Synthetic Biology: Scope, Applications and Implications
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Venter Institute
Genomics:GTL Program Projects J. Craig Venter Institute 42 Estimation of the Minimal Mycoplasma Gene Set Using Global Transposon Mutagenesis and Comparative Genomics John I. Glass* ([email protected]), Nina Alperovich, Nacyra Assad-Garcia, Shibu Yooseph, Mahir Maruf, Carole Lartigue, Cynthia Pfannkoch, Clyde A. Hutchison III, Hamilton O. Smith, and J. Craig Venter J. Craig Venter Institute, Rockville, MD The Venter Institute aspires to make bacteria with specific metabolic capabilities encoded by artificial genomes. To achieve this we must develop technologies and strategies for creating bacterial cells from constituent parts of either biological or synthetic origin. Determining the minimal gene set needed for a functioning bacterial genome in a defined laboratory environment is a necessary step towards our goal. For our initial rationally designed cell we plan to synthesize a genome based on a mycoplasma blueprint (mycoplasma being the common name for the class Mollicutes). We chose this bacterial taxon because its members already have small, near minimal genomes that encode limited metabolic capacity and complexity. We took two approaches to determine what genes would need to be included in a truly minimal synthetic chromosome of a planned Mycoplasma laboratorium: determination of all the non-essential genes through random transposon mutagenesis of model mycoplasma species, Mycoplasma genitalium, and comparative genomics of a set of 15 mycoplasma genomes in order to identify genes common to all members of the taxon. Global transposon mutagenesis has been used to predict the essential gene set for a number of bac- teria. In Bacillus subtilis all but 271 of bacterium’s ~4100 genes could be knocked out. -
Microbial Identification Framework for Risk Assessment
Microbial Identification Framework for Risk Assessment May 2017 Cat. No.: En14-317/2018E-PDF ISBN 978-0-660-24940-7 Information contained in this publication or product may be reproduced, in part or in whole, and by any means, for personal or public non-commercial purposes, without charge or further permission, unless otherwise specified. You are asked to: • Exercise due diligence in ensuring the accuracy of the materials reproduced; • Indicate both the complete title of the materials reproduced, as well as the author organization; and • Indicate that the reproduction is a copy of an official work that is published by the Government of Canada and that the reproduction has not been produced in affiliation with or with the endorsement of the Government of Canada. Commercial reproduction and distribution is prohibited except with written permission from the author. For more information, please contact Environment and Climate Change Canada’s Inquiry Centre at 1-800-668-6767 (in Canada only) or 819-997-2800 or email to [email protected]. © Her Majesty the Queen in Right of Canada, represented by the Minister of the Environment and Climate Change, 2016. Aussi disponible en français Microbial Identification Framework for Risk Assessment Page 2 of 98 Summary The New Substances Notification Regulations (Organisms) (the regulations) of the Canadian Environmental Protection Act, 1999 (CEPA) are organized according to organism type (micro- organisms and organisms other than micro-organisms) and by activity. The Microbial Identification Framework for Risk Assessment (MIFRA) provides guidance on the required information for identifying micro-organisms. This document is intended for those who deal with the technical aspects of information elements or information requirements of the regulations that pertain to identification of a notified micro-organism. -
NASA Resources for Biology Classes
NASA Resources for Biology classes For NC Bio. Obj. 1.2.3 - Cell adaptations help cells survive in particular environments Lesson Plan: Is it Alive? This lesson is designed to be a review of the characteristics of living things. http://marsed.asu.edu/sites/default/files/stem_resources/Is_it_Alive_HS_Lesson_2_16.pdf Lesson Plan: Building Blocks of Life Experiment with Yeast to simulate carbonaceous meteorites. https://er.jsc.nasa.gov/seh/Exploring_Meteorite_Mysteries.pdf#page=138 Video: ● Subsurface Astrobiology: Cave Habitats on Earth, Mars and Beyond: In our quest to explore other planets, we only have our own planet as an analogue to the environments we may find life. By exploring extreme environments on Earth, we can model conditions that may be present on other celestial bodies and select locations to explore for signatures of life. https://images.nasa.gov/details-ARC-20160809-AAV2863-SummerSeries-15-PenelopeBoston- Youtube.html ● Real World: Heart Rate and Blood Pressure: Learn about the physiological effects reduced gravity environments have on the human body. Use multiplication to calculate cardiac output and find out what effect space travel has on sensory-motor skills, stroke volume and heart rates of the astronauts. https://nasaeclips.arc.nasa.gov/video/realworld/real-world-heart-rate-and-blood- pressure ● Launchpad: Astrobiology: Are we alone in the universe? Where do we come from? Join NASA in the search for answers to these and many more questions about life in our solar system. Learn how astrobiologists use what we know about Earth to investigate Titan, Europa and other far-off worlds. https://nasaeclips.arc.nasa.gov/video/launchpad/launchpad-astrobiology Article: ● Synthetic Biology - ‘Worker Microbes’ for Deep Space Missions https://www.nasa.gov/content/synthetic-biology For NC Bio. -
The Principles for the Oversight of Synthetic Biology the Principles for the Oversight of Synthetic Biology
The Principles for the Oversight of Synthetic Biology The Principles for the Oversight of Synthetic Biology Drafted through a collaborative process among civil society groups. For more information or copies of this declaration, contact: The Principles for the Eric Hoffman Food and technology policy campaigner Friends of the Earth U.S. Oversight of Synthetic Biology 1100 15th St. NW, 11th Floor Washington, D.C. 20005 202.222.0747 [email protected] www.foe.org Jaydee Hanson Policy director International Center for Technology Assessment 660 Pennsylvania Ave., SE, Suite 302 Washington, D.C. 20003 202.547.9359 [email protected] www.icta.org Jim Thomas Research program manager ETC Group 5961 Rue Jeanne Marce Montreal, Quebec Canada +1.514.273.9994 [email protected] The views expressed in this declaration represent those of the signers and do not necessarily represent those of individual contributors to Friends of the Earth U.S., International Center for Technology Assessment, ETC Group or the funding organizations. Funding thanks to CS Fund and Appleton Foundation. The Principles for the Oversight of Synthetic Biology The undersigned, a broad coalition of civil society groups, social movements, local and indigenous communities, public interest, environmental, scientif ic, human rights, religious and labor organizations concerned about various aspects of synthetic biology’s human health, environmental, social, economic, ethical and other impacts, offer the following declaration, The Principles for the Oversight of Synthetic Biology. Executive Summary Synthetic biology, an extreme form of genetic engi- and should include consideration of synthetic biology’s neering, is developing rapidly with little oversight or wide-ranging effects, including ethical, social and eco- regulation despite carrying vast uncertainty. -
Role of Protein Phosphorylation in Mycoplasma Pneumoniae
Pathogenicity of a minimal organism: Role of protein phosphorylation in Mycoplasma pneumoniae Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades „Doctor rerum naturalium“ der Georg-August-Universität Göttingen vorgelegt von Sebastian Schmidl aus Bad Hersfeld Göttingen 2010 Mitglieder des Betreuungsausschusses: Referent: Prof. Dr. Jörg Stülke Koreferent: PD Dr. Michael Hoppert Tag der mündlichen Prüfung: 02.11.2010 “Everything should be made as simple as possible, but not simpler.” (Albert Einstein) Danksagung Zunächst möchte ich mich bei Prof. Dr. Jörg Stülke für die Ermöglichung dieser Doktorarbeit bedanken. Nicht zuletzt durch seine freundliche und engagierte Betreuung hat mir die Zeit viel Freude bereitet. Des Weiteren hat er mir alle Freiheiten zur Verwirklichung meiner eigenen Ideen gelassen, was ich sehr zu schätzen weiß. Für die Übernahme des Korreferates danke ich PD Dr. Michael Hoppert sowie Prof. Dr. Heinz Neumann, PD Dr. Boris Görke, PD Dr. Rolf Daniel und Prof. Dr. Botho Bowien für das Mitwirken im Thesis-Komitee. Der Studienstiftung des deutschen Volkes gilt ein besonderer Dank für die finanzielle Unterstützung dieser Arbeit, durch die es mir unter anderem auch möglich war, an Tagungen in fernen Ländern teilzunehmen. Prof. Dr. Michael Hecker und der Gruppe von Dr. Dörte Becher (Universität Greifswald) danke ich für die freundliche Zusammenarbeit bei der Durchführung von zahlreichen Proteomics-Experimenten. Ein ganz besonderer Dank geht dabei an Katrin Gronau, die mich in die Feinheiten der 2D-Gelelektrophorese eingeführt hat. Außerdem möchte ich mich bei Andreas Otto für die zahlreichen Proteinidentifikationen in den letzten Monaten bedanken. Nicht zu vergessen ist auch meine zweite Außenstelle an der Universität in Barcelona. Dr. Maria Lluch-Senar und Dr. -
Synthetic Biology and the CBD Five Key Decisions for COP 13 & COP-MOP 8
Synthetic Biology and the CBD Five key decisions for COP 13 & COP-MOP 8 Synthetic biology threatens to undermine all What Is Synthetic Biology? three objectives of the Convention if Parties fail to act on the following 5 key issues: Synthetic biology describes the next generation of biotechnologies that attempt to engineer, re- 1. Operational Definition. It’s time for the design, re-edit and synthesize biological systems, CBD to adopt an operational definition of including at the genetic level. synthetic biology. Synthetic biology goes far beyond the first 2. Precaution: Gene drives. Gene drives pose generation of ‘transgenic’ engineered organisms. wide ecological and societal threats and should Predicted to be almost a 40 billion dollar (US) be placed under a moratorium. market by 2020, industrial activity in synthetic 3. Biopiracy: Digital Sequences. Synthetic biology is rapidly exploding as new genome biology allows for digital theft and use of DNA editing tools and cheaper synthesis of DNA sequences – this must be addressed by both the make it easier and faster to genetically re-design CBD and the Nagoya Protocol. or alter biological organisms. Synthetic biology-derived products already on 4. Socio-economic Impacts: Sustainable Use. the market include biosynthesized versions of The CBD needs a process to address impacts flavors, fragrances, fuels, pharmaceuticals, of synthetic biology on sustainable use of textiles, industrial chemicals, cosmetic and food biodiversity. ingredients. A next generation of synthetically 5. Cartagena Protocol: Risk Assessment. engineered (including ‘genome edited’) crops, Parties to the COP-MOP 8 need to clearly insects and animals are also nearing move forward with elaborating risk assessment commercialization. -
Future Directions of Synthetic Biology for Energy & Power
Future Directions of Synthetic Biology for Energy & Power March 6–7, 2018 Michael C. Jewett, Northwestern University Workshop funded by the Basic Research Yang Shao-Horn, Massachusetts Institute of Technology Office, Office of the Under Secretary of Defense Christopher A. Voigt, Massachusetts Institute of Technology for Research & Engineering. This report does not necessarily reflect the policies or positions Prepared by: Kate Klemic, VT-ARC of the US Department of Defense Esha Mathew, AAAS S&T Policy Fellow, OUSD(R&E) Preface OVER THE PAST CENTURY, SCIENCE AND TECHNOLOGY HAS BROUGHT RE- MARKABLE NEW CAPABILITIES TO ALL SECTORS OF THE ECONOMY; from telecommunications, energy, and electronics to medicine, transpor- tation and defense. Technologies that were fantasy decades ago, such as the internet and mobile devices, now inform the way we live, work, and interact with our environment. Key to this technologi- cal progress is the capacity of the global basic research community to create new knowledge and to develop new insights in science, technology, and engineering. Understanding the trajectories of this fundamental research, within the context of global challenges, em- powers stakeholders to identify and seize potential opportunities. The Future Directions Workshop series, sponsored by the Basic Re- search Directorate of the Office of the Under Secretary of Defense for Research and Engineering, seeks to examine emerging research and engineering areas that are most likely to transform future tech- nology capabilities. These workshops gather distinguished academic researchers from around the globe to engage in an interactive dia- logue about the promises and challenges of emerging basic research areas and how they could impact future capabilities. -
Methylase-Assisted Subcloning for High Throughput Biobrick Assembly
Methylase-assisted subcloning for high throughput BioBrick assembly Ichiro Matsumura Emory University School of Medicine, Department of Biochemistry, Atlanta, GA, United States of America ABSTRACT The BioBrick standard makes possible iterated pairwise assembly of cloned parts with- out any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join. Subjects Bioengineering, Molecular Biology, Synthetic Biology Keywords BioBrick assembly, Methylase-assisted cloning, Synthetic biology, Laboratory automation, DNA methyltransferase Submitted 27 April 2020 Accepted 10 August 2020 Published 11 September 2020 INTRODUCTION Corresponding author A bottleneck in many synthetic biology projects is the physical linkage of cloned synthetic Ichiro Matsumura, [email protected] genes (``parts'') to each other to form longer functional assemblies (``devices''). -
Synthetic Biology an Overview of the Debates
SYNTHETIC BIOLOGY PROJECT / SYNBIO 3 SYNTHETIC BIOLOGY Ethical Issuesin SYNBIO 3/JUNE2009 An overview ofthedebates Contents Preface 3 Executive Summary 4 Who is doing what, where are they doing it and how is this current work funded? 6 How distinct is synthetic biology from other emerging areas of scientific and technological innovation? 9 Ethics: What harms and benefits are associated with synthetic biology? 12 The pro-actionary and pre-cautionary frameworks 18 N OVERVIEW OF THE DEBATES N OVERVIEW OF A Competing—and potentially complementary—views about non-physical harms (harms to well-being) 23 The most contested harms to well-being 25 Conclusion: Moving the debate forward 26 References 29 ETHICAL ISSUES IN SYNTHETIC BIOLOGY: ETHICAL ISSUES IN SYNTHETIC BIOLOGY: ii The opinions expressed in this report are those of the authors and do not necessarily reflect views Sloan Foundation. Wilson International Center for Scholars or the Alfred P. of the Woodrow Ethical Issues in SYNTHETIC BIOLOGY An overview of the debates Erik Parens, Josephine Johnston, and Jacob Moses The Hastings Center, Garrison, New York SYNBIO 3 / JUNE 2009 2 ETHICAL ISSUES IN SYNTHETIC BIOLOGY: AN OVERVIEW OF THE DEBATES Preface Synthetic biology will allow scientists and where such topics are divided into two broad engineers to create biological systems categories: concerns about physical and non- that do not occur naturally as well as to physical harms. While physical harms often re-engineer existing biological systems to trigger debates about how to proceed among perform novel and beneficial tasks. This researchers, policymakers, and the public, emerging field presents a number of non-physical harms present more difficult opportunities to address ethical issues early conundrums. -
Genome Mining and Synthetic Biology in Marine Natural Product Discovery
marine drugs Editorial Genome Mining and Synthetic Biology in Marine Natural Product Discovery Maria Costantini Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; [email protected]; Tel.: +39-081-583-3285 Received: 17 November 2020; Accepted: 22 November 2020; Published: 3 December 2020 Oceans cover nearly 70% of the earth’s surface and host a huge ecological, chemical, and biological diversity. The natural conditions of the sea favor, in marine organisms, the production of a large variety of novel molecules with great pharmaceutical potential. Marine organisms are unique in their structural and functional features compared to terrestrial ones [1,2]. Innovation in this field is very rapid, as revealed by the funding of several Seventh Framework Programme (FP7) and Horizon 2020 projects under the topic “Blue Growth”. The major parts of these projects have the common final goal of meeting the urgent need to discover new drug entities to counteract the increased incidence of severe diseases (such as cancer) and the reduced efficacy of existing drugs [3]. For this reason, the application of molecular biology techniques in biotechnological field is very important. Driven by the rapidly-decreasing cost and increasing throughput of DNA-sequencing technologies, significant progress in genomics has renewed interest in the discovery of natural products. Rapidly-expanding genomic and metagenomic datasets reveal a vast number of biosynthetic gene clusters (BGCs) in nature, which are predicted to encode novel biomedically-relevant molecules. This ‘top-down’ discovery approach can only provide access to a small fraction of biosynthetic compounds, given that the majority of microorganisms cannot be isolated or cultured. -
Eukaryotic Cell Eukaryotic Cells Are Defined As Cells Containing Organized Nucleus and Organelles Which Are Enveloped by Membrane-Bound Organelles
Eukaryotic Cell Eukaryotic cells are defined as cells containing organized nucleus and organelles which are enveloped by membrane-bound organelles. Examples of eukaryotic cells are plants, animals, protists, fungi. Their genetic material is organized in chromosomes. Golgi apparatus, Mitochondria, Ribosomes, Nucleus are parts of Eukaryotic Cells. Let’s learn about the parts of eukaryotic cells in detail. Parts ot Eukaryotic Cells Cytoplasmic Membrane: Description: It is also called plasma membrane or cell membrane. The plasma membrane is a semi-permeable membrane that separates the inside of a cell from the outside. Structure and Composition: In eukaryotic cells, the plasma membrane consists of proteins , carbohydrates and two layers of phospholipids (i.e. lipid with a phosphate group). These phospholipids are arranged as follows: • The polar, hydrophilic (water-loving) heads face the outside and inside of the cell. These heads interact with the aqueous environment outside and within a cell. • The non-polar, hydrophobic (water-repelling) tails are sandwiched between the heads and are protected from the aqueous environments. Scientists Singer and Nicolson(1972) described the structure of the phospholipid bilayer as the ‘Fluid Mosaic Model’. The reason is that the bi-layer looks like a mosaic and has a semi-fluid nature that allows lateral movement of proteins within the bilayer. Image: Fluid mosaic model. Orange circles – Hydrophilic heads; Lines below – Hydrophobic tails. Functions • The plasma membrane is selectively permeable i.e. it allows only selected substances to pass through. • It protects the cells from shock and injuries. • The fluid nature of the membrane allows the interaction of molecules within the membrane. -
A New Biobrick Assembly Strategy Designed for Facile Protein Engineering
A New Biobrick Assembly Strategy Designed for Facile Protein Engineering Ira E. Phillips∗ and Pamela A. Silver∗ April 18, 2006 Abstract The existing biobrick assembly technique[1] provides a straightforward way to combine standardized biological components, termed biobricks. This system, however, is limited in that each protein-encoding biobrick must contain a complete translated region. Signal sequences or other pro- tein domains often convey a specific function to the protein to which they are attached; hence, each domain should be considered an independent biological part. With the current assembly technique, assembling such parts is not possible. This paper presents a revised assembly strategy that is compatible with the current biobrick definition and permits the construction of fusion proteins. Introduction The standard biobrick assembly technique was created in an attempt to simplify the construction of long concatemeric pieces of DNA often used in synthetic biology [1]. Previously existing techniques were limiting in that one often needed to design a unique cloning strategy for each desired construct. Moreover, the intermediates in the cloning of one construct would be of little value in creating other constructs. As a solution to these problems, T. Knight developed a novel cloning strategy that permits standardization of biological parts or biobricks [1]. Each biobrick can be placed in front of or behind another biobrick using a standard protocol that is independent of the content of the parts involved. (To insert a biobrick in front of another, simply digest the upstream biobrick with EcoRI and SpeI. Cut out this insert and ligate into a vector containing the second part cut with EcoRI and XbaI.