Regulation of Synthetic Biology
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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. -
Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation
G C A T T A C G G C A T genes Review Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation Christian Diwo 1 and Nediljko Budisa 1,2,* 1 Institut für Chemie, Technische Universität Berlin Müller-Breslau-Straße 10, 10623 Berlin, Germany; [email protected] 2 Department of Chemistry, University of Manitoba, 144 Dysart Rd, 360 Parker Building, Winnipeg, MB R3T 2N2, Canada * Correspondence: [email protected] or [email protected]; Tel.: +49-30-314-28821 or +1-204-474-9178 Received: 27 November 2018; Accepted: 21 December 2018; Published: 28 December 2018 Abstract: The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. -
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. -
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. -
Flourishing and Discordance: on Two Modes of Human Science Engagement with Synthetic Biology
Flourishing and Discordance: On Two Modes of Human Science Engagement with Synthetic Biology by Anthony Stavrianakis A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Anthropology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Paul Rabinow, Chair Professor Xin Liu Professor Charis Thompson Fall 2012 Abstract Flourishing and Discordance: On Two Modes of Human Science Engagement with Synthetic Biology by Anthony Stavrianakis Doctor of Philosophy in Anthropology University of California, Berkeley Professor Paul Rabinow, Chair This dissertation takes up the theme of collaboration between the human sciences and natural sciences and asks how technical, veridictional and ethical vectors in such co-labor can be inquired into today. I specify the problem of collaboration, between forms of knowledge, as a contemporary one. This contemporary problem links the recent past of the institutional relations between the human and natural sciences to a present experience of anthropological engagement with a novel field of bioengineering practice, called synthetic biology. I compare two modes of engagement, in which I participated during 2006–2011. One project, called Human Practices, based within the Synthetic Biology Engineering Research Center (SynBERC), instantiated an anthropological mode of inquiry, explicitly oriented to naming ethical problems for collaboration. This project, conducted in collaboration with Paul Rabinow and Gaymon Bennett, took as a challenge the invention of an appropriate practice to indeterminate ethical problems. Flourishing, a translation of the ancient Greek term eudaemonia, was a central term in orienting the Human Practices project. This term was used to posit ethical questions outside of the instrumental rationality of the sciences, and on which the Human Practices project would seek to work. -
21St Century Borders/Synthetic Biology: Focus on Responsibility and Governance
Social science Engineering Framework Institute on Science for Global Policy (ISGP) Risk-benefit Media Public Synthetic Biology Genetic Governance Regulation Voluntary Anticipatory Databases Xenobiology 21st Century Borders/Synthetic Biology: Focus on Responsibility and Governance Conference convened by the ISGP Dec. 4–7, 2012 at the Hilton El Conquistador, Tucson, Arizona Risk Technology Oversight Plants Uncertainty Product Less-affluent countries DIYBIO Biotechnology Emerging Dynamic Environmental Government Biosafety Self-regulation Nefarious Genetically modified Protein Standards Dual use Distribution Applications Food Microbial Authority Assessment Agricultural Institute on Science for Global Policy (ISGP) 21st Century Borders/Synthetic Biology: Focus on Responsibility and Governance Conference convened by the ISGP in partnership with the University of Arizona at the Hilton El Conquistador Hotel Tucson, Arizona, U.S. Dec. 4–7, 2012 An ongoing series of dialogues and critical debates examining the role of science and technology in advancing effective domestic and international policy decisions Institute on Science for Global Policy (ISGP) Tucson, AZ Office 845 N. Park Ave., 5th Floor PO Box 210158-B Tucson, AZ 85721 Washington, DC Office 818 Connecticut Ave. NW Suite 800 Washington, DC 20006 www.scienceforglobalpolicy.org © Copyright Institute on Science for Global Policy, 2013. All rights reserved. ISBN: 978-0-9803882-4-0 ii Table of contents Executive summary • Introduction: Institute on Science for Global Policy (ISGP) .............. 1 Dr. George H. Atkinson, Founder and Executive Director, ISGP, and Professor Emeritus, University of Arizona • Conference conclusions: Areas of consensus and Actionable next steps ...................................... 7 Conference program ........................................................................................... 11 Policy position papers and debate summaries • Synthetic Biology — Do We Need New Regulatory Systems? Prof. -
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. -
Astrobiology Life in the Universe
Astrobiology Astrobiology is the study of the origin, evolution, distribution, and future of life in the universe. In simplest terms, it is the study of life in the universe–both on Earth and off it. It combines the search for habitable environments in the Solar System and beyond with research into the evolution and adaptability of life here on Earth. By knitting together research in astrophysics, earth science, and heliophysics as well as planetary science, astrobiology seeks to answer fundamental scientific questions about life: how it begins and evolves; what biological, planetary, and cosmic conditions must exist in order for it to take hold; and whether there is/was/can be life elsewhere in the galaxy. Dr. Alka Misra Assistant Professor Department of Mathematics & Astronomy University of Lucknow What is Astrobiology! Astrobiology is the study of life in the Universe – where it is, how it came to be there, what it is like, and where it might be going. As the only life we know about for sure is on Earth, a lot of astrobiology is about trying to predict where we might find life elsewhere. Astrobiology is the study of the origin, evolution, distribution, and future of life in the universe. This interdisciplinary field encompasses the search for habitable environments in our Solar System and habitable planets outside our Solar System, the search for evidence of prebiotic chemistry, laboratory and field research into the origins and early evolution of life on Earth, and studies of the potential for life to adapt to challenges on Earth and in outer space. -
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. -
Synthetic Biology in Agriculture and Challenges for Risk Governance
Synthetic biology in agriculture and challenges for risk governance STOA Workshop on Ethical and social challenges of agricultural technologies European Parliament, 25th January 2017 Helge Torgersen Synthetic biology, agriculture and risk govenance 1. What is synthetic biology? 2. Novel risk aspects – what relevance for agriculture? 3. Gene editing – the pertinent example: Definition: what is a GMO? Assessment: how to compare an edited organism? Containment: gene drive Public perception: edited animals 4. Risk governance 5. Strategies 1) What is Synthetic Biology? • Introducing into biotechnology concepts from computer science and systems engineering (Endy 2005) The design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural systems (UK Royal Society 2014) • ‘Extreme genetic engineering’ (ETC Group 2007) The application of science, technology and engineering to facilitate and accelerate the design, manufacture and/or modification of genetic materials in living organisms (SCHER/SCENIHR/SCCS 2015) Synthetic biology is a compilation of novel bio-engineering approaches with no clear distinction from genetic engineering, from which it evolves (1) Relevant fields (SCHER/SCENHIR/SCCS 2015) a. Genetic parts: pieces of DNA governing particular functions in an organism, to be deliberately combined b. Protocells: artificial cell-like devices that perform some functions of a living cell c. Minimal cells deprived of all non-essential genes used as a “chassis” for genetic parts d. Xenobiology: -
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.