Realizing the Potential of Synthetic Biology
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Informa Tics for Genome Analysis, Biomarkers,And Ta Rget Disco Very
Register by March 14 and Save up to $200! Final Agenda Cambridge Healthtech Institute’s Sixth Annual April 28 – 30, 2008 • World Trade Center • Boston, MA Keynote Presentations by: Concurrent Tracks: • Informatics and IT Infrastructure & Operations • Informatics for Genome Analysis, Biomarkers, and Target Discovery Linda Avey co-Founder • Predictive and in silico Science 23andMe, Inc. • eChemistry Solutions • Clinical and Medical Informatics Joshua Boger, Ph.D. President & Chief Executive Offi cer Keynote Panel: A Must-Attend Event for the Life Vertex Pharmaceuticals, Inc. The Future of Personal Genomics: A special plenary panel discussion featuring George Church,Science Ph.D., Harvard IT Medical& Informatics School Community Dietrich Stephan, Ph.D., Navigenics John Reynders, Ph.D. Jeffrey M. Drazen, M.D., New England Journal of Medicine/Harvard Vice President & Chief Information Offi cer Medical School Johnson & Johnson, Pharma R&D Fred D. Ledley, M.D., Bentley College ...and more 2008 Benjamin Franklin Award EEventvent FFeatures:eatures: presented by Bioinformatics.org • Access All Five Tracks for One Price • Network with 1,500+ Delegates Platinum Sponsors: • Hear 85+ Technology and Scientifi c Presentations • Choose from Four Pre-conference Workshops, the Oracle Life Sciences and Healthcare User Group Meeting, and Symyx Software Symposium 2008 Gold Sponsors: • Attend Bio-IT World’s Best Practices Awards NEW Bronze Sponsor: • Connect with Attendees Using CHI’s Intro-Net Corporate Support: • Participate in the Poster Competition • See the Winners of the following 2008 Awards: Offi cial Publication: Benjamin Franklin Best of Show Lead Sponsoring Publications: Best Practices • View Who’s Who & What’s New in the Exhibit Hall • And Much More! www.Bio-ITWorldExpo.com Organized & Managed by: Cambridge Healthtech Institute 250 First Avenue, Suite 300, Needham, MA 02494 • Phone: 781-972-5400 • Fax: 781-972-5425 • Toll-free in the U.S. -
Design Principles of Genetic Circuits Justin Bois Caltech Spring, 2018
BE 150: Design Principles of Genetic Circuits Justin Bois Caltech Spring, 2018 This document was prepared at Caltech with financial support from the Donna and Benjamin M. Rosen Bioengineering Center. © 2018 Justin Bois. All rights reserved except for figures taken from literature sources. 8 The repressilator Today we will talk about an oscillating genetic circuit developed by Elowitz and Leibler and published in 2000, called the repressilator. As we work through this example, we will learn a valuable technique for analyzing dynamical systems, including many of those we encounter in systems biology, linear stability analysis. 8.1 Design of the repressilator The repressilator consists of three repressors on a plasmid, as shown in Fig. 7. They are TetR, λ cI, and LacI. For our analysis here, the names are unimportant, and we will call them repressor 1, 2, and 3. Repressorletters 1 represses to production nature of repressor 2, which in turn represses production of repressor 3. Finally, repressor 3 represses production or repressor 1, completing the loop. a Repressilator Reporter 30 8C. At least 100 individual cell lineages in each of three micro- colonies were tracked manually, and their ¯uorescence intensity was P lac01 L quanti®ed. ampR tetR-lite The timecourse of the ¯uorescence of one such cell is shown in PLtet01 Fig. 2. Temporal oscillations (in this case superimposed on an kanR overall increase in ¯uorescence) occur with a period of around Tet R Tet R pSC101 gfp-aav 150 minutes, roughly threefold longer than the typical cell-division λP origin R time. The amplitude of oscillations is large compared with baseline λ cI LacI GFP levels of GFP ¯uorescence. -
The Plant Circadian Clock and Chromatin Modifications
G C A T T A C G G C A T genes Review The Plant Circadian Clock and Chromatin Modifications Ping Yang 1,2, Jianhao Wang 1,2, Fu-Yu Huang 3 , Songguang Yang 1,* and Keqiang Wu 3,* 1 Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; [email protected] (P.Y.); [email protected] (J.W.) 2 University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China 3 Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan; [email protected] * Correspondence: [email protected] (S.Y.); [email protected] (K.W.) Received: 3 October 2018; Accepted: 5 November 2018; Published: 20 November 2018 Abstract: The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized transcriptional feedback regulation of several clock components, additional regulatory mechanisms, such as alternative splicing, regulation of protein stability, and chromatin modifications are beginning to emerge. In this review, we discuss recent findings in the regulation of the circadian clock function in Arabidopsis thaliana. The involvement of chromatin modifications in the regulation of the core circadian clock genes is also discussed. Keywords: circadian clock; oscillators; transcriptional and post-transcriptional regulation; chromatin modifications; Arabidopsis 1. Introduction Plants, like animals, exhibit rhythmic biological activity, with a periodicity of 24 h. -
Research Laboratory of Electronics
Research Laboratory of Electronics The Research Laboratory of Electronics (RLE) at MIT is a vibrant intellectual community and was one of the Institute’s earliest modern interdepartmental academic research centers. RLE research encompasses both basic and applied science and engineering in an extensive range of natural and man-made phenomena. Integral to RLE’s efforts is the furthering of scientific understanding and leading innovation to provide great service to society. The lab’s research spans the fundamentals of quantum physics and information theory to synthetic biology and power electronics and extends to novel engineering applications, including those that produce significant advances in communication systems or enable remote sensing from aircraft and spacecraft, and the development of new biomaterials and innovations in diagnostics and treatment of human diseases. RLE was founded in 1946 following the groundbreaking research that led to the development of ultra-high-frequency radar, a technology that changed the course of World War II. It was home to some of the great discoveries made in the 20th century at MIT. Cognizant of its rich history and focus on maintaining its position as MIT’s leading interdisciplinary research organization, RLE fosters a stimulating and supportive environment for innovative research and impact. What distinguishes RLE today from all other entities at MIT is its breadth of intellectual pursuit and diversity of research themes. The lab supports its researchers by providing a wide array of services spanning financial and human resources (HR), information technology, and renovations. It is fiscally independent and maintains a high level of loyalty from its principal investigators (PIs) and staff. -
The Plant Circadian Oscillator
biology Review The Plant Circadian Oscillator C. Robertson McClung Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA; [email protected]; Tel.: +1-603-646-3940 Received: 19 December 2018; Accepted: 9 March 2019; Published: 12 March 2019 Abstract: It has been nearly 300 years since the first scientific demonstration of a self-sustaining circadian clock in plants. It has become clear that plants are richly rhythmic, and many aspects of plant biology, including photosynthetic light harvesting and carbon assimilation, resistance to abiotic stresses, pathogens, and pests, photoperiodic flower induction, petal movement, and floral fragrance emission, exhibit circadian rhythmicity in one or more plant species. Much experimental effort, primarily, but not exclusively in Arabidopsis thaliana, has been expended to characterize and understand the plant circadian oscillator, which has been revealed to be a highly complex network of interlocked transcriptional feedback loops. In addition, the plant circadian oscillator has employed a panoply of post-transcriptional regulatory mechanisms, including alternative splicing, adjustable rates of translation, and regulated protein activity and stability. This review focuses on our present understanding of the regulatory network that comprises the plant circadian oscillator. The complexity of this oscillatory network facilitates the maintenance of robust rhythmicity in response to environmental extremes and permits nuanced control of multiple clock outputs. Consistent with this view, the clock is emerging as a target of domestication and presents multiple targets for targeted breeding to improve crop performance. Keywords: circadian rhythms; circadian clock; transcriptional feedback loops; plant circadian clock; posttranscriptional; posttranslational; alternative splicing; protein stability 1. Introduction This special issue celebrates the 2017 Nobel Prize in Physiology awarded to Jeff Hall, Michael Rosbash, and Mike Young. -
View Publication
Downloaded from rsif.royalsocietypublishing.org on 20 April 2009 Towards programming languages for genetic engineering of living cells Michael Pedersen and Andrew Phillips J. R. Soc. Interface published online 15 April 2009 doi: 10.1098/rsif.2008.0516.focus Supplementary data "Data Supplement" http://rsif.royalsocietypublishing.org/content/suppl/2009/04/15/rsif.2008.0516.focus.D C1.html References This article cites 19 articles, 7 of which can be accessed free http://rsif.royalsocietypublishing.org/content/early/2009/04/14/rsif.2008.0516.focus.full. html#ref-list-1 P<P Published online 15 April 2009 in advance of the print journal. Subject collections Articles on similar topics can be found in the following collections synthetic biology (9 articles) Email alerting service Receive free email alerts when new articles cite this article - sign up in the box at the top right-hand corner of the article or click here Advance online articles have been peer reviewed and accepted for publication but have not yet appeared in the paper journal (edited, typeset versions may be posted when available prior to final publication). Advance online articles are citable and establish publication priority; they are indexed by PubMed from initial publication. Citations to Advance online articles must include the digital object identifier (DOIs) and date of initial publication. To subscribe to J. R. Soc. Interface go to: http://rsif.royalsocietypublishing.org/subscriptions This journal is © 2009 The Royal Society Downloaded from rsif.royalsocietypublishing.org on 20 April 2009 J. R. Soc. Interface doi:10.1098/rsif.2008.0516.focus Published online Towards programming languages for genetic engineering of living cells Michael Pedersen1,2 and Andrew Phillips1,* 1Microsoft Research Cambridge, Cambridge CB3 0FB, UK 2LFCS, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK Synthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. -
Building and Understanding Repressilators and Synchrony
BUILDING AND UNDERSTANDING: REPRESSILATORS AND SYNCHRONY THREE CELLS IN A BUBBLE BATH Brenton Munson Clara Posner Jonathan Pekar October 23, 2016 UNIVERSITY OF CALIFORNIA SAN DIEGO DEPARTMENT OF BIOENGINNERING BENG 221 PROJECT i Contents ii CONTENTS 1 Introduction 1 1.1 Problem Statement . .2 2 Methods 2 2.1 Simplifying and Parameterization . .2 2.2 Numerical Method . .5 3 Results and Discussion6 References 14 4 Appendix 16 4.1 Code............................................. 16 4.1.1 Single Cell Repressilator Model . 16 4.1.2 Repressilator Model with Drug Sensing . 23 LISTOFFIGURES Figure 1 Repressilator System . .2 Figure 2 Repressilator with Drug Sensing . .4 Figure 3 Multicell Environment . .5 Figure 4 Starting a Repressilator . .7 Figure 5 Repressilator at Steady State . .8 Figure 6 Model Sensitivity to Transcription Rate . .8 Figure 7 Model Sensitivity to Translation Rate . .9 Figure 8 Model Sensitivity to Protein Degradation Rates . 10 Figure 9 Model Sensitivity to Hill Parameters . 11 Figure 10 Controlling a Repressilator with an External Stimulus . 11 Figure 11 Cell Synchronization . 12 Figure 12 Cell Synchronization . 12 INTRODUCTION 1 1 INTRODUCTION The demands placed upon modern medicine are rapidly driving scientists and engineers to inves- tigate the mechanisms of disease and biological function to ever-increasing complexity. Much of this frontier lies in modeling not only the outcome of individual genetic perturbations but also how the networks of genetic interactions coordinate cellular- and tissue-level phenotypes [1]. While progress has been made in describing living systems, these networks often become too complex and cumbersome to interrogate with the current tools of bioinformatics [2,3]. As such, the problem is often broken down into more discrete subunits, with which they can be modeled, perturbed, and hopefully understood on a more functional level [4]. -
SYNTHETIC BIOLOGY and ITS POTENTIAL IMPLICATIONS for BIOTRADE and ACCESS and BENEFIT-SHARING ©2019, United Nations Conference on Trade and Development
UNITED NATIONS CONFERENCE ON TRADE AND DEVELOPMENT SYNTHETIC BIOLOGY AND ITS POTENTIAL IMPLICATIONS FOR BIOTRADE AND ACCESS AND BENEFIT-SHARING ©2019, United Nations Conference on Trade and Development. All rights reserved. The trends, figures and views expressed in this publication are those of UNCTAD and do not necessarily represent the views of its member States. The designations employed and the presentation of material on any map in this work do not imply the expression of any opinion whatsoever on the part of the United Nations concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. This study can be freely cited provided appropriate acknowledgment is given to UNCTAD. For further information on UNCTAD’s BioTrade Initiative please consult the following website: http://www.unctad. org/biotrade or contact us at: [email protected] This publication has not been formally edited. UNCTAD/DITC/TED/INF/2019/12 AND ITS POTENTIAL IMPLICATIONS FOR BIOTRADE AND ACCESS AND BENEFIT-SHARING iii Contents Acknowledgements ................................................................................................................................iv Abbreviations ...........................................................................................................................................v EXECUTIVE SUMMARY ............................................................................................. vi SECTION 1: INTRODUCTION TO BIOTRADE, -
Synthetic Biology Approaches in Cancer Immunotherapy, Genetic
Integrative Biology REVIEW ARTICLE Synthetic biology approaches in cancer immunotherapy, genetic network engineering, Downloaded from https://academic.oup.com/ib/article-abstract/8/4/504/5163774 by Columbia University user on 27 March 2020 Cite this: Integr. Biol., 2016, 8, 504 and genome editing Deboki Chakravarti,* Jang Hwan Cho,† Benjamin H. Weinberg,† Nicole M. Wong† and Wilson W. Wong* Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad Received 24th December 2015, and vital role that the synthetic biology approach has played in applying fundamental biological Accepted 31st March 2016 discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields DOI: 10.1039/c5ib00325c of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when www.rsc.org/ibiology developing systems around living cells. Insight, innovation, integration Investigations into cells and their contents have provided evolving insight into the emergence of complex behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending basic discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. -
2018 Semiconductor Synthetic Biology Roadmap
2018 Semiconductor Synthetic Biology Roadmap Editor’s Note Victor Zhirnov Chief Scientist at Semiconductor I am delighted to introduce the 1st Edition of the SemiSynBio Roadmap, a collective Research Corporation and Editor of work by many dedicated contributors from industry, academia and government. the 1st Edition of the Semiconductor It can be argued that innovation explosions often occur at the intersection of Roadmap. scientific disciplines, and Semiconductor Synthetic Biology or SemiSynBio is an excellent example of this. The objective of this Roadmap is to serve as a vehicle to realize the transformative potential of the new technology emerging at the interface between semiconductors and synthetic biology. The SemiSynBio Roadmap is intended to catalyze both interest in and rapid technological advances that provide new capabilities that benefit humankind. Victor Zhirnov is Chief Scientist at the Semiconductor Research Corporation. His research interests include nanoelectronics devices and systems, properties of materials at the nanoscale, bio-inspired electronic systems etc. He has authored and co-authored over 100 technical papers and contributions to books. Victor Zhirnov served as the Chair of the Emerging Research Device (ERD) Working Group for the International Technology Roadmap for Semiconductors (ITRS). Victor Zhirnov also holds adjunct faculty position at North Carolina State University and has served as an advisor to a number of government, industrial, and academic institutions. Victor Zhirnov received the M.S. in applied physics from the Ural Polytechnic Institute, Ekaterinburg, Russia, and the Ph.D. in solid state electronics and microelectronics from the Institute of Physics and Technology, Moscow, in 1989 and 1992, respectively. From 1992 to 1998 he was a senior scientist at the Institute of Crystallography of Russian Academy of Science in Moscow. -
Genocad Introduction
GenoCAD Introduction Computer-Assisted Design Software for Synthetic Biology Materials prepared by: Mary E. Mangan PhD www.openhelix.com/genocad Version 1 GenoCAD Introduction Agenda Introduction to GenoCAD genocad.org Introduction and Credits Register and Log In Step 1: Parts Parts Grammar Import the Training Set Step 2: Design Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/ Computer-assisted design software for synthetic biology Visit GenoCAD.org 1 Support for GenoCAD Process Flow click peccoud.org nsf.gov Parts and grammars, public or custom collections Peccoud team Design constructs NSF support Simulate processes Conceptual Framework for GenoCAD Data Model, Concepts Promoters Coding Seqs Terminators peccoud.vbi.vt.edu/publications 2007: 10.1093/bioinformatics/btm446 2009: 10.1371/journal.pcbi.1000529 Promoter A Coding Seq A Promoter B Coding Seq B Your constructs Parts form the foundation, stored in project libraries Aspects of DNA function explained with language metaphors: transcription, translation, code Grammar rules specify the way the parts work in series GenoCAD lets you develop language for programming cells Parts + Grammars give you synthetic construct designs 2 Further Reading Getting Assistance doi: 10.1093/bioinformatics/btm446 doi: 10.1371/journal.pcbi.1000529 doi: 10.1093/nar/gkp361 doi: 10.1016/j.tibtech.2011.09.001 support Help: context-sensitive help from ? Button Publications: theoretical, software, ongoing development Support link for asking questions or offering feedback -
Computational Tools and Algorithms for Designing Customized
View metadata, citation and similar papers at core.ac.uk brought to you by CORE REVIEW ARTICLE published: 06provided October by 2014 Frontiers - Publisher Connector BIOENGINEERING AND BIOTECHNOLOGY doi: 10.3389/fbioe.2014.00041 Computational tools and algorithms for designing customized synthetic genes Nathan Gould 1, Oliver Hendy 2 and Dimitris Papamichail 1* 1 Department of Computer Science, The College of New Jersey, Ewing, NJ, USA 2 Department of Biology, The College of New Jersey, Ewing, NJ, USA Edited by: Advances in DNA synthesis have enabled the construction of artificial genes, gene cir- Ilias Tagkopoulos, University of cuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs California, Davis, USA provides significant power in studying the impact of mutations in sequence features, and Reviewed by: verifying hypotheses on the functional information that is encoded in nucleic and amino Yinjie Tang, Washington University, USA acids. To aid this goal, a large number of software tools of variable sophistication have M. Kalim Akhtar, University College been implemented, enabling the design of synthetic genes for sequence optimization London, UK based on rationally defined properties. The first generation of tools dealt predominantly *Correspondence: with singular objectives such as codon usage optimization and unique restriction site incor- Dimitris Papamichail, Department of Computer Science, The College of poration. Recent years have seen the emergence of sequence design tools that aim to New Jersey, 2000 Pennington Road, evolve sequences toward combinations of objectives.The design of optimal protein-coding Ewing, NJ 08628, USA sequences adhering to multiple objectives is computationally hard, and most tools rely on e-mail: [email protected] heuristics to sample the vast sequence design space.