DOCSLIB.ORG

Mouse Ppp2r5b Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Ppp2r5b Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Ppp2r5b Knockout Project (CRISPR/Cas9) Objective: To create a Ppp2r5b knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ppp2r5b gene (NCBI Reference Sequence: NM_198168 ; Ensembl: ENSMUSG00000024777 ) is located on Mouse chromosome 19. 14 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 14 (Transcript: ENSMUST00000025695). Exon 2~11 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from the coding region. Exon 2~11 covers 74.85% of the coding region. The size of effective KO region: ~4944 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 10 1 2 3 4 5 6 7 8 9 11 14 Legends Exon of mouse Ppp2r5b Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 412 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 806 bp section downstream of Exon 11 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 8 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(412bp) | A(19.9% 82) | C(30.1% 124) | T(21.84% 90) | G(28.16% 116) Note: The 412 bp section upstream of Exon 2 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(806bp) | A(23.7% 191) | C(27.17% 219) | T(24.19% 195) | G(24.94% 201) Note: The 806 bp section downstream of Exon 11 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 4 of 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 412 1 412 412 100.0% chr19 - 6234832 6235243 412 browser details YourSeq 25 113 144 412 96.3% chr14 - 78577730 78577763 34 browser details YourSeq 23 359 383 412 87.5% chr5 - 8364365 8364388 24 browser details YourSeq 21 101 121 412 100.0% chr19 - 15753905 15753925 21 browser details YourSeq 21 31 51 412 100.0% chr16 + 13923634 13923654 21 browser details YourSeq 20 31 50 412 100.0% chr14 - 35486923 35486942 20 Note: The 412 bp section upstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 806 1 806 806 100.0% chr19 - 6229350 6230155 806 browser details YourSeq 30 656 805 806 65.7% chr11 + 109379423 109379547 125 browser details YourSeq 23 264 287 806 100.0% chr10 + 15231316 15231343 28 browser details YourSeq 22 784 805 806 100.0% chr10 - 125674781 125674802 22 browser details YourSeq 21 186 206 806 100.0% chr1 + 126925227 126925247 21 browser details YourSeq 20 82 101 806 100.0% chr10 - 36960978 36960997 20 browser details YourSeq 20 604 623 806 100.0% chr12 + 108359086 108359105 20 Note: The 806 bp section downstream of Exon 11 is BLAT searched against the genome. No significant similarity is found. Page 5 of 8 https://www.alphaknockout.com Gene and protein information: Ppp2r5b protein phosphatase 2, regulatory subunit B', beta [ Mus musculus (house mouse) ] Gene ID: 225849, updated on 12-Aug-2019 Gene summary Official Symbol Ppp2r5b provided by MGI Official Full Name protein phosphatase 2, regulatory subunit B', beta provided by MGI Primary source MGI:MGI:2388480 See related Ensembl:ENSMUSG00000024777 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as B'beta; BC026670 Expression Ubiquitous expression in adrenal adult (RPKM 89.9), cerebellum adult (RPKM 51.2) and 23 other tissues See more Orthologs human all Genomic context Location: 19; 19 A See Ppp2r5b in Genome Data Viewer Exon count: 15 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (6227765..6236264, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 19 NC_000085.5 (6227767..6235840, complement) Chromosome 19 - NC_000085.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 4 transcripts Gene: Ppp2r5b ENSMUSG00000024777 Description protein phosphatase 2, regulatory subunit B', beta [Source:MGI Symbol;Acc:MGI:2388480] Gene Synonyms B'beta Location Chromosome 19: 6,227,765-6,235,872 reverse strand. GRCm38:CM001012.2 View alleles of this gene on alternative sequences About this gene This gene has 4 transcripts (splice variants), 1 gene allele, 175 orthologues, 4 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Ppp2r5b-201 ENSMUST00000025695.9 2742 497aa ENSMUSP00000025695.9 Protein coding CCDS29499 Q6PD28 TSL:1 GENCODE basic APPRIS P1 Ppp2r5b-204 ENSMUST00000236699.1 740 No protein - Retained intron - - - Ppp2r5b-203 ENSMUST00000153155.1 389 No protein - Retained intron - - TSL:3 Ppp2r5b-202 ENSMUST00000148693.1 467 No protein - lncRNA - - TSL:5 28.11 kb Forward strand 6.22Mb 6.23Mb 6.24Mb Genes Majin-201 >protein coding Gpha2-201 >protein coding Atg2a-201 >protein coding (Comprehensive set... Majin-202 >protein coding Gpha2-202 >protein coding Atg2a-204 >protein coding Contigs AC127556.4 > Genes (Comprehensive set... < Ppp2r5b-201protein coding < Ppp2r5b-204retained intron < Ppp2r5b-202lncRNA < Ppp2r5b-203retained intron Regulatory Build 6.22Mb 6.23Mb 6.24Mb Reverse strand 28.11 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript RNA gene Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000025695 < Ppp2r5b-201protein coding Reverse strand 8.11 kb ENSMUSP00000025... MobiDB lite Low complexity (Seg) Superfamily Armadillo-type fold Pfam Protein phosphatase 2A, regulatory B subunit, B56 PIRSF Protein phosphatase 2A, regulatory B subunit, B56 PANTHER PTHR10257:SF4 Protein phosphatase 2A, regulatory B subunit, B56 Gene3D Armadillo-like helical All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 60 120 180 240 300 360 420 497 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
Load more

Recommended publications
  • Deregulated Gene Expression Pathways in Myelodysplastic Syndrome Hematopoietic Stem Cells
    Leukemia (2010) 24, 756–764 & 2010 Macmillan Publishers Limited All rights reserved 0887-6924/10 $32.00 www.nature.com/leu ORIGINAL ARTICLE Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells A Pellagatti1, M Cazzola2, A Giagounidis3, J Perry1, L Malcovati2, MG Della Porta2,MJa¨dersten4, S Killick5, A Verma6, CJ Norbury7, E Hellstro¨m-Lindberg4, JS Wainscoat1 and J Boultwood1 1LRF Molecular Haematology Unit, NDCLS, John Radcliffe Hospital, Oxford, UK; 2Department of Hematology Oncology, University of Pavia Medical School, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; 3Medizinische Klinik II, St Johannes Hospital, Duisburg, Germany; 4Division of Hematology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden; 5Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK; 6Albert Einstein College of Medicine, Bronx, NY, USA and 7Sir William Dunn School of Pathology, University of Oxford, Oxford, UK To gain insight into the molecular pathogenesis of the the World Health Organization.6,7 Patients with refractory myelodysplastic syndromes (MDS), we performed global gene anemia (RA) with or without ringed sideroblasts, according to expression profiling and pathway analysis on the hemato- poietic stem cells (HSC) of 183 MDS patients as compared with the the French–American–British classification, were subdivided HSC of 17 healthy controls. The most significantly deregulated based on the presence or absence of multilineage dysplasia. In pathways in MDS include interferon signaling, thrombopoietin addition, patients with RA with excess blasts (RAEB) were signaling and the Wnt pathways. Among the most signifi- subdivided into two categories, RAEB1 and RAEB2, based on the cantly deregulated gene pathways in early MDS are immuno- percentage of bone marrow blasts.
    [Show full text]
  • PPP2R3C Gene Variants Cause Syndromic 46,XY Gonadal
    5 180 T Guran and others PPP2R3C in testis developmentQ1 180:5 291–309 Clinical Study and spermatogenesis PPP2R3C gene variants cause syndromic 46,XY gonadal dysgenesis and impaired spermatogenesis in humans Tulay Guran1, Gozde Yesil2, Serap Turan1, Zeynep Atay3, Emine Bozkurtlar4, AghaRza Aghayev5, Sinem Gul6, Ilker Tinay7, Basak Aru8, Sema Arslan9, M Kutay Koroglu10, Feriha Ercan10, Gulderen Y Demirel8, Funda S Eren4, Betul Karademir9 and Abdullah Bereket1 1Department of Paediatric Endocrinology and Diabetes, Marmara University, 2Department of Genetics, Bezm-i Alem University, 3Department of Paediatric Endocrinology and Diabetes, Medipol University, 4Department of Pathology, Marmara University, School of Medicine, Istanbul, Turkey, 5Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey, 6Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey, 7Department of Urology, Marmara University, School of Medicine, Istanbul, Turkey, 8Department of Immunology, Yeditepe Correspondence University, Faculty of Medicine, Istanbul, Turkey, 9Department of Biochemistry, Genetic and Metabolic Diseases should be addressed Research and Investigation Center, and 10Department of Histology and Embryology, Marmara University, School of to T Guran Medicine, Istanbul, Turkey Email [email protected] Abstract Context: Most of the knowledge on the factors involved in human sexual development stems from studies of rare cases with disorders of sex development. Here, we have described a novel 46, XY complete gonadal dysgenesis syndrome caused by homozygous variants in PPP2R3C gene. This gene encodes B″gamma regulatory subunit of the protein phosphatase 2A (PP2A), which is a serine/threonine phosphatase involved in the phospho-regulation processes of most mammalian cell types. PPP2R3C gene is most abundantly expressed in testis in humans, while its function was hitherto unknown.
    [Show full text]
  • Temporal Proteomic Analysis of HIV Infection Reveals Remodelling of The
    1 1 Temporal proteomic analysis of HIV infection reveals 2 remodelling of the host phosphoproteome 3 by lentiviral Vif variants 4 5 Edward JD Greenwood 1,2,*, Nicholas J Matheson1,2,*, Kim Wals1, Dick JH van den Boomen1, 6 Robin Antrobus1, James C Williamson1, Paul J Lehner1,* 7 1. Cambridge Institute for Medical Research, Department of Medicine, University of 8 Cambridge, Cambridge, CB2 0XY, UK. 9 2. These authors contributed equally to this work. 10 *Correspondence: [email protected]; [email protected]; [email protected] 11 12 Abstract 13 Viruses manipulate host factors to enhance their replication and evade cellular restriction. 14 We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a 15 comprehensive time course analysis of >6,500 viral and cellular proteins during HIV 16 infection. To enable specific functional predictions, we categorized cellular proteins regulated 17 by HIV according to their patterns of temporal expression. We focussed on proteins depleted 18 with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be 19 necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the 20 B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). 21 Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent 22 hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. 23 The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral 2 24 lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and 25 conserved Vif function.
    [Show full text]
  • Loss of PPP2R2A Inhibits Homologous Recombination DNA Repair and Predicts
    Author Manuscript Published OnlineFirst on October 18, 2012; DOI: 10.1158/0008-5472.CAN-12-1667 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Loss of PPP2R2A inhibits homologous recombination DNA repair and predicts tumor sensitivity to PARP inhibition Peter Kalev1, Michal Simicek1, Iria Vazquez1, Sebastian Munck1, Liping Chen2, Thomas Soin1, Natasha Danda1, Wen Chen2 and Anna Sablina1,* 1VIB Center for the Biology of Disease; Center for Human Genetics, KULeuven, Leuven 3000 Belgium 2Department of Toxicology, Faculty of Preventive Medicine, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China *Corresponding author information: [email protected] Contact information: Anna A. Sablina, Ph.D. CME Department, KULeuven O&N I Herestraat 49, bus 602 Leuven, Belgium 3000 Tel: +3216330790 Fax: +3216330145 Running title: The role of PPP2R2A in DNA repair Keywords: PP2A, ATM, DNA repair, cancer, PARP inhibition Conflict of interests: The authors claim no conflict of interest. - 1 - Downloaded from cancerres.aacrjournals.org on September 27, 2021. © 2012 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 18, 2012; DOI: 10.1158/0008-5472.CAN-12-1667 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Abstract Reversible phosphorylation plays a critical role in DNA repair. Here we report the results of a loss-of-function screen that identifies the PP2A heterotrimeric serine/threonine phosphatases PPP2R2A, PPP2R2D, PPP2R5A and PPP2R3C in double-strand break (DSB) repair. In particular, we found that PPP2R2A-containing complexes directly dephosphorylated ATM at S367, S1893, and S1981 to regulate its retention at DSB sites.
    [Show full text]
  • Therapeutic Re-Activation of Protein Phosphatase 2A in Acute Myeloid
    MINI REVIEW ARTICLE published: 02 February 2015 doi: 10.3389/fonc.2015.00016 Therapeutic re-activation of protein phosphatase 2A in acute myeloid leukemia Kavitha Ramaswamy, Barbara Spitzer and Alex Kentsis* Molecular Pharmacology and Chemistry Program, Department of Pediatrics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, New York, NY, USA Edited by: Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase that is required for nor- Peter Ruvolo, The University of Texas mal cell growth and development. PP2A is a potent tumor suppressor, which is inactivated MD Anderson Cancer Center, USA in cancer cells as a result of genetic deletions and mutations. In myeloid leukemias, genes Reviewed by: encoding PP2A subunits are generally intact. Instead, PP2A is functionally inhibited by Peter Ruvolo, The University of Texas MD Anderson Cancer Center, USA post-translational modifications of its catalytic C subunit, and interactions with negative Alejandro Gutierrez, Boston Children’s regulators by its regulatory B and scaffold A subunits. Here, we review the molecular Hospital, USA mechanisms of genetic and functional inactivation of PP2A in human cancers, with a par- *Correspondence: ticular focus on human acute myeloid leukemias (AML). By analyzing expression of genes Alex Kentsis, Molecular Pharmacology and Chemistry encoding PP2A subunits using transcriptome sequencing, we find that PP2A dysregulation Program, Department of Pediatrics, in AML is characterized by silencing
    [Show full text]
  • Protein Family Members. the GENE.FAMILY
    Table 3: Protein family members. The GENE.FAMILY col- umn shows the gene family name defined either by HGNC (superscript `H', http://www.genenames.org/cgi-bin/family_ search) or curated manually by us from Entrez IDs in the NCBI database (superscript `C' for `Custom') that we have identified as corresonding for each ENTITY.ID. The members of each gene fam- ily that are in at least one of our synaptic proteome datasets are shown in IN.SYNAPSE, whereas those not found in any datasets are in the column OUT.SYNAPSE. In some cases the intersection of two HGNC gene families are needed to specify the membership of our protein family; this is indicated by concatenation of the names with an ampersand. ENTITY.ID GENE.FAMILY IN.SYNAPSE OUT.SYNAPSE AC Adenylate cyclasesH ADCY1, ADCY2, ADCY10, ADCY4, ADCY3, ADCY5, ADCY7 ADCY6, ADCY8, ADCY9 actin ActinsH ACTA1, ACTA2, ACTB, ACTC1, ACTG1, ACTG2 ACTN ActininsH ACTN1, ACTN2, ACTN3, ACTN4 AKAP A-kinase anchoring ACBD3, AKAP1, AKAP11, AKAP14, proteinsH AKAP10, AKAP12, AKAP17A, AKAP17BP, AKAP13, AKAP2, AKAP3, AKAP4, AKAP5, AKAP6, AKAP8, CBFA2T3, AKAP7, AKAP9, RAB32 ARFGEF2, CMYA5, EZR, MAP2, MYO7A, MYRIP, NBEA, NF2, SPHKAP, SYNM, WASF1 CaM Endogenous ligands & CALM1, CALM2, EF-hand domain CALM3 containingH CaMKK calcium/calmodulin- CAMKK1, CAMKK2 dependent protein kinase kinaseC CB CalbindinC CALB1, CALB2 CK1 Casein kinase 1C CSNK1A1, CSNK1D, CSNK1E, CSNK1G1, CSNK1G2, CSNK1G3 CRHR Corticotropin releasing CRHR1, CRHR2 hormone receptorsH DAGL Diacylglycerol lipaseC DAGLA, DAGLB DGK Diacylglycerol kinasesH DGKB,
    [Show full text]
  • Protein Phosphatase 2A Regulatory Subunits and Cancer
    Biochimica et Biophysica Acta 1795 (2009) 1–15 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbacan Review Protein phosphatase 2A regulatory subunits and cancer Pieter J.A. Eichhorn 1, Menno P. Creyghton 2, René Bernards ⁎ Division of Molecular Carcinogenesis, Center for Cancer Genomics and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands article info abstract Article history: The serine/threonine protein phosphatase (PP2A) is a trimeric holoenzyme that plays an integral role in the Received 7 April 2008 regulation of a number of major signaling pathways whose deregulation can contribute to cancer. The Received in revised form 20 May 2008 specificity and activity of PP2A are highly regulated through the interaction of a family of regulatory B Accepted 21 May 2008 subunits with the substrates. Accumulating evidence indicates that PP2A acts as a tumor suppressor. In this Available online 3 June 2008 review we summarize the known effects of specific PP2A holoenzymes and their roles in cancer relevant pathways. In particular we highlight PP2A function in the regulation of MAPK and Wnt signaling. Keywords: Protein phosphatase 2A © 2008 Elsevier B.V. All rights reserved. Signal transduction Cancer Contents 1. Introduction ............................................................... 1 2. PP2A structure and function ....................................................... 2 2.1. The catalytic subunit (PP2Ac).................................................... 2 2.2. The structural subunit (PR65) ................................................... 3 2.3. The regulatory B subunits ..................................................... 3 2.3.1. The B/PR55 family of B subunits .............................................. 3 2.3.2. The B′/PR61 family of β subunits ............................................. 4 2.3.3. The B″/PR72 family of β subunits ............................................
    [Show full text]
  • Regulation of the Phosphoprotein Phosphatase 2A System and Its Modulation During Oxidative Stress: a Potential Therapeutic Target?
    Pharmacology & Therapeutics 198 (2019) 68–89 Contents lists available at ScienceDirect Pharmacology & Therapeutics journal homepage: www.elsevier.com/locate/pharmthera Regulation of the phosphoprotein phosphatase 2A system and its modulation during oxidative stress: A potential therapeutic target? I.S. Elgenaidi, J.P. Spiers ⁎ Department of Pharmacology and Therapeutics, Trinity College Dublin, Ireland article info abstract Phosphoprotein phosphatases are of growing interest in the pathophysiology of many diseases and are often the Keywords:: neglected partner of protein kinases. One family member, PP2A, accounts for dephosphorylation of ~55-70% of all Ischaemia serine/threonine phosphosites. Interestingly, dysregulation of kinase signalling is a hallmark of many diseases in PP2A HIF1α which an increase in oxidative stress is also noted. With this in mind, we assess the evidence to support oxidative CIP2A stress-mediated regulation of the PP2A system SMAPs In this article, we first present an overview of the PP2A system before providing an analysis of the regulation hypoxia of PP2A by endogenous inhibitors, post translational modification, and miRNA. Next, a detailed critique of data miRNA implicating reactive oxygen species, ischaemia, ischaemia-reperfusion, and hypoxia in regulating the PP2A holoenzyme and associated regulators is presented. Finally, the pharmacological targeting of PP2A, its endoge- nous inhibitors, and enzymes responsible for its post-translational modification are covered. There is extensive evidence that oxidative stress modulates multiple components of the PP2A system, however, most of the data pertains to the catalytic subunit of PP2A. Irrespective of the underlying aetiology, free radical- mediated attenuation of PP2A activity is an emerging theme. However, in many instances, a dichotomy exists, which requires clarification and mechanistic insight.
    [Show full text]
  • Genetic Risk Factors for PTSD: a Gene-Set Analysis of Neurotransmitter Receptors
    Genetic Risk Factors for PTSD: A Gene-Set Analysis of Neurotransmitter Receptors Michael Lewis Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Psychology Russell T. Jones Bruce H. Scarpa-Friedman Margaret T. Davis Rachel A. Diana May 12, 2020 Blacksburg, VA Keywords: PTSD, Gene-set analysis, GSA-SNP2, Neurotransmitter receptors, serotonin, glutamate, intracellular signaling Genetic Risk Factors for PTSD: A Gene-Set Analysis of Neurotransmitter Receptors Michael Lewis Abstract (Academic) PTSD is a moderately heritable disorder that causes intense and chronic suffering in afflicted individuals. The pathogenesis of PTSD is not well understood, and genetic mechanisms are particularly elusive. Neurotransmitter systems are thought to contribute to PTSD etiology and are the targets of most pharmacotherapies used to treat PTSD, including the only two FDA approved options and a wide array of off-label options. However, the degree to which variations in genes which encode for and regulate neurotransmitter receptors increase risk of developing PTSD is unclear. Recently, large collaborative groups of PTSD genetics researchers have completed genome-wide association studies (GWAS) using massive sample sizes and have made summary statistics available for public use. In 2018, a new technique for high-powered analysis of GWAS summary statistics called GSA-SNP2 was introduced. In order to explore the relationship between PTSD and genetic variants in widely theorized molecular targets, this study applied GSA-SNP2 to manually curated neurotransmitter receptor gene-sets. Curated gene-sets included nine total “neurotransmitter receptor group” gene-sets and 45 total “receptor subtype” gene-sets.
    [Show full text]
  • Novel Protein Phosphatase 2A Complexes in Skeletal Muscle from Obese Insulin Resistant Human Participants Divyasri Damacharla Wayne State University
    Wayne State University Wayne State University Theses 1-1-2015 Novel Protein Phosphatase 2a Complexes In Skeletal Muscle From Obese Insulin Resistant Human Participants Divyasri Damacharla Wayne State University, Follow this and additional works at: http://digitalcommons.wayne.edu/oa_theses Part of the Medicinal Chemistry and Pharmaceutics Commons, and the Pharmacology Commons Recommended Citation Damacharla, Divyasri, "Novel Protein Phosphatase 2a Complexes In Skeletal Muscle From Obese Insulin Resistant Human Participants" (2015). Wayne State University Theses. Paper 371. This Open Access Thesis is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Theses by an authorized administrator of DigitalCommons@WayneState. NOVEL PROTEIN PHOSPHATASE 2A COMPLEXES IN SKELETAL MUSCLE FROM OBESE INSULIN RESISTANT HUMAN PARTICIPANTS by DIVYASRI DAMACHARLA THESIS Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE 2015 MAJOR: PHARMACEUTICAL SCIENCES Approved By: Advisor Date i © COPYRIGHT BY DIVYASRI DAMACHARLA 2015 All Rights Reserved ii TABLE OF CONTENTS LIST OF FIGURES…………………………………………………………..……..….…….v LIST OF TABLES……………………………………………………………….……..…....vi CHAPTER 1 INTRODUCTION……………………………………………………….……1 1.1 INTRODUCTION TO DIABETES AND INSULIN SIGNALING PATHWAY........1 1.1.1 INTRODUCTION TO DIABETES……………………..……………...…......1 1.1.2 INSULIN SIGNALING PATHWAY…..………………………….….….…...2
    [Show full text]
  • ORAOV1 Is a Probable Target Within the 11Q13.3 Amplicon in Lymph Node Metastases from Gastric Adenocarcinoma
    INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 29: 81-87, 2012 ORAOV1 is a probable target within the 11q13.3 amplicon in lymph node metastases from gastric adenocarcinoma JI UN KANG1 and SUN HOE KOO2 1Department of Biomedical Laboratory Science, Korea Nazarene University, Cheonan 331-718; 2Department of Laboratory Medicine, Chungnam National University College of Medicine, Taejeon 301-721, Republic of Korea Received July 29, 2011; Accepted September 21, 2011 DOI: 10.3892/ijmm.2011.811 Abstract. The lymph node metastatic (LNM) spread of overall incidence of GAC has declined, the incidence remains tumor cells is a frequent event in the initial process of cancer high in Asian countries and there is a compelling need to dissemination and is a powerful independent prognostic indi- explore novel therapeutic targets for its management (2). cator in gastric adenocarcinoma (GAC). High density genomic Lymph node metastasis (LNM) is a frequent event in arrays were conducted to identify molecular markers associ- the initial process of GAC dissemination and is the major ated with lymph node metastasis in GAC. In the genome-wide determinant of GAC-related mortality (3). In most solid profile, large copy number gains involving chromosomes 1p, tumors, including GAC, the spread of cancer cells through the 3q, 8q, 9q, 11q, 16p, 19p, and 20q (log2 ratio >0.25) (>40% of lymphatics to the regional lymph nodes (LN) is considered as patients) were more prevalent than copy number losses. The an important prognostic indicator for patient outcome (4-8). most notable finding was copy number gains at the long arm Therefore, a better understanding of molecules promoting LNM of chromosome 11, which occurred in 75.0% of lymphatic may open the way to a host of innovative therapeutic strategies metastasis GAC cases, and the delineated minimal common for GAC and could provide additional information concerning region was 11q24.2-q12.1.
    [Show full text]
  • Structure-Function Relationships of Rna and Protein in Synaptic Plasticity
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Structure-Function Relationships Of Rna And Protein In Synaptic Plasticity Sarah Middleton University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Biology Commons, and the Neuroscience and Neurobiology Commons Recommended Citation Middleton, Sarah, "Structure-Function Relationships Of Rna And Protein In Synaptic Plasticity" (2017). Publicly Accessible Penn Dissertations. 2474. https://repository.upenn.edu/edissertations/2474 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2474 For more information, please contact [email protected]. Structure-Function Relationships Of Rna And Protein In Synaptic Plasticity Abstract Structure is widely acknowledged to be important for the function of ribonucleic acids (RNAs) and proteins. However, due to the relative accessibility of sequence information compared to structure information, most large genomics studies currently use only sequence-based annotation tools to analyze the function of expressed molecules. In this thesis, I introduce two novel computational methods for genome-scale structure-function analysis and demonstrate their application to identifying RNA and protein structures involved in synaptic plasticity and potentiation—important neuronal processes that are thought to form the basis of learning and memory. First, I describe a new method for de novo identification of RNA secondary structure motifs enriched in co-regulated transcripts. I show that this method can accurately identify secondary structure motifs that recur across three or more transcripts in the input set with an average recall of 0.80 and precision of 0.98. Second, I describe a tool for predicting protein structural fold from amino acid sequence, which achieves greater than 96% accuracy on benchmarks and can be used to predict protein function and identify new structural folds.
    [Show full text]