Genetic Engineering – the Foundation of Cutting-Edge Extramural Research
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Rnase a Cleanup of DNA Samples Version Number: 1.0 Version 1.0 Date: 12/21/2016 Author(S): Yuko Yoshinaga, Eileen Dalin Reviewed/Revised By
SAMPLE MANAGEMENT STANDARD OPERATING PROCEDURE RNase A Cleanup of DNA Samples Version Number: 1.0 Version 1.0 Date: 12/21/2016 Author(s): Yuko Yoshinaga, Eileen Dalin Reviewed/Revised by: Summary RNase A treatment is used for the removal of RNA from genomic DNA samples. RNase A cleaves the phosphodiester bond between the 5'-ribose of a nucleotide and the phosphate group attached to the 3'- ribose of an adjacent pyrimidine nucleotide. The resulting 2', 3'-cyclic phosphate is hydrolyzed to the corresponding 3'-nucleoside phosphate. Materials & Reagents Materials Vendor Stock Number Disposables 1.5 ml microcentrifuge tubes Reagents TE Buffer, pH 8.0 Ambion 9849 RNase A, DNase and protease-free (10 mg/ml) ThermoFisher EN0531 Sodium acetate buffer solution (3M, pH 5.2) VWR 567422 Ethanol, 200 proof Pharmco-Aaper 111000200CSPP 50x TAE Buffer Life Technologies/ Invitrogen MRGF-4210 SYBR® Safe DNA gel stain (10,000x concentrate in Life Technologies/ Invitrogen S33102 DMSO) DNA Molecular Weight Marker II Sigma 10236250001 Gel Loading Dye, Blue (6x) New England BioLabs B7021S Equipment Centrifuge 4°C Heat block 37°C Gel electrophoresis device Gel Imager Bio-Rad EH&S PPE Requirements: 1.1 Safety glasses, lab coat, and nitrile gloves should be worn at all times while performing work in the lab during this protocol. 1.2 Ethanol is a highly flammable and irritating to the eyes. Vapors may cause drowsiness and dizziness. Keep containers closed and keep away from sources of ignition such as smoking. 1 SAMPLE MANAGEMENT STANDARD OPERATING PROCEDURE Avoid contact with skin and eyes. In case of contact with eyes, rinse immediately with plenty of water and seek medical advice. -
Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity
Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity 82 SYNTHETIC BIOLOGY FOREWORD To be added by SCBD at a later stage. 1 BACKGROUND 2 In decision X/13, the Conference of the Parties invited Parties, other Governments and relevant 3 organizations to submit information on, inter alia, synthetic biology for consideration by the Subsidiary 4 Body on Scientific, Technical and Technological Advice (SBSTTA), in accordance with the procedures 5 outlined in decision IX/29, while applying the precautionary approach to the field release of synthetic 6 life, cell or genome into the environment. 7 Following the consideration of information on synthetic biology during the sixteenth meeting of the 8 SBSTTA, the Conference of the Parties, in decision XI/11, noting the need to consider the potential 9 positive and negative impacts of components, organisms and products resulting from synthetic biology 10 techniques on the conservation and sustainable use of biodiversity, requested the Executive Secretary 11 to invite the submission of additional relevant information on this matter in a compiled and synthesised 12 manner. The Secretariat was also requested to consider possible gaps and overlaps with the applicable 13 provisions of the Convention, its Protocols and other relevant agreements. A synthesis of this 14 information was thus prepared, peer-reviewed and subsequently considered by the eighteenth meeting 15 of the SBSTTA. The documents were then further revised on the basis of comments from the SBSTTA 16 and peer review process, and submitted for consideration by the twelfth meeting of the Conference of 17 the Parties to the Convention on Biological Diversity. -
U6 Small Nuclear RNA Is Transcribed by RNA Polymerase III (Cloned Human U6 Gene/"TATA Box"/Intragenic Promoter/A-Amanitin/La Antigen) GARY R
Proc. Nati. Acad. Sci. USA Vol. 83, pp. 8575-8579, November 1986 Biochemistry U6 small nuclear RNA is transcribed by RNA polymerase III (cloned human U6 gene/"TATA box"/intragenic promoter/a-amanitin/La antigen) GARY R. KUNKEL*, ROBIN L. MASERt, JAMES P. CALVETt, AND THORU PEDERSON* *Cell Biology Group, Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545; and tDepartment of Biochemistry, University of Kansas Medical Center, Kansas City, KS 66103 Communicated by Aaron J. Shatkin, August 7, 1986 ABSTRACT A DNA fragment homologous to U6 small 4A (20) was screened with a '251-labeled U6 RNA probe (21, nuclear RNA was isolated from a human genomic library and 22) using a modified in situ plaque hybridization protocol sequenced. The immediate 5'-flanking region of the U6 DNA (23). One of several positive clones was plaque-purified and clone had significant homology with a potential mouse U6 gene, subsequently shown by restriction mapping to contain a including a "TATA box" at a position 26-29 nucleotides 12-kilobase-pair (kbp) insert. A 3.7-kbp EcoRI fragment upstream from the transcription start site. Although this containing U6-hybridizing sequences was subcloned into sequence element is characteristic of RNA polymerase II pBR322 for further restriction mapping. An 800-base-pair promoters, the U6 gene also contained a polymerase III "box (bp) DNA fragment containing U6 homologous sequences A" intragenic control region and a typical run of five thymines was excised using Ava I and inserted into the Sma I site of at the 3' terminus (noncoding strand). The human U6 DNA M13mp8 replicative form DNA (M13/U6) (24). -
Prebiotic Chemistry, Origin, and Early Evolution of Life
Say what you are going to say, say it, say what you said Guiding theory Richard Feynman Polyelectrolytes with uniform structure are universal for Darwinism A specific hypothesis to provide context The polyelectrolyte that supported Earth’s first Darwinism was RNA Focus on paradoxes to constrain human self-deception "Settled science" says that RNA is impossible to form prebiotically Strategies for paradox resolution Mineral-guided processes allow RNA to form nonetheless Natural history context The needed chemistry-mineral combination was transient on Earth Your reward A relatively simple path to form RNA prebiotically A relatively narrow date when life on Earth originated prebiotically A clear statement of the next round of paradoxes Elisa Biondi, Hyo-Joong Kim, Daniel Hutter, Clemens Richert, Stephen Mojzsis, Ramon Brasser, Dustin Trail, Kevin Zahnle, David Catling, Rob Lavinsky Say what you are going to say, say it, say what you said Guiding theory Richard Feynman Polyelectrolytes with uniform structure are universal for Darwinism A specific hypothesis to provide context The polyelectrolyte that supported Earth’s first Darwinism was RNA Focus on paradoxes to constrain human self-deception "Settled science" says that RNA is impossible to form prebiotically Strategies for paradox resolution Mineral-guided processes allow RNA to form nonetheless Natural history context The needed chemistry-mineral combination was transient on Earth Your reward A relatively simple path to form RNA prebiotically A relatively narrow date when life on Earth originated prebiotically A clear statement of the next round of paradoxes Elisa Biondi, Hyo-Joong Kim, Daniel Hutter, Clemens Richert, Stephen Mojzsis, Ramon Brasser, Dustin Trail, Kevin Zahnle, David Catling, Rob Lavinsky What does a repeating backbone charge do for informational molecule? O 1. -
Expanding the Genetic Code Lei Wang and Peter G
Reviews P. G. Schultz and L. Wang Protein Science Expanding the Genetic Code Lei Wang and Peter G. Schultz* Keywords: amino acids · genetic code · protein chemistry Angewandte Chemie 34 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim DOI: 10.1002/anie.200460627 Angew. Chem. Int. Ed. 2005, 44,34–66 Angewandte Protein Science Chemie Although chemists can synthesize virtually any small organic molecule, our From the Contents ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, 1. Introduction 35 modifications are largely restricted to substitutions among the common 20 2. Chemical Approaches 35 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and 3. In Vitro Biosynthetic eukaryotic organisms. Over 30 novel amino acids have been genetically Approaches to Protein encoded in response to unique triplet and quadruplet codons including Mutagenesis 39 fluorescent, photoreactive, and redox-active amino acids, glycosylated 4. In Vivo Protein amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom- Mutagenesis 43 containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps 5. An Expanded Code 46 entire organisms with new or enhanced properties. 6. Outlook 61 1. Introduction The genetic codes of all known organisms specify the same functional roles to amino acid residues in proteins. Selectivity 20 amino acid building blocks. These building blocks contain a depends on the number and reactivity (dependent on both limited number of functional groups including carboxylic steric and electronic factors) of a particular amino acid side acids and amides, a thiol and thiol ether, alcohols, basic chain. -
A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis
Microorganisms 2015, 3, 500-517; doi:10.3390/microorganisms3030500 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis Violetta La Cono 1, Erika Arcadi 1, Gina La Spada 1, Davide Barreca 2, Giuseppina Laganà 2, Ersilia Bellocco 2, Maurizio Catalfamo 1, Francesco Smedile 1, Enzo Messina 1, Laura Giuliano 1,3 and Michail M. Yakimov 1,* 1 Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina 98122, Italy; E-Mails: [email protected] (V.L.C.); [email protected] (E.A.); [email protected] (G.L.S.); [email protected] (M.C.); [email protected] (F.S.); [email protected] (E.M.); [email protected] (L.G.) 2 Department of Organic and Biological Chemistry, University of Messina, Salita Sperone 31, Villaggio S. Agata, Messina 98166, Italy; E-Mails: [email protected] (D.B.); [email protected] (G.L.); [email protected] (E.B.) 3 Mediterranean Science Commission (CIESM), 16 bd de Suisse, MC 98000, Monaco * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-090-6015-437. Academic Editors: Ricardo Amils and Elena González Toril Received: 1 July 2015 / Accepted: 1 September 2015 / Published: 9 September 2015 Abstract: Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. -
Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2014-07-01 Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biochemistry Commons, and the Chemistry Commons BYU ScholarsArchive Citation Taylor, Ryan M., "Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules" (2014). Theses and Dissertations. 5585. https://scholarsarchive.byu.edu/etd/5585 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy John T. Prince, Chair Mark Clement Steven W. Graves Barry M. Willardson Dixon J. Woodbury Department of Chemistry and Biochemistry Brigham Young University July 2014 Copyright © 2014 Ryan M. Taylor All Rights Reserved ABSTRACT Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Department of Chemistry and Biochemistry, BYU Doctor of Philosophy Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. -
"Modified" RNA (And DNA) World
July editorial The "modified" RNA (and DNA) world A few months ago, as COVID-19 vaccinations were getting underway in the U.S., a non-scientist friend said he was uneasy because had heard that the RNA in them had been "doped". Leaning in, I asked "How?" (I knew of course, vide infra). "With some chemical" he replied. This struck me as a perfect storm of an educated, reasonably informed non- scientist being led astray by how the media often doesn't get it quite right, though we all recognize that too much detail can be narcoleptic. The art is to convey the science in just the right dose, as Lewis Thomas and Carl Sagan did for example (1). I told my friend what the "doping" was, using lay terms. He listened thoughtfully and then I came in with my final shot: nature is full of RNA that is "doped", and even DNA is as well. These chemical modifications are not done by mad scientists but the very biological systems in which these RNAs and DNAs reside, using their own enzymes. He left somewhat convinced and hopefully is now vaccinated. This encounter gave me the thought that I, and my readers, should take a step back and think about all the "modified" RNAs and DNAs out there. For transfer RNAs alone, there are 120 known base modifications, with their prevalence as high as 13 of the 76 nucleotides in human cytosolic tRNAtyr(2). N6- adenosine methylation of messenger RNA, discovered in 1974, has recently come to the fore, although not all experts agree on its functional significance (3,4). -
Chapter 3. the Beginnings of Genomic Biology – Molecular
Chapter 3. The Beginnings of Genomic Biology – Molecular Genetics Contents 3. The beginnings of Genomic Biology – molecular genetics 3.1. DNA is the Genetic Material 3.6.5. Translation initiation, elongation, and termnation 3.2. Watson & Crick – The structure of DNA 3.6.6. Protein Sorting in Eukaryotes 3.3. Chromosome structure 3.7. Regulation of Eukaryotic Gene Expression 3.3.1. Prokaryotic chromosome structure 3.7.1. Transcriptional Control 3.3.2. Eukaryotic chromosome structure 3.7.2. Pre-mRNA Processing Control 3.3.3. Heterochromatin & Euchromatin 3.4. DNA Replication 3.7.3. mRNA Transport from the Nucleus 3.4.1. DNA replication is semiconservative 3.7.4. Translational Control 3.4.2. DNA polymerases 3.7.5. Protein Processing Control 3.4.3. Initiation of replication 3.7.6. Degradation of mRNA Control 3.4.4. DNA replication is semidiscontinuous 3.7.7. Protein Degradation Control 3.4.5. DNA replication in Eukaryotes. 3.8. Signaling and Signal Transduction 3.4.6. Replicating ends of chromosomes 3.8.1. Types of Cellular Signals 3.5. Transcription 3.8.2. Signal Recognition – Sensing the Environment 3.5.1. Cellular RNAs are transcribed from DNA 3.8.3. Signal transduction – Responding to the Environment 3.5.2. RNA polymerases catalyze transcription 3.5.3. Transcription in Prokaryotes 3.5.4. Transcription in Prokaryotes - Polycistronic mRNAs are produced from operons 3.5.5. Beyond Operons – Modification of expression in Prokaryotes 3.5.6. Transcriptions in Eukaryotes 3.5.7. Processing primary transcripts into mature mRNA 3.6. Translation 3.6.1. -
Evaluation of the Quality, Safety and Efficacy of Messenger RNA
1 2 3 WHO/BS/2021.2402 4 ENGLISH ONLY 5 6 7 8 9 Evaluation of the quality, safety and efficacy of messenger RNA vaccines for 10 the prevention of infectious diseases: regulatory considerations 11 12 13 14 15 16 NOTE: 17 18 This draft document has been prepared for the purpose of inviting comments and suggestions on 19 the proposals contained therein which will then be considered by the WHO Expert Committee on 20 Biological Standardization (ECBS). The distribution of this draft document is intended to 21 provide information on the proposed document: Evaluation of the quality, safety and efficacy of 22 messenger RNA vaccines for the prevention of infectious diseases: regulatory considerations to a 23 broad audience and to ensure the transparency of the consultation process. 24 25 The text in its present form does not necessarily represent the agreed formulation of the 26 ECBS. Written comments proposing modifications to this text MUST be received by 17 27 September 2021 using the Comment Form available separately and should be addressed to 28 the Department of Health Products Policy and Standards, World Health Organization, 20 Avenue 29 Appia, 1211 Geneva 27, Switzerland. Comments may also be submitted electronically to the 30 Responsible Officer: Dr Tiequn Zhou at: [email protected]. 31 32 The outcome of the deliberations of the Expert Committee will be published in the WHO 33 Technical Report Series. The final agreed formulation of the document will be edited to be in 34 conformity with the second edition of the WHO style guide (KMS/WHP/13.1). -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Supplementary Figure Legends for Rands Et Al. 2019
Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018).