Nahar Et Al. Supplementary Figure 1 (%) 10
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Manuscript for Proximity Interactome Analysis of Lassa
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.16.452739; this version posted July 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC 4.0 International license. 1 Main Manuscript for 2 Proximity interactome analysis of Lassa polymerase reveals 3 eRF3a/GSPT1 as a druggable target for host directed antivirals. 4 Jingru Fang1,2, Colette Pietzsch3,4, George Tsaprailis5, Gogce Crynen5, Kelvin Frank Cho6, Alice 5 Y. Ting7,8, Alexander Bukreyev3,4,9, Erica Ollmann Saphire2* and Juan Carlos de la Torre1* 6 1 Department of Immunology and Microbiology, Scripps Research, La Jolla CA 92037 7 2La Jolla Institute for Immunology, La Jolla CA 92037 8 3Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550 9 4Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550 10 5Proteomics Core, Scripps Research, Jupiter, FL 33458 11 6Cancer Biology Program, Stanford University, Stanford, CA 94305 12 7Department of Genetics, Department of Biology and Department of Chemistry, Stanford 13 University, Stanford, CA 94305 14 8Chan Zuckerberg Biohub, San Francisco, CA 94158 15 9Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 16 TX 77550 17 *Erica Ollmann Saphire; Juan Carlos de la Torre. 18 Email: [email protected] and [email protected] 19 Author Contributions: J.F., E.O.S., and J.C.T designed research; J.F. performed all non-BSL4 20 experiments and analyzed data; C.P. -
Methods in and Applications of the Sequencing of Short Non-Coding Rnas" (2013)
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Methods in and Applications of the Sequencing of Short Non- Coding RNAs Paul Ryvkin University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Ryvkin, Paul, "Methods in and Applications of the Sequencing of Short Non-Coding RNAs" (2013). Publicly Accessible Penn Dissertations. 922. https://repository.upenn.edu/edissertations/922 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/922 For more information, please contact [email protected]. Methods in and Applications of the Sequencing of Short Non-Coding RNAs Abstract Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields angingr from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non- coding RNAs, as well as a study in which they are applied to Alzheimer's Disease (AD). The computational methods presented here include High-throughput Annotation of Modified Ribonucleotides (HAMR), which enables researchers to detect post-transcriptional covalent modifications ot RNAs in a high-throughput manner. In addition, I describe Classification of RNAs by Analysis of Length (CoRAL), a computational method that allows researchers to characterize the pathways responsible for short non-coding RNA biogenesis. -
(KPNA7), a Divergent Member of the Importin a Family of Nuclear Import
Kelley et al. BMC Cell Biology 2010, 11:63 http://www.biomedcentral.com/1471-2121/11/63 RESEARCH ARTICLE Open Access Karyopherin a7 (KPNA7), a divergent member of the importin a family of nuclear import receptors Joshua B Kelley1, Ashley M Talley1, Adam Spencer1, Daniel Gioeli2, Bryce M Paschal1,3* Abstract Background: Classical nuclear localization signal (NLS) dependent nuclear import is carried out by a heterodimer of importin a and importin b. NLS cargo is recognized by importin a, which is bound by importin b. Importin b mediates translocation of the complex through the central channel of the nuclear pore, and upon reaching the nucleus, RanGTP binding to importin b triggers disassembly of the complex. To date, six importin a family members, encoded by separate genes, have been described in humans. Results: We sequenced and characterized a seventh member of the importin a family of transport factors, karyopherin a 7 (KPNA7), which is most closely related to KPNA2. The domain of KPNA7 that binds Importin b (IBB) is divergent, and shows stronger binding to importin b than the IBB domains from of other importin a family members. With regard to NLS recognition, KPNA7 binds to the retinoblastoma (RB) NLS to a similar degree as KPNA2, but it fails to bind the SV40-NLS and the human nucleoplasmin (NPM) NLS. KPNA7 shows a predominantly nuclear distribution under steady state conditions, which contrasts with KPNA2 which is primarily cytoplasmic. Conclusion: KPNA7 is a novel importin a family member in humans that belongs to the importin a2 subfamily. KPNA7 shows different subcellular localization and NLS binding characteristics compared to other members of the importin a family. -
WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US). -
Mir-17-92 Fine-Tunes MYC Expression and Function to Ensure
ARTICLE Received 31 Mar 2015 | Accepted 22 Sep 2015 | Published 10 Nov 2015 DOI: 10.1038/ncomms9725 OPEN miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth Marija Mihailovich1, Michael Bremang1, Valeria Spadotto1, Daniele Musiani1, Elena Vitale1, Gabriele Varano2,w, Federico Zambelli3, Francesco M. Mancuso1,w, David A. Cairns1,w, Giulio Pavesi3, Stefano Casola2 & Tiziana Bonaldi1 The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 30 untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c- MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 30 UTR shortening at different stages of tumorigenesis. 1 Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy. 2 Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Mouse Anti-Human Karyopherin Α Monoclonal Antibody, Clone 3 (CABT-B9227) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Mouse anti-Human Karyopherin α monoclonal antibody, clone 3 (CABT-B9227) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Immunogen Human Rch-1 aa. 254-497 Isotype IgG1 Source/Host Mouse Species Reactivity Human, Mouse, Rat, Dog, Fly Clone 3 Purification The monoclonal antibody was purified from tissue culture supernatant or ascites by affinity chromatography. Conjugate Unconjugated Applications WB; IHC; IF; IP Format Liquid Concentration 250 µg/ml Size 50ug, 150ug Buffer Aqueous buffered solution containing BSA, glycerol, and ≤0.09% sodium azide. Storage Store undiluted at -20°C. BACKGROUND Introduction The two step process of importing proteins into the nucleus involves the binding and interaction of several cytosolic and nuclear pore proteins. Proteins to be translocated into the nucleus contain a nuclear localization sequence (NLS) which is recognized and bound by carrier proteins in the cytosol. Heterodimers belonging to a highly conserved family of proteins called karyopherins are required for successful nuclear localization of cytosolic proteins. The α-subunits appear to function in the binding of NLS (both simple and bitartite NLS motifs), but both α- and β- subunits are required for successful docking to the nuclear envelope. ATP is required for 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved complete translocation of proteins into the nucleus. Karyopherin α2 was first identified as Rch-1, an NLS receptor which interacts with the RAG-1 recombination-activating protein in developing B and T cells. -
Functional Interactomes of the Ebola Virus Polymerase Identified by Proximity Proteomics 2 in the Context of Viral Replication
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.20.453153; this version posted July 21, 2021. 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-NC 4.0 International license. 1 Functional interactomes of the Ebola virus polymerase identified by proximity proteomics 2 in the context of viral replication 3 Jingru Fang1,2, Colette Pietzsch3,4, George Tsaprailis5, Gogce Crynen6, Kelvin Frank Cho7, Alice 4 Y. Ting8,9, Alexander Bukreyev3,4,10*, Juan Carlos de la Torre2*, Erica Ollmann Saphire1* 5 1La Jolla Institute for Immunology, La Jolla CA 92037 6 2Department of Immunology and Microbiology, Scripps Research, La Jolla CA 92037 7 3Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550 8 4Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550 9 5Proteomics Core, Scripps Research, Jupiter, FL 33458 10 6Bioinformatics and Statistics Core, Scripps Research, Jupiter, FL 33458 11 7Cancer Biology Program, Stanford University, Stanford, CA 94305 12 8Department of Genetics, Department of Biology and Department of Chemistry, Stanford 13 University, Stanford, CA 94305 14 9Chan Zuckerberg Biohub, San Francisco, CA 94158 15 10 Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 16 TX 77550 17 Correspondence: [email protected], [email protected], [email protected] 18 Lead contact: [email protected] 19 SUMMARY 20 Ebola virus (EBOV) critically depends on the viral polymerase to replicate and transcribe the viral 21 RNA genome. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
Mrna Export Through an Additional Cap-Binding Complex Consisting of NCBP1 and NCBP3
ARTICLE Received 2 Mar 2015 | Accepted 28 Jul 2015 | Published 18 Sep 2015 DOI: 10.1038/ncomms9192 OPEN mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3 Anna Gebhardt1,*, Matthias Habjan1,*, Christian Benda2, Arno Meiler1, Darya A. Haas1, Marco Y. Hein3, Angelika Mann1, Matthias Mann3, Bianca Habermann4 & Andreas Pichlmair1 The flow of genetic information from DNA to protein requires polymerase-II-transcribed RNA characterized by the presence of a 50-cap. The cap-binding complex (CBC), consisting of the nuclear cap-binding protein (NCBP) 2 and its adaptor NCBP1, is believed to bind all capped RNA and to be necessary for its processing and intracellular localization. Here we show that NCBP1, but not NCBP2, is required for cell viability and poly(A) RNA export. We identify C17orf85 (here named NCBP3) as a cap-binding protein that together with NCBP1 forms an alternative CBC in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to poly(A) RNA export. Loss of NCBP3 can be compensated by NCBP2 under steady-state conditions. However, NCBP3 becomes pivotal under stress conditions, such as virus infection. We propose the existence of an alternative CBC involving NCBP1 and NCBP3 that plays a key role in mRNA biogenesis. 1 Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany. 2 Department of Structural Cell Biology, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany. 3 Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany. 4 Bioinformatics Core Facility, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany. -
Influence of Erf3a/GSPT1 Gene Expression on Susceptibility to Carcinogenesis
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL INFLUENCE OF ERF3 A/GSPT1 GENE EXPRESSI ON ON SUSCEPTIBILITY TO CARCINOGENESIS JOANA FERREIRA TOMÉ MALTA VACAS Tese orientada por: Professor Doutor Rui Miguel Brito Professora Doutora Maria Manuela Coelho DOUTORAMENTO EM BIOLOGIA (Biologia Molecular) 2009 This study was supported by the Fundação Para a Ciência e a Tecnologia: PhD fellowship SFRH/BD/21468/2005, projects POCTI/MGI/40071/2001 and PTDC/SAU-GMG/67031/2006. This dissertation should be cited as: Malta-Vacas J. (2009) Influence of eRF3a/GSPT1 gene expression on susceptibility to carcinogenesis. PhD Thesis, University of Lisbon, Portugal. “O erro é a noite dos espíritos e a armadilha da inocência” Luc de Clapiers, Marquês de Vauvenargues NOTAS PRÉVIAS Nos termos do n.º 1 do Artigo 40, Capítulo V, do Regulamento de Estudos Pós-Graduados da Universidade de Lisboa, publicado no Diário da República – II Série N.º 153, de 5 de Julho de 2003, esclarece-se que na elaboração da presente dissertação foram usados integralmente artigos científicos já publicados (4) ou submetidos para publicação (1) em revistas indexadas de circulação internacional, os quais integram os Capítulos II e III da presente tese. Tendo os referidos trabalhos sido realizados em colaboração, a candidata esclarece que participou integralmente no planeamento e na elaboração de todos os trabalhos, assim como na análise e discussão dos resultados. Esclarece-se ainda que a formatação dos vários artigos que integram a presente dissertação obedece às regras das revistas em que foram publicados ou submetidos para publicação. Por este motivo, não foi possível adoptar um critério uniforme ao longo dos vários capítulos.