Engineering Bacterial Populations Via Dna Messaging

Total Page:16

File Type:pdf, Size:1020Kb

Engineering Bacterial Populations Via Dna Messaging ENGINEERING BACTERIAL POPULATIONS VIA DNA MESSAGING ADISSERTATION SUBMITTED TO THE DEPARTMENT OF BIOENGINEERING AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Monica Elise Ortiz June 2013 © 2013 by Monica Elise Ortiz. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial 3.0 United States License. http://creativecommons.org/licenses/by-nc/3.0/us/ This dissertation is online at: http://purl.stanford.edu/ht577gs4955 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Andrew Endy, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Daniel Fisher I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Hans Riedel-Kruse Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii iv Abstract Evolution has selected for organisms that benefit from genetically encoded cell-cell communication. We observe cell-cell communication throughout every scale in na- ture, from simple single-celled bacteria to complex multicellular mammals. Engineers have begun to repurpose elements of natural communication systems to coordinate their own population-level behaviors, including oscillations and programmed pat- tern formation. Existing engineered systems, however, rely on small, system-specific biomolecules to send messages among cells. However, such molecules are capable of sending only a single message, typically “regulate transcription.” Thus, the informa- tion transmission capacity of such biological communication systems is fundamentally limited. Through this thesis, I demonstrated the decoupling of messages from a common communication channel via the autonomous transmission of numerous arbitrary ge- netic messages. To do so, I engineered a cell-cell communication platform using bacte- riophage M13 gene products to autonomously package and deliver heterologous DNA messages of varying lengths and encoded functions. Further, I increased the range of engineered DNA messaging across semisolid media by coupling message transmis- sion or receipt to active cellular chemotaxis. Through this coupling, I demonstrated that our system is adaptable to di↵erent contexts by creating simple patterns. Fi- nally, using recombinase-mediated logic gates developed within the Endy laboratory, Idemonstratedtheabilitytoprogrambacteriabytransmittinglogicgatestosur- rounding cells. Overall, this work significantly enhances the suite of cell-cell communication tools available to engineers. I have shown that a variety of DNA messages can be trans- mitted among cells and have moved the field of synthetic biology closer to designing synthetic ecologies with more complex communication schemes and varied behaviors. v Acknowledgements This dissertation would not have been possible without the love and support of my family. To my parents, Brenda and Edgar Ortiz, for instilling in me a confidence and drive without which I would not be where I am today. To Nicole, my sister and first roommate, for being a force of nature and an inspiration. To my grandparents and extended family for always making me feel special, even when I was actually a brat. To Stephen, my partner and best friend, for his support over the better part of the last decade. To Olive and Sprout for their unconditional love and incessant purring. Iwouldnextliketothankmyadvisor,DrewEndy,foracceptingmeintohislab when I had no academic home, and for fostering an environment where good work is valued above all. Drew embodies the “dream it and achieve it” mentality better than anyone I know, and I am a better engineer for joining Drew’s group. I am grateful to Daniel Fisher and Ingmar Riedel-Kruse for serving on my disser- tation reading committee. I thank Daniel Fisher, who has provided hours of advice and wonderful conversation on a myriad of topics. I will particularly miss Daniel’s insight and booming voice. I thank Ingmar Riedel-Kruse, who was unselfish with his time and provided a number of interesting research avenues. I also thank Jan Skotheim, chair of my dissertation defense committee, and Christina Smolke, also a member of my dissertation defense committee, for their time and counsel. I thank past and present members of the Endy Lab—Sara Aguiton, Jerome Bon- net, Paul Jaschke, Xiaofan Jin, Linda Kahl, Lance Martin, Megan Palmer, Je↵Quinn, C´esar Rodriguez, Pablo Schyfter, Fran¸cois St.-Pierre, Pakpoom (Ton) Subsoontorn, Brent Townshend, Peter Yin—and Smolke Lab for not only providing guidance and discussion to help push forward this work, but also for preserving my sanity. The “En- dolke Lab” has been a wonderful place to work. I am sad to lose these co-workers, but glad to have gained many wonderful friends. Teaching has been an integral part of my graduate education. For this, I thank my past mentors—Jennifer Cochran, Christina Smolke, and Daniel Fisher. I also thank my fellow TAs—Aakash Basu, Ryan Bloom, and Kathy Wei. Finally, I thank Norbert Pelc, Isis Trenchard, Jennifer Lahti, and Hedi Razavi, all of whom I had the pleasure of working with as a TA coordinator. vi As a member of the fifth incoming Ph.D. class to Stanford Bioengineering, I have been fortunate to witness the transformation of an initially small department into a powerhouse of high-impact research and home to many talented students. I thank the faculty for the education I was provided and for their continuous support. I thank Olgalydia Urbano-Winegar profusely for being supportive, for always having her door open, and for tolerating my perpetually late forms. I also thank my tal- ented Bioengineering classmates, especially Amy Lam, Jayodita Sanghvi, and Tony Schindler. Finally, I felt fortunate to have a supportive group of friends spread around the country who were always just a phone call away. Thanks to Disha Shah, Julie Young, Elissa and Ben Cosgrove, Emily Schwartz, David Ritchie, D. Paul Golden, Kevin Lar- son, Amanda Cannata, Andrew Chow, Arup Chakrabarti, Michael Dini, and Gian Merlino for providing a constant stream of encouragement and entertaining voice- mails. vii Contents Abstract v Acknowledgements vi 1 Introduction 1 1.1 Anintroductiontocell-cellcommunication . 1 1.2 A Shannon framework . 4 1.3 Anoverviewofthisdissertation . 13 1.4 Collaborations . 15 1.4.1 Chapter 2 . 15 1.4.2 Chapter 3 . 15 1.4.3 Chapter 4 . 15 2 Achieving decoupled and scalable cell-cell communication via M13 16 2.1 Introduction . 16 2.2 Materials and Methods . 18 2.2.1 Strains and media . 18 2.2.2 Messaging phagemid and plasmid construction . 19 2.2.3 Preparation of sender and receiver cells . 22 2.2.4 Liquid-based experiments . 23 2.3 Results . 27 2.3.1 Requirements of M13-based message transmission . 27 2.3.2 Multiple messages can be sent through a single channel . 32 2.4 Discussion . 35 viii 3 Expanding phage-based communication to 2-D space 37 3.1 Introduction . 37 3.2 Materials and methods . 40 3.2.1 Di↵usion experiments . 40 3.2.2 Motility experiments . 41 3.3 Results . 45 3.3.1 Information channel capacities for AHL- and M13-based com- municationsystems. 45 3.3.2 Di↵usion analysis for AHL- and bacteriophage M13-based cell- cell communication systems . 49 3.3.3 E↵ective range of a DNA message transmission coupled to bac- terial chemotaxis . 51 3.4 Discussion . 57 4 Bacterial programming by transmission of DNA logic gates 60 4.1 Introduction . 62 4.2 Materials and Methods . 66 4.2.1 Molecular biology . 66 4.2.2 Site specific chromosomal integration . 67 4.2.3 Cell culture and gate operating conditions . 67 4.2.4 Transmission experiments . 68 4.3 Results . 72 4.3.1 Uniform populations can be programmed with di↵erent logic elements . 72 4.3.2 Intermediate states of logic elements can be transmitted . 76 4.3.3 Logic elements can be remotely activated . 76 4.4 Discussion . 78 5 Future Work and Final Remarks 81 5.1 Future work . 81 5.1.1 Improvements to the M13-based platform. 82 5.1.2 Next steps with respect to pattern formation . 85 ix 5.1.3 Firstapplications . 86 5.2 Conclusions . 88 A Vector maps and DNA sequences 90 A.1 VectormapsforChapters2and3 . 90 A.2 VectormapsandsequencesforChapter4. 92 A.2.1 pWSK29mod XOR........................ 92 A.2.2 pWSK29mod AND . 96 A.2.3 Othersequencesandaddedinformation. 99 Bibliography 100 x List of Figures 1.1 Existing cell-cell communication systems are limited by message-channel coupling .................................. 3 1.2 Generic communication systems have five components . 5 2.1 Biological communication systems can be represented formally . 18 2.2 Targeted and autonomous communication of arbitrary DNA messages via a reusable cell-cell communication channel . 28 2.3 Growth and fluorescence measurements of co-cultures under antibiotic selection . 30 2.4 M13-based cell-cell communication does not occur in absence of the F-plasmid.................................. 31 2.5 Additional DNA messages sent via M13-based cell-cell communication. 34 3.1 Channel capacity and transmission distances di↵er between AHL- and M13- based cell-cell communication systems. 48 3.2 Activation of beta-galactosidase activity in receiver cells via message particle di↵usion alone. 52 3.3 Viable M13 particles are produced during active chemotaxis . 53 3.4 Active chemotaxis enables DNA messaging across centimeter lengths 55 4.1 Using transcriptors to implement three-terminal Boolean integrase logic gates .
Recommended publications
  • Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions
    Overview of Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions Synthetic Biology: DNA Digital Storage, Computation and the Organic Computer Alex Widdel University of Minnesota, Morris 1 / 27 Overview of Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions Outline 1 Overview of Synthetic Biology 2 Background: Systems Architecture and Biology 3 Memory: DNA Storage 4 Building a Biological CPU 5 Conclusions 2 / 27 Overview of Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions What is Synthetic Biology? Biology is viewed as technology. One central goal: construction of a universal bio-computer. A union of biology, computer science, and engineering. The interdisciplinary nature and youth of synthetic biology has led to debate over the term. 3 / 27 Overview of Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions Background: Systems Architecture 4 / 27 Overview of Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions Systems: Von Neumann Architecture Four parts: Memory Input/output device (IO) Control Unit Arithmetic Logic Unit (ALU) I Arithmetic I/O Logic O Memory Control 5 / 27 Overview of Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions Background: Biology 6 / 27 Overview of Synthetic Biology Background: Systems Architecture and Biology Memory: DNA Storage Building a Biological CPU Conclusions Biology: DNA and Protein Synthesis Structure of DNA: DNA can encode bits in a way that is compatible with the way computers store information.
    [Show full text]
  • TRANSCRIPT Applications
    Presidential Commission for the Study of Bioethical Issues TRANSCRIPT Applications J. Craig Venter, Ph.D. Founder and President, J. Craig Venter Institute George Church, Ph.D. Professor of Genetics, Harvard Medical School Kristala L. J. Prather, Ph.D. Assistant Professor, Dept. of Chemical Engineering, Massachu- setts Institute of Technology Meeting 1, Session 2 July 8, 2010 Washington, D.C. Jim Wagner: Could we have our speakers come to the table. And if others could take their chairs, we’ll get under way. Thank you. Commission members, we need you as well, actually. I see them filter- ing up. I saw Nita out there. And there’s Bonnie in the back of the room. So that there is ample time for our speakers to present and for us to ask questions, let’s do get under way. Really, again, appreciate this morning’s conversation and the presenta- tions, helping us to — wow. Helping us to define what is and is not synthetic biology and to understand a little bit more about some of the science involved. This particular session, we are going to focus and we have asked our experts to focus more on applications. We’ll try to use a similar format. Have our speakers present for a brief period. You have the timer in front of you. Make sure after all of you have pre- sented the commission has time to ask questions. And then we’ll try to throw it open — not try to – we will, certainly, throw it open to the public for other questions they may have.
    [Show full text]
  • Driving Diffusion of Scientific Innovation
    Driving Diffusion of Scientific Innovation - The Role of Institutional Entrepreneurship and Open Science in Synthetic Biology Vom Promotionsausschuss der Technischen Universit¨at Hamburg-Harburg zur Erlangung des akademischen Grades Doktor der Wirtschafts- und Sozialwissenschaften (Dr. rer. pol.) genehmigte Dissertation von Giulio Barth aus M¨unster 2018 Advisors: Prof. Dr. C. Ihl, Prof. Dr. M. G. M¨ohrle Institute of Entrepreneurship, TUHH i Gutachter: Prof. Dr. C. Ihl Prof. Dr. M. G. Mohrle¨ Vorsitz: Prof. Dr. C. Luthje¨ Tag der mundlichen¨ Prufung:¨ 14. September 2018 ”Our victory: inevitable; our timing: uncertain.” (Drew Endy, Assistant Professor Stanford University) i Abstract Scientific innovations need to widely diffuse to fully exploit their potential. Prior research investigated levers on the diffusion of scientific innovation with particular interest on institutions, e.g., settings of property rights. As institutional theory lacks in explaining emergence and shaping of institu- tions, the institutional entrepreneur approach faces these limitations. Key actors combine logics from multiple fields and convince their social context of their ideas to legitimate the creation of new institutions and shape an emerging field. This thesis validates theories on institutional entrepreneurs and investigates the end-to process from diffusing a logic to the impact of an established insti- tution on scientific innovations in context of the emerging synthetic biology. The field is expected to introduce the 5th revolution and characterized by the central logic of making biology an engineering discipline. In chapter 4 theories on institutional entrepreneurs driving diffusion of in- stitutional logics to shape an emerging field are validated. To measure the social influence mechanisms, the heterogeneous diffusion model is adapted to the institutional logic.
    [Show full text]
  • CBD/DSI/AHTEG/2018/1/3 12 January 2018
    CBD Distr. GENERAL CBD/SBSTTA/22/INF/3 CBD/DSI/AHTEG/2018/1/3 12 January 2018 ENGLISH ONLY AD HOC TECHNICAL EXPERT GROUP ON SUBSIDIARY BODY ON SCIENTIFIC, DIGITAL SEQUENCE INFORMATION ON TECHNICAL AND TECHNOLOGICAL GENETIC RESOURCES ADVICE Montreal, Canada, 13-16 February 2018 Twenty-second meeting Item 3 of the provisional agenda** Montreal, Canada, 2-7 July 2018 Item 3 of the provisional agenda*** FACT-FINDING AND SCOPING STUDY ON DIGITAL SEQUENCE INFORMATION ON GENETIC RESOURCES IN THE CONTEXT OF THE CONVENTION ON BIOLOGICAL DIVERSITY AND THE NAGOYA PROTOCOL Note by the Executive Secretary 1. In decision XIII/16, paragraph 3(b), the Executive Secretary was requested to commission a fact-finding and scoping study, subject to the availability of funds, to clarify terminology and concepts and to assess the extent and the terms and conditions of the use of digital sequence information on genetic resources in the context of the Convention and the Nagoya Protocol. 2. Accordingly, the Executive Secretary commissioned a research team led by Ms. Sarah Laird of People and Plants International and Ms. Rachel Wynberg of the University of Cape Town, to carry out this study. The study was undertaken with the generous financial support of Canada, the European Union and Switzerland. 3. A draft of the study was made available online for peer review from 8 November to 1 December 2017. 1 The comments received in response have been made available online.2 The research team revised the study in the light of the comments received and the final version is presented below in the form and language in which it was received by the Secretariat of the Convention on Biological Diversity.
    [Show full text]
  • February Newsletter
    Systematic Innovation e-zine Issue 132, March 2013 In this month’s issue: Article – Ten Innovation Trilemmas Article – Holes Not So Funny – Killer Flapjacks Patent of the Month – Temperature Responsive Textiles Best of The Month – Yes To The Mess Conference Report – Hargraves 2013, Sydney Investments – Biological Transistor Generational Cycles – The Wise Prophet Biology – Silver Ant II Short Thort News The Systematic Innovation e-zine is a monthly, subscription only, publication. Each month will feature articles and features aimed at advancing the state of the art in TRIZ and related problem solving methodologies. Our guarantee to the subscriber is that the material featured in the e-zine will not be published elsewhere for a period of at least 6 months after a new issue is released. Readers’ comments and inputs are always welcome. Send them to [email protected] 2013, DLMann, all rights reserved Ten Innovation Trilemmas One day in the not too distant future, we’re hoping to finish the third part in our series on trilemmas. We see the trilemma as the next logical evolution stage to the dilemma (contradiction) story that presently sits at the heart of TRIZ and SI. The basic theory goes something like this: it is relatively easy to resolve a conflict between a pair of system attributes because there is an implied freedom to adversely affect any third attribute that wasn’t part of the problem definition. Solving contradictions helps deliver ‘more ideal’ solutions only in so far as there is an expectation that the two conflicting parameters under consideration are more important than any of the others that might be present in or around the system.
    [Show full text]
  • 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.
    [Show full text]
  • The Biological Microprocessor, Or How to Build a Computer with Biological Parts
    Volume No: 7, Issue: 8, April 2013, e201304003, http://dx.doi.org/10.5936/csbj.201304003 CSBJ The biological microprocessor, or how to build a computer with biological parts Gerd HG Moe-Behrens a,* Abstract: Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system. Introduction Nature and computers are words that used to mean unrelated Other important contributions to systemics are by the Nobel-prize things. However, this view changed, starting in the 1940s, when a winning work of Ilya Prigogine on self-organization and his systems revolutionary scientific paradigm, systemics based on platonic theory concepts in thermodynamics [10]. Furthermore: Mitchell idealistic philosophy, gained popularity [1] [2] [3]. Feigenbaums work on Chaos theory [11]. Contemporary application The roots of philosophical idealism based systemics goes back to finds systems theory in bioscience in fields such as systems biology, Plato. A centerpiece of Plato’s (428/7 to 348/7 BC) work is his and its practical application synthetic biology [12]. The term systems theory of forms, also called theory of ideas [2].
    [Show full text]
  • Systems and Control Theoretic Approaches to Engineer Robust
    Systems and Control Theoretic Approaches to Engineer Robust Biological Systems by Yili Qian Submitted to the Department of Mechanical Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY September 2020 ○c Massachusetts Institute of Technology 2020. All rights reserved. Author................................................................ Department of Mechanical Engineering August 7, 2020 Certified by. Domitilla Del Vecchio Professor of Mechanical Engineering Thesis Supervisor Accepted by . Nicolas G. Hadjiconstantinou Chairman, Department Committee on Graduate Theses 2 Systems and Control Theoretic Approaches to Engineer Robust Biological Systems by Yili Qian Submitted to the Department of Mechanical Engineering on August 7, 2020, in partial fulfillment of the requirements for the degree of Doctor of Philosophy Abstract Synthetic biology is an emerging field of research aimed to engineer biological systems by inserting programmed DNA molecules into living cells. These DNAs encode the production and subsequent interactions of biomolecules that allow the cells to have novel sensing, computing, and actuation capabilities. However, most success stories to date rely heavily on trial and error. This is mainly because genetic systems are context-dependent: the expression level of a synthetic gene often depends not only on its own regulatory inputs, but also on the expression of other supposedly unconnected genes. This lack of modularity leads to unexpected behaviors when multiple genetic subsystems are composed together, making it difficult to engineer complex systems that function predictably and robustly in practice. This thesis characterizes resource competition as a form of context dependence, and presents control theoretic approaches to engineer robust, context-independent gene networks.
    [Show full text]
  • Synthetic Biology in the United States a Brief History of an Emerging Innovation System
    Synthetic Biology in the United States A Brief History of an Emerging Innovation System David Rejeski Global Fellow Wilson Center March 2016 Acknowledgments: I was lucky. I had a front seat during the development of a new field — synthetic biology. Not being a scientist, I had not expected those in the field to open their arms to a foreigner with obvious leanings towards the often maligned and un-scientific field of public policy. But it happened. Dozens of people took the time to talk to me, in person or by phone, about their involvement in the field, their hopes, and their concerns. My special thanks to Paula Olsiewski of the Alfred P. Sloan foundation, who supported the Synthetic Biology Project, myself and my staff, at the Woodrow Wilson Center for eight years. Special thanks also to Drew Endy, who, like a magician pulling rabbits from a hat, seemed to have an endless library of important historical documents and photos he was willing to share. Tom Knight and Peter Carr reviewed early versions of the history section and provided valuable feedback. Thanks to my colleague at the International Institute of Applied Systems Analysis, Leena Ilmola, who integrated me into the proposal for the Finnish Academy, an opportunity I would have certainly missed. This story is my construction and I take responsibility for the interpretation, including any errors or failures of inclusion. Maybe we can make it better. Dave Rejeski Washington, DC The research leading to these results has received funding from the Strategic Research Council at the Academy of Finland under grant agreement no: 293446 - Platform Value Now: Value Capturing in the fast emerging platform ecosystems.
    [Show full text]
  • Can We Make Biology Easy to Engineer?
    FEATURE COMMENTARY Synthetic biology: Can we make biology easy to engineer? Drew Endy This is how I want to frame my remarks today: How do we make biology easy to engineer? How do we enable all of biotechnology to “come true”, not in some notional point in the future, but over a The following is an edited transcription of a plenary talk given by period of 10, 20, or 30 years? This is my starting point. Dr. Drew Endy at the BIO Pacific Rim Summit, Vancouver, British My thoughts on this resolve to two obvious things — we need more Columbia, Canada, 11 September 2008. people working on the problem, and we need better tools. As far as the people requirement goes: I’ve been working on this problem for a little while. One fun project I got caught up in was mak- ing a comic strip trying to explain to teenagers and others how one ’ll start by relating an anecdote from a friend who’s a young might begin to think about programming DNA. In that comic strip, you venture capitalist. He had sought out an old, successful partner have a young boy learning from his elder and who gets excited about at a firm near San Francisco, a fellow who had made a lot of doing something with a bacteria: finding some genetic material inside, I money by investing in biosynthesis companies. My young friend thinking about reprogramming it, trying to brainstorm an idea. asked for some advice, inquiring of the colleague how he decided Now, in this case, the young gentleman would like to make a what investments to make in biosynthesis and industrial biotechnol- bacterial balloon, some sort of self-assembling biofilm that goes off ogy.
    [Show full text]
  • This New Discovery Will Finally Allow Us to Build Biological Computers
    This new discovery will finally allow us to build biological computers The dawn of biological computers is at hand. In a major first for synthetic biology, Stanford engineers have used genetic material to create a biological transistor. Called the "transcriptor," the creation is the final, missing component necessary for the creation of a biological computer that could enable researchers to program functions into living cells. Modern computers rely on three standard functions. One: they must be able to store information. Two: they have to be able to transmit information. Three: they need a basic system of logic – a set of rules that governs how they should function given one or more forms of input. A biological computer would implement all three on a cellular level, using proteins and DNA in place of silicon chips. The first two functions have been demonstrated with cellular materials before. Several labs have now demonstrated the ability to store digital data in DNA,some of them at jaw-dropping densities; and last year, a team led by Stanford bioengineer Drew Endy developed a system for transmitting genetic information between cells. Now, in a study recounted in the latest issue ofScience, Endy's team has developed what it calls a "transcriptor" – the biological equivalent of a digital transistor – and with it a system of logic that can control cellular function. Soon you'll be backing up your hard drive using DNA Think the memory card in your camera is high-capacity? It's got nothing on DNA. With data…Read more io9.com In your standard computer, transistors govern the flow of electricity by playing red light/green light with electrons along a circuit.
    [Show full text]
  • Speaker Biographies
    SPEAKER BIOGRAPHIES George W. Anderson, Jr., PhD, RBP Chair of the Institutional Biosafety Committee at Lawrence Livermore National Labs George W. Anderson, Jr. received his BS and MS degrees in biology from the Florida Institute of Technology and his doctorate in immunology from the Johns Hopkins University. Dr. Anderson’s research experience includes work with rickettsia, hemorrhagic fever viruses and bacterial agents in high containment laboratories. Dr. Anderson’s research interests include animal models for infectious diseases, pathogenesis, and vaccine development and testing. Dr. Anderson was responsible for the set-up and commissioning of a Biosafety Level (BSL) 3/Animal Biosafety Level (ABSL) 3 laboratory in the United States that operated under the Good Laboratory Practices to meet Federal Drug Administration (FDA) requirements. Dr. Anderson has training and experience in Good Manufacturing Practices as well as Good Clinical Practices. Dr. Anderson has been an associate investigator on clinical protocols as well as the principal investigator on numerous animal protocols. Dr. Anderson has been engaged in biological safety assessments at research and production facilities in the former Soviet Union (FSU) as well as biological safety and laboratory training for BSL-2/BSL-3 laboratories in the FSU for the Defense Threat Reduction Agency (DTRA). This work also included responsible for the set-up and operation of a number of BSL-2 laboratories. Dr. Anderson participated in the laboratory oversight of Defense Advanced Research Project Agency (DARPA) funded research projects at a number of high containment laboratories in Russia, which also included facility upgrades and training personnel to meet the US Animal Welfare regulations and US Department of Defense requirements for care and use of animals in biological research as well as biosafety.
    [Show full text]