Bioinformatics Analysis of the Target Gene of Fibroblast Growth Factor Receptor 3 in Bladder Cancer and Associated Molecular Mechanisms
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32-2709: PPIL1 Recombinant Protein Description Product Info Application
9853 Pacific Heights Blvd. Suite D. San Diego, CA 92121, USA Tel: 858-263-4982 Email: [email protected] 32-2709: PPIL1 Recombinant Protein Alternative Name : Peptidyl-Prolyl Cis-Trans Isomerase-Like 1,PPIL-1,CYPL1,hCyPX,MGC678,PPIase,CGI-124,PPIL1. Description Source : Escherichia Coli. PPIL1 Human Recombinant protein produced in E.Coli is a single, non-glycosylated, polypeptide chain containing 174 amino acids (1-166) and having a molecular mass of 19.3 kDa. PPIL1 is fused to 8 amino acid His Tag at C-terminus and is purified by proprietary chromatographic techniques. PPIL1 belongs to the cyclophilin family of peptidylprolyl isomerases (PPIases). The cyclophilins are a well conserved, ubiquitous family, members of which take an significant part in protein folding, immunosuppression by cyclosporin A, and infection of HIV-1 virions. PPIL1 protein increases the folding of proteins and catalyze the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. PPIL1 is involved in proliferation of cancer cells through modulation of phosphorylation of stathmin. PPIL1 is a novel molecular target for colon- cancer therapy. Product Info Amount : 50 µg Purification : Greater than 95.0% as determined by SDS-PAGE. Content : PPIL1 solution containing 20 mM Tris-HCl buffer (pH 8.0) and 20% glycerol PPIL1 Human Recombinant although stable at 4°C for 1 week, should be stored desiccated below Storage condition : -18°C. Please prevent freeze thaw cycles. Amino Acid : MAAIPPDSWQ PPNVYLETSM GIIVLELYWK HAPKTCKNFA ELARRGYYNG TKFHRIIKDF MIQGGDPTGT GRGGASIYGK QFEDELHPDL KFTGAGILAM ANAGPDTNGS QFFVTLAPTQ WLDGKHTIFG RVCQGIGMVN RVGMVETNSQ DRPVDDVKII KAYPSGLEHH HHHH. Application Note Specific activity is > 300 nmoles/min/mg, and is defined as the amount of enzyme that cleaves 1umole of suc-AAFP-pNA per minute at 25C in Tris-Hcl pH8.0 using chymotrypsin. -
Environmental Influences on Endothelial Gene Expression
ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community. -
In This Table Protein Name, Uniprot Code, Gene Name P-Value
Supplementary Table S1: In this table protein name, uniprot code, gene name p-value and Fold change (FC) for each comparison are shown, for 299 of the 301 significantly regulated proteins found in both comparisons (p-value<0.01, fold change (FC) >+/-0.37) ALS versus control and FTLD-U versus control. Two uncharacterized proteins have been excluded from this list Protein name Uniprot Gene name p value FC FTLD-U p value FC ALS FTLD-U ALS Cytochrome b-c1 complex P14927 UQCRB 1.534E-03 -1.591E+00 6.005E-04 -1.639E+00 subunit 7 NADH dehydrogenase O95182 NDUFA7 4.127E-04 -9.471E-01 3.467E-05 -1.643E+00 [ubiquinone] 1 alpha subcomplex subunit 7 NADH dehydrogenase O43678 NDUFA2 3.230E-04 -9.145E-01 2.113E-04 -1.450E+00 [ubiquinone] 1 alpha subcomplex subunit 2 NADH dehydrogenase O43920 NDUFS5 1.769E-04 -8.829E-01 3.235E-05 -1.007E+00 [ubiquinone] iron-sulfur protein 5 ARF GTPase-activating A0A0C4DGN6 GIT1 1.306E-03 -8.810E-01 1.115E-03 -7.228E-01 protein GIT1 Methylglutaconyl-CoA Q13825 AUH 6.097E-04 -7.666E-01 5.619E-06 -1.178E+00 hydratase, mitochondrial ADP/ATP translocase 1 P12235 SLC25A4 6.068E-03 -6.095E-01 3.595E-04 -1.011E+00 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 Protein kinase C and casein Q9BY11 PACSIN1 3.837E-03 -5.863E-01 3.680E-06 -1.824E+00 kinase substrate in neurons protein 1 Tubulin polymerization- O94811 TPPP 6.466E-03 -5.755E-01 6.943E-06 -1.169E+00 promoting protein MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Mitochondrial 2- -
The Genetic Architecture of Secretory PLA2 (Spla2) Genes and Their Impact on Spla2 Activity/Mass and Association with CHD Risk
The Genetic Architecture of Secretory PLA2 (sPLA2) Genes and their Impact on sPLA2 Activity/Mass and Association with CHD Risk Holly Jane Exeter University College London A thesis submitted in accordance with the regulations of the University College London for the degree of Doctor of Philosophy Centre for Cardiovascular Genetics UCL Institute of Cardiovascular Science 1 For Mum and Dad 2 Declaration I, Holly Jane Exeter confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. In relation to specific chapters I would like to clarify my role: In Chapter 3 I was responsible for identifying SNPs of interest from the results of previously genotyped studies. I was then responsible for the in depth literature and bioinformatics study undertaken for PLA2G2A, sPLA2-IIA and the SNPs of interest. I designed the primers for all cloning and EMSA work and carried out all of the cloning experiments, luciferase assays, TaqMan Gene Expression assays and EMSAs according to the methods described. I also carried out the statistical work relating to the luciferase assay experiments. In Chapter 4 I was responsible for genotyping 2 of the studies in the final meta-analysis; IMPROVE and CYPRUS. I used the PRISMA guidelines to compile an in depth literature search of the sPLA2 inhibitor, varespladib. I was part of the core group of investigators who met to discuss the results and direction of the study (participants of the MR study are at the end of the thesis). -
Datasheet: VMA00345KT Product Details
Datasheet: VMA00345KT Description: NUCLEOSIDE DIPHOSPHATE KINASE A ANTIBODY WITH CONTROL LYSATE Specificity: NUCLEOSIDE DIPHOSPHATE KINASE A Format: Purified Product Type: PrecisionAb™ Monoclonal Isotype: IgG2b Quantity: 2 Westerns Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Species Cross Reacts with: Mouse, Rat Reactivity N.B. Antibody reactivity and working conditions may vary between species. Product Form Purified IgG - liquid Preparation 20μl Mouse monoclonal antibody prepared by affinity chromatography on Protein G Buffer Solution Phosphate buffered saline Preservative 0.09% Sodium Azide (NaN3) Stabilisers Immunogen Recombinant human nucleoside diphosphate kinase A External Database Links UniProt: P15531 Related reagents Entrez Gene: 4830 NME1 Related reagents Synonyms NDPKA, NM23 Page 1 of 3 Specificity Mouse anti Human nucleoside diphosphate kinase A antibody recognizes nucleoside diphosphate kinase A, also known as NDP kinase A, granzyme A-activated DNase, metastasis inhibition factor nm23, non-metastatic cells 1 and tumor metastatic process-associated protein. The NME1 gene was identified because of its reduced mRNA transcript levels in highly metastatic cells. -
Frontiers Medicine Csa 2021
1 Frontiers Medicine 2 February 3, 2021 3 Title: Cyclosporin A: a repurposable drug in the treatment of COVID-19 ? 4 5 Running title: Cyclosporin A and COVID-19 6 7 Christian A. DEVAUX,1,2*, Cléa MELENOTTE1, Marie-Dominique 8 PIERCECCHI-MARTI3,4, Clémence DELTEIL3,4, and Didier RAOULT1 9 10 1Aix-Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, 11 France 12 2 CNRS, Marseille, France 13 3 Department of Legal Medicine, Hôpital de la Timone, Marseille University Hospital 14 Center, Marseille, France 15 4 Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France 16 17 *Corresponding author : 18 Christian Devaux, PhD 19 IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, France 20 Phone: (+33) 4 13 73 20 51 21 Fax : (+33) 4 13 73 20 52 22 E-mail: [email protected] 23 24 Abstract length: 190 words; Manuscript length:,7817 words 25 Figures: 7 26 Table 4 27 Keywords: SARS-CoV-2; COVID-19; Cyclosporin A; Cyclophilin; ACE2 28 Summary: 29 COVID-19 is now at the forefront of major health challenge faced globally, creating an urgent 30 need for safe and efficient therapeutic strategies. Given the high attrition rates, high costs and 31 quite slow development of drug discovery, repurposing of known FDA-approved molecules is 32 increasingly becoming an attractive issue in order to quickly find molecules capable of 33 preventing and/or curing COVID-19 patients. Cyclosporin A (CsA), a common anti-rejection 34 drug widely used in transplantation, has recently been shown to exhibit substantial anti- 35 SARS-CoV-2 antiviral activity and anti-COVID-19 effect. -
Global Screening of Sentrin-Specific Protease Family Substrates in Sumoylation
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.25.964072; this version posted February 26, 2020. 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. Global Screening of Sentrin-Specific Protease Family Substrates in SUMOylation Yunzhi Wang, 1, 4 Xiaohui Wu,1, 4 Rui Ge,1, 4 Lei Song, 2 Kai Li, 2 Sha Tian,1 Lili Cai, 1 Mingwei Liu, 2 Wenhao Shi, 2Guoying Yu, 3 Bei Zhen, 2 Yi Wang, 2 Fuchu He, 1, 2, * Jun Qin, 1, 2, * Chen Ding1, 2, * 1State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China 2State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China 3State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, Henan 453007 4Co-first author *Correspondence: [email protected] (C.D.); [email protected] (J.Q.); [email protected] (F.H.); Key Words 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.25.964072; this version posted February 26, 2020. 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. Posttranslational modification; SUMO; Sentrin/SUMO-specific proteases; Mass Spectrometry; Innate Immunity Abstract Post-translational modification of proteins by the addition of small ubiquitin-related modifier (SUMO) is a dynamic process, in which deSUMOylation is carried out by members of the Sentrin/SUMO-specific protease (SENP) family. -
Identi Cation of Crucial Genes in Metastatic Osteosarcoma And
Identication of crucial genes in metastatic osteosarcoma and prognostic biomarker in osteosarcoma patients Weihao Wang First Aliated Hospital of Shantou University Medical College Zhaoyong Liu First Aliated Hospital of Shantou University Medical College Weiqing Lu First Aliated Hospital of Shantou University Medical College Huancheng Guo First Aliated Hospital of Shantou University Medical College Chunbin Zhou First Aliated Hospital of Shantou University Medical College Youbin Lin First Aliated Hospital of Shantou University Medical College Hu Wang ( [email protected] ) the First Aliated Hospital of Shantou University Medical Collegethe First Aliated Hospital of Shantou University Medical Collegethe First Aliated Hospital of Shantou University Medical Collegethe First Aliated Hospital of Shantou University Med Research article Keywords: osteosarcoma, metastasis, crucial genes, prognostic biomarker Posted Date: July 22nd, 2020 DOI: https://doi.org/10.21203/rs.3.rs-44119/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract Background Osteosarcoma is still a challenging cancer that poses a huge threat to human health worldwide, especially in young people. The aim of this study was to identify prognostic genes associated with neoplasm metastasis in osteosarcoma, and construct a prognostic nomogram to help the orthopedist to assess prognosis of osteosarcoma patients. Methods Gene expression and clinical information were extracted from the TARGET database. Differentially expressed genes (DEGs) associated with osteosarcoma metastasis were identied and subjected to GO functional and KEGG pathway enrichment analyses. Survival and Cox analyses were used to identify prognostic genes. Results First, 214 DEGs were identied as crucial genes associated with osteosarcoma metastasis. -
Transcriptome Analysis of Paralichthys Olivaceus Erythrocytes Reveals Profound Immune Responses Induced by Edwardsiella Tarda Infection
International Journal of Molecular Sciences Article Transcriptome Analysis of Paralichthys olivaceus Erythrocytes Reveals Profound Immune Responses Induced by Edwardsiella tarda Infection Bin Sun 1,2,3 , Xuepeng Li 1, Xianhui Ning 1 and Li Sun 1,2,* 1 CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; [email protected] (B.S.); [email protected] (X.L.); [email protected] (X.N.) 2 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China 3 University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China * Correspondence: [email protected]; Tel.: +86-532-82898829 Received: 13 March 2020; Accepted: 3 April 2020; Published: 28 April 2020 Abstract: Unlike mammalian red blood cells (RBCs), fish RBCs are nucleated and thus capable of gene expression. Japanese flounder (Paralichthys olivaceus) is a species of marine fish with important economic values. Flounder are susceptible to Edwardsiella tarda, a severe bacterial pathogen that is able to infect and survive in flounder phagocytes. However, the infectivity of and the immune response induced by E. tarda in flounder RBCs are unclear. In the present research, we found that E. tarda was able to invade and replicate inside flounder RBCs in both in vitro and in vivo infections. To investigate the immune response induced by E. tarda in RBCs, transcriptome analysis of the spleen RBCs of flounder challenged with E. tarda was performed. Six sequencing libraries were constructed, and an average of 43 million clean reads per library were obtained, with 85% of the reads being successfully mapped to the genome of flounder. -
Immunosuppression by Cyclosporine Cyclophilin A-Deficient Mice Are
Cyclophilin A-Deficient Mice Are Resistant to Immunosuppression by Cyclosporine John Colgan, Mohammed Asmal, Bin Yu and Jeremy Luban This information is current as J Immunol 2005; 174:6030-6038; ; of October 2, 2021. doi: 10.4049/jimmunol.174.10.6030 http://www.jimmunol.org/content/174/10/6030 References This article cites 53 articles, 28 of which you can access for free at: Downloaded from http://www.jimmunol.org/content/174/10/6030.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision http://www.jimmunol.org/ • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: by guest on October 2, 2021 http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2005 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Cyclophilin A-Deficient Mice Are Resistant to Immunosuppression by Cyclosporine1 John Colgan,2* Mohammed Asmal,* Bin Yu,* and Jeremy Luban3*† Cyclosporine is an immunosuppressive drug that is widely used to prevent organ transplant rejection. Known intracellular ligands for cyclosporine include the cyclophilins, a large family of phylogenetically conserved proteins that potentially regulate protein folding in cells. -
Structural and Functional Insights Into Human Nuclear Cyclophilins
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 2 November 2018 doi:10.20944/preprints201811.0037.v1 Peer-reviewed version available at Biomolecules 2018, 8, 161; doi:10.3390/biom8040161 1 Review 2 Structural and Functional Insights into Human 3 Nuclear Cyclophilins 4 Caroline Rajiv12 and Tara L. Davis13,* 5 1 Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 6 Philadelphia PA USA 19102. 7 2 Janssen Pharmaceuticals, Inc., 22-21062, 1400 McKean Rd, Spring House, PA 19477; 8 [email protected] 9 3 FORMA Therapeutics, 550 Arsenal St. Ste. 100, Boston, MA 02472; [email protected] 10 11 * Correspondence: [email protected]; Tel.: +01-857-209-2342 12 13 Abstract: The peptidyl-prolyl isomerases of the cyclophilin type are distributed throughout human 14 cells, including eight found solely in the nucleus. Nuclear cyclophilins are involved in complexes 15 that regulate chromatin modification, transcription, and pre-mRNA splicing. This review collects 16 what is known about the eight human nuclear cyclophilins: PPIH, PPIE, PPIL1, PPIL2, PPIL3, PPIG, 17 CWC27, and PPWD1. Each “spliceophilin” is evaluated in relation to the spliceosomal complex in 18 which it has been studied, and current work studying the biological roles of these cyclophilins in 19 the nucleus are discussed. The eight human splicing complexes available in the RCSB are analyzed 20 from the viewpoint of the human spliceophilins. Future directions in structural and cellular biology, 21 and the importance of developing spliceophilin-specific inhibitors, are considered. 22 23 Keywords: Peptidyl-prolyl isomerases; nuclear cyclophilins; spliceophilins; alternative splicing; 24 spliceosomes; NMR; x-ray crystallography 25 26 27 1. -
RNA-Seq and GSEA Identifies Suppression of Ligand-Gated
www.nature.com/scientificreports OPEN RNA‑seq and GSEA identifes suppression of ligand‑gated chloride efux channels as the major gene pathway contributing to form deprivation myopia Loretta Giummarra Vocale1,4*, Sheila Crewther1, Nina Riddell1, Nathan E. Hall1,2, Melanie Murphy1 & David Crewther1,3 Currently there is no consensus regarding the aetiology of the excessive ocular volume that characterizes high myopia. Thus, we aimed to test whether the gene pathways identifed by gene set enrichment analysis of RNA‑seq transcriptomics refutes the predictions of the Retinal Ion Driven Efux (RIDE) hypothesis when applied to the induction of form‑deprivation myopia (FDM) and subsequent recovery (post‑occluder removal). We found that the induction of profound FDM led to signifcant suppression in the ligand‑gated chloride ion channel transport pathway via suppression of glycine, GABAA and GABAC ionotropic receptors. Post‑occluder removal for short term recovery from FDM of 6 h and 24 h, induced signifcant upregulation of the gene families linked to cone receptor phototransduction, mitochondrial energy, and complement pathways. These fndings support a model of form deprivation myopia as a Cl− ion driven adaptive fuid response to the modulation of the visual signal cascade by form deprivation that in turn afects the resultant ionic environment of the outer and inner retinal tissues, axial and vitreal elongation as predicted by the RIDE model. Occluder removal and return to normal light conditions led to return to more normal upregulation of phototransduction, slowed growth rate, refractive recovery and apparent return towards physiological homeostasis. Myopia (short-sightedness) is the most common visual disorder worldwide and the greatest risk factor for severe ophthalmic diseases in older individuals especially those with high (-5D) refractive errors1.