Mammalian Synthetic Systems PDF Download

Author: Francesca Ceroni
Publisher: Springer Nature
ISBN: 1071637185
Category :
Languages : en
Pages : 319

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Author: Jamie Davies
Publisher:
ISBN: 019884154X
Category :
Languages : en
Pages : 137

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Book Description
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.

Author: Institute of Medicine
Publisher: National Academies Press
ISBN: 0309219396
Category : Science
Languages : en
Pages : 570

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Book Description
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.

Author: Noah Justin Davidsohn
Publisher:
ISBN:
Category :
Languages : en
Pages : 129

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Book Description
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.

Author: Xavier Duportet
Publisher:
ISBN:
Category :
Languages : en
Pages : 108

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Book Description
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.

Author: Robert E. Rhoads
Publisher: Humana
ISBN: 9781493936236
Category : Medical
Languages : en
Pages : 0

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Book Description
This volume presents detailed laboratory protocols for in vitro synthesis of mRNA with favorable properties, its introduction into cells by a variety of techniques, and the measurement of physiological and clinical consequences such as protein replacement and cancer immunotherapy. Synthetic techniques are described for structural features in mRNA that provide investigational tools such as fluorescence emission, click chemistry, photo-chemical crosslinking, and that produce mRNA with increased stability in the cell, increased translational efficiency, and reduced activation of the innate immune response. Protocols are described for clinical applications such as large-scale transfection of dendritic cells, production of GMP-grade mRNA, redirecting T cell specificity, and use of molecular adjuvants for RNA vaccines. 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Synthetic mRNA: Production, Introduction into Cells, and Physiological Consequences is a valuable and cutting-edge resource for both laboratory investigators and clinicians interested in this powerful and rapidly evolving technology.

Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
ISBN: 0309465184
Category : Technology & Engineering
Languages : en
Pages : 189

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Book Description
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.

Author: Daniel G. Gibson
Publisher: Perspectives Cshl
ISBN: 9781621821182
Category : Science
Languages : en
Pages : 0

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Book Description
Synthetic biology involves the rational design and construction of biological components and systemsfrom genetic elements and metabolic pathways to entirely new organisms. Progress in this field has been rapid, and it promises to significantly expand our capabilities in biotechnology, medicine, and agriculture. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines the tools and techniques employed by synthetic biologists, how these may be used to develop new drugs, diagnostic approaches, food sources, and clean energy, and what the field of synthetic biology has taught us about natural living systems. The contributors discuss advances in DNA synthesis and assembly, genome editing (e.g., CRISPR/Cas9), and artificial genetic systems. Progress in designing complex genetic switches and circuits, expanding the genetic code, modifying cellular organization, producing proteins using cell-free systems, and developing biodesign automation tools is also covered. The authors also explore ways to produce new organisms and products that have particular attributesfor example, microbial "molecular factories," synthetic organs and tissues, and plants with novel traits. This volume is an essential resource for molecular, cell, and systems biologists who seek to engineer living systems for human benefit.

Author: Cameron Michael Kim
Publisher:
ISBN:
Category :
Languages : en
Pages :

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From the approximately 20,000 genes embedded in DNA genomes to the functional proteins they encode for, much of the functional diversity of mammals can be attributed to alternative splicing, a pre-messenger RNA processing mechanism that produces multiple proteins from a single gene through careful arrangement of exons into a final transcript. While synthetic biology harnesses natural sequences refined by genetic evolution to build new functions from modular DNA components in engineered biological systems, few systems have leveraged alternative splicing as a precision tool for genetic control in mammalian systems. Combining the evolved mechanisms of splicing regulation with the ability to produce multiple, distinct proteins from a single gene, alternative splicing in synthetic genetic devices expands our capacity to control mammalian systems for medical, industrial, and biological discovery platforms. We have developed a class of mutually exclusive alternative splicing devices that can express two distinct isoforms based on which one of two internal exons is included in the final RNA molecule. In our efforts to engineer these devices for novel functions to control biological systems, we expanded the functional outputs of our alternative splicing devices using modular protein domains and fluorescent proteins, in addition to updating previous design considerations that limited our initial efforts, such as size and sequence constraints. Our ability to regulate outcomes from alternative splicing devices is important for their use as genetic transcriptional tools for mammalian synthetic biology. We modify our intron framework to support the production of both isoforms at various ratios based on mutations and truncations to consensus elements responsible for alterna- tive splicing. We explored synthetic approaches to controlling isoforms, such as the CRISPR-Cas13 RNA-targeting system and the MS2 protein aptamer, that allowed us to shift splicing patterns in a dynamic fashion. Our strategy to controlling isoform outcomes and protein functionality replicates how evolution evolved RNA splicing for a synthetic alternative splicing device. We present the design, construction, regulation, and versatility of alternative splicing devices. Their unique ability to compress genetic information combined with transcriptional regulation tools, both naturally encoded and artificially introduced, advances the novel mechanism we can harness to engineer biology.

Author: Pengcheng Fu
Publisher: John Wiley & Sons
ISBN: 9780470437971
Category : Technology & Engineering
Languages : en
Pages : 672

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Book Description
The genomic revolution has opened up systematic investigations and engineering designs for various life forms. Systems biology and synthetic biology are emerging as two complementary approaches, which embody the breakthrough in biology and invite application of engineering principles. Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems. This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.