BIOTECHNOLOGY RISK ASSESSMENT: STATE of the FIELD Editing Biosecurity Working Paper No
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Efficient Genome Editing of an Extreme Thermophile, Thermus
www.nature.com/scientificreports OPEN Efcient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant Bjorn Thor Adalsteinsson1*, Thordis Kristjansdottir1,2, William Merre3, Alexandra Helleux4, Julia Dusaucy5, Mathilde Tourigny4, Olafur Fridjonsson1 & Gudmundur Oli Hreggvidsson1,2 Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. We identifed CaldoCas9 and designed an associated guide RNA and showed that the pair have targetable nuclease activity in vitro at temperatures up to 65 °C. We performed a detailed characterization of the protospacer adjacent motif specifcity of CaldoCas9, which revealed a preference for 5′-NNNNGNMA. We constructed a plasmid vector for the delivery and use of the CaldoCas9 based genome editing system in the extreme thermophile Thermus thermophilus at 65 °C. Using the vector, we generated gene knock-out mutants of T. thermophilus, targeting genes on the bacterial chromosome and megaplasmid. Mutants were obtained at a frequency of about 90%. We demonstrated that the vector can be cured from mutants for a subsequent round of genome editing. CRISPR-Cas9 based genome editing has not been reported previously in the extreme thermophile T. thermophilus. These results may facilitate development of genome editing tools for other extreme thermophiles and to that end, the vector has been made available via the plasmid repository Addgene. -
Steven H. Strauss 21 December 2018
CV STEVEN H. STRAUSS 21 DECEMBER 2018 Distinguished Professor of Forest Biotechnology Phone: 541/737-6578 Department of Forest Ecosystems and Society Fax: 541/737-1393 Oregon State University Email: [email protected] Corvallis, Oregon, USA 97331-5752 Born: November 28, 1955 Home page / TBGRC Coop / Posters-Presentations PROFESSIONAL EXPERIENCE 7/09-present Distinguished Professor, Oregon State University 1/18-present Graduate Faculty, Environmental Sciences 1/18-present Graduate Faculty, Environmental Sciences 3/14 Visiting Scientist, Scion (Forest Biotechnology), New Zealand 11/04-12/13 Director, Outreach in Biotechnology, Oregon State University 2003-2012 Editor, New Phytologist 7/95-present Professor, Forest Ecosystems and Society; Molecular & Cellular Biology 1/01-4/01 Visiting Senior Fellow, Linacre College, Oxford University, UK 1/01-4/01 Visiting Scientist, Department of Plant Science, Oxford Forestry Institute , UK 7/90-6/95 Associate Professor, Department of Forest Science, OSU 7/94-present Director, Tree Genomics and Biosafety Research Cooperative, OSU 7/99-6/04 Director, National Science Foundation Center for Tree Genetics (Industry/University Cooperative Research Centers Program) 6/93-8/93 Visiting Scientist, INRA, Versailles & Orleans, France 9/91-6/92 Visiting Professor, Australian National University, Canberra, Australia 9/91-6/92 Visiting Scientist, CSIRO Division of Plant Industry, Canberra, Australia 6/90-7/90 Visiting Scientist, Department of Botany, Tromsø University, Norway 7/85-6/90 Assistant Professor, Department of Forest Science and Genetics Program, OSU 7/85-9/85 Visiting Scientist, US Forest Service, Berkeley, California (Sederoff laboratory) EDUCATION Ph.D. 1985 University of California at Berkeley, Forest Resources (Genetics) M.F.S. -
CRISPR/Cas9: Tools and Applications for Eukaryotic Genome Editing
CRISPR/Cas9: Tools and Applications for Eukaryotic Genome Editing Fei Ann Ran Broad Institute Cambridge, Massachusetts [email protected] I will provide some background on the CRISPR/Cas9 technology, some of the rationale for how we came to develop and use this tool, and I will address immediate questions concerning the specificity of the technology. I will also discuss some of the more interest- ing applications. Figure 1 reflects how the cost of DNA sequencing has decreased dramatically over the past two decades due to technological progress. As a result, there has been an explo- sion of data, not only in the sequences of different species, but in sequence differences between individuals within species, between cell types and between diseased and healthy cells. It suffices to say that this is an exciting time to be working in the field of genome engineering. Genome Engineering Typically, genome engineering is achieved by leveraging the cell’s own repair machinery. This can come from the error-prone NHEJ pathway that leads to insertion/deletion (in- del) mutations, which can be used to knock out genes, or, alternatively, we can supply a repair template to overwrite the site of a double-stranded break (DSB) for more-precise genome engineering via the HDR pathway (Figure 2). Figure 1. Advances in DNA-sequencing technologies. (Stratton MR et al., 2009) When we started working on CRISPR/Cas technology1, several well developed tools were already being used—and still are being used—to achieve impressive results in bio- technology, medicine, agriculture, and other fields. At the outset, we were interested in developing an alternative technology to make cloning easier at lower cost with greater scalability. -
Artificial Intelligence As a Dual-Use Technology Éva AMBRUS1
AARMS Vol. 19, No. 2 (2020) 19–28. 10.32565/aarms.2020.2.2 Artificial Intelligence as a Dual-use Technology Éva AMBRUS1 The aim of this article is to give an overview of the state of artificial intelligence regarding malware attacks, its uses in the military and views regarding if it should be classified as a dual-use technology. As an emerging technology, with a wide variety of use and capabilities, more could be done to overview its uses, and some form of control over it. While the classical exports control might be counterproductive, a more closed approach towards critical information dissemination might be advisable until the full range of capabilities of artificial intelligence will be known. Keywords: artificial intelligence, dual-use technology, military use, malware Introduction The security paradigm is changing. Until a new definition comes forward, policy-makers, academia and users will debate its nature and possible effects. Asymmetrical warfare, hybrid warfare, ‘grey area’ warfare, (dis)information warfare, unpeace are just a few names used trying to pinpoint the development of (IT) technology on security. Warfare and security includes more and more cyberspace, including cyber weapons, cyber espionage and cybersecurity. One driver of this change is the advances made in the last decade regarding artificial intelligence (AI). In this article I will present the idea that AI should be classified as a dual-use technology, meaning that it can be used for both civilian and military applications. I will start with presenting where AI weapons are today, followed by the nature of the relationship between state and technology. -
Genetic Modification for Agriculture—Proposed Revision of GMO Regulation in Australia
plants Opinion Genetic Modification for Agriculture—Proposed Revision of GMO Regulation in Australia Robert Redden RJR Agriculture Consultants, 62 Schier Drive, Horsham 340, Australia; [email protected] Abstract: Genetic engineering (GM) of crops, modified with DNA transfer between species, has been highly regulated for over two decades. Now, genome editing (GE) enables a range of DNA alterations, from single base pair changes to precise gene insertion with site-directed nucleases (SDNs). Past regulations, established according to the precautionary principle of avoiding potential risks to human health and the environment, are predicated on fears fanned by well-funded and emotional anti-GM campaigns. These fears ignore the safety record of GM crops over the last 25 years and the benefits of GM to crop productivity, disease and pest resistance, and the environment. GE is now superseding GM, and public education is needed about its benefits and its potential to meet the challenges of climate change for crops. World population will exceed 9 billion by 2050, and world CO2 levels are now over 400 ppm in contrast with a pre-industrial 280 ppm, leading to a projected 1.5 ◦C global warming by 2050, with more stressful crop environments. The required abiotic and biotic stress tolerances can be introgressed from crop wild relatives (CWR) into domestic crops via GE. Restrictive regulations need to be lifted to facilitate GE technologies for sustainable agriculture in Australia and the world. Keywords: genetic engineering; genome editing; regulation; climate change; precautionary principle Citation: Redden, R. Genetic Modification for Agriculture—Proposed Revision of 1. Introduction GMO Regulation in Australia. -
The Environmental Ethics of Domestication
The Environmental Ethics of Domestication when biotechnology reframes nature by Samantha McLean, BAppSc (Hons) Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy School of Geography and Environmental Studies University of Tasmania December 2008 Declaration of Originality This thesis contains no material which has been accepted for the award of any other degree or diploma in any university or other tertiary institution and, to the best of my knowledge and belief, contains no material previously published or written by another person, except where due reference has been made in the text. amantha McLean Statement of Authority of Access This thesis may be made available for loan and limited copying in accordance with the Copyright Act 1968. Abstract Controversies about genetic engineering in agriculture mobilise the concept of nature in ways that reframe nature with significant conceptual implications for the field of environmental ethics. The political economy and regulatory environment of genetic engineering excludes non- technical, non-expert and non-market perspectives in official assessments of biotechnological risk, but broader public conceptions of risk include philosophical concerns about the implications of genetic engineering for nature. Critical attention to the philosophical substance of these concerns is moderated by the conceptual ambiguity of their articulation in terms of unnaturalness and the ubiquity of other rhetorical appeals to nature as a source of precedence, legitimacy and morality. These discourses of naturalness are primarily concerned with whether genetic engineering represents a significant departure from conventional and traditional crop breeding practices or merely their continuation. This tension is seen in contrasting visions of biotechnology as either evolutionary or revolutionary and is resolved by recourse to particular narratives of domesticatory, evolutionary and cultural histories. -
Preparing for Future Products of Biotechnology
THE NATIONAL ACADEMIES PRESS This PDF is available at http://nap.edu/24605 SHARE Preparing for Future Products of Biotechnology DETAILS 230 pages | 7 x 10 | PAPERBACK ISBN 978-0-309-45205-2 | DOI 10.17226/24605 CONTRIBUTORS GET THIS BOOK Committee on Future Biotechnology Products and Opportunities to Enhance Capabilities of the Biotechnology Regulatory System; Board on Life Sciences; Board on Agriculture and Natural Resources; Board on Chemical Sciences and FIND RELATED TITLES Technology; Division on Earth and Life Studies; National Academies of Sciences, Engineering, and Medicine Visit the National Academies Press at NAP.edu and login or register to get: – Access to free PDF downloads of thousands of scientific reports – 10% off the price of print titles – Email or social media notifications of new titles related to your interests – Special offers and discounts Distribution, posting, or copying of this PDF is strictly prohibited without written permission of the National Academies Press. (Request Permission) Unless otherwise indicated, all materials in this PDF are copyrighted by the National Academy of Sciences. Copyright © National Academy of Sciences. All rights reserved. Preparing for Future Products of Biotechnology Preparing for Future Products of Biotechnology Committee on Future Biotechnology Products and Opportunities to Enhance Capabilities of the Biotechnology Regulatory System Board on Life Sciences Board on Agriculture and Natural Resources Board on Chemical Sciences and Technology Division on Earth and Life Studies A Report of Copyright National Academy of Sciences. All rights reserved. Preparing for Future Products of Biotechnology THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001 This activity was supported by Contract No. -
Biotechnology and Genetic Engineering
GLOBAL ISSUES BIOTECHNOLOGY AND GENETIC ENGINEERING GLOBAL ISSUES BIOTECHNOLOGY AND GENETIC ENGINEERING Kathy Wilson Peacock Foreword by Charles Hagedorn, Ph.D. Professor, Environmental Microbiology, Virginia Tech GLOBAL ISSUES: BioTECHNologY AND GENETIC ENgiNeeRING Copyright © 2010 by Infobase Publishing All rights reserved. No part of this book may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage or retrieval systems, without permission in writing from the publisher. For information contact: Facts On File, Inc. An imprint of Infobase Publishing 132 West 31st Street New York NY 10001 Library of Congress Cataloging-in-Publication Data Peacock, Kathy Wilson. Biotechnology and genetic engineering / Kathy Wilson Peacock; foreword by Charles Hagedorn. p.; cm. — (Global issues) Includes bibliographical references and index. ISBN 978-0-8160-7784-7 (alk. paper) 1. Biotechnology—Popular works. 2. Genetic engineering—Popular works. I. Title. II. Series: Global issues (Facts on File, Inc.) [DNLM: 1. Biotechnology. 2. Genetic Engineering. 3. Organisms, Genetically Modified—genetics. QU 450 P352b 2010] TP248.215.P43 2010 660.6—dc22 2009025794 Facts On File books are available at special discounts when purchased in bulk quantities for businesses, associations, institutions, or sales promotions. Please call our Special Sales Department in New York at (212) 967-8800 or (800) 322-8755. You can find Facts On File on the World Wide Web at http://www.factsonfile.com Text design by Erika K. Arroyo Illustrations by Dale Williams Composition by Mary Susan Ryan-Flynn Cover printed by Art Print, Taylor, Pa. Book printed and bound by Maple Press, York, Pa. -
EURORDIS Introduction on the Topic of Genome Editing for Rare Disease
Introduction on the topic of genome editing for rare disease patients Introduction In early 2016, health and science news outlets were talking about research studies using mouse models and human cells in which Duchenne Muscular Dystrophy was partially treated using genome editing. This is just one example of an increasing build-up of editorials, blog posts, reviews and position statements surrounding recent scientific advances in genome editing technologies. Why so much interest and debate? How is it different to gene therapy? How does it work? What can genome editing do? Genome editing essentially allows DNA in a living cell to be modified in a predetermined manner. This technology has the potential to treat many genetic diseases which are caused by alterations in the genetic code (mutations). All genes are made of DNA and form the blue prints of the proteins that build the body. When a gene is mutated, part of the DNA is changed in such a way that the protein it encodes no longer functions correctly. Theoretically, genome editing technology could allow these mutations to be corrected, restoring the function of the protein, and potentially alleviating the disease. This is an exciting prospect as currently most genetic diseases do not have a cure. If treatments are available they are usually aimed at managing the symptoms or slowing the progression of the disease. Genome editing tools allow scientists in the lab to address the cause and not just the symptoms of genetic diseases by performing a sort of genetic surgery. Technically, they are able to change genes by adding, replacing and/or removing sections of DNA, thus correcting the mutation responsible for causing the disease. -
Are We Ready for Designer Babies? Analysis of Law, Policy and Ethics Surrounding Germline Genetic Engineering
MUMBAI SILICON VALLEY BANGALORE SINGAPORE MUMBAI BKC NEW DELHI MUNICH NEW YORK Are we ready for Designer Babies? Analysis of law, policy and ethics surrounding germline genetic engineering Strategic, Legal, Tax and Ethical issues June 2019 © Copyright 2019 Nishith Desai Associates www.nishithdesai.com Are we ready for Designer Babies? Analysis of law, policy and ethics surrounding germline genetic engineering Strategic, Legal, Tax and Ethical Issues June 2019 [email protected] DMS Code: No 480049v2 © Nishith Desai Associates 2019 Are we ready for Designer Babies? Analysis of law, policy and ethics surrounding germline genetic engineering About NDA At Nishith Desai Associates, we have earned the reputation of being Asia’s most Innovative Law Firm – and the go-to specialists for companies around the world, looking to conduct businesses in India and for Indian companies considering business expansion abroad. In fact, we have conceptualized and created a state-of-the-art Blue Sky Thinking and Research Campus, Imaginarium Aligunjan, an international institution dedicated to designing a premeditated future with an embedded strategic foresight capability. We are a research and strategy driven international firm with offices in Mumbai, Palo Alto (Silicon Valley), Bangalore, Singapore, New Delhi, Munich, and New York. Our team comprises of specialists who provide strategic advice on legal, regulatory, and tax related matters in an integrated manner basis key insights carefully culled from the allied industries. As an active participant in shaping India’s regulatory environment, we at NDA, have the expertise and more importantly – the VISION – to navigate its complexities. Our ongoing endeavors in conducting and facilitating original research in emerging areas of law has helped us develop unparalleled proficiency to anticipate legal obstacles, mitigate potential risks and identify new opportunities for our clients on a global scale. -
CRISPR/Cas9 Genome Editing Brochure
mirusbio.com Cas9 Target Sequence Guide RNA GENOME EDITING: CRISPR/CAS9 DELIVERY METHODS GENOME EDITING: CRISPR/CAS9 DELIVERY What is CRISPR/Cas9 Genome Editing? The CRISPR/Cas9 system is a powerful tool for genome editing in mammalian cells that allows researchers to generate genetic variants at lower cost and with higher throughput than alternative methods like zinc finger nuclease (ZFN) or transcription activator-like effector nuclease (TALEN) genome editing. Cas9 PAM Genomic DNA Target Sequence Guide RNA crRNA tracrRNA The CRISPR/Cas9 RNP Complex. The CRISPR associated protein 9 (Cas9) endonuclease (blue) is targeted to DNA by a guide RNA (gRNA), which can be supplied as a two-part system consisting of CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) or as a single guide RNA (sgRNA), where the crRNA and tracrRNA are connected by a linker (dotted line). Target recognition is facilitated by the protospacer-adjacent motif (PAM). A double strand break (DSB) occurs 3 bp upstream of the PAM. CRISPR Facilitates Multiple Types of Genome Modification Cleavage of Target DNA By Cas9 Deletion Modication Insertion Multiple Genomic Alterations are Possible Following Cleavage of Target DNA by Cas9. Variable length insertions and/ or deletions (indels) can result near the DNA break due to mistakes in DNA repair by the endogenous non-homologous end joining (NHEJ) pathway. These indels frequently result in disruption of gene function. Alternatively, by supplying a DNA repair template, researchers can leverage the homology-directed repair (HDR) pathway to create defined deletions, insertions or other modifications. 2 TO ORDER | Toll Free 888.530.0801 | Direct 608.441.2852 | www.mirusbio.com Glossary of CRISPR Terms Term Definition CRISPR Associated Protein 9 - Cas9 is an RNA-guided DNA endonuclease from the type Cas9 II CRISPR system of Streptococcus pyogenes that has been adapted for use in genome editing applications. -
A Modular Cloning Toolkit for Genome Editing in Plants Florian Hahn1 , Andrey Korolev1,2, Laura Sanjurjo Loures1 and Vladimir Nekrasov1*
Hahn et al. BMC Plant Biology (2020) 20:179 https://doi.org/10.1186/s12870-020-02388-2 METHODOLOGY ARTICLE Open Access A modular cloning toolkit for genome editing in plants Florian Hahn1 , Andrey Korolev1,2, Laura Sanjurjo Loures1 and Vladimir Nekrasov1* Abstract Background: CRISPR/Cas has recently become a widely used genome editing tool in various organisms, including plants. Applying CRISPR/Cas often requires delivering multiple expression units into plant and hence there is a need for a quick and easy cloning procedure. The modular cloning (MoClo), based on the Golden Gate (GG) method, has enabled development of cloning systems with standardised genetic parts, e.g. promoters, coding sequences or terminators, that can be easily interchanged and assembled into expression units, which in their own turn can be further assembled into higher order multigene constructs. Results: Here we present an expanded cloning toolkit that contains 103 modules encoding a variety of CRISPR/Cas- based nucleases and their corresponding guide RNA backbones. Among other components, the toolkit includes a number of promoters that allow expression of CRISPR/Cas nucleases (or any other coding sequences) and their guide RNAs in monocots and dicots. As part of the toolkit, we present a set of modules that enable quick and facile assembly of tRNA-sgRNA polycistronic units without a PCR step involved. We also demonstrate that our tRNA- sgRNA system is functional in wheat protoplasts. Conclusions: We believe the presented CRISPR/Cas toolkit is a great resource that will contribute towards wider adoption of the CRISPR/Cas genome editing technology and modular cloning by researchers across the plant science community.