Linley1,5, Georgios Baskozos6 , Benedikt M Kessler2, James J Cox1, Annette C Dolphin7, Frank Zufall3, John N Wood1,* & Jing Zhao1,** Abstract Introduction The voltage-gated sodium channel NaV1.7 plays a critical role in Pain is a major clinical problem. A 2012 National Health Interview pain pathways. We generated an epitope-tagged NaV1.7 mouse Survey (NHIS) in the United States revealed that 25.3 million adults that showed normal pain behaviours to identify channel-inter- (11.2%) suffered from daily (chronic) pain and 23.4 million acting proteins. Analysis of NaV1.7 complexes affinity-purified (10.3%) reported severe pain within a previous 3-month period under native conditions by mass spectrometry revealed 267 (Nahin, 2015). Many types of chronic pain are difficult to treat as proteins associated with Nav1.7 in vivo. The sodium channel b3 most available drugs have limited efficacy and can cause side (Scn3b), rather than the b1 subunit, complexes with Nav1.7, and effects. There is thus a huge unmet need for novel analgesics we demonstrate an interaction between collapsing-response medi- (Woodcock, 2009). Recent human and animal genetic studies have ator protein (Crmp2) and Nav1.7, through which the analgesic drug indicated that the voltage-gated sodium channel (VGSC) NaV1.7 lacosamide regulates Nav1.7 current density. Novel NaV1.7 protein plays a crucial role in pain signalling (Nassar et al, 2004; Cox et al, interactors including membrane-trafficking protein synaptotag- 2006; Dib-Hajj et al, 2013), highlighting NaV1.7 as a promising drug min-2 (Syt2), L-type amino acid transporter 1 (Lat1) and trans- target for development of novel analgesics (Habib et al, 2015; membrane P24-trafficking protein 10 (Tmed10) together with Emery et al, 2016). -
Genes and Symptoms of Schizophrenia: Modifiers, Networks, and Interactions in Complex Disease
Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2009 Genes and Symptoms of Schizophrenia: Modifiers, Networks, and Interactions in Complex Disease Sarah Bergen Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Medical Genetics Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/1940 This Dissertation is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Genes and Symptoms of Schizophrenia: Modifiers, Networks, and Interactions in Complex Disease A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University by: Sarah E. Bergen B.A., Macalester College, 2000 M.S., University of Pittsburgh, 2004 Director: Kenneth S. Kendler, M.D. Distinguished Professor, Departments of Psychiatry and Human and Molecular Genetics Virginia Commonwealth University Richmond, VA September, 2009 Acknowledgements First, I want to thank my parents whose unconditional love and only slightly conditional support has carried me through every bump and rough patch on my journey through grad school (and life). None of my work would have been accomplished without all you have done for me, and I am profoundly grateful. I have been extremely fortunate in my experiences here to not only have been quite productive scientifically, but also to have enjoyed the graduate school experience. This is almost entirely due to the brilliant and kind people I have had the opportunity to work with. -
Calcium Control of Neurotransmitter Release
Downloaded from http://cshperspectives.cshlp.org/ on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Calcium Control of Neurotransmitter Release Thomas C. Su¨dhof Department of Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 Correspondence: [email protected] Upon entering a presynaptic terminal, an action potential opens Ca2þ channels, and transiently increases the local Ca2þ concentration at the presynaptic active zone. Ca2þ then triggers neurotransmitter release within a few hundred microseconds by activating synaptotagmins Ca2þ. Synaptotagmins bind Ca2þ via two C2-domains, and transduce the Ca2þ signal into a nanomechanical activation of the membrane fusion machinery; this acti- vation is mediated by the Ca2þ-dependent interaction of the synaptotagmin C2-domains with phospholipids and SNARE proteins. In triggering exocytosis, synaptotagmins do not act alone, but require an obligatory cofactor called complexin, a small protein that binds to SNARE complexes and simultaneously activates and clamps the SNARE complexes, thereby positioning the SNARE complexes for subsequent synaptotagmin action. The con- served function of synaptotagmins and complexins operates generally in most, if not all, Ca2þ-regulated forms of exocytosis throughout the body in addition to synaptic vesicle exo- cytosis, including in the degranulation of mast cells, acrosome exocytosis in sperm cells, hormone secretion from endocrine cells, and neuropeptide release. ynaptic transmission is initiated when an in the brainstem (Fig. 1B; reviewed in Mein- Saction potential invades a nerve terminal, renken et al. 2003). Overall, these high-resolution opening Ca2þ channels, which gate a highly electrophysiological studies on neurotrans- localized, transient increase in intracellular mitter release revealed that a presynaptic action Ca2þ at the active zone (Fig. -
Drosophila and Human Transcriptomic Data Mining Provides Evidence for Therapeutic
Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome Author Abhay Sharma Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research Delhi University Campus, Mall Road Delhi 110007, India Tel: +91-11-27666156, Fax: +91-11-27662407 Email: [email protected] Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 Running head: Pentylenetetrazole mechanism in Down syndrome 1 Abstract Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation.