An RNA-Centric Dissection of Host Complexes Controlling Flavivirus Infection
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Function and Gene Expression of Circulating Neutrophils in Dairy Cows: Impact of Micronutrient Supplementation
FUNCTION AND GENE EXPRESSION OF CIRCULATING NEUTROPHILS IN DAIRY COWS: IMPACT OF MICRONUTRIENT SUPPLEMENTATION A Dissertation Presented to The Faculty of the Graduate School At The University of Missouri In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy By Xavier S. Revelo Dr. Matthew R. Waldron, Dissertation Supervisor July, 2012 ©Copyright by Xavier S. Revelo 2012 All rights reserved The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled: FUNCTION AND GENE EXPRESSION OF CIRCULATING NEUTROPHILS IN DAIRY COWS: IMPACT OF MICRONUTRIENT SUPPLEMENTATION Presented by Xavier Revelo A candidate for the degree of Doctor of Philosophy in Animal Sciences And hereby certify that, in their opinion, it is worthy of acceptance. Dissertation Examination Committee: ________________________ Advisor Matthew R. Waldron, Ph.D. ________________________ Kevin L. Fritsche, Ph.D. ________________________ Matthew C. Lucy, Ph.D. ________________________ James W. Perfield, Ph.D. ACKNOWLEDGEMENTS First of all, I would like to thank my family for their patience, love and inseparable support even after all the years that I have been away from home. Thanks to my mother Sonia for dedicating her life to the guidance, inspiration, and nurturance of our family. I have been blessed with a loving and devoted family who gave me the motivation I needed to pursue my professional goals. I would also like to offer my sincerest gratitude to the friends I made while pursuing my doctorate degree at the University of Missouri. Special thanks to Daniel Mathew, Brad Scharf, Ky Pohler, Eric Coate, and Emma Jinks for sharing their time and friendship. -
S41467-020-18249-3.Pdf
ARTICLE https://doi.org/10.1038/s41467-020-18249-3 OPEN Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain Lei Zhao1,2,17, Zhongqi Li 1,2,17, Joaquim S. L. Vong2,3,17, Xinyi Chen1,2, Hei-Ming Lai1,2,4,5,6, Leo Y. C. Yan1,2, Junzhe Huang1,2, Samuel K. H. Sy1,2,7, Xiaoyu Tian 8, Yu Huang 8, Ho Yin Edwin Chan5,9, Hon-Cheong So6,8, ✉ ✉ Wai-Lung Ng 10, Yamei Tang11, Wei-Jye Lin12,13, Vincent C. T. Mok1,5,6,14,15 &HoKo 1,2,4,5,6,8,14,16 1234567890():,; The molecular signatures of cells in the brain have been revealed in unprecedented detail, yet the ageing-associated genome-wide expression changes that may contribute to neurovas- cular dysfunction in neurodegenerative diseases remain elusive. Here, we report zonation- dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which pro- minently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier (BBB) and glucose/energy metabolism especially in capillary ECs (capECs). An overrepresentation of Alzheimer disease (AD) GWAS genes is evident among the human orthologs of the differentially expressed genes of aged capECs, while comparative analysis revealed a subset of concordantly downregulated, functionally important genes in human AD brains. Treatment with exenatide, a glucagon-like peptide-1 receptor agonist, strongly reverses aged mouse brain EC transcriptomic changes and BBB leakage, with associated attenuation of microglial priming. We thus revealed tran- scriptomic alterations underlying brain EC ageing that are complex yet pharmacologically reversible. -
Common Variant Near the Endothelin Receptor Type a (EDNRA)
Common variant near the endothelin receptor type A(EDNRA) gene is associated with intracranial aneurysm risk Katsuhito Yasunoa,b,c, Mehmet Bakırcıog˘ lua,b,c, Siew-Kee Lowd, Kaya Bilgüvara,b,c, Emília Gaála,b,c,e, Ynte M. Ruigrokf, Mika Niemeläe, Akira Hatag, Philippe Bijlengah, Hidetoshi Kasuyai, Juha E. Jääskeläinenj, Dietmar Krexk, Georg Auburgerl, Matthias Simonm, Boris Krischekn, Ali K. Ozturka,b,c, Shrikant Maneo, Gabriel J. E. Rinkelf, Helmuth Steinmetzl, Juha Hernesniemie, Karl Schallerh, Hitoshi Zembutsud, Ituro Inouep, Aarno Palotieq, François Cambienr, Yusuke Nakamurad, Richard P. Liftonc,s,t,1, and Murat Günela,b,c,1 Departments of aNeurosurgery, bNeurobiology, and cGenetics, Yale Program on Neurogenetics, Yale Center for Human Genetics and Genomics, and sDepartment of Internal Medicine and tHoward Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510; dHuman Genome Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; eDepartment of Neurosurgery, Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland; fDepartment of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; gDepartment of Public Health, School of Medicine, Chiba University, Chiba 260-8670, Japan; hService de Neurochirurgie, Department of Clinical Neurosciences, Geneva University Hospital, 1211 Geneva 4, Switzerland; iDepartment of Neurosurgery, Medical Center East, Tokyo Women’s University, Tokyo 116-8567, Japan; jDepartment -
RRBP1 (NM 001042576) Human Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC218816L3 RRBP1 (NM_001042576) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: RRBP1 (NM_001042576) Human Tagged ORF Clone Tag: Myc-DDK Symbol: RRBP1 Synonyms: ES/130; ES130; hES; p180; RRp Vector: pLenti-C-Myc-DDK-P2A-Puro (PS100092) E. coli Selection: Chloramphenicol (34 ug/mL) Cell Selection: Puromycin ORF Nucleotide The ORF insert of this clone is exactly the same as(RC218816). Sequence: Restriction Sites: SgfI-MluI Cloning Scheme: ACCN: NM_001042576 ORF Size: 2931 bp This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 RRBP1 (NM_001042576) Human Tagged ORF Clone – RC218816L3 OTI Disclaimer: Due to the inherent nature of this plasmid, standard methods to replicate additional amounts of DNA in E. coli are highly likely to result in mutations and/or rearrangements. Therefore, OriGene does not guarantee the capability to replicate this plasmid DNA. Additional amounts of DNA can be purchased from OriGene with batch-specific, full-sequence verification at a reduced cost. Please contact our customer care team at [email protected] or by calling 301.340.3188 option 3 for pricing and delivery. The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. -
Loss of Conserved Ubiquitylation Sites in Conserved Proteins During Human Evolution
INTERNATIONAL JOURNAL OF MOleCular meDICine 42: 2203-2212, 2018 Loss of conserved ubiquitylation sites in conserved proteins during human evolution DONGBIN PARK, CHUL JUN GOH, HYEIN KIM, JI SEOK LEE and YOONSOO HAHN Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea Received January 30, 2018; Accepted July 6, 2018 DOI: 10.3892/ijmm.2018.3772 Abstract. Ubiquitylation of lysine residues in proteins serves Introduction a pivotal role in the efficient removal of misfolded or unused proteins and in the control of various regulatory pathways Ubiquitylation, in which the highly conserved 76‑residue poly- by monitoring protein activity that may lead to protein peptide ubiquitin is covalently attached to a lysine residue of degradation. The loss of ubiquitylated lysines may affect substrate proteins, mediates the targeted destruction of ubiq- the ubiquitin‑mediated regulatory network and result in the uitylated proteins by the ubiquitin‑proteasome system (1‑4). emergence of novel phenotypes. The present study analyzed The ubiquitin‑mediated protein degradation pathway serves a mouse ubiquitylation data and orthologous proteins from crucial role in the efficient and specific removal of misfolded 62 mammals to identify 193 conserved ubiquitylation sites from proteins and certain key regulatory proteins (5,6). Ubiquitin 169 proteins that were lost in the Euarchonta lineage leading and other ubiquitin‑like proteins, including autophagy‑related to humans. A total of 8 proteins, including betaine homo- protein 8, Ubiquitin‑like -
Discovery and Systematic Characterization of Risk Variants and Genes For
medRxiv preprint doi: https://doi.org/10.1101/2021.05.24.21257377; this version posted June 2, 2021. 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. It is made available under a CC-BY 4.0 International license . 1 Discovery and systematic characterization of risk variants and genes for 2 coronary artery disease in over a million participants 3 4 Krishna G Aragam1,2,3,4*, Tao Jiang5*, Anuj Goel6,7*, Stavroula Kanoni8*, Brooke N Wolford9*, 5 Elle M Weeks4, Minxian Wang3,4, George Hindy10, Wei Zhou4,11,12,9, Christopher Grace6,7, 6 Carolina Roselli3, Nicholas A Marston13, Frederick K Kamanu13, Ida Surakka14, Loreto Muñoz 7 Venegas15,16, Paul Sherliker17, Satoshi Koyama18, Kazuyoshi Ishigaki19, Bjørn O Åsvold20,21,22, 8 Michael R Brown23, Ben Brumpton20,21, Paul S de Vries23, Olga Giannakopoulou8, Panagiota 9 Giardoglou24, Daniel F Gudbjartsson25,26, Ulrich Güldener27, Syed M. Ijlal Haider15, Anna 10 Helgadottir25, Maysson Ibrahim28, Adnan Kastrati27,29, Thorsten Kessler27,29, Ling Li27, Lijiang 11 Ma30,31, Thomas Meitinger32,33,29, Sören Mucha15, Matthias Munz15, Federico Murgia28, Jonas B 12 Nielsen34,20, Markus M Nöthen35, Shichao Pang27, Tobias Reinberger15, Gudmar Thorleifsson25, 13 Moritz von Scheidt27,29, Jacob K Ulirsch4,11,36, EPIC-CVD Consortium, Biobank Japan, David O 14 Arnar25,37,38, Deepak S Atri39,3, Noël P Burtt4, Maria C Costanzo4, Jason Flannick40, Rajat M 15 Gupta39,3,4, Kaoru Ito18, Dong-Keun Jang4, -
The DNA Sequence and Comparative Analysis of Human Chromosome 20
articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M. -
(RRBP1) Expression Through Internal Ribosome Entry Site (IRES)-Mediated Translation During Cellular Stress Condition
International Journal of Molecular Sciences Article La Autoantigen Induces Ribosome Binding Protein 1 (RRBP1) Expression through Internal Ribosome Entry Site (IRES)-Mediated Translation during Cellular Stress Condition Wenqing Gao †, Qi Li †, Ruiyu Zhu * and Jian Jin * Laboratory of Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; [email protected] (W.G.); [email protected] (Q.L.) * Correspondence: [email protected] (R.Z.); [email protected] (J.J.); Tel.: +86-510-8591-8219 (R.Z. & J.J.) † These authors contributed equally to this work. Academic Editor: Kotb Abdelmohsen Received: 3 June 2016; Accepted: 13 July 2016; Published: 20 July 2016 Abstract: The function of ribosome binding protein 1 (RRBP1) is regulating the transportation and secretion of some intracellular proteins in mammalian cells. Transcription of RRBP1 is induced by various cytokines. However, few studies focused on the process of RRPB1 mRNA translation. The RRBP1 mRNA has a long 51 untranslated region that potentially formed a stable secondary structure. In this study, we show that the 51 UTR of RRBP1 mRNA contains an internal ribosome entry site (IRES). Moreover, the RRBP1 expression is induced by chemotherapeutic drug paclitaxel or adriamycin in human hepatocellular carcinoma cells and accompanied with the increased expression of La autoantigen (La), which binds to RRBP1 IRES element and facilitates translation initiation. Interestingly, we found IRES-mediated RRBP1 translation is also activated during serum-starvation condition which can induce cytoplasmic localization of La. After mapping the entire RRBP1 51 UTR, we determine the core IRES activity is located between nt-237 and -58. -
UK Lipoedema’ Cohort
medRxiv preprint doi: https://doi.org/10.1101/2021.06.15.21258988; this version posted June 18, 2021. 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. It is made available under a CC-BY 4.0 International license . Investigation of clinical characteristics and genome associations in the ‘UK Lipoedema’ cohort Authors Dionysios Grigoriadis1*, Ege Sackey1*, Katie Riches2**, Malou van Zanten1**, Glen Brice3, Ruth England2, Mike Mills1, Sara E Dobbins1, Lipoedema Consortium, Genomics England Research Consortium4, Steve Jeffery1, Liang Dong5, David B. Savage5, Peter S. Mortimer1,6, Vaughan Keeley2,7, Alan Pittman1, Kristiana Gordon1,6 ‡, Pia Ostergaard1 ‡ Affiliations 1. Molecular and Clinical Sciences Institute, St George’s University of London, London, UK 2. University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK 3. South West Thames Regional Genetics Unit, St George's University of London, London, UK 4. Genomics England, London, UK 5. Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK 6. Dermatology & Lymphovascular Medicine, St George's Universities NHS Foundation trust, London, UK 7. University of Nottingham Medical School, Nottingham, UK *These two authors contributed equally; ** These two authors contributed equally ‡Clinical correspondence to Kristiana Gordon [email protected] and research- related correspondence to Pia Ostergaard, [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2021.06.15.21258988; this version posted June 18, 2021. -
13Q Deletion Syndrome Involving RB1: Characterization of a New Minimal Critical Region for Psychomotor Delay
G C A T T A C G G C A T genes Article 13q Deletion Syndrome Involving RB1: Characterization of a New Minimal Critical Region for Psychomotor Delay Flavia Privitera 1,2, Arianna Calonaci 3, Gabriella Doddato 1,2, Filomena Tiziana Papa 1,2, Margherita Baldassarri 1,2 , Anna Maria Pinto 4, Francesca Mari 1,2,4, Ilaria Longo 4, Mauro Caini 3, Daniela Galimberti 3, Theodora Hadjistilianou 5, Sonia De Francesco 5, Alessandra Renieri 1,2,4 and Francesca Ariani 1,2,4,* 1 Medical Genetics, University of Siena, 53100 Siena, Italy; fl[email protected] (F.P.); [email protected] (G.D.); fi[email protected] (F.T.P.); [email protected] (M.B.); [email protected] (F.M.); [email protected] (A.R.) 2 Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy 3 Unit of Pediatrics, Department of Maternal, Newborn and Child Health, Azienda Ospedaliera Universitaria Senese, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; [email protected] (A.C.); [email protected] (M.C.); [email protected] (D.G.) 4 Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; [email protected] (A.M.P.); [email protected] (I.L.) 5 Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; [email protected] (T.H.); [email protected] (S.D.F.) * Correspondence: [email protected]; Tel.: +39-057-723-3303 Citation: Privitera, F.; Calonaci, A.; Abstract: Retinoblastoma (RB) is an ocular tumor of the pediatric age caused by biallelic inactivation Doddato, G.; Papa, F.T.; Baldassarri, of the RB1 gene (13q14). -
Proteomic Mapping of Cytosol-Facing Outer Mitochondrial and ER
TOOLS AND RESOURCES Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation Victoria Hung1†‡, Stephanie S Lam1†§, Namrata D Udeshi2, Tanya Svinkina2, Gaelen Guzman2, Vamsi K Mootha2,3, Steven A Carr2, Alice Y Ting1,2#* 1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States; 2Broad Institute of MIT and Harvard, Cambridge, United States; 3Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, United States *For correspondence: [email protected] Abstract The cytosol-facing membranes of cellular organelles contain proteins that enable signal †These authors contributed transduction, regulation of morphology and trafficking, protein import and export, and other equally to this work specialized processes. Discovery of these proteins by traditional biochemical fractionation can be Present address: ‡Departments plagued with contaminants and loss of key components. Using peroxidase-mediated proximity of Developmental Biology and biotinylation, we captured and identified endogenous proteins on the outer mitochondrial Genetics, Stanford University, membrane (OMM) and endoplasmic reticulum membrane (ERM) of living human fibroblasts. The Stanford, United States; proteomes of 137 and 634 proteins, respectively, are highly specific and highlight 94 potentially §Department of Molecular novel mitochondrial or ER proteins. Dataset intersection identified protein candidates potentially Biology, Howard Hughes localized to mitochondria-ER contact sites. We found that one candidate, the tail-anchored, PDZ- Medical Institute, Massachusetts domain-containing OMM protein SYNJ2BP, dramatically increases mitochondrial contacts with General Hospital, Harvard rough ER when overexpressed. Immunoprecipitation-mass spectrometry identified ribosome- Medical School, Boston, United binding protein 1 (RRBP1) as SYNJ2BP’s ERM binding partner. -
Supplementary Information
-- SUPPLEMENTARY INFORMATION-- Responder and nonresponder patients exhibit different peripheral transcriptional signatures during Major Depressive Episode Raoul Belzeaux1,2,3; Aurélie Bergon2,4,5; Valérie Jeanjean1,2; Béatrice Loriod4,5; Christine Formisano-Tréziny6,7; Lore Verrier2; Anderson Loundou8,9; Karine Baumstarck-Barrau8,9; Laurent Boyer9,10; Valérie Gall4,5; Jean Gabert6,7,11; Catherine Nguyen4,5; Jean-Michel Azorin2,3, Jean Naudin2; El Chérif Ibrahim1,*. 1Aix-Marseille Université, CNRS, CRN2M UMR 7286, 2Pôle de Psychiatrie Universitaire Solaris, Hôpital Sainte Marguerite, Assistance Publique–Hôpitaux de Marseille, Marseille, France, 3FondaMental, Fondation de Recherche et de Soins en Santé Mentale, Paris, France, 4INSERM, TAGC-UMR 1090, 5Aix-Marseille Université, TAGC-UMR 1090, Parc scientifique de Luminy, Marseille, France, 6INSERM, UNIS, U-1072, 7Aix-Marseille Université, UNIS, U-1072, 13015, Marseille, France, 8Unité d’aide méthodologique, Faculté de Médecine Timone, 9Department of Public Health, Hôpital La Timone, Assistance Publique–Hôpitaux de Marseille, France, 10Aix-Marseille Université, Research Unit EA 3279, 11Laboratoire de Biochimie-Biologie Moléculaire, Hôpital Nord, Assistance Publique– Hôpitaux de Marseille, France *To whom correspondence should be addressed. E-mail: [email protected] CONTENTS Page 1 SUPPLEMENTARY METHODS 2 1.1 DESIGN SETTING AND SUBJECTS 2 1.2 BLOOD MRNA EXTRACTION 3 1.3 PREPARATION OF SAMPLES AND MICORARRAY ASSAY 3 1.4 GENE AND CHROMOSOME BAND ENRICHMENT ANALYSES 4 1.5 MIRNA QUANTIFICATION