Download or read book Developing New Tools and Platforms for Mammalian Synthetic Biology written by Xavier Duportet and published by . This book was released on 2014 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mammalian synthetic biology may provide novel therapeutic strategies, help decipher new paths for drug discovery and facilitate synthesis of valuable molecules. Yet, our capacity to program cells is currently hampered both by the lack of efficient approaches to streamline the design, construction and screening of synthetic gene networks, and also by the complexity of mammalian systems and our poor understanding of cellular processes context¬dependencies.To address these problems, I proposed and validated a number of concepts and approaches during my PhD. First, I created a framework for modular and combinatorial assembly of functional (multi)gene expression vectors and their efficient and specific targeted integration into a well-defined chromosomal context in mammalian cells. Second, I developed a platform to identify and characterize new serine reconnbinase systems from Mycobacteriophage genomes in order to extend the toolbox of genome engineering techniques available for mammalian cells progranning. To overcome the apparent limitations in our single-tell rational engineering capacity, I also engineered two new artificial intercellular communication systems for mammalian cells, in order to facilitate the spatial decoupling of different modules of a synthetic circuit. Even though we are still years away from therapies using engineered cells carrying synthetic circuits to repair damaged or non-functional organs or to create de-novo tissues, I believe the contributions developed during the course of my PhD could potentially be used to help fasten the development of therapeutically relevant DNA circuits or to provide new means to understand mechanisms of cellular processes.
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 Foundational Platform for Mammalian Synthetic Biology written by Noah Justin Davidsohn and published by . This book was released on 2013 with total page 129 pages. Available in PDF, EPUB and Kindle. Book excerpt: The emergent field of synthetic biology is different from many other biological engineering efforts, in that its roots, design principles, and forward engineering perspective have been adopted from electrical engineering and computer science. Synthetic biology is uniquely poised to make great contributions to numerous fields such as bio-fuel, energy production, agriculture and eco-remediation, national defense, and biomedical and tissue engineering. Considerable progress has been made in engineering novel genetic circuits in many different organisms. However, not much progress has been made toward developing a formal methodology to engineer complex genetic systems in mammalian cells. One of the most promising areas of research is the study of embryonic and adult stem cells. Synthetic biology has the potential to greatly impact the progression and development of research in this area of study. A critical impediment to the development of stem cell engineering is the innate complexity, little to no characterization of parts, and limited compositional predictive capabilities. In this thesis, I discuss the strategies used for constructing and optimizing the performance of signaling pathways, the development of a large mammalian genetic part and circuit library, and the characterization and implementation of novel genetic parts and components aimed at developing a foundation for mammalian synthetic biology. I have designed and tested several orthogonal strategies aimed at cell-cell communication in mammalian cells. I have designed a characterization framework for the complete and proper characterization of genetic parts that allows for modular predictive composition of genetic circuits. With this characterization framework I have generated a small library of characterized parts and composite circuits that have well defined input-output relationships that can be used in novel genetic architectures. I also aided in the development of novel analysis and computational tools necessary for accurate predictive composition of these novel circuits. This work collectively provides a foundation for engineering complex intracellular transcriptional networks and intercellular signaling systems in mammalian cells.
Download or read book Mammalian Synthetic Systems written by Francesca Ceroni and published by Springer Nature. This book was released on with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 Engineering Self assembling Living Structures with Mammalian Synthetic Biology written by Jessica Jane Tordoff and published by . This book was released on 2020 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt: The shapes and structures created by living organisms have properties that any engineer would desire: they are self-healing, growing, adaptive, and range in complexity and material property from the strength of bone to the lightweight flexibility of an insect wing. The goal of this thesis is to use synthetic biology to design, control, and understand the range of structures that can be constructed using a ubiquitous tool for self-organization in animal development: cell sorting. We first use experiments and computational modeling to demonstrate how incompletely sorted structures can be systematically designed by quantitative control of cell composition. By varying the number of highly adhesive and less adhesive cells in multicellular aggregates, we find that cell type ratio and total number of cells are controllers of pattern formation, and the resulting structures are maintained over the course of days. Next, we establish a set of design rules for cell sorting-driven shape assembly using cell lines with engineered genetic circuits that can induce expression of different cadherins. We show that, even when well mixed, populations of cells with different cadherin expression profiles sort themselves in predictable ways. The resulting shapes vary significantly, including planes of semi-regular polka dots, a sphere engulfed by an outer shell, maze-like intertwined populations, and radial protrusions from a core. We can reliably select between these shapes and control their properties by changing induction of cadherin expression, population ratio, cadherin identity, and total aggregate size. Finally, we have designed and constructed a recombinase-based tool to break symmetry in a population of cells, with the ultimate goal of controlling the autonomous creation of different subpopulations from a single cell. By creating a platform to programmably generate multicellular forms, this thesis aims to establish design principles for synthetic morphogenesis and provide a framework to control living shapes.
Download or read book BioBuilder written by Natalie Kuldell PhD. and published by "O'Reilly Media, Inc.". This book was released on 2015-06-22 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt: Today’s synthetic biologists are in the early stages of engineering living cells to help treat diseases, sense toxic compounds in the environment, and produce valuable drugs. With this manual, you can be part of it. Based on the BioBuilder curriculum, this valuable book provides open-access, modular, hands-on lessons in synthetic biology for secondary and post-secondary classrooms and laboratories. It also serves as an introduction to the field for science and engineering enthusiasts. Developed at MIT in collaboration with award-winning high school teachers, BioBuilder teaches the foundational ideas of the emerging synthetic biology field, as well as key aspects of biological engineering that researchers are exploring in labs throughout the world. These lessons will empower teachers and students to explore and be part of solving persistent real-world challenges. Learn the fundamentals of biodesign and DNA engineering Explore important ethical issues raised by examples of synthetic biology Investigate the BioBuilder labs that probe the design-build-test cycle Test synthetic living systems designed and built by engineers Measure several variants of an enzyme-generating genetic circuit Model "bacterial photography" that changes a strain’s light sensitivity Build living systems to produce purple or green pigment Optimize baker’s yeast to produce ?-carotene
Download or read book Computational and Experimental Approaches to Understanding Mammalian Gene Regulation with Synthetic Biology written by Aditya Mukund and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcriptional regulation is a key pathway cells use to regulate gene expression in response to temporal signaling, and is becoming widely used as a platform for synthetic biology applications. Transcription in mammalian cells is in large part driven by the actions of transcription factors, which consist of DNA-binding domains that recognize and bind to specific genomic locations and effector domains that recruit transcriptional machinery and chromatin regulators to activate or repress target genes. This work uses mathematical modeling and high-throughput experimental approaches to dissect the temporal and combinatorial logic of gene regulation in mammalian cells. First, we build a mathematical framework for analyzing the response of genetic circuits containing chromatin regulators to temporal signals in mammalian cell populations, elaborating on prior models in which individual cells stochastically transitioning between active, reversibly silent, and irreversibly silent gene states at constant rates over time. We analyze classical gene regulatory motifs such as feedforward and autoregulatory loops in the context of duration-dependent signaling, and find that repressive regulators with epigenetic memory can sum up and encode the total duration of their recruitment in the fraction of cells irreversibly silenced. Last, we use an information theoretic approach to show that all-or-none stochastic silencing can be used by populations to transmit information reliably and with high fidelity even in very simple genetic circuits. Second, we use a high-throughput approach to dissecting how distinct effector domains within a single transcription factor can be combined to regulate gene expression. We measure transcriptional activity for 8,400 effector domain combinations by recruiting them to reporter genes in human cells. We find that weak and moderate activation domains synergize to drive strong gene expression, while combining strong activators often results in weaker activation. In contrast, weaker repressor domains tend to average each other out, and moderate to strong repressor domains often overpower activation domains. We use this information to build a synthetic transcription factor whose function can be tuned between repression and activation independent of recruitment to target genes by using a small molecule drug. Altogether, this work helps to advance our understanding of how to build synthetic transcription factors, and how to design and model chromatin regulation-based circuits. Our hope is that these efforts will help advance mammalian synthetic biology as a tool for biological research and a reliable strategy for developing medical therapies.
Download or read book Synthetic Biology written by Shailza Singh and published by Springer. This book was released on 2018-10-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book uses an integrated approach to predict the behavior of various biological interactions. It further discusses how synthetic biology gathers the information about various systems, in order to either devise an entirely new system, or, to modulate existing systems. The book also tackles the concept of modularity, where biological systems are visualized in terms of their parts. The chapters discuss how the principles of engineering are being used in biomedical sciences, to design biological circuits that can harbor multiple inputs and generate multiple outputs; to create genetic networks and control gene activity, in order to generate a desired response. The book aims to help the readers develop an array of biological parts, and to use these parts to develop synthetic circuits that can be assembled like electronic circuits. The ultimate aim of the book will be to serve as an amalgamation of key ideas of how judiciously synthetic biology could be exploited in therapeutic device and delivery mechanism.
Download or read book Developing Tools and Techniques for Expanding the Synthetic Biology Toolkit written by Thomas Jacobsen and published by . This book was released on 2019 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Development of Synthetic Biology Tools Driven by Membrane Potential written by Marco A. Delise and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Gene Networks written by Wilfried Weber and published by Humana Press. This book was released on 2011-11-17 with total page 393 pages. Available in PDF, EPUB and Kindle. Book excerpt: The rapid expansion of synthetic biology is due to the design and construction of synthetic gene networks that have opened many new avenues in fundamental and applied research. Synthetic Gene Networks: Methods and Protocols provides the necessary information to design and construct synthetic gene networks in different host backgrounds. Divided into four convenient sections, this volume focuses on design concepts to devise synthetic gene networks and how mathematical models can be applied to the predictable engineering of desired network features. The volume continues by highlighting the construction and validation of biologic tools, describing strategies to optimize and streamline the host cell for optimized network performance, and covering how optimally designed gene networks can be implemented in a large variety of host cells ranging from bacteria over yeast and insect cells to plant and mammalian cell culture. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Synthetic Gene Networks: Methods and Protocols serves as an invaluable resource for established biologists, engineers, and computer scientists or novices just entering into the rapidly growing field of synthetic biology
Download or read book New Frontiers and Applications of Synthetic Biology written by Vijai Singh and published by Academic Press. This book was released on 2022-01-12 with total page 487 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Frontiers and Applications of Synthetic Biology presents a collection of chapters from eminent synthetic biologists across the globe who have established experience and expertise working with synthetic biology. This book offers several important areas of synthetic biology which allow us to read and understand easily. It covers the introduction of synthetic biology and design of promoter, new DNA synthesis and sequencing technology, genome assembly, minimal cells, small synthetic RNA, directed evolution, protein engineering, computational tools, de novo synthesis, phage engineering, a sensor for microorganisms, next-generation diagnostic tools, CRISPR-Cas systems, and more. This book is a good source for not only researchers in designing synthetic biology, but also for researchers, students, synthetic biologists, metabolic engineers, genome engineers, clinicians, industrialists, stakeholders and policymakers interested in harnessing the potential of synthetic biology in many areas. Offers basic understanding and knowledge in several aspects of synthetic biology Covers state-of-the-art tools and technologies of synthetic biology, including promoter design, DNA synthesis, DNA sequencing, genome design, directed evolution, protein engineering, computational tools, phage design, CRISPR-Cas systems, and more Discusses the applications of synthetic biology for smart drugs, vaccines, therapeutics, drug discovery, self-assembled materials, cell free systems, microfluidics, and more
Download or read book Industrialization of Biology written by National Research Council and published by National Academies Press. This book was released on 2015-06-29 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: The tremendous progress in biology over the last half century - from Watson and Crick's elucidation of the structure of DNA to today's astonishing, rapid progress in the field of synthetic biology - has positioned us for significant innovation in chemical production. New bio-based chemicals, improved public health through improved drugs and diagnostics, and biofuels that reduce our dependency on oil are all results of research and innovation in the biological sciences. In the past decade, we have witnessed major advances made possible by biotechnology in areas such as rapid, low-cost DNA sequencing, metabolic engineering, and high-throughput screening. The manufacturing of chemicals using biological synthesis and engineering could expand even faster. A proactive strategy - implemented through the development of a technical roadmap similar to those that enabled sustained growth in the semiconductor industry and our explorations of space - is needed if we are to realize the widespread benefits of accelerating the industrialization of biology. Industrialization of Biology presents such a roadmap to achieve key technical milestones for chemical manufacturing through biological routes. This report examines the technical, economic, and societal factors that limit the adoption of bioprocessing in the chemical industry today and which, if surmounted, would markedly accelerate the advanced manufacturing of chemicals via industrial biotechnology. Working at the interface of synthetic chemistry, metabolic engineering, molecular biology, and synthetic biology, Industrialization of Biology identifies key technical goals for next-generation chemical manufacturing, then identifies the gaps in knowledge, tools, techniques, and systems required to meet those goals, and targets and timelines for achieving them. This report also considers the skills necessary to accomplish the roadmap goals, and what training opportunities are required to produce the cadre of skilled scientists and engineers needed.
Download or read book Synthetic Biology Handbook written by Darren N. Nesbeth and published by CRC Press. This book was released on 2016-04-06 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Synthetic Biology Handbook explains the major goals of the field of synthetic biology and presents the technical details of the latest advances made in achieving those goals. Offering a comprehensive overview of the current areas of focus in synthetic biology, this handbook:Explores the standardisation of classic molecular bioscience approaches
