DOCSLIB.ORG

Encapsulation of Biomolecules in Bacteriophage MS2 Viral Capsids

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Encapsulation of Biomolecules in Bacteriophage MS2 Viral Capsids Encapsulation of Biomolecules in Bacteriophage MS2 Viral Capsids By Jeff Edward Glasgow A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Chemistry in the Graduate Division of the University of California, Berkeley Committee in Charge: Professor Matthew Francis, Co-Chair Professor Danielle Tullman-Ercek, Co-Chair Professor Michelle Chang Professor John Dueber Spring 2014 Encapsulation of Biomolecules in Bacteriophage MS2 Viral Capsids Copyright ©2014 By: Jeff Edward Glasgow Abstract Encapsulation of Biomolecules in Bacteriophage MS2 Viral Capsids By Jeff Edward Glasgow Doctor of Philosophy in Chemistry University of California, Berkeley Professor Matthew Francis, Co-Chair Professor Danielle Tullman-Ercek, Co-Chair Nanometer-scale molecular assemblies have numerous applications in materials, catalysis, and medicine. Self-assembly has been used to create many structures, but approaches can match the extraordinary combination of stability, homogeneity, and chemical flexibility found in viral capsids. In particular, the bacteriophage MS2 capsid has provided a porous scaffold for several engineered nanomaterials for drug delivery, targeted cellular imaging, and photodynamic thera- py by chemical modification of the inner and outer surfaces of the shell. This work describes the development of new methods for reassembly of the capsid with concomitant encapsulation of large biomolecules. These methods were then used to encapsulate a variety of interesting cargoes, including RNA, DNA, protein-nucleic acid and protein-polymer conjugates, metal nanoparticles, and enzymes. To develop a stable, scalable method for encapsulation of biomolecules, the assembly of the capsid from its constituent subunits was analyzed in detail. It was found that combinations of negatively charged biomolecules and protein stabilizing agents could enhance reassembly, while electrostatic interactions of the biomolecules with the positively charged inner surface led to en- capsulation. To investigate the role protein shells play in encapsulated enzymatic processes, this method was then used to a model enzyme in a series of capsids with altered characteristics around the pores. The method was then used to develop a potential system for delivery of therapeutic pro- teins to the cytoplasm of cancer cells by encapsulating conjugates of these proteins to a negatively charged, membrane-lysing polymer. 1 Dedicated to my parents, Joe and Heidi Glasgow. i Table of Contents Abstract ..................................................................................................................... 1 Acknowledgments .................................................................................................... iv 1. Production and Applications of Engineered Viral Capsids ................................... 1 1.1 Abstract ......................................................................................................................................1 1.2 Introduction ................................................................................................................................2 1.3 Production: Recombinant vs. Infection ......................................................................................2 1.4 Production: Capsid Size and Assembly ......................................................................................3 1.5 Production: Surface Chemistry ..................................................................................................4 1.6 Applications: Drug Delivery ......................................................................................................4 1.7 Applications: Imaging Agents ....................................................................................................6 1.8 Applications: Templated Synthesis .............................................................................................7 1.9 Applications: Nanoreactors and Scaffolds .................................................................................9 1.10 Nonviral Protein Scaffolds .....................................................................................................10 1.11 Conclusions and Perspectives ................................................................................................11 1.12 References ..............................................................................................................................11 2. Osmolyte-Mediated Encapsulation of Proteins inside MS2 Viral Capsids......... 21 2.1 Abstract ....................................................................................................................................21 2.2 Introduction ..............................................................................................................................22 2.3 Reassembly of Wild-type MS2 ..................................................................................................23 2.4 Encapsulation of GFP ..............................................................................................................25 2.5 Encapsulation and Activity of Alkaline Phosphatase ..............................................................27 2.6 Summary ..................................................................................................................................29 2.7 Materials and Methods ............................................................................................................30 2.8 References ................................................................................................................................34 ii 3. The Influence of Electrostatics on Small Molecule Flux through a Protein Nano- reactor .................................................................................................................. 38 3.1 Abstract ....................................................................................................................................38 3.2 Introduction ..............................................................................................................................39 3.3 PhoA Kinetics in MS2 Pore Mutants .......................................................................................41 3.4 Modeling of Encapsulated Reactions .......................................................................................43 3.5 Conclusion ...............................................................................................................................45 3.6 Materials and Methods ............................................................................................................46 3.7 References ................................................................................................................................52 4. Toward Therapeutic Protein Delivery with MS2-Encapsulated Protein-polymer Conjugates ........................................................................................................... 55 4.1 Abstract ....................................................................................................................................55 4.2 Targeted Delivery of Therapeutic Proteins .............................................................................56 4.3 Polymer Conjugates in Cytosolic Protein Delivery .................................................................57 4.4 Conjugation of Negatively Charged Polymer Amphiphiles .....................................................57 4.5 Encapsulation of Protein-polymer Conjugates ........................................................................61 4.6 Therapeutic Protein Encapsulation .........................................................................................63 4.7 Materials and Methods ............................................................................................................66 4.8 References ................................................................................................................................73 iii Acknowledgments Berkeley has been such a great place for me to grow into a scientist, with so many people eager to lend help or support in developing this dissertation. As such there are innumerable people I should thank. Here are a few: Matt and Danielle—thank you for agreeing to take me on and start a new collaboration. You’ve both been so helpful with your ideas, enthusiasm, discussion, and support. The DTE lab—thank you for giving me such a fun, stimulating place to work. I have really en- joyed watching how the lab’s personality has grown and shifted since the first year. You have all made a huge impact on me as a scientist. Thanks to Chris for all the math help. Thanks to Anum, who has always been a great partner. The Francis lab—thank you for also taking me in and teaching me a little chemistry. The diversity of the both the research ideas and the people that have come through the lab has helped me see things from many different perspectives. Thanks to Stacy for lots of help and puppy pictures and Adel, Allie, Ioana, and Farkas for all their contributions. Other labs—there have been several other groups that have helped me over the years. Thanks to the M. Chang lab for basically being my third home in the department. Thanks to the Fréchet, Ber- tozzi, and Sarpong labs for being so generous with useful discussion and equipment. My Berkeley friends—both in and out of lab, I was lucky to have a great group of friends. I couldn’t
Load more

Recommended publications
  • Asymmetric Cryo-EM Reconstruction of Phage MS2 Reveals Genome Structure in Situ
    ARTICLE Received 8 Feb 2016 | Accepted 11 Jul 2016 | Published 26 Aug 2016 DOI: 10.1038/ncomms12524 OPEN Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ Roman I. Koning1,2, Josue Gomez-Blanco3, Inara Akopjana4, Javier Vargas3, Andris Kazaks4, Kaspars Tars4, Jose´ Marı´a Carazo3 & Abraham J. Koster1,2 In single-stranded ribonucleic acid (RNA) viruses, virus capsid assembly and genome packaging are intertwined processes. Using cryo-electron microscopy and single particle analysis we determined the asymmetric virion structure of bacteriophage MS2, which includes 178 copies of the coat protein, a single copy of the A-protein and the RNA genome. This reveals that in situ, the viral RNA genome can adopt a defined conformation. The RNA forms a branched network of stem-loops that almost all allocate near the capsid inner surface, while predominantly binding to coat protein dimers that are located in one-half of the capsid. This suggests that genomic RNA is highly involved in genome packaging and virion assembly. 1 Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands. 2 Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. 3 Biocomputing Unit, Centro Nacional de Biotecnologı´a, Consejo Superior de Investigaciones Cientı´ficas (CNB-CSIC), Darwin 3, Campus Universidad Auto´noma, Cantoblanco, Madrid 28049, Spain. 4 Biomedical Research and Study Centre, Ratsupites 1, LV-1067 Riga, Latvia. Correspondence and requests for materials should be addressed to R.I.K. (email: [email protected]).
    [Show full text]
  • Guide for Common Viral Diseases of Animals in Louisiana
    Sampling and Testing Guide for Common Viral Diseases of Animals in Louisiana Please click on the species of interest: Cattle Deer and Small Ruminants The Louisiana Animal Swine Disease Diagnostic Horses Laboratory Dogs A service unit of the LSU School of Veterinary Medicine Adapted from Murphy, F.A., et al, Veterinary Virology, 3rd ed. Cats Academic Press, 1999. Compiled by Rob Poston Multi-species: Rabiesvirus DCN LADDL Guide for Common Viral Diseases v. B2 1 Cattle Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 2 Deer and Small Ruminants Please click on the principle system involvement Generalized viral disease Respiratory viral disease Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 3 Swine Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 4 Horses Please click on the principle system involvement Generalized viral diseases Neurological viral diseases Respiratory viral diseases Enteric viral diseases Abortifacient/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 5 Dogs Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Back to the Beginning DCN LADDL Guide for Common Viral Diseases v.
    [Show full text]
  • 25 May 7, 2014
    Joint Pathology Center Veterinary Pathology Services Wednesday Slide Conference 2013-2014 Conference 25 May 7, 2014 ______________________________________________________________________________ CASE I: 3121206023 (JPC 4035610). Signalment: 5-week-old mixed breed piglet, (Sus domesticus). History: Two piglets from the faculty farm were found dead, and another piglet was weak and ataxic and, therefore, euthanized. Gross Pathology: The submitted piglet was in good body condition. It was icteric and had a diffusely pale liver. Additionally, petechial hemorrhages were found on the kidneys, and some fibrin was present covering the abdominal organs. Laboratory Results: The intestine was PCR positive for porcine circovirus (>9170000). Histopathologic Description: Mesenteric lymph node: Diffusely, there is severe lymphoid depletion with scattered karyorrhectic debris (necrosis). Also scattered throughout the section are large numbers of macrophages and eosinophils. The macrophages often contain botryoid basophilic glassy intracytoplasmic inclusion bodies. In fewer macrophages, intranuclear basophilic inclusions can be found. Liver: There is massive loss of hepatocytes, leaving disrupted liver lobules and dilated sinusoids engorged with erythrocytes. The remaining hepatocytes show severe swelling, with micro- and macrovesiculation of the cytoplasm and karyomegaly. Some swollen hepatocytes have basophilic intranuclear, irregular inclusions (degeneration). Throughout all parts of the liver there are scattered moderate to large numbers of macrophages (without inclusions). Within portal areas there is multifocally mild to moderate fibrosis and bile duct hyperplasia. Some bile duct epithelial cells show degeneration and necrosis, and there is infiltration of neutrophils within the lumen. The limiting plate is often obscured mainly by infiltrating macrophages and eosinophils, and fewer neutrophils, extending into the adjacent parenchyma. Scattered are small areas with extra medullary hematopoiesis.
    [Show full text]
  • Sensitive Detection of Live Escherichia Coli by Bacteriophage Amplification-Coupled
    bioRxiv preprint doi: https://doi.org/10.1101/318071; this version posted May 9, 2018. 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. 1 Sensitive detection of Live Escherichia coli by bacteriophage amplification-coupled 2 immunoassay on the Luminex® MAGPIX instrument 3 Tomotaka Midoa*, Eric M. Schafferb,c, Robert W. Dorseyc, Shanmuga Sozhamannand,e, E. 4 Randal Hofmannc,f 5 6 CBRN Detection Technology Section, CBRN Defense Technology Division, Advanced Defense 7 Technology Center, Acquisition, Technology and Logistics Agency (ATLA), Tokyo, Japana; 8 Leidos, Inc., Aberdeen Proving Ground, Maryland, USAb; Biosciences Division, U.S. Army 9 Edgewood Chemical Biological Center, Aberdeen Proving Grounds, Edgewood, MD, USAc; The 10 Tauri Group, LLC, Alexandria, VA, USAd; Defense Biological Product Assurance Office, JPM 11 G, JPEO, Frederick, MD, USAe; EXCET, Inc. Springfield, VA, USAf. 12 13 Running Head: Bacterial detection via phage on a MAGPIX instrument 14 15 #Address correspondence to [email protected] 16 *Present address: International Affairs Office, International Cooperation Division, Department 17 of Equipment Policy, Acquisition, Technology and Logistics Agency (ATLA), Tokyo, Japan 18 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/318071; this version posted May 9, 2018. 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. 21 Abstract (250 words) 22 Phages are natural predators of bacteria and have been exploited in bacterial detection because of 23 their exquisite specificity to their cognate bacterial hosts.
    [Show full text]
  • Canine Circovirus in Foxes from Northern Italy: Where Did It All Begin?
    pathogens Article Canine Circovirus in Foxes from Northern Italy: Where Did It All Begin? Giovanni Franzo 1,* , Maria Luisa Menandro 1 , Claudia Maria Tucciarone 1 , Giacomo Barbierato 1, Lorenzo Crovato 1 , Alessandra Mondin 1, Martina Libanora 2, Federica Obber 2, Riccardo Orusa 3, Serena Robetto 3, Carlo Citterio 2 and Laura Grassi 1 1 Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; [email protected] (M.L.M.); [email protected] (C.M.T.); [email protected] (G.B.); [email protected] (L.C.); [email protected] (A.M.); [email protected] (L.G.) 2 O.U. of Ecopathology, SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 32100 Belluno, Italy; [email protected] (M.L.); [email protected] (F.O.); [email protected] (C.C.) 3 S.C. Valle d.’Aosta—National Reference Centre Wildlife Diseases, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZS PLV)—Ce.R.M.A.S., 11020 Quart, AO, Italy; [email protected] (R.O.); [email protected] (S.R.) * Correspondence: [email protected]; Tel.: +39-049-827-2968 Abstract: Canine circovirus (CanineCV) is a recently identified virus affecting both domestic and wild carnivores, including foxes, sometimes in presence of severe clinical signs. Its circulation in wild animals can thus represent a potential threat for endangered species conservation and an infection Citation: Franzo, G.; Menandro, source for dogs. Nevertheless, no data were available on its circulation in the Alps region of Northern M.L.; Tucciarone, C.M.; Barbierato, G.; Italy.
    [Show full text]
  • Viruses in Transplantation - Not Always Enemies
    Viruses in transplantation - not always enemies Virome and transplantation ECCMID 2018 - Madrid Prof. Laurent Kaiser Head Division of Infectious Diseases Laboratory of Virology Geneva Center for Emerging Viral Diseases University Hospital of Geneva ESCMID eLibrary © by author Conflict of interest None ESCMID eLibrary © by author The human virome: definition? Repertoire of viruses found on the surface of/inside any body fluid/tissue • Eukaryotic DNA and RNA viruses • Prokaryotic DNA and RNA viruses (phages) 25 • The “main” viral community (up to 10 bacteriophages in humans) Haynes M. 2011, Metagenomic of the human body • Endogenous viral elements integrated into host chromosomes (8% of the human genome) • NGS is shaping the definition Rascovan N et al. Annu Rev Microbiol 2016;70:125-41 Popgeorgiev N et al. Intervirology 2013;56:395-412 Norman JM et al. Cell 2015;160:447-60 ESCMID eLibraryFoxman EF et al. Nat Rev Microbiol 2011;9:254-64 © by author Viruses routinely known to cause diseases (non exhaustive) Upper resp./oropharyngeal HSV 1 Influenza CNS Mumps virus Rhinovirus JC virus RSV Eye Herpes viruses Parainfluenza HSV Measles Coronavirus Adenovirus LCM virus Cytomegalovirus Flaviviruses Rabies HHV6 Poliovirus Heart Lower respiratory HTLV-1 Coxsackie B virus Rhinoviruses Parainfluenza virus HIV Coronaviruses Respiratory syncytial virus Parainfluenza virus Adenovirus Respiratory syncytial virus Coronaviruses Gastro-intestinal Influenza virus type A and B Human Bocavirus 1 Adenovirus Hepatitis virus type A, B, C, D, E Those that cause
    [Show full text]
  • Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics
    viruses Article Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics Ashleigh F. Porter 1, Mang Shi 1, John-Sebastian Eden 1,2 , Yong-Zhen Zhang 3,4 and Edward C. Holmes 1,3,* 1 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] (A.F.P.); [email protected] (M.S.); [email protected] (J.-S.E.) 2 Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia 3 Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 201500, China; [email protected] 4 Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China * Correspondence: [email protected]; Tel.: +61-2-9351-5591 Received: 17 October 2019; Accepted: 23 November 2019; Published: 25 November 2019 Abstract: DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date.
    [Show full text]
  • Internal Control for Real-Time Polymerase Chain Reaction Based on MS2 Bacteriophage for RNA Viruses Diagnostics
    Mem Inst Oswaldo Cruz, Rio de Janeiro, Vol. 112(5): 339-347, May 2017 339 Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics Miriam Ribas Zambenedetti1,2, Daniela Parada Pavoni1/+, Andreia Cristine Dallabona1, Alejandro Correa Dominguez1, Celina de Oliveira Poersch1, Stenio Perdigão Fragoso1, Marco Aurélio Krieger1,3 1Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil 2Universidade Federal do Paraná, Departamento de Bioprocessos e Biotecnologia, Curitiba, PR, Brasil 3Fundação Oswaldo Cruz-Fiocruz, Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil BACKGROUND Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV), hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC) is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. OBJECTIVES The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. METHODS The MS2 genome was cloned into the pET47b(+) plasmid, generating pET47b(+)-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+)-MS2, which produces a non-propagating MS2 particle.
    [Show full text]
  • Insights Into Circovirus Host Range from the Genomic Fossil Record
    bioRxiv preprint doi: https://doi.org/10.1101/246777; this version posted March 8, 2018. 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-ND 4.0 International license. Insights into circovirus host range from the genomic fossil record. Running title: Circovirus host range Authors: Tristan P.W. Dennis1*, Peter J. Flynn2,3*, William Marciel de Souza1,4, Joshua B. Singer1, Corrie S. Moreau2, Sam J. Wilson1, Robert J. Gifford1 Affiliations: 1 MRC-University of Glasgow Centre for Virus Research, Glasgow, UK 2 Field Museum of Natural History, Department of Science and Education, Chicago, IL 60605, USA 3University of Chicago, Committee on Evolutionary Biology, Chicago IL 60637, USA 4 Virology Research Center, School of Medicine of Ribeirão Preto of University of São Paulo, Ribeirão Preto, Brazil * These authors contributed equally Corresponding author: Robert J. Gifford MRC-University of Glasgow Centre for Virus Research 464 Bearsden Road Glasgow, Scotland, UK E-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/246777; this version posted March 8, 2018. 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-ND 4.0 International license. Abstract A diverse range of DNA sequences derived from circoviruses (family Circoviridae) have been identified in samples obtained from humans and domestic animals, often in association with pathological conditions.
    [Show full text]
  • Downloaded from Transcriptome Shotgun Assembly (TSA) Database on 29 November 2020 (Ftp://Ftp.Ddbj.Nig.Ac.Jp/Ddbj Database/Tsa/, Table S3)
    viruses Article Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing Xin-Xin Chen, Wei-Chen Wu and Mang Shi * School of Medicine, Sun Yat-sen University, Shenzhen 518107, China; [email protected] (X.-X.C.); [email protected] (W.-C.W.) * Correspondence: [email protected] Abstract: In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray- finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups.
    [Show full text]
  • What Is a Gene, Post-ENCODE? History and Updated Definition
    Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Perspective What is a gene, post-ENCODE? History and updated definition Mark B. Gerstein,1,2,3,9 Can Bruce,2,4 Joel S. Rozowsky,2 Deyou Zheng,2 Jiang Du,3 Jan O. Korbel,2,5 Olof Emanuelsson,6 Zhengdong D. Zhang,2 Sherman Weissman,7 and Michael Snyder2,8 1Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut 06511, USA; 2Molecular Biophysics & Biochemistry Department, Yale University, New Haven, Connecticut 06511, USA; 3Computer Science Department, Yale University, New Haven, Connecticut 06511, USA; 4Center for Medical Informatics, Yale University, New Haven, Connecticut 06511, USA; 5European Molecular Biology Laboratory, 69117 Heidelberg, Germany; 6Stockholm Bioinformatics Center, Albanova University Center, Stockholm University, SE-10691 Stockholm, Sweden; 7Genetics Department, Yale University, New Haven, Connecticut 06511, USA; 8Molecular, Cellular, & Developmental Biology Department, Yale University, New Haven, Connecticut 06511, USA While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century—from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity.
    [Show full text]
  • Porcine Circovirus Type 2 Suppresses IL-12P40 Induction Via Capsid/Gc1qr-Mediated Micrornas and Signalings This Information Is Current As of September 27, 2021
    Porcine Circovirus Type 2 Suppresses IL-12p40 Induction via Capsid/gC1qR-Mediated MicroRNAs and Signalings This information is current as of September 27, 2021. Qian Du, Xingchen Wu, Tongtong Wang, Xuefeng Yang, Zhenyu Wang, Yingying Niu, Xiaomin Zhao, Shan-Lu Liu, Dewen Tong and Yong Huang J Immunol published online 1 June 2018 http://www.jimmunol.org/content/early/2018/05/31/jimmun Downloaded from ol.1800250 Supplementary http://www.jimmunol.org/content/suppl/2018/05/31/jimmunol.180025 http://www.jimmunol.org/ Material 0.DCSupplemental Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on September 27, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: 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 © 2018 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published June 1, 2018, doi:10.4049/jimmunol.1800250 The Journal of Immunology Porcine Circovirus Type 2 Suppresses IL-12p40 Induction via Capsid/gC1qR-Mediated MicroRNAs and Signalings Qian Du,*,1 Xingchen Wu,*,1 Tongtong Wang,*,1 Xuefeng Yang,* Zhenyu Wang,* Yingying Niu,* Xiaomin Zhao,* Shan-Lu Liu,†,‡,x,{ Dewen Tong,* and Yong Huang* Porcine circovirus (PCV) type 2 (PCV2), an immunosuppression pathogen, is often found to increase the risk of other pathogenic infections.
    [Show full text]