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John Snow Lecture, by George Davey Smith
Published by Oxford University Press on behalf of the International Epidemiological Association International Journal of Epidemiology 2011;40:537–562 ß The Author 2011; all rights reserved. doi:10.1093/ije/dyr117 IEA JOHN SNOW LECTURE 2011 Epidemiology, epigenetics and the ‘Gloomy Prospect’: embracing randomness in population health research and practice George Davey Smith MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK Epidemiologists aim to identify modifiable causes of disease, this often being a prerequisite for the application of epidemiological findings in public health pro- grammes, health service planning and clinical medicine. Despite successes in identifying causes, it is often claimed that there are missing additional causes for even reasonably well-understood conditions such as lung cancer and coronary heart disease. Several lines of evidence suggest that largely chance events, from the biographical down to the sub-cellular, contribute an important stochastic element to disease risk that is not epidemiologically tractable at the individual level. Epigenetic influences provide a fashionable contemporary explanation for such seemingly random processes. Chance events—such as a particular lifelong smoker living unharmed to 100 years—are averaged out at the group level. As a consequence population-level differences (for example, secular trends or differ- ences between administrative areas) can be entirely explicable by causal factors that appear to account for only a small proportion of individual-level risk. In public health terms, a modifiable cause of the large majority of cases of a disease may have been identified, with a wild goose chase continuing in an attempt to discipline the random nature of the world with respect to which particular indi- viduals will succumb. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
UCK2 Polyclonal Antibody Allele of This Gene May Play a Role in Mediating Nonhumoral Immunity to Hemophilus Influenzae Type B
UCK2 polyclonal antibody allele of this gene may play a role in mediating nonhumoral immunity to Hemophilus influenzae type B. Catalog Number: PAB2754 [provided by RefSeq] Regulatory Status: For research use only (RUO) References: 1. Crude Extracts, Flavokawain B and Alpinetin Product Description: Rabbit polyclonal antibody raised Compounds from the Rhizome of Alpinia mutica Induce against synthetic peptide of UCK2. Cell Death via UCK2 Enzyme Inhibition and in Turn Reduce 18S rRNA Biosynthesis in HT-29 Cells. Malami Immunogen: A synthetic peptide (conjugated with KLH) I, Abdul AB, Abdullah R, Kassim NK, Rosli R, Yeap SK, corresponding to N-terminus of human UCK2. Waziri P, Etti IC, Bello MB. PLoS One. 2017 Jan 19;12(1):e0170233. Host: Rabbit 2. A crucial role of uridine/cytidine kinase 2 in antitumor activity of 3'-ethynyl nucleosides. Murata D, Endo Y, Reactivity: Human Obata T, Sakamoto K, Syouji Y, Kadohira M, Matsuda A, Applications: IHC-P, WB-Ce Sasaki T. Drug Metab Dispos. 2004 Oct;32(10):1178-82. (See our web site product page for detailed applications Epub 2004 Jul 27. information) 3. Reaction of human UMP-CMP kinase with natural and analog substrates. Pasti C, Gallois-Montbrun S, Protocols: See our web site at Munier-Lehmann H, Veron M, Gilles AM, Deville-Bonne http://www.abnova.com/support/protocols.asp or product D. Eur J Biochem. 2003 Apr;270(8):1784-90. page for detailed protocols Form: Liquid Purification: Protein G purification Recommend Usage: Western Blot (1:1000) Immunohistochemistry (1:50-100) The optimal working dilution should be determined by the end user. -
A Path Towards SARS-Cov-2 Attenuation: Metabolic Pressure on CTP Synthesis Rules the Virus Evolution
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.162933; this version posted June 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 A path towards SARS-CoV-2 attenuation: metabolic pressure on CTP synthesis rules the virus evolution Zhihua Ou1,2, Christos Ouzounis3, Daxi Wang1,2, Wanying Sun1,2,4, Junhua Li1,2, Weijun Chen2,5*, Philippe Marlière6, Antoine Danchin7,8* 1. BGI-Shenzhen, Shenzhen 518083, China. 2. Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China. 3. Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica 57001, Greece 4. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China. 5. BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China. 6. TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 81 rue Réaumur, 75002, Paris, France 7. Kodikos Labs, Institut Cochin, 24, rue du Faubourg Saint-Jacques Paris 75014, France. 8. School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, 21 Sassoon Road, Pokfulam, Hong Kong. * To whom correspondence should be addressed Tel: +331 4441 2551; Fax: +331 4441 2559 E-mail: [email protected] Correspondence may also be addressed to [email protected] Keywords ABCE1; cytoophidia; innate immunity; Maxwell’s demon; Nsp1; phosphoribosyltransferase; queuine bioRxiv preprint doi: https://doi.org/10.1101/2020.06.20.162933; this version posted June 21, 2020. -
ABSTRACT DATA DRIVEN APPROACHES to IDENTIFY DETERMINANTS of HEART DISEASES and CANCER RESISTANCE Avinash Das Sahu, Doctor Of
ABSTRACT Title of dissertation: DATA DRIVEN APPROACHES TO IDENTIFY DETERMINANTS OF HEART DISEASES AND CANCER RESISTANCE Avinash Das Sahu, Doctor of Philosophy, 2016 Dissertation directed by: Professor Sridhar Hannenhalli Department of Computer Science Cancer and cardio-vascular diseases are the leading causes of death world-wide. Caused by systemic genetic and molecular disruptions in cells, these disorders are the manifestation of profound disturbance of normal cellular homeostasis. People suffering or at high risk for these disorders need early diagnosis and personalized therapeutic intervention. Successful implementation of such clinical measures can significantly improve global health. However, development of effective therapies is hindered by the challenges in identifying genetic and molecular determinants of the onset of diseases; and in cases where therapies already exist, the main challenge is to identify molecular determinants that drive resistance to the therapies. Due to the progress in sequencing technologies, the access to a large genome-wide biolog- ical data is now extended far beyond few experimental labs to the global research community. The unprecedented availability of the data has revolutionized the ca- pabilities of computational researchers, enabling them to collaboratively address the long standing problems from many different perspectives. Likewise, this thesis tackles the two main public health related challenges using data driven approaches. Numerous association studies have been proposed to identify genomic variants that determine disease. However, their clinical utility remains limited due to their inability to distinguish causal variants from associated variants. In the presented thesis, we first propose a simple scheme that improves association studies in su- pervised fashion and has shown its applicability in identifying genomic regulatory variants associated with hypertension. -
Mysteries of Partial Dihydroorotate Dehydrogenase Inhibition And
Editorials 2. Silver RT. Recombinant interferon-alpha for treatment of poly - 8. Kiladjian JJ, Cassinat B, Chevret S, et al. Pegylated interferon-alfa-2a cythaemia vera. Lancet. 1988;2(8607):403. induces complete hematologic and molecular responses with low 3. Gilbert HS. Long term treatment of myeloproliferative disease with toxicity in polycythemia vera. Blood. 2008;112(8):3065-3072. interferon-alpha-2b: feasibility and efficacy. Cancer. 1998;83(6): 9. Pizzi M, Silver RT, Barel AC, Orazi A. Recombinant interferon- a in 1205-1213. myelofibrosis reduces bone marrow fibrosis, improves its morphol - 4. Silver RT. Long-term effects of the treatment of polycythemia vera ogy and is associated with clinical response. Mod. Pathol. with recombinant interferon-alpha. Cancer. 2006;107(3):451-458. 2015;28(10):1315-1323. 5. Jones AV, Silver RT, Waghorn K, et al. Minimal molecular response 10. Silver RT, Barel AC, Lascu E, et al. The effect of initial molecular in polycythemia vera patients treated with imatinib or interferon profile on response to recombinant interferon- a (rIFN a) treatment in alpha. Blood. 2006;107(8):3339-3341. early myelofibrosis. Cancer. 2017;123(14):2680-2687. 6. Barbui T, Tefferi A, Vannucchi AM, et al. Philadelphia chromosome- 11. Mikkelsen SU, Kjaer L, Bjorn ME, et al. Safety and efficacy of com - negative classical myeloproliferative neoplasms: revised manage - bination therapy of interferon a-2 and ruxolitinib in polycythemia ment recommendations from European LeukemiaNet. Leukemia. vera and myelofibrosis. Cancer Med. 2018;7(8):3571-3581. 2018;32(5):1057-1069. 12. Sørensen AL, Mikkelsen SU, Knudsen TA, et al. -
A Systems-Genetics Analyses of Complex Phenotypes
A systems-genetics analyses of complex phenotypes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 David Ashbrook Table of contents Table of contents Table of contents ............................................................................................... 1 Tables and figures ........................................................................................... 10 General abstract ............................................................................................... 14 Declaration ....................................................................................................... 15 Copyright statement ........................................................................................ 15 Acknowledgements.......................................................................................... 16 Chapter 1: General introduction ...................................................................... 17 1.1 Overview................................................................................................... 18 1.2 Linkage, association and gene annotations .............................................. 20 1.3 ‘Big data’ and ‘omics’ ................................................................................ 22 1.4 Systems-genetics ..................................................................................... 24 1.5 Recombinant inbred (RI) lines and the BXD .............................................. 25 Figure 1.1: -
A Preliminary Study on the Impact of UCK2 Knockdown in DLD-1
Sains Malaysiana 50(7)(2021): 1935-1946 http://doi.org/10.17576/jsm-2021-5007-09 A Preliminary Study on the Impact of UCK2 Knockdown in DLD-1 Colorectal Cells Treated with DHODH Inhibitor (Kajian Awal ke atas Kesan Penyahfungsian UCK2 di dalam Sel Kolorektum DLD-1 yang Dirawat dengan Perencat DHODH) MOHAMAD FAIRUS ABDUL KADIR, PUTERI SHAFINAZ ABDUL-RAHMAN, KAVITHA NELLORE & SHATRAH OTHMAN* ABSTRACT Brequinar sodium (BQR) is a well-studied inhibitor of the dihydroorotate dehydrogenase (DHODH) enzyme. Both the DHODH and uridine-cytidine kinase 2 (UCK2) enzymes have been reported to be over-expressed in cancer cells to maintain the cells high demand for DNA and RNA for their proliferation. In this study, we aim to further sensitize cells to the effects of BQR by knocking down the UCK2 activity. In DLD-1 UCK2 knockdown cells, no change in the sensitivity of cells to BQR was observed. Uridine is known to reverse the anti-proliferative effect ofDHODH inhibitors via the salvage pathway. We observed abrogation of approximately 30% of the uridine reversal effect inUCK 2 knockdown cells compared to the wild type cells. Our finding indicates that the loss ofUCK 2 activity in the salvage pathway did not enhance the BQR-mediated cell proliferation inhibition but it abrogates the uridine reversal in the cells. Keywords: BQR; DHODH; TAS-106; UCK2; uridine abrogation ABSTRAK Natrium Brequinar (BQR) dikenali sebagai salah satu perencat enzim dihidroorotat dehidrogenase (DHODH). Kedua- dua enzim DHODH dan uridina-sitidina kinase 2 (UCK2) diekspreskan secara berlebihan di dalam sel kanser untuk mengekalkan permintaan tinggi ke atas DNA dan RNA bagi pembahagian sel. -
Brain Pyrimidine Nucleotide Synthesis and Alzheimer Disease
www.aging-us.com AGING 2019, Vol. 11, No. 19 Research Paper Brain pyrimidine nucleotide synthesis and Alzheimer disease Alba Pesini1,2, Eldris Iglesias1,2, M. Pilar Bayona-Bafaluy1,2,3, Nuria Garrido-Pérez1,2,3, Patricia Meade1,2, Paula Gaudó1,2, Irene Jiménez-Salvador1, Pol Andrés-Benito4,5,6, Julio Montoya1,2,3, Isidro Ferrer4,5,6,7,8, Pedro Pesini9, Eduardo Ruiz-Pesini1,2,3,10 1Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain 2Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain 3Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain 4Departamento de Patología y Terapéutica Experimental, Universidad de Barcelona, Hospitalet de Llobregat, Barcelona, Spain 5Centro de Investigaciones Biomédicas en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain 6Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain 7Servicio de Anatomía Patológica, Hospital Universitario de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain 8Instituto de Neurociencias, Universidad de Barcelona, Barcelona, Spain 9Araclon Biotech, Zaragoza, Spain 10Fundación ARAID, Zaragoza, Spain Correspondence to: Eduardo Ruiz-Pesini; email: [email protected] Keywords: Alzheimer disease, brain, de novo pyrimidine biosynthesis, pyrimidine salvage pathway, oxidative phosphorylation Received: June 25, 2019 Accepted: September 22, 2019 Published: September 27, 2019 Copyright: Pesini et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Many patients suffering late-onset Alzheimer disease show a deficit in respiratory complex IV activity. -
1 Epidemiology and Genetics of Preserved Ratio Impaired Spirometry
medRxiv preprint doi: https://doi.org/10.1101/2020.10.14.20212613; this version posted October 20, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license . Epidemiology and Genetics of Preserved Ratio Impaired SpiroMetry (PRISm): An Analysis of UK Biobank Daniel H Higbee MBBS1,2, Raquel Granell PhD1, George Davey Smith FRS1, James W Dodd MB ChB, PhD1,2 1 MRC Integrative Epidemiology Unit (IEU), University of Bristol, Oakfield Grove, Bristol, BS8 2BN, UK. 2 Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, BS10 5NB UK Corresponding Author: Dr James W. Dodd [email protected] Tel +44117 4142012 Fax +44117 4149496 ORCID 0000-00034805-5759 JD & DH conceived the study and initial draft, all authors made substantial contributions to the analysis, drafting and final approval of the paper. Funding: This work was supported by the Medical Research Council and the University of Bristol Integrative Epidemiology Unit (MC_UU_00011). MRC CARP Fellowship (Grant ref: MR/T005114/1) 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/10.1101/2020.10.14.20212613; this version posted October 20, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. -
Regulation of Pancreatic Islet Gene Expression in Mouse Islets by Pregnancy
265 Regulation of pancreatic islet gene expression in mouse islets by pregnancy B T Layden, V Durai, M V Newman, A M Marinelarena, C W Ahn, G Feng1, S Lin1, X Zhang2, D B Kaufman2, N Jafari3, G L Sørensen4 and W L Lowe Jr Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Tarry 15, Chicago, Illinois 60611, USA 1Northwestern University Biomedical Informatics Center, 2Division of Transplantation Surgery, Department of Surgery and 3Genomics Core, Center for Genetic Medicine, Northwestern University, Chicago, Illinois 60611, USA 4Medical Biotechnology Center, University of Southern Denmark, DK-5000 Odense C, Denmark (Correspondence should be addressed to W L Lowe Jr; Email: [email protected]) Abstract Pancreatic b cells adapt to pregnancy-induced insulin were confirmed in murine islets. Cytokine-induced resistance by unclear mechanisms. This study sought to expression of SP-D in islets was also demonstrated, suggesting identify genes involved in b cell adaptation during pregnancy. a possible role as an anti-inflammatory molecule. Comple- To examine changes in global RNA expression during menting these studies, an expression array was performed to pregnancy, murine islets were isolated at a time point of define pregnancy-induced changes in expression of GPCRs increased b cell proliferation (E13.5), and RNA levels were that are known to impact islet cell function and proliferation. determined by two different assays (global gene expression This assay, the results of which were confirmed using real- array and G-protein-coupled receptor (GPCR) array). time reverse transcription-PCR assays, demonstrated that free Follow-up studies confirmed the findings for select genes. -
Multivariable Two-Sample Mendelian Randomization Estimates of The
RESEARCH ARTICLE Multivariable two-sample Mendelian randomization estimates of the effects of intelligence and education on health Neil Martin Davies1,2*, W David Hill3,4, Emma L Anderson1,2, Eleanor Sanderson1,2, Ian J Deary3,4, George Davey Smith1,2 1Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; 2Bristol Medical School, University of Bristol, Bristol, United Kingdom; 3Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom; 4Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom Abstract Intelligence and education are predictive of better physical and mental health, socioeconomic position (SEP), and longevity. However, these associations are insufficient to prove that intelligence and/or education cause these outcomes. Intelligence and education are phenotypically and genetically correlated, which makes it difficult to elucidate causal relationships. We used univariate and multivariable Mendelian randomization to estimate the total and direct effects of intelligence and educational attainment on mental and physical health, measures of socioeconomic position, and longevity. Both intelligence and education had beneficial total effects. Higher intelligence had positive direct effects on income and alcohol consumption, and negative direct effects on moderate and vigorous physical activity. Higher educational attainment had positive direct effects on income, alcohol consumption, and vigorous physical activity,