https://hdl.handle.net/1721.1/18186 2026-04-08T11:08:56Z 2026-04-08T11:08:56Z Kahl, Linda https://hdl.handle.net/1721.1/111012 2025-02-27T21:04:33Z 2017-08-24T00:00:00Z

Draft OpenMTA 11 June 2017, for comment Kahl, Linda The Open Material Transfer Agreement (OpenMTA) is designed to allow researchers to share materials on an open basis while working within the practical realities of technology transfer. Our goal it to help reduce transaction costs, support collaboration among researchers across institutional and international boundaries, promote access to materials for researchers in less privileged institutions and world regions, and provide an avenue for researchers and their institutions to be credited for materials made openly available. The OpenMTA was developed as a collaborative effort led by the BioBricks Foundation and OpenPlant Synthetic Biology Research Centre, with input from researchers, technology transfer professionals, legal experts, social scientists and other stakeholders. Design goals for the OpenMTA include access, attribution, reuse, redistribution, and nondiscrimination, in line with open access and open data principles. A proposed draft of the OpenMTA Master Agreement is herewith made available for public review and comment. Please send comments to Linda Kahl via linda@biobricks.org.

2017-08-24T00:00:00Z Endy, Drew Zoloth, Laurie https://hdl.handle.net/1721.1/102449 2025-02-27T21:05:22Z 2016-05-10T00:00:00Z

Should We Synthesize A Human Genome? Endy, Drew; Zoloth, Laurie Given that human genome synthesis is a technology that could be used to completely redefine the core of what now joins all of humanity together as a species, we argue that discussions of making such capacities real, like today's meeting at Harvard, should not take place without open and advance consideration of whether and under what circumstances it is morally right to proceed.

2016-05-10T00:00:00Z Knight, Thomas Matsudaira, Paul https://hdl.handle.net/1721.1/101009 2025-02-27T21:04:33Z 2016-01-27T00:00:00Z

Cellular Computing, ISAT Summer Study, August 1996 Knight, Thomas; Matsudaira, Paul Create and exploit a novel technology for information processing and manufacturing by controlling processes in living cells. Final slide deck from very early (1996) DARPA ISAT study. This seminal effort helped create foundation for the 2003 DARPA ISAT on synthetic biology and other activities.

2016-01-27T00:00:00Z Endy, Drew https://hdl.handle.net/1721.1/78009 2025-02-27T21:04:33Z 2013-03-27T00:00:00Z

Integrases, Aliens, & Bill Joy Endy, Drew Research presentation on recent and unpublished work before the MIT Synthetic Biology Working Group on 24 September 2012 in MIT Building 56. synthetic biology, engineering genetic data storage, logic, and communication systems using phage and integrases

2013-03-27T00:00:00Z Shetty, Reshma Lizarazo, Meagan Rettberg, Randy Knight, Thomas F., Jr. https://hdl.handle.net/1721.1/65066 2025-02-27T21:05:22Z 2011-05-20T00:00:00Z

Assembly of BioBrick standard biological parts using three antibiotic assembly Shetty, Reshma; Lizarazo, Meagan; Rettberg, Randy; Knight, Thomas F., Jr. An underlying goal of synthetic biology is to make the process of engineering biological systems easier and more reliable. In support of this goal, we developed BioBrick assembly standard 10 to enable the construction of systems from standardized genetic parts. The BioBrick standard underpins the distributed efforts by the synthetic biology research community to develop a collection of more than 6000 standard genetic parts available from the Registry of Standard Biological Parts. Here, we describe the three antibiotic assembly method for physical composition of BioBrick parts and provide step-by-step protocols. The method relies on a combination of positive and negative selection to eliminate time- and labor-intensive steps such as column cleanup and agarose gel purification of DNA during part assembly. This is a revised personal version of the text of the final journal article available via DOI: 10.1016/B978-0-12-385120-8.00013-9

2011-05-20T00:00:00Z Endy, Drew Grewal, David Schultz, Jason Lynch, Jennifer Crews, Lee Fischer, Mark https://hdl.handle.net/1721.1/50999 2025-02-27T21:04:33Z 2010-01-25T16:29:55Z

The BioBrick Public Agreement v1a Endy, Drew; Grewal, David; Schultz, Jason; Lynch, Jennifer; Crews, Lee; Fischer, Mark We present an updated, clean draft for additional public comment of a new legal framework supporting the future of biotechnology. The framework, named here as the BioBrick Public Agreement, is based upon the contribution of promises not to assert any property rights against users of so-contributed standard biological parts. Comments and feedback on this working draft are requested. This draft, BPA v1a, replaces and earlier draft, BPA v1.

2010-01-25T16:29:55Z Fischer, Mark Crews, Lee Lynch, Jennifer Schultz, Jason Grewal, David Endy, Drew https://hdl.handle.net/1721.1/49434 2025-02-27T21:05:22Z 2009-10-18T14:13:45Z

The BioBrick Public Agreement v1 (draft) Fischer, Mark; Crews, Lee; Lynch, Jennifer; Schultz, Jason; Grewal, David; Endy, Drew We present a draft for public comment of a new legal framework supporting the future of biotechnology. The framework, named here as the BioBrick Public Agreement, is based upon the contribution of promises not to assert any property rights against users of so-contributed standard biological parts. Comments and feedback on this working draft are requested.

2009-10-18T14:13:45Z Win, Maung Nyan Smolke, Christina https://hdl.handle.net/1721.1/46338 2025-02-27T21:04:33Z 2009-07-29T06:23:51Z

Raw Data, Win MN, Smolke CD. 2008. Higher-order cellular information processing with synthetic RNA devices. Science. 322: 456-60. DOI: 10.1126/science.1160311 Win, Maung Nyan; Smolke, Christina This supplement provides additional detail on the data analysis methods and the raw data for the RNA devices presented in the published manuscript and supporting online material. The information provided in the current supplement is organized as follows: 1. Gating methods for the raw flow cytometry data 2. Correction methods for nonspecific effects on fluorescence of chemical effectors controlling the RNA devices 3. Selection of standard against which to report device performance 4. Relevance to conclusions published in the Science paper 5. Example calculations 6. Raw data for RNA devices

2009-07-29T06:23:51Z Wadey, Chuck Deese, Isadora Endy, Drew https://hdl.handle.net/1721.1/46337 2025-02-27T21:04:34Z 2005-11-24T00:00:00Z

Adventures in Synthetic Biology Wadey, Chuck; Deese, Isadora; Endy, Drew 3 chapter comic book reflecting the early engineering period of synthetic biology ~2005. Translations freely available by searching online.

2005-11-24T00:00:00Z Smolke, CD Win, MN https://hdl.handle.net/1721.1/45668 2025-02-27T21:04:33Z 2009-06-30T06:48:12Z

Advance Online Correction to PNAS v104 p14283 Smolke, CD; Win, MN We are publishing the following draft correction and clarification to Proc Natl Acad Sci U S A. 2007 Sep 4;104(36):14283-8. We are now working directly with the PNAS Editor to have this correction published by the journal as well. Early publication of correction and clarification to referenced article in PNAS USA.

2009-06-30T06:48:12Z Lazowska, Ed Endy, Drew https://hdl.handle.net/1721.1/43950 2025-02-27T21:04:33Z 2008-12-23T23:49:40Z

The Imperative of Synthetic Biology: A Proposed National Research Initiative Lazowska, Ed; Endy, Drew A 2.5 page report outlining why the United States should launch a strategic national research initiative in synthetic biology

2008-12-23T23:49:40Z Soergel, David Choi, Kirindi Thomson, Ty Doane, Jay George, Brian Morgan-Linial, Ross Brent, Roger Endy, Drew https://hdl.handle.net/1721.1/41867 2025-02-27T21:04:34Z 2008-06-19T13:10:14Z

MONOD, a Collaborative Tool for Manipulating Biological Knowledge Soergel, David; Choi, Kirindi; Thomson, Ty; Doane, Jay; George, Brian; Morgan-Linial, Ross; Brent, Roger; Endy, Drew We describe an open source software tool called MONOD, for Modeler’s Notebook and Datastore, designed to capture and communicate knowledge generated during the process of building models of many-component biological systems. We used MONOD to construct a model of the pheromone response signaling pathway of Saccharomyces cerevisiae. MONOD allowed the accumulation, documentation, and exchange of data, valuations, assumptions, and decisions generated during the model building process. MONOD thus helped preserve a record of the steps taken on the path between from the experimental data to the computable model. We believe that MONOD and its successors may streamline the processes of building models, communicating with other researchers, and managing and manipulating biological knowledge. "Collaborative annotation"-- fine-grained, structured, searchable communication enabled by software tools of this type-- could positively affect the practice of biological research. Research article written in 2004 describing MONOD, an early biological knowledge management system

2008-06-19T13:10:14Z Shetty, Reshma P https://hdl.handle.net/1721.1/41843 2025-02-27T21:04:33Z 2008-05-27T20:53:42Z

Applying engineering principles to the design and construction of transcriptional devices Shetty, Reshma P The aim of this thesis is to consider how fundamental engineering principles might best be applied to the design and construction of engineered biological systems. I begin by applying these principles to a key application area of synthetic biology: metabolic engineering. Abstraction is used to compile a desired system function, reprogramming bacterial odor, to devices with human-defined function, then to biological parts, and finally to genetic sequences. Standardization is used to make the process of engineering a multi-component system easier. I then focus on devices that implement digital information processing through transcriptional regulation in Escherichia coli. For simplicity, I limit the discussion to a particular type of device, a trancriptional inverter, although much of the work applies to other devices as well. First, I discuss basic issues in transcriptional inverter design. Identification of key metrics for evaluating the quality of a static device behavior allows informed device design that optimizes digital performance. Second, I address the issue of ensuring that transcriptional devices work in combination by presenting a framework for developing standards for functional composition. The framework relies on additional measures of device performance, such as error rate and the operational demand the device places on the cellular chassis, in order to proscribe standard device signal thresholds. Third, I develop an experimental, proof-of-principle implementation of a transcriptional inverter based on a synthetic transcription factor derived from a zinc finger DNA binding domain and a leucine zipper dimerization domain. Zinc fingers and leucine zippers offer a potential scalable solution to the challenge of building libraries of transcription-based logic devices for arbitrary information processing in cells. Finally, I extend the principle of physical composition standards from parts and devices to the vectors that propagate those parts and devices. The new vectors support the assembly of biological systems. Taken together, the work helps to advance the transformation of biological system design from an ad hoc, artisanal craft to a more predictable, engineering discipline. Ph.D. thesis (user submitted)

2008-05-27T20:53:42Z Bügl, Hans Danner, John Molinari, Robert Mulligan, John Roth, David Wagner, Ralf Budowle, Bruce Scripp, Robert Smith, Jenifer Steele, Scott Church, George Endy, Drew https://hdl.handle.net/1721.1/40280 2025-02-27T21:04:33Z 2006-12-12T20:16:41Z

A Practical Perspective on DNA Synthesis and Biological Security (12/4/2006 Draft) Bügl, Hans; Danner, John; Molinari, Robert; Mulligan, John; Roth, David; Wagner, Ralf; Budowle, Bruce; Scripp, Robert; Smith, Jenifer; Steele, Scott; Church, George; Endy, Drew Few developments have leapfrogged over predecessor technology as quickly and extensively as synthetic biology. Based on cutting-edge DNA synthesis technology, synthetic biology has already fueled an expansion of opportunities in biological engineering, with advanced capabilities that surpass those provided by traditional recombinant DNA technology. Improvements in synthesis technology are accelerating the pace of innovation in everything from the development of renewable energy to the production of bulk and fine chemicals, from information processing to environmental monitoring, and from agricultural productivity to breakthroughs in human health and medicine. Synthetic biology promises vast improvements to our well-being and our understanding of the living world. Like any powerful technology, DNA synthesis has the potential to be misused. In the wrong hands, the new capabilities enabled by synthetic biology could give rise to both known and unforeseeable threats to our biological safety and security. Current government oversight of the DNA synthesis industry falls short of addressing this unfortunate reality. Here, we introduce and outline a practical plan for developing an effective governance framework for the DNA synthesis industry. A thoughtfully crafted and effectively implemented framework would protect our continued well-being in at least two ways. First, the framework would promote our biological safety and security. Second, the framework would encourage the further responsible development of synthetic biology technologies and their continued, overwhelmingly constructive application. The proposed plan represents the collective views of the International Consortium for Polynucleotide Synthesis, the U.S. Federal Bureau of Investigation, the Chief Executive Officers or Presidents of several of the principal synthetic biology companies, and representatives from academia. Our framework calls for the immediate and systematic implementation of a tiered DNA synthesis screening process. In order to establish accountability at the user level, individuals who place orders for DNA synthesis would be required to identify themselves, their home organization, and all relevant biosafety level information. Next, individual companies would use software tools to check synthesis orders against a set of select agents or sequences to help ensure regulatory compliance and flag synthesis orders for further review. Finally, DNA synthesis and synthetic biology companies would work together, and interface with appropriate government agencies, to rapidly and continually improve the underlying technologies used to screen orders and identify potentially dangerous sequences, as well as develop a clearly defined process to report behavior that falls outside of agreed-upon guidelines. This is the unabridged draft of the manuscript "DNA synthesis and biological security." An abridged form of this manuscript was later published as a peer review commentary in Nature Biotechnology (doi:10.1038/nbt0607-627)

2006-12-12T20:16:41Z Garfinkel, Michele Endy, Drew Epstein, Gerald Friedman, Robert https://hdl.handle.net/1721.1/39658 2025-02-27T21:04:33Z 2007-12-04T17:33:37Z

Working Papers for Synthetic Genomics: Risks and Benefits for Science and Society Garfinkel, Michele; Endy, Drew; Epstein, Gerald; Friedman, Robert The following papers were commissioned for the project Synthetic Genomics: Risks and Benefits for Science and Society. These papers formed the basis of many discussions at project workshops and at a large invitational meeting. The information elicited from these meetings, and from the commissioned papers themselves, formed the basis of our report Synthetic Genomics: Options for Governance (http://dspace.mit.edu/handle/1721.1/39141). The views and opinions expressed in these commissioned papers are those of the authors of the papers and not necessarily those of the authors of the report, or of the institutions at which the authors work. Citation: Working Papers for Synthetic Genomics: Risks and Benefits for Science and Society. Garfinkel MS, Endy D, Epstein GL, Friedman RM, editors. 2007. Compilation of Technical Reports in Support of Sloan Foundation study on DNA synthesis and governance options

2007-12-04T17:33:37Z Sanghvi, Yogesh https://hdl.handle.net/1721.1/39657 2025-02-27T21:05:22Z 2007-12-04T17:33:04Z

A Roadmap to the Assembly of Synthetic DNA from Raw Materials Sanghvi, Yogesh Until recently, the synthesis of DNA has been a tedious, time consuming, expensive and experimentally challenging task. But advances in automated instrumentation and improved chemistry have now made it possible to make any moderate-length sequence of DNA in any quantity. The ease of automated chemical synthesis of DNA has triggered a whole new industry of low-cost DNA suppliers around the globe. The convenience of ordering DNA sequence by mail has opened new avenues in research both in academia and in the healthcare products developed by pharmaceutical companies. At the same time, these advances have made it theoretically possible to synthesize DNA that could be used to do harm. This article aims to describe the first stages of DNA synthesis, from readily available raw materials to medium-sized segments with a desired sequence (oligonucleotides), and examines whether there are points at which such activities could be, for example, monitored or controlled. Some academic and commercial applications of DNA synthesis require the construction of very small quantities of the desired sequence; others involve synthesis at the gram scale or larger. I provide comments on possible intervention points for both types of application. Terms shown in bold are defined in the glossary. Technical Report in support of Sloan Foundation study on DNA synthesis and governance options.

2007-12-04T17:33:04Z Jones, Robert https://hdl.handle.net/1721.1/39656 2025-02-27T21:05:22Z 2007-12-04T17:32:25Z

Sequence Screening Jones, Robert Currently the vast majority of DNA synthesis is performed by service companies or by in-house central facilities in universities and large companies. The DNA synthesis industry provides researchers with custom DNA at such low cost and with such convenience that almost all synthesis work takes place in a relatively small number of facilities. A request for DNA synthesis requires that the customer provide the sequence of the molecule. This creates the opportunity to monitor or screen input sequences for matches to a database of pathogen sequences. Finding a positive match at the time the order was received would allow the vendor to alert the relevant authority and to delay shipment of that DNA. I have written a software package, called BlackWatch, that implements sequence screening. This paper will describe the operation of this system, its current shortcomings and ways that these might be addressed. Technical Report in support of the Sloan Foundation study on DNA synthesis and governance options.

2007-12-04T17:32:25Z Furger, Franco https://hdl.handle.net/1721.1/39655 2025-02-27T21:04:33Z 2007-12-04T17:31:44Z

From Genetically Modified Organisms To Synthetic Biology: Legislation in the European Union, in Six Member Countries and in Switzerland Furger, Franco This report is based on the assumption that in Europe and in its member countries—with the exception perhaps of Switzerland—“synthetic genomics” as a distinct policy domain does not yet exist. This conclusion is based on considerable empirical evidence. Since I was approached last October (2005) by the project leaders I have systematically been monitoring the use of this term in the news media around the (English speaking) world. I have done so in two ways: with the help of several Google search robots and by scanning various Lexis-Nexis news databases using the term “synthetic genomics” and its translation in German, Italian French, Spanish and Dutch. The search has produced very modest results. To date, there has been very few instances of news reporting focused on synthetic genomics. One of them was the founding by Dr. Craig Venter of Synthetic Genomics. Another one has been the launch of the project this review paper has been prepared for. And the third one was the appointment of Dr. Ari Patrinos to President of Synthetic Genomics. In addition, there has been sporadic report on the discipline itself, but rarely in connection with possible novel risks. With regard to Europe, no news stories have been found focusing on synthetic genomics per se or on possible new dangers stemming from its development. Technical report in support of the Sloan Foundation study on DNA synthesis and governance options.

2007-12-04T17:31:44Z Fleming, Diane https://hdl.handle.net/1721.1/39654 2025-02-27T21:04:33Z 2007-12-04T17:30:46Z

Risk Assessment of Synthetic Genomics: A Biosafety and Biosecurity Perspective Fleming, Diane The ability to synthesize molecules found in living organisms is not new for scientists in the fields of biochemistry and molecular biology. However, the “synthetic biology” made possible by the genetic mapping of microorganisms, plants and animals, including the human genome, has taken this area of science into new and relatively uncharted territory. The focus here will be on “synthetic genomics” in which genetic information is synthesized using chemical components and the genomic DNA sequence of an organism. This is how investigators at the State University of New York in Stony Brook, using a published genetic sequence, synthesized a DNA version of poliovirus in 2002. Using an enzyme, reverse transcriptase, they converted the DNA to RNA and were able to grow the virus in a cell-free extract. Their synthesized poliovirus caused paralysis in animals (Cello et al., 2002). One of the authors, Eckard Wimmer, warned: “The world had better be prepared. This shows you can re-create a virus from written information.” From a biosafety and biosecurity perspective the synthesis of etiologic agents is of concern because of the potential to create completely new combinations or chimeric genomes with enhanced virulence, extended host range, and resistance to antimicrobials, antivirals or vaccines. A major concern is that an agent which has been eradicated as a source of infectious disease, such as smallpox, and one which is in the process of being eradicated, such as poliovirus, will never be truly eliminated because the information for their synthesis is readily available in sequence databases. Technical report in support of the Sloan Foundation funded study on DNA synthesis and governance.

2007-12-04T17:30:46Z Collett, Marc https://hdl.handle.net/1721.1/39653 2025-02-27T21:04:33Z 2007-12-04T17:28:43Z

Impact of Synthetic Genomics on the Threat of Bioterrorism with Viral Agents Collett, Marc In 2002, a team of researchers at the State University of New York led by Eckard Wimmer assembled a DNA template for the RNA poliovirus using an internet-available nucleotide sequence and mail order synthetic oligonucleotides. Using a routine laboratory procedure, they then converted the DNA into RNA and produced an infectious, neurovirulent poliovirus capable of paralyzing and killing mice.1 This work demonstrated clearly for the first time the feasibility of chemically synthesizing a pathogen knowing only its nucleotide sequence. Some called the work “irresponsible,” and there was widespread speculation in the press that bioterrorists might use the technology to create more virulent viruses, such as smallpox, from published gene sequences or create novel, more lethal viruses. Wimmer countered that “an evildoer would not use that very tedious method to synthesize a virus. That terrorist would rather use already existing viruses in nature.” 2 Indeed, all viruses, from the common cold to the deadliest, originate in nature, being identified and isolated from infected humans or animals or the virus’s animal or insect vector. However, the rapidly advancing technology of whole genome assembly (“synthetic genomics”) is making the chemical synthesis of viral genomes a much less tedious endeavor.3 This paper will explore the potential impact of synthetic genomics technology on the risks of a bioterrorist attack using viral pathogens. Technical report in support of Sloan Foundation study on DNA synthesis and governance.

2007-12-04T17:28:43Z Baric, Ralph https://hdl.handle.net/1721.1/39652 2025-02-27T21:05:21Z 2007-12-04T17:28:00Z

Synthetic Viral Genomics: Risks and Benefits for Science and Society Baric, Ralph Viral disease outbreaks have long inspired fear in human populations. Highly pathogenic infectious disease has shaped world history, primarily by impacting the outcome of wars and other global conflicts and precipitating human movement. Historic accounts have documented the catastrophic consequences and human suffering associated with widespread viral outbreaks like smallpox virus, yellow fever virus, measles virus, human immunodeficiency virus (HIV), the severe acute respiratory syndrome coronavirus (SARS-CoV), the 1918 influenza virus and others (51). News accounts and film have reinforced the serious threat posed by the emergence of new viral diseases as well as the catastrophic consequences of intentional release of highly pathogenic viruses in human populations. As illustrated by the SARS epidemic and the continuing evolution of the H5N1 avian influenza, global and national infectious disease outbreaks can overwhelm disaster medical response networks and medical facilities, disrupt global economies, and paralyze health and medical services by targeting health care workers and medical staff (21). This review focuses on viruses of humans, animals and plants that are viewed as potential weapons of mass disruption to human populations, critical plant and animal food sources, and national economies; and will consider whether and how the availability of synthetic genomics technologies will change this landscape. Technical Report in support of Sloan Foundation sponsored study on DNA synthesis governance options

2007-12-04T17:28:00Z Garfinkel, Michele Endy, Drew Epstein, Gerald Friedman, Robert https://hdl.handle.net/1721.1/39141 2025-02-27T21:05:22Z 2007-10-17T17:50:40Z

Synthetic Genomics: Options for Governance Garfinkel, Michele; Endy, Drew; Epstein, Gerald; Friedman, Robert Gene and genome synthesis, that is, constructing long stretches of DNA from constituent chemicals, provides scientists with new and unparalleled capabilities both for understanding biology and for using it for beneficial purposes. But along with new capabilities come new risks. Discussion of policy options for regulation of DNA synthesis technology.

2007-10-17T17:50:40Z Vincent Rouilly, Barry Canton Poul Nielsen, Richard Kitney https://hdl.handle.net/1721.1/39120 2025-02-27T21:05:22Z 2007-10-04T21:47:21Z

Registry of BioBricks Models using CellML Vincent Rouilly, Barry Canton; Poul Nielsen, Richard Kitney One of the main goals in Synthetic Biology is to assess the feasibility of building novel biological systems from interchangeable and standardized parts. In order to collect and share parts, a Registry of standardized DNA BioBricks[1] has been established at MIT. BioBricks can be assembled to form devices and systems to operate in living cells. Design of reliable devices and systems would benefit from accurate models of system function. To predict the function of systems built from many parts, we need to have accurate models for the parts and mechanisms to easily compose those part models into a system model. Therefore, in parallel to increasing the number of parts available and characterising them experimentally, a logical extension to the Registry would be to build a Registry of BioBrick models to complement the physical parts. A poster presented at BioSysBio 2007 and at SB3.0

2007-10-04T21:47:21Z Endy, Drew https://hdl.handle.net/1721.1/38455 2025-02-27T21:05:22Z 2007-08-14T22:52:47Z

2003 Synthetic Biology study Endy, Drew Biology is a technology for processing information, materials, and energy. As a technology platform, biological systems provide access to artifacts and processes across a range of scales (e.g., the ribosome is a programmable nanoassembler, a bamboo shoot can grow 12” per day). Biology also forms the basis for human welfare (e.g., modest amounts of memory and logic, implemented as genetically encoded systems,would directly impact biological research and medicine). However, our ability to deploy biology as a technology and to interact intentionally with the living world is now limited; the charge to our study was to begin to specify enabling technologies that, if developed, would provide a general foundation for the engineering of biology and make routine the creation of synthetic biological systems that behave as predicted. This is the final report of the 2002-2003 synthetic biology study, which brought together ~50 researchers to discuss an improved framework for engineering biology. The report itself takes the form of an annotated presentation and was written for a general technical audience. This study built upon a smaller, earlier study led by Tom Knight (unpublished at this time).

2007-08-14T22:52:47Z Shetty, Reshma P. Endy, Drew Knight, Thomas F. Jr https://hdl.handle.net/1721.1/37820 2025-02-27T21:05:22Z 2007-07-17T03:09:54Z

Engineering transcription-based digital logic devices Shetty, Reshma P.; Endy, Drew; Knight, Thomas F. Jr Implementing in vivo information processing is a key challenge in synthetic biology. We describe the construction and characterization of digital transcription-based devices from zinc fingers and leucine zippers. We also present a framework around device design and performance. Poster presented at Synthetic Biology 3.0: The third international conference in synthetic biology.

2007-07-17T03:09:54Z Mallet, Alex https://hdl.handle.net/1721.1/35880 2025-02-27T21:05:22Z 2007-02-06T16:41:27Z

Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation Mallet, Alex I performed computational analyses of various approaches to generating re- engineered versions of the genome of bacteriophage T7. I analyzed a proposed design for a re-engineered genome by examining conservation of T7 genes across related phages, and looking for RNA secondary structure arising from the re-engineered genome that might contribute to unwanted regulation. In addition, I proposed two methods of generating libraries of T7 genomes, and implemented simulations showing that the proposed methods are theoretically feasible. I conclude with thoughts on how to further validate my proposed approaches to genome generation, and suggest a specific high-throughput method of characterizing rebuilt genomes.

2007-02-06T16:41:27Z Kosuri, Sriram https://hdl.handle.net/1721.1/35864 2025-02-27T21:05:22Z 2007-02-02T13:46:50Z

Simulation, Models, and Refactoring of Bacteriophage T7 Kosuri, Sriram Our understanding of why biological systems are designed in a particular way would benefit from biophysically-realistic models that can make accurate predictions on the time-evolution of molecular events given arbitrary arrangements of genetic components. This thesis is focused on constructing such models for gene expression during bacteriophage T7 infection. T7 gene expression is a particularly well suited model system because knowledge of how the phage functions is thought to be relatively complete. My work focuses on two questions in particular. First, can we address deficiencies in past simulations and measurements of bacteriophage T7 to improve models of gene expression? Second, can we design and build refactored surrogates of T7 that are easier to understand and model? To address deficiencies in past simulations and measurements, I developed a new single-molecule, base-pair-resolved gene expression simulator named Tabasco that can faithfully represent mechanisms thought to govern phage gene expression. I used Tabasco to construct a model of T7 gene expression that encodes our mechanistic understanding. The model displayed significant discrepancies from new system-wide measurements of absolute T7 mRNA levels during infection. I fit transcript-specific degradation rates to match the measured RNA levels and as a result corrected discrepancies in protein synthesis rates that confounded previous models. I also developed and used a fitting procedure to the data that let us evaluate assumptions related to promoter strengths, mRNA degradation, and polymerase interactions. To construct surrogates of T7 that are easier to understand and model, I began the process of refactoring the T7 genome to construct an organism that is a more direct representation of the models that we build. In other words, instead of making our models evermore detailed to explain wild-type T7, we started to construct new phage that are more direct representations of our models. The goal of our original design, T7.1, was to physically define, separate, and enable unique manipulation of primary genetic elements. To test our initial design, we replaced the left 11,515 bp of the wild-type genome with 12,179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. I also present a second generation design, T7.2, that extends the original goals of T7.1 by constructing a more direct physical representation of the T7 model.

2007-02-02T13:46:50Z Brent, Roger https://hdl.handle.net/1721.1/34914 2025-02-27T21:04:33Z 2006-11-22T00:00:00Z

In the valley of the shadow of death Brent, Roger During the 20th century, advances in biological understanding sparked a global revolution in biological capability, or RBC. Since that time, the revolution has proceeded in a Moore's-law-like fashion for many decades. One negative consequence of the RBC is that the US now faces a large and growing threat of catastrophic biological attack. To deal with the threat, this article advocates a two-part strategy. First, during the current period of high and growing risk, Period 1, "the Valley of the Shadow of Death", the US should bring into being a patchwork of agile technical capabilities to detect and respond to attacks, and social and normative policies to diminish their risk of occurrence. Second and simultaneously, the US should initiate research whose fruits will eventually deter biological attacks by rendering them "impotent and obsolete". Creation of effective, responsive, and agile Period 1 capabilities will buy time, by lowering the probability of attacks and blunting their impact, until strong technical defenses enabled by longer-term research can become operational in Period 2. Executing the two components of this strategy will be far more costly and complex than is generally contemplated, albeit probably less expensive and difficult than execution of the containment strategy during the Cold War. However, the increased security, human health and felicity, and economic growth that this activity will engender will repay the effort and cost many times over. Entry into Period 2, defense so strong as to deter attack by making it unlikely to have any effect, coincides with the effective elimination of most naturally occurring infectious diseases as a factor in human affairs. But at the moment, the best names for Period 2 seem to be "Partial Victory" or "Basin and Range", in that later trends may shift once again to favor attack. Roger Brent provides a commentary on current and future biological security challenges and possible strategies / approaches.

2006-11-22T00:00:00Z Brent, Roger https://hdl.handle.net/1721.1/34913 2025-02-27T21:04:33Z 2006-11-21T23:56:44Z

Power and responsibility Brent, Roger Peter Parker and Uncle Ben are on my mind. The reason is that is that a month ago I was jumped by Craig Venter. There were TV cameras around. The live audience was an interesting, edgy mix, on the interface between "technology", meaning computer technology, and culture/ media/ journalism; I had just given a closely prepared talk on the history, promises, and perils of biology, 20 minutes from solar system formation to origin of life to photosynthesis to agriculture to Asilomar to now; and I had paid particular attention to the existing threat from remade and lightly engineered viruses, and the various technology-empowered approaches that could contribute to a defense against unpredictable viral and bacterial pathogens. The whole set of ways the defense strategy needs to shift. A commentary from Roger Brent on synthetic biology and its relation to issues of personal responsibility and biological security.

2006-11-21T23:56:44Z Rai, Arti Boyle, James https://hdl.handle.net/1721.1/34274 2025-02-27T21:04:33Z 2006-11-05T00:00:00Z

SYNTHETIC BIOLOGY: CAUGHT BETWEEN PROPERTY RIGHTS, THE PUBLIC DOMAIN, AND THE COMMONS Rai, Arti; Boyle, James Preprint of Rai and Boyle article to be published in PLoS Biology. Pre-published here with permission of author's and PLoS Editor (below). From: RAI@law.duke.edu Subject: Re: quick question Date: November 3, 2006 1:20:42 PM EST To: endy@MIT.EDU Here you go. (You can post it as a draft, forthcoming in PLoS Biology.) EIC is editor in chief. Thanks so much for doing this!

2006-11-05T00:00:00Z Endy, Drew https://hdl.handle.net/1721.1/33001 2025-02-27T21:05:22Z 2006-06-15T14:39:41Z

May 2006 correspondance between James Randerson and Drew Endy Endy, Drew I am a science journalist with the Guardian newspaper in London. We are a national daily paper. I am hoping to put together an investigative piece on how easy (or not) it would be for a would-be terrorist to put together the genome of a nasty organism like anthrax from scratch. For the purposes of the piece I am planning to approach a DNA synthesis company and ask them to make a fragment of a nasty toxin gene. Some companies have safeguards in place to prevent this kind of thing but others do not. (continued)

2006-06-15T14:39:41Z Conferees, SB2.0 https://hdl.handle.net/1721.1/32982 2025-02-27T21:05:22Z 2006-05-30T19:27:35Z

Public Draft of the Declaration of the Second International Meeting on Synthetic Biology Conferees, SB2.0 Draft public declaration from the Second International Meeting on Synthetic Biology (May 20-22, 2006, Berkeley, CA)

2006-05-30T19:27:35Z Anand, Ishan Kosuri, Sriram Endy, Drew https://hdl.handle.net/1721.1/32981 2025-02-27T21:05:22Z 2006-05-26T19:40:06Z

GeneJax: A Prototype CAD tool in support of Genome Refactoring Anand, Ishan; Kosuri, Sriram; Endy, Drew Refactoring is a technique used by computer scientists for improving program design. The Endy Laboratory has adapted this process to make the genomes of biological organisms more amenable to human understanding and design goals. To assist in this endeavor, we implemented GeneJax, a prototype JavaScript web application for the dissection and visualization stages of the genome refactoring process. This paper reviews key genome refactoring concepts and then discusses the features, development history, user-interface, and underlying implementation issues faced during the making of GeneJax. In addition, we provide recommendations for future GeneJax development. This paper may be of interest to engineers of CAD tools for synthetic biology.

2006-05-26T19:40:06Z Phillips, Ira Silver, Pamela https://hdl.handle.net/1721.1/32535 2025-02-27T21:05:22Z 2006-04-20T23:42:53Z

A New Biobrick Assembly Strategy Designed for Facile Protein Engineering Phillips, Ira; Silver, Pamela 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 protein 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.

2006-04-20T23:42:53Z Conboy, Caitlin Braff, Jen Endy, Drew https://hdl.handle.net/1721.1/31335 2025-02-27T21:04:33Z 2006-03-16T02:20:49Z

Definitions and Measures of Performance for Standard Biological Parts Conboy, Caitlin; Braff, Jen; Endy, Drew We are working to enable the engineering of integrated biological systems. Specifically, we would like to be able to build systems using standard parts that, when combined, have reliable and predictable behavior. Here, we define standard characteristics for describing the absolute physical performance of genetic parts that control gene expression. The first characteristic, PoPS, defines the level of transcription as the number of RNA polymerase molecules that pass a point on DNA each second, on a per DNA copy basis (PoPS = Polymerase Per Second; PoPSdc = PoPS per DNA copy). The second characteristic, RiPS, defines the level of translation as the number of ribosome molecules that pass a point on mRNA each second, on a per mRNA copy basis (RiPS = Ribosomes Per Second; RiPSmc = RiPS per mRNA copy). In theory, it should be possible to routinely combine devices that send and receive PoPS and RiPS signals to produce gene expression-based systems whose quantiative behavior is easy to predict. To begin to evaluate the utility of the PoPS and RIPS framework we are characterizing the performance of a simple gene expression device in E. coli growing at steady state under standard operating conditions; we are using a simple ordinary differential equation model to estimate the steady state PoPS and RiPS levels. Poster presented at the 2005 ICSB meeting, held at Harvard Medical School in Boston, MA.

2006-03-16T02:20:49Z Endy, Drew https://hdl.handle.net/1721.1/30595 2025-02-27T21:04:33Z 2003-10-01T00:00:00Z

Strategy for Biological Risk & Security Endy, Drew Why do biological risks exist? Can we develop and implement a strategy for thoughtfully approaching future biological risks? This short, working report provides an abstract introduction to the problem of biological risk and outlines how technical and societal approaches should be combined in order to best address the challenge.

2003-10-01T00:00:00Z Sutton, Samantha Neves, Sara Leung, Lauren Endy, Drew https://hdl.handle.net/1721.1/29804 2025-02-27T21:05:22Z 2005-12-07T23:32:00Z

Engineered Post-Translational Logic (PTL) Sutton, Samantha; Neves, Sara; Leung, Lauren; Endy, Drew Current synthetic biological circuits make use of protein-DNA and RNA-RNA interactions to control gene expression in bacteria. Systems that rely on the regulation of gene expression are relatively slow and unsuitable for many applications. Here, we describe our work to engineer synthetic biological systems in yeast using post-translational modifications of proteins to define system state and control cell function; such systems should have faster performance time and enable a wider range of applications. We have specifically chosen to focus on building phosphorylation-driven protein circuits. We modeled a specific instance of a post-translational circuit using methods such as Lyapunov exponents, and showed that the circuit should behave as desired within a large parameter space. We developed a set of peptide tags that can be used to drive the phosphorylation of a chosen substrate by a desired mitogen-activated protein kinase (MAPK). Each phosphorylation event alters a substrate output activity, such as translocation, degradation, or other binding event. These tags were developed using the Phospholocator – a construct whose phosphorylation-mediated translocation is controlled by MAPK activity. Specifically, MAPK phosphorylation of the Phospholocator nuclear localization sequence (NLS) controls recognition of the NLS by cellular import machinery. The Phospholocator serves three purposes: to determine the docking sites of MAPKs of interest, to measure the in vivo activity of such MAP Kinases, and to serve as a first set of post-translational logic parts. Currently, we have built a version of the Phospholocator that is targeted by Cdc28; our next step is to build Fus3-, p38-, and Hog1-activated instances. This poster was presented at the 2005 International Conference on Systems Biology, October 21, 2005.

2005-12-07T23:32:00Z Thomson, Ty M Endy, Drew https://hdl.handle.net/1721.1/29803 2025-02-27T21:05:22Z 2005-10-21T00:00:00Z

Rapid Characterization of Cellular Pathways Using Time-Varying Signals Thomson, Ty M; Endy, Drew The use of traditional tools for the discovery and characterization of biological systems has resulted in a wealth of biological knowledge. Unfortunately, only a small portion of the biological world is well-understood to date, and the study of the rest remains a daunting task. This work involves using time-varying stimuli in order to more rapidly interrogate and characterize signaling pathways. The time-dependent stimulation of a signaling pathway can be used in conjunction with a model of the pathway to efficiently evaluate and test hypotheses. We are developing this technology using the yeast pheromone signal transduction pathway as a model system. The time-varying stimuli will be applied to the yeast cells via a novel microfluidic device, and the pathway output will be measured via various fluorescent reporters. The output of the pathway can then be compared to the output from a computational model of the pathway in order to test hypotheses and constrain our knowledge of the pathway. Initial work shows that a computational model can be used to identify stimuli time-courses that increase the parameter sensitivity, meaning that corresponding experiments could potentially be much more informative. Poster presented at the 2005 ICSB meeting, held at Harvard Medical School in Boston, MA.

2005-10-21T00:00:00Z Canton, Bartholomew Endy, Drew https://hdl.handle.net/1721.1/29802 2025-02-27T21:05:21Z 2005-10-21T00:00:00Z

Engineering the Interface Between Cellular Chassis and Integrated Biological Systems Canton, Bartholomew; Endy, Drew The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help enable the future engineering of biological systems, we are studying and optimizing the interface between an engineered biological system and its host cell or ``chassis''. Other engineering disciplines use modularity to make interacting systems interchangeable and to insulate one system from another. Engineered biological systems are more likely to work as predicted if system function is decoupled from the state of the host cell. Also, specifying and standardizing the interfaces between a system and the chassis will allow systems to be engineered independent of chassis and allow systems to be interchanged between different chassis. To this end, we have assembled orthogonal transcription and translation systems employing dedicated machinery, independent from the equivalent host cell machinery. In parallel, we are developing test systems and metrics to measure the interactions between an engineered system and its chassis. Lastly, we are exploring methods to``port'' a simple engineered system from a prokaryotic to a eukaryotic organism so that the system can function in both organisms. Poster presented at the 2005 ICSB meeting, held at Harvard Medical School in Boston, MA.

2005-10-21T00:00:00Z Shetty, Reshma P. Knight, Thomas F. Jr https://hdl.handle.net/1721.1/29800 2025-02-27T21:05:22Z 2005-10-20T00:00:00Z

Engineering transcription-based digital logic devices Shetty, Reshma P.; Knight, Thomas F. Jr The goal of Synthetic Biology is to engineer systems from biological parts. One class of systems are those whose purpose is to process information. My work seeks to build transcription-based devices for use in combinational digital logic. Preliminary characterization experiments show that existing devices fall short of desired device behavior. I propose to develop a novel implementation of transcription-based logic by designing synthetic transcription factors from well-characterized DNA binding and dimerization domains. Initial modeling work serves to inform design of these devices. Poster presented at the 2005 ICSB meeting, held at Harvard Medical School in Boston, MA.

2005-10-20T00:00:00Z Kelly, Jason Michener, Josh Endy, Drew https://hdl.handle.net/1721.1/29799 2025-02-27T21:04:33Z 2005-10-20T00:00:00Z

Design and Evolution of Engineered Biological Systems Kelly, Jason; Michener, Josh; Endy, Drew To date, engineered biological systems have been constructed via a variety of ad hoc approaches. The resulting systems should be thought of as pieces of art. We are interested in exploring how existing forward engineering approaches might be combined with directed evolution to make routine the construction of engineered biological systems. We have specified a procedure for construction of biological systems via screening of subcomponent libraries and rational re-assembly. We have begun development of tools to enable this approach, including a FACS-based screening system to rapidly measure the input/output function of a genetic circuit. Additionally, we have designed a microfluidic system that enables more sophisticated screening and selection functions. Specifically, a microfluidic chemostat integrated with a cell sorter (i.e., a sortostat). This microscope-based system will enable us to evaluate whether or not more complicated screens and selections will be of practical use in service of evolving engineered biological systems. Poster presented at the 2005 ICSB meeting, held at Harvard Medical School in Boston, MA.

2005-10-20T00:00:00Z Arkin, Adam P Endy, Drew https://hdl.handle.net/1721.1/29794 2025-02-27T21:05:22Z 1999-10-07T00:00:00Z

A Standard Parts List for Biological Circuitry Arkin, Adam P; Endy, Drew One of the hallmarks of biochemical circuits found in nature is analog, asymmetric, asynchronous design. That is, there is little standardization of parts, e.g. all the promoters have different strengths and kinetics, transcription factors are designed to have different effects at different loci, and each enzymatic reaction has its own idiosyncratic mechanism and rates. In addition, all of the heterogeneous circuit elements are executing their functions concurrently and asynchronously. Biological circuits are seemingly designed to deal with the fluctuating delays, different time-scales and energy requirements associated with each component process of the overall network. These factors also make design of novel biochemical circuitry from existent parts difficult to achieve. Without standardization, the qualitative design methods used in other engineering fields are simply inapplicable. The de facto design methodology for biological circuitry is natural selection. Rational design of biological systems by humans has remained restricted to rather small or hit-or-miss efforts and has often relied on the ability to "select" for biochemical parts that fulfill some criteria. In practice however biological-designers are rare, and solutions are usually realized through an expensive stepwise trial and error approach or through mutation and selection. Furthermore, these otherwise practical approaches are limited in terms of the problems they can solve. We believe that implementation of designed biological circuitry is limited by issues of practice.

1999-10-07T00:00:00Z Knight, Thomas F. Sussman, Gerald Jay https://hdl.handle.net/1721.1/29793 2025-02-27T21:05:22Z 1998-01-05T00:00:00Z

Cellular Gate Technology Knight, Thomas F.; Sussman, Gerald Jay We propose a biochemically plausible mechanism for constructing digital logic signals and gates of significant complexity within living cells. These mechanisms rely largely on co-opting existing biochemical machinery and binding proteins found naturally within the cell, replacing difficult protein engineering problems with more straightforward engineering of novel combinations of gene control sequences and gene coding regions. The resulting logic technology, although slow, allows us to engineer the chemical behavior of cells for use as sensors and effectors. One promising use of such technology is the control of fabrication processes at the molecular scale.

1998-01-05T00:00:00Z Endy, Drew https://hdl.handle.net/1721.1/29183 2025-02-27T21:04:33Z 2005-09-29T17:09:25Z

iGEM 2005 Invitation Supplement Endy, Drew This document provides background material in support of the 2005 intercollegiate Genetically Engineered Machine Competition (aka iGEM). Herein, you can read quick summaries of earlier competitions and courses, obtain a general view of the work from both a technical and educational perspective, and read about our current understanding of how to engineering biology (e.g., PoPS, abstraction, and so on).

2005-09-29T17:09:25Z Chan, Leon Kosuri, Sriram Endy, Drew https://hdl.handle.net/1721.1/27501 2025-02-27T21:05:22Z 2004-10-01T00:00:00Z

Refactoring Bacteriophage T7 (2004 version) Chan, Leon; Kosuri, Sriram; Endy, Drew Natural biological systems are selected by evolution to continue to exist. Evolution might give rise to complicated systems that are difficult to discover, measure, model, and direct. Here, we redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered alternative that is easier to study, understand, and extend. We replaced the left 11,515 base pairs of the wild-type genome with 12,179 base pairs of redesigned DNA. The resulting chimeric genome encodes a viable bacteriophage that maintains key features of the original while being simpler to model and easier to manipulate. This document is an prior version of the manuscript 'Refactoring Bacteriophage T7' that is now published in Nature/EMBO Molecular Systems Biology (DOI: 10.1038/msb4100025). This DSpace manuscript is more concise but provides less context than the MSB manuscript.

2004-10-01T00:00:00Z Weiss, Ron, 1970- https://hdl.handle.net/1721.1/8228 2022-01-13T07:54:29Z 2001-01-01T00:00:00Z

Cellular computation and communications using engineered genetic regulatory networks Weiss, Ron, 1970- In this thesis, I present an engineering discipline for obtaining complex, predictable, and reliable cell behaviors by embedding biochemical logic circuits and programmed intercellular communications into cells. To accomplish this goal, I provide a well-characterized component library, a biocircuit design methodology, and software design tools. I have built and characterized an initial cellular gate library with biochemical gates that implement the NOT, IMPLIES, and AND logic functions in E. coli cells. The logic gates perform computation using DNA-binding proteins, small molecules that interact with these proteins, and segments of DNA that regulate the expression of the proteins. I introduce genetic process engineering, a methodology for modifying the DNA encoding of existing genetic elements to achieve the desired input/output behavior for constructing reliable circuits of significant complexity. I demonstrate the feasibility of digital computation in cells by building several operational in-vivo digital logic circuits, each composed of three gates that have been optimized by genetic process engineering.; (cont.) I also demonstrate engineered intercellular communications with programmed enzymatic activity and chemical diffusions to carry messages, using DNA from the Vibrio fischeri lux operon. The programmed communications is essential for obtaining coordinated behavior from cell aggregates. In addition to the above experimental contributions, I have developed BioSPICE, a prototype software tool for biocircuit design. It supports both static and dynamic simulations and analysis of single cell environments and small cell aggregates. Finally, I present the Microbial Colony Language (MCL), a model for programming cell aggregates. The language is expressive enough for interesting applications, yet relies on simple primitives that can be mapped to the engineered biological processes described above. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.; Includes bibliographical references (p. 130-138).

2001-01-01T00:00:00Z Kelly, Jason https://hdl.handle.net/1721.1/21169 2025-02-27T21:04:33Z 2005-08-11T03:54:14Z

Design and Evolution of Engineered Biological Systems Kelly, Jason To date, engineered biological systems have been constructed via a variety of ad hoc approaches. The resulting systems should be thought of as pieces of art. Here, I propose to explore how existing forward engineering approaches might be combined with evolution to make routine the construction of engineered biological systems. I will specify a procedure for construction of biological systems via screening of subcomponent libraries and rational re-assembly. I will develop tools to enable this approach including a high-throughput screening system to measure the input/output function of an arbitrary genetic device. I will apply this approach to construct a collection of ring oscillators and bi-stable switches. Furthermore, I anticipate that performance of these devices will decay over time due to spontaneous errors in replication of the genetic information encoding the systems. As an engineer, I would like to be able to design systems with behavior that is predictable in the face of mutation and selection. I will explore mechanisms for increasing or decreasing the susceptibility of engineered biological systems to loss of function as a result of mutation.

2005-08-11T03:54:14Z Knight, Thomas https://hdl.handle.net/1721.1/21168 2025-02-27T21:04:34Z 2003-01-01T00:00:00Z

Idempotent Vector Design for Standard Assembly of Biobricks Knight, Thomas The lack of standardization in assembly techniques for DNA sequences forces each DNA assembly reaction to be both an experimental tool for addressing the current research topic, and an experiment in and of itself. One of our goals is to replace this ad hoc experimental design with a set of standard and reliable engineering mechanisms to remove much of the tedium and surprise during assembly of genetic components into larger systems.

2003-01-01T00:00:00Z Knight, Thomas https://hdl.handle.net/1721.1/21167 2025-02-27T21:05:22Z 2002-05-22T00:00:00Z

DARPA BioComp Plasmid Distribution 1.00 of Standard Biobrick Components Knight, Thomas This distribution consists of 300 ng aliquots of plasmid DNA for each of twelve components and compound constructs utilizing our idempotent assembly strategy. The dried DNA should be stable at room temperature for many weeks, but long term storage at -20 or -80 in the resealable foil pouch with desiccant is recommended. This document and much additional information, protocols, and detailed sequences is or will be available from the site http://ks.ai.mit.edu

2002-05-22T00:00:00Z Canton, Bartholomew https://hdl.handle.net/1721.1/19813 2025-02-27T21:05:22Z 2005-08-08T18:36:16Z

Engineering the Interface Between Cellular Chassis and Integrated Biological Systems Canton, Bartholomew The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help enable the future engineering of biological systems, I will study and optimize the interface between an engineered biological system and its host cell or “chassis”. Other engineering disciplines use modularity to make interacting systems interchangeable and to insulate one system from another. Engineered biological systems are more likely to work as predicted if system function is decoupled from the state of the host cell. Also, specifying and standardizing the interfaces between a system and the chassis will allow systems to be engineered independent of chassis and allow systems to be interchanged between different chassis. To this end, I will build dedicated transcription and translation systems, independent from the equivalent host cell systems. In parallel, I will develop test systems and metrics to measure the interactions between an engineered system and its chassis. Lastly, I will explore methods to “port” a simple engineered system from a prokaryotic to a eukaryotic organism so that the system can function in both organisms.

2005-08-08T18:36:16Z Che, Austin, 1979- https://hdl.handle.net/1721.1/16618 2022-01-13T07:54:29Z 2004-01-01T00:00:00Z

Fluorescence assay for polymerase arrival rates Che, Austin, 1979- To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate. Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2004.; Includes bibliographical references (p. 87-100).; This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.

2004-01-01T00:00:00Z Goler, Jonathan A. https://hdl.handle.net/1721.1/7115 2025-02-27T21:04:34Z 2004-05-28T00:00:00Z

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems Goler, Jonathan A. The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.

2004-05-28T00:00:00Z Che, Austin https://hdl.handle.net/1721.1/7112 2025-02-27T21:05:22Z 2003-08-31T00:00:00Z

Fluorescence Assay for Polymerase Arrival Rates Che, Austin To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate.

2003-08-31T00:00:00Z Abelson, Harold Allen, Don Coore, Daniel Hanson, Chris Homsy, George Knight, Thomas F., Jr. Nagpal, Radhika Rauch, Erik Sussman, Gerald Jay Weiss, Ron https://hdl.handle.net/1721.1/5929 2025-02-27T21:05:22Z 1999-08-29T00:00:00Z

Amorphous Computing Abelson, Harold; Allen, Don; Coore, Daniel; Hanson, Chris; Homsy, George; Knight, Thomas F., Jr.; Nagpal, Radhika; Rauch, Erik; Sussman, Gerald Jay; Weiss, Ron Amorphous computing is the development of organizational principles and programming languages for obtaining coherent behaviors from the cooperation of myriads of unreliable parts that are interconnected in unknown, irregular, and time-varying ways. The impetus for amorphous computing comes from developments in microfabrication and fundamental biology, each of which is the basis of a kernel technology that makes it possible to build or grow huge numbers of almost-identical information-processing units at almost no cost. This paper sets out a research agenda for realizing the potential of amorphous computing and surveys some initial progress, both in programming and in fabrication. We describe some approaches to programming amorphous systems, which are inspired by metaphors from biology and physics. We also present the basic ideas of cellular computing, an approach to constructing digital-logic circuits within living cells by representing logic levels by concentrations DNA-binding proteins.

1999-08-29T00:00:00Z Che, Austin https://hdl.handle.net/1721.1/39832 2025-02-27T21:04:33Z 2004-06-09T23:50:11Z

BioBricks++: Simplifying Assembly of Standard DNA Components Che, Austin Construction of complex biological systems can require assembling many modules together. However, existing assembly schemes are lacking in generality, ease of use, or power to perform some desirable operations. Currently, biological modules are most easily specified and manipulated as DNA sequences. A general system, called BioBricks++, for assembling and manipulating DNA modules is proposed. BioBricks++ was inspired by the BioBricks assembly scheme but provides for more possible module operations. BioBricks++ uses commercially available restriction enzymes and standard biological techniques for assembling modules. The key to the method is in the specification of the standard DNA module. Modules are packaged with a standard prefix and suffix DNA sequence containing several restriction enzyme sites, which are used for different module operations. The following operations can be performed on all BioBricks++ modules. The most fundamental operation is the arbitrary assembly of any two modules. In addition, the assembly of the two modules can be made seamless, with no extra intervening sequence inserted between the modules. Modules can also be easily reversed with no extra bases added during the operation. Another useful capability is being able to remove bases from either end of a module, allowing for operations such as protein fusions or addition of tags.

2004-06-09T23:50:11Z