Download or read book Synthetic Gene Network written by Bor-Sen Chen and published by CRC Press. This book was released on 2014-05-02 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book develops a rational design and systematic approach to construct a gene network with desired behaviors. In order to achieve this goal, the registry of standard biological parts and experimental techniques are introduced at first. Then these biological components are characterized by a standard modeling method and collected in the component libraries, which can be efficiently reused in engineering synthetic gene networks. Based on the system theory, some design specifications are provided to engineer the synthetic gene networks to robustly track the desired trajectory by employing the component libraries.
Download or read book Synthetic Gene Networks written by Wilfried Weber and published by Humana Press. This book was released on 2016-05-01 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book shows how to design and build synthetic gene networks in different host backgrounds. Coverage includes concepts for devising synthetic gene networks and application of mathematical models to the predictable engineering of desired network features.
Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.
Download or read book Synthetic Gene Network written by Bor-Sen Chen and published by . This book was released on 2014-01-01 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book develops a rational design and systematic approach to construct a gene network with desired behaviors. In order to achieve this goal, the registry of standard biological parts and experimental techniques are introduced at first. Then these biological components are characterized by a standard modeling method and collected in the component libraries, which can be efficiently reused in engineering synthetic gene networks. Based on the system theory, some design specifications are provided to engineer the synthetic gene networks to robustly track the desired trajectory by employing the component libraries.
Download or read book Advances in Synthetic Biology written by Vijai Singh and published by Springer Nature. This book was released on 2020-04-13 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses the design of emerging conceptual tools, technologies and systems including novel synthetic parts, devices, circuits, oscillators, biological gates, and small regulatory RNAs (riboregulators and riboswitches), which serve as versatile control elements for regulating gene expression. Synthetic biology, a rapidly growing field that involves the application of engineering principles in biology, is now being used to develop novel systems for a wide range of applications including diagnostics, cell reprogramming, therapeutics, enzymes, vaccines, biomaterials, biofuels, fine chemicals and many more. The book subsequently summarizes recent developments in technologies for assembling synthetic genomes, minimal genomes, synthetic biology toolboxes, CRISPR-Cas systems, cell-free protein synthesis systems and microfluidics. Accordingly, it offers a valuable resource not only for beginners in synthetic biology, but also for researchers, students, scientists, clinicians, stakeholders and policymakers interested in the potential held by synthetic biology.
Download or read book Design and Engineering of Synthetic Gene Networks written by Fuqing Wu and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic gene networks have evolved from simple proof-of-concept circuits to complex therapy-oriented networks over the past fifteen years. This advancement has greatly facilitated expansion of the emerging field of synthetic biology. Multistability is a mechanism that cells use to achieve a discrete number of mutually exclusive states in response to environmental inputs. However, complex contextual connections of gene regulatory networks in natural settings often impede the experimental establishment of the function and dynamics of each specific gene network. In this work, diverse synthetic gene networks are rationally designed and constructed using well-characterized biological components to approach the cell fate determination and state transition dynamics in multistable systems. Results show that unimodality and bimodality and trimodality can be achieved through manipulation of the signal and promoter crosstalk in quorum-sensing systems, which enables bacterial cells to communicate with each other. Moreover, a synthetic quadrastable circuit is also built and experimentally demonstrated to have four stable steady states. Experiments, guided by mathematical modeling predictions, reveal that sequential inductions generate distinct cell fates by changing the landscape in sequence and hence navigating cells to different final states. Circuit function depends on the specific protein expression levels in the circuit. We then establish a protein expression predictor taking into account adjacent transcriptional regions' features through construction of 120 synthetic gene circuits (operons) in Escherichia coli. The predictor's utility is further demonstrated in evaluating genes' relative expression levels in construction of logic gates and tuning gene expressions and nonlinear dynamics of bistable gene networks. These combined results illustrate applications of synthetic gene networks to understand the cell fate determination and state transition dynamics in multistable systems. A protein-expression predictor is also developed to evaluate and tune circuit dynamics.
Download or read book Synthetic Gene Circuits written by Filippo Menolascina and published by Humana. This book was released on 2022-01-21 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides clear and direct protocols to implement automated Design-Build-Test-Learn (DBTL) into synthetic biology research. Chapters detail techniques to model and simulate biological systems, redesign biological systems, setting up of an automated biolaboratory, step-by-step guide on how to perform computer aided design, RNA sequencing, microfluidics -using bacterial cell free extracts, live mammalian cells, computational and experimental procedures, metabolic burden, computational techniques to predict such burden from models, and how DNA parts can be engineered in mammalian cells to sense, and respond to, and intracellular signals in general. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Synthetic Gene Circuits: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Download or read book Mammalian Synthetic Biology written by Jamie Davies and published by . This book was released on 2019-12-12 with total page 137 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written primarily for mid-to-upper level undergraduates, this primer will introduce students to topics at the forefront of the subject that are being applied to probe biological problems, or to address the most pressing issues facing society. These topics will include those that form thecornerstone of contemporary research, helping students to make the transition to active researcher.This primer introduces the challenges and opportunities of applying synthetic biological techniques to mammalian cells, tissues, and organisms. It covers the special features that make engineering mammalian systems different from engineering bacteria, fungi, and plants, and provides an overview ofcurrent techniques. A variety of cutting-edge examples illustrate the different purposes of mammalian synthetic biology, including pure biomedical research, drug production, tissue engineering, and regenerative medicine.
Download or read book A Synthetic Gene Network that Counts written by Ari Edward Friedland and published by . This book was released on 2010 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing. A counter is one such device that would enable a new type of memory and allow for complex synthetic programming and novel behaviors. Here we report a synthetic genetic counter in Escherchia coli that counts up to three identical induction events, expressing a unique protein species to signify each number. The counter is comprised of a transcriptional cascade in which transcription is de-coupled from translation by riboregulators. The modularity of this device permits counting of varied user-defined inputs and its open-ended architecture provides a potent biotechnology platform for counting higher numbers, which is supported by mathematical modeling.
Download or read book Design Analysis and Construction of Novel Synthetic Gene Networks written by and published by . This book was released on 2011 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biodefense in the Age of Synthetic Biology written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-01-05 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused. Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.
Download or read book A Breadboard for Synthetic Gene Networks written by Kevin Daniel Litcofsky and published by . This book was released on 2012 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Interest in the development of increasingly complex synthetic gene networks for the study of natural networks and engineering novel functions has necessitated new approaches to the design and construction of the plasmids upon which they are encoded. Current methods that focus on additive DNA assembly hinder post-construction substitutions. Such modifications are important in facilitating iterative design strategies, which are prevalent due to imperfectly characterized biological components and contexts. We present an approach for the design, construction, and modification of synthetic gene networks termed the Gene Circuit Breadboard. It focuses on the ability to modify constructs to allow for tuning, troubleshooting, or repurposing of networks. We use a specified set of restriction enzymes in conjunction with a library of components that lack those restriction sites to maintain the uniqueness of the sites used for construction. Using this approach, we constructed a genetic toggle switch, added modified ssrA degradation tags to the genes in the toggle, and transformed the toggle into three- and four-node coherent feed-forward loops. The construction and tuning of these networks demonstrated both the need for and performance of our approach, as each circuit required modifications to achieve its intended behavior.
Download or read book Synthetic Biology written by Huimin Zhao and published by Academic Press. This book was released on 2013-03-21 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems. Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems. Includes contributions from leaders in the field presents examples of ambitious synthetic biology efforts including creation of artificial cells from scratch, cell-free synthesis of chemicals, fuels, and proteins, engineering of artificial photosynthesis for biofuels production, and creation of unnatural living organisms Describes the latest state-of-the-art tools developed for low-cost synthesis of ever-increasing sizes of DNA and efficient modification of proteins, pathways, and genomes Highlights key technologies for analyzing biological systems at the genomic, proteomic, and metabolomic levels which are especially valuable in pathway, whole cell, and multi-cell applications Details mathematical modeling tools and computational tools which can dramatically increase the speed of the design process as well as reduce the cost of development
Download or read book Synthetic Gene Circuits written by Filippo Menolascina and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides clear and direct protocols to implement automated Design-Build-Test-Learn (DBTL) into synthetic biology research. Chapters detail techniques to model and simulate biological systems, redesign biological systems, setting up of an automated biolaboratory, step-by-step guide on how to perform computer aided design, RNA sequencing, microfluidics -using bacterial cell free extracts, live mammalian cells, computational and experimental procedures, metabolic burden, computational techniques to predict such burden from models, and how DNA parts can be engineered in mammalian cells to sense, and respond to, and intracellular signals in general. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Synthetic Gene Circuits: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Download or read book A Formal Framework for Analysis and Design of Synthetic Gene Networks written by Boyan Yordanov Yordanov and published by . This book was released on 2011 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Synthetic biology has recently emerged as an attempt to study biological systems by construction rather than through observation. Work in the field has demonstrated that synthetic gene networks with a specific function can be designed and constructed experimentally and is expected to lead to important application in bioremediation, biosensing, clean fuel and drug bioproduction, and therapeutics. However, designing biological systems that work as expected remains a challenge. Mathematical modeling is often used to guide the design efforts in synthetic biology but the types of models arc often complex and cannot be easily analyzed. In addition, only simple specifications such as the existence of equilibria, limit cycles, or invariance sets are usually considered. In contrast, methods for proving (or disproving) the correctness of software programs and digital circuits have been developed in the field of formal verification. Such systems can be modeled as simple finite transition graphs and algorithms for automatically deciding whether a model satisfies a specification, expressed in temporal logic, are available. Temporal logics are rich enough to capture properties of biological systems relevant to synthetic biology. However, only simple, unrealistic models are directly amenable to formal verification. In this work, we bridge the gap and develop a theoretical framework and a set of computational tools allowing the analysis of realistic models from rich temporal logic specifications. We consider discrete time, piece-wise affine (PWA) systems, which evolve along different affine dynamics in different regions of the continuous state space. This structure results in models that are globally complex and can approximate nonlinear systems with arbitrary accuracy, but are also locally simple, which allows us to construct finite abstractions. Based on this, we develop formal methods for the analysis, parameter synthesis and control of PWA systems from temporal logic specifications.We apply our methods to analyze the synthetic gene networks that can be constructed from a set of available parts. We demonstrate how our tools can identify device designs that fail to meet the required specifications. Such an approach can be used to filter flawed designs before they are implemented experimentally, thereby decreasing the time and cost involved in synthetic biology projects.
Download or read book Cell Free Synthetic Biology written by Jian Li and published by Frontiers Media SA. This book was released on 2022-01-13 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Synthetic Genomics written by Miguel Fernández-Niño and published by BoD – Books on Demand. This book was released on 2022-02-02 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: The current advances in sequencing, data mining, DNA synthesis, cloning, in silico modeling, and genome editing have opened a new field of research known as Synthetic Genomics. The main goal of this emerging area is to engineer entire synthetic genomes from scratch using pre-designed building blocks obtained by chemical synthesis and rational design. This has opened the possibility to further improve our understanding of genome fundamentals by considering the effect of the whole biological system on biological function. Moreover, the construction of non-natural biological systems has allowed us to explore novel biological functions so far not discovered in nature. This book summarizes the current state of Synthetic Genomics, providing relevant examples in this emerging field.
