Download or read book Scalable Genetic System Design Using Synthetic RNA Regulators written by Lei Qi and published by . This book was released on 2012 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Our ability to efficiently and predictably program cells is central to the fields of bioengineering and synthetic biology. Once thought to be a passive carrier of genetic information, RNA is now more appreciated as the main organizer of cellular networks. To harness the unique abilities of RNA molecules for programming cells, we show here how to rationally design novel synthetic RNA elements to recapitulate the functions of natural noncoding RNAs (ncRNAs), and how to assemble these synthetic elements into higher-order biological systems. To create synthetic RNA elements, we start with two primary types of ncRNA-mediated natural systems. Both modulate RNA-level regulatory signals encoded in the 5' untranslated region, and are mediated by ncRNAs. In the first system the ncRNA represses transcription elongation, whereas in the second system the ncRNA inhibits translation initiation. To create orthogonal RNA elements that work independently in the same cell, we systematically modify the RNA-RNA interaction in the natural systems. Our characterization results in families of orthogonally acting RNA elements for both transcription and translation controls. Furthermore, we develop mathematical thermodynamic models to predict new RNA elements in silico for translation controls. To engineer synthetic RNAs to sense and integrate cellular signals, we design allosteric RNA chimera molecules by fusing ncRNAs to RNA aptamers. We demonstrate the design principles for creating such chimeric RNA molecules that can sense proteins or small molecules and control transcription or translation. We show that the design strategy is modular, which allows us to reconfigure different ncRNA mutants and RNA aptamers to engineer orthogonal RNA chimeras that respond to different ligands and regulate different gene targets. We further show that multiple RNA chimeras allow logical integration of molecular signals in the same cell for cellular information processing. We assemble multiple synthetic RNA elements to create basic regulatory network motifs. These include independent control, logic control, and cascading control. We characterize the performance and properties of these engineered RNA circuits such as their time response, signal sensitivity, and noises across cell populations. We further explore a strategy that can effectively convert orthogonal translational regulators into orthogonal transcriptional regulators, which can be used to perform multi-input logic computation. In an effort to engineer feedback circuits, we demonstrate the use of translational repressor and activator based on RNA-binding proteins. The designed positive or negative feedback circuits form a basis for programming complex functions. To improve the predictability of engineered biological systems, we develop a synthetic RNA processing platform from the bacterial CRISPR genetic immune pathway. The synthetic RNA processing system can efficiently and specifically cleave desired precursor mRNAs at designed loci. Using this system, we show that transcript cleavage enables quantitative programming of gene expression by modular assembly of promoters, ribosome binding sites, cis regulatory elements, and riboregulators. These basic components can be grouped into multi-gene synthetic operons that behave predictably only after RNA processing. Physical separation of otherwise linked elements within biological assemblies allows design of sophisticated RNA-level regulatory systems that are not possible without it. Thus, our results exemplify a crucial design principle based on controllable RNA processing for improving the modularity and reliability of genetic systems. To sum, our work established bacterial ncRNAs as an intriguing engineering substrate for scalable genetic circuit design and for programming cells. We provide a set of engineering principles for designing synthetic RNA elements as well as using them to sense signals and form genetic circuits. Our RNA-based engineering platform provides a versatile and powerful strategy for designing higher-order cellular information processing and computation systems, which can be readily applied to practical applications including chemical production, environment remediation, and therapeutics.

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 High throughput Strategies for the Scalable Generation of RNA Component Functions written by Joe Chih Yao Liang and published by . This book was released on 2012 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: Engineered biological systems hold great promise in providing solutions to many global challenges, including environmental remediation, sustainability, scalable manufacturing, and health and medicine. Synthetic biology is an emerging research field with a primary goal of making the engineering of biology more streamlined and reliable. Recent advances in synthetic RNA biology have led to design of RNA-based gene-regulatory devices from assembly of functional RNA components that encode more basic functions, including sensing, information transmission, and actuation functions. These synthetic RNA control devices allow access and control information on cellular state, thereby advancing our ability to interact with and program biology. A modular ribozyme device platform was recently described to link an aptamer (sensor) to a hammerhead ribozyme (actuator) through a distinct sequence (information transmitter) capable of a strand-displacement event. The utilization of ribozyme as the actuator in the platform, whose mechanism of action is independent of cell-specific machinery, allows transport of the resultant devices to in vitro or different cellular environments. The broad implementation of these devices requires enabling technologies to support efficient generation of new functional RNA components and quantitative tailoring of device regulatory performance for specific cellular applications. Current component generation and device tailoring strategies are limited in their throughputs and efficiencies, and thus have hampered our ability to generate new ribozyme devices for cellular engineering applications. To support scalable generation and tailoring of ribozyme devices, we have described high-throughput in vitro selection and in vivo screening strategies based on the modular ribozyme device platform. We proposed a high-throughput solution-based in vitro selection strategy to generate new sensing functions within the device platform. A high-throughput and quantitative two-color FACS-based screening strategy was developed to complement the in vitro selection strategy by allowing efficient tailoring of device regulatory activities in the cellular environments. We further developed quantitative assays based on the surface plasmon resonance (SPR) technology to allow rapid measurements of the device and component activities. Together, these enabling strategies will offer a scalable and integrated process for the construction and programming of RNA control devices for broad cellular engineering applications, thus laying an important foundation for engineering more complex biological systems.

Download or read book Developing Design Principles for Engineering RNA Transcription Regulators and RNA Synthetic Gene Networks written by Melissa Kimie Takahashi and published by . This book was released on 2015 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: A major goal of synthetic biology is to reliably engineer microorganisms to perform a variety of functions with impact in the fields of biotechnology and medicine. Cells naturally control their behavior and process information via genetic networks - webs of interactions between cellular regulatory molecules that ultimately control when specific genes are expressed. Therefore, the route that synthetic biologists have taken to engineer microorganisms has been through constructing synthetic gene networks. Historically, these networks were built using proteins that regulate transcription, but recently RNAs have emerged as versatile molecules that can be engineered to regulate all aspects of gene expression. Aside from their versatility, RNAs offer potential advantages over protein regulators for engineering synthetic gene networks. RNAs are relatively easy to engineer due to the direct relationship between their structure and function as well as the abundance of new technologies that allow us to determine RNA secondary structures. RNA regulators are typically compact in size making networks constructed out of them easier to build. Finally, RNA networks have the potential to propagate signals faster than protein networks due to their fast degradation rates. For these reasons the focus of the work presented here has been to develop new RNA transcription regulators and to lay the groundwork for using them to build RNA synthetic gene networks. Antisense RNA transcriptional attenuators (repressors) were shown to be a key component of the synthetic biology toolbox, with their ability to serve as building blocks for both signal integration logic networks and transcriptional cascades. However, in order to build more sophisticated networks, larger libraries of orthogonal attenuators that function independently are required. To address this bottleneck we developed a strategy to create chimeric fusions between the pT181 transcriptional attenuator and other natural antisense RNA translational regulators. This strategy resulted in a library of 7 orthogonal regulators. While the strategy was successful, many of the attenuators engineered during the process did not regulate gene expression. To help understand the relationship between the structure and function of these RNA regulators we characterized their structures using in-cell SHAPE-Seq and molecular dynamics simulations. In-cell SHAPE-Seq provides nucleotide-resolution chemical reactivity spectra for RNAs that reflect their structural state within the cell. By probing functional and non-functional regulators we uncovered a design principle that brings us closer to designing chimeric attenuators in silico, thus expanding the synthetic biology toolbox even further. Next, we expand the capabilities of RNAs by engineering small transcription activating RNAs (STARs). In order to build complex RNA synthetic gene networks the ability to both activate and repress gene expression is required. However, there are no known natural small RNA (sRNA) mechanisms that activate transcription. To fill this gap, we developed two sRNA regulators to activate transcription. These STAR regulators were then used to engineer new RNA logic gates, thus expanding the RNA synthetic biology toolbox. One of the bottlenecks to developing new RNA gene networks is the slow process of testing network designs in cells. To prevent this we adapted a cell- free transcription-translation (TX-TL) system to rapidly test our RNA parts and to prototype new networks. TX-TL systems incorporate all the cellular machinery necessary for gene expression, but do so in an in vitro environment therefore bypassing the limitations that come with growing cells. We use TX-TL to prototype a new RNA network, an RNA single input module and to show that RNA networks do in fact propagate signals on the fast timescales of RNA degradation rates. Finally, we aim to expand the capabilities of RNA networks by developing an RNA genetic oscillator. Our goal is to build a dual-feedback oscillator that combines two autoregulatory network motifs - negative autoregulation and positive autoregulation using the pT181 attenuator and the best STAR regulator, respectively. We describe the progress that has been made in building these two networks as well as a path forward to engineering the RNA oscillator. Altogether the work presented here has made significant progress in our ability to engineer RNA synthetic gene networks. We anticipate that the RNA regulators and tools developed here will pave the way toward future studies of RNA structure-function principles as well as the development of new RNA networks.

Download or read book Evolutionary Computation in Gene Regulatory Network Research written by Hitoshi Iba and published by John Wiley & Sons. This book was released on 2016-01-21 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.

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 Cell targeted Regulation of Gene Expression Through Synthetic RNA Devices written by James Vincent Vowles and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to interface with and program cellular function remains a challenging research frontier in biotechnology. Although the emerging field of synthetic biology has recently generated a variety of gene-regulatory strategies based on synthetic RNA molecules, few strategies exist through which to control such regulatory effects in response to specific exogenous or endogenous molecular signals. Here, we present the development of an engineered RNA-based device platform to detect and act on endogenous protein signals, linking these signals to the regulation of genes and thus cellular function. We describe efforts to develop an RNA-based device framework for regulating endogenous genes in human cells. Previously developed RNA control devices have demonstrated programmable ligand-responsive genetic regulation in diverse cell types, and we attempted to adapt this class of cis-acting control elements to function in trans. We divided the device into two strands that reconstitute activity upon hybridization. Device function was optimized using an in vivo model system, and we found that device sequence is not as flexible as previously reported. After verifying the in vitro activity of our optimized design, we attempted to establish gene regulation in a human cell line using additional elements to direct device stability, structure, and localization. The significant limitations of our platform prevented endogenous gene regulation. We next describe the development of a protein-responsive RNA-based regulatory platform. Employing various design strategies, we demonstrated functional devices that both up- and downregulate gene expression in response to a heterologous protein in a human cell line. The activity of our platform exceeded that of a similar, small-molecule-responsive platform. We demonstrated the ability of our devices to respond to both cytoplasmic- and nuclear-localized protein, providing insight into the mechanism of action and distinguishing our platform from previously described devices with more restrictive ligand localization requirements. Finally, we demonstrated the versatility of our device platform by developing a regulatory device that responds to an endogenous signaling protein. The foundational tool we present here possesses unique advantages over previously described RNA-based gene-regulatory platforms. This genetically encoded technology may find future applications in the development of more effective diagnostic tools and targeted molecular therapy strategies.

Download or read book Strategies and Technologies for Engineering Gene regulatory RNA Devices written by Andrew B. Kennedy and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Engineered biological systems will provide solutions to diverse global challenges, enabling new and enhanced products for application in chemical processing, materials synthesis, sustainable technologies, and human health. Ability to manipulate and probe biological systems is limited by our ability to noninvasively access, process, report on, and respond to information encoded in the properties of molecules in living systems. Developing genetically encoded information processing and control technologies is critical to addressing and overcoming fundamental challenges in basic and applied biomedical research. RNA poses a strong candidate for a substrate in which to build genetic control devices. Examples of functional RNA molecules playing key roles in controlling the behavior of natural biological systems have grown over the past decade. The relative ease in modeling RNA molecules has enabled design of synthetic counterparts, act with diverse function as components including sensors, regulators, controllers (ligand-responsive RNA regulators), and scaffolds. These synthetic regulatory RNAs are providing new tools for temporal and spatial control in biological systems. A modular platform was described for the construction of RNA devices composed of distinct domains that encode sensing, transmission and actuation functions. The sensor domain is composed of an RNA aptamer, a nucleic acid structure evolved in vitro to bind with high affinity to a given ligand. The actuator domain is composed of a hammerhead ribozyme, which self-cleaves at a specific sequence under proper secondary and tertiary folding. The transmitter domain couples the sensor and actuator domains and communicates the ligand-bound conformational state of the sensor domain to the actuator domain by affecting the folded state of the actuator into either its ribozyme-active or -inactive conformation. The devices are placed in the 3' untranslated region of a target transcript, where self-cleavage inactivates the transcript, thereby lowering gene expression. This framework has been extended to the assembly of devices exhibiting higher-order information processing operations, including logic gates, signal filters and programmed cooperativity. As a demonstration of the broader significance of this class of devices, they have been successfully implemented as biological control systems to regulate signaling pathways and clinically-relevant phenotypes. However, it is critical to develop an improved understanding of the underlying molecular mechanisms and parameters guiding the activities of these devices in vivo in order to develop improved design strategies and associated regulatory activity to extend the utility of these genetic devices for a broader range of applications. To advance the RNA device design, we have developed and implemented novel methods to measure important parameters. We characterized the causal relationship between the in vitro device cleavage rate constant device parameter and in vivo gene- regulatory activity, and utilized this for efficient device performance characterization and design. We described a have novel, two-color, in vivo fluorescent activated cell sorting-based approach to identify sequences that yielded improved catalytic activities within the device platform and enabled efficient tailoring of device regulatory activities. We further developed a quantitative assay based on surface plasmon resonance technology for rapid measurements of device cleavage and ligand binding, the important parameters governing the underlying device mechanism. We incorporate this assay into the RNA device design cycle, pre-filtering candidate devices by in vitro cleavage and binding activity for subsequent in vivo testing. By this method we efficiently developed of new protein-responsive RNA devices in both yeast and mammalian hosts. Finally, we devised a platform utilizing next generation sequencing and fluorescent activated cell sorting for simultaneous measurements of in vitro cleavage and in vivo gene-regulatory activities of large RNA device libraries. Enabled by the large screening capacity, we develop a new RNA device architecture, with modularity instilled at the design level. By this approach we generate RNA devices without a programmed conformational change that results in improved device gene- regulatory performance. Taken together, these new technologies for characterizing important device performance characters and resultant gene-regulatory activity provide a comprehensive framework for designing, testing and implementing RNA genetic controllers for engineering biological systems.

Download or read book Versatile and Dynamic Gene Regulation Using Synthetic Non coding RNAs written by Young Je Lee and published by . This book was released on 2018 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria hold great potential as a platform to produce hundreds or thousands of natural products derived from organisms across the tree of life, which can be applied towards a number of diverse applications, including environmental remediation, commodity chemical synthesis, and health and medicine. Accessing these products is solely dependent on our ability to reprogram bacteria through the design and implementation of synthetic devices. Recently, RNA regulators have emerged as a reliable tool for the construction of devices that can create desired patterns of gene expression. These RNA regulators are highly structured molecules that exhibit diverse functionalities, including sensing, regulatory, and scaffolding activities. In this work, we combine the CRISPR system and synthetic antisense RNAs in Escherichia coli strains to repress or derepress a target gene in a programmable manner. Next, we demonstrate an integrated genetic circuit compiled from the STAR system and synthetic antisense RNAs to activate or deactivate a target gene. Furthermore, two A AND NOT B logic gates are constructed and tested in the same cell using the combined STAR and antisense RNA system to demonstrate sophisticated multi-gene regulation. Finally, a data-driven model is developed for predictable and tunable antisense RNA-mediated repression. This predictive model is validated in a number of different genetic contexts and organisms. Together, this work establishes a methodology for integrating multiple RNA regulators to modulate multiple genes' expression and provide a generalizable model that enables predictable antisense RNA-mediated gene repression in diverse bacterial species.

Download or read book Towards Modular Scalable and Optimal Design of Transcriptional Logic Systems written by Nicolae Radu Zabet and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Living organisms can perform computations through various mechanisms. Understanding the limitations of these computations is not only of practical relevance (for example in the context of synthetic biology) but will most of all provide new insights into the design principles of living systems. This thesis investigates the conditions under which genes can perform logical computations and how this behaviour can be enhanced. In particular, we identified three properties which characterise genes as computational units, namely: the noise of the gene expression, the slow response times and the energy cost of the logical operation. This study examined how biological parameters control the computational properties of genes and what is the functional relationship between various computational properties. Specifically, we found that there is a three-way trade-off between speed, accuracy and metabolic cost, in the sense that under fixed metabolic cost the speed can be increased only by reducing the accuracy and vice-versa. Furthermore, higher metabolic cost resulted in better trade-offs between speed and accuracy. In addition, we showed that genes with leak expression are sub-optimal compared with leak-free genes. However, the cost to reduce the leak rate can be significant and, thus, genes prefer to handle poorer speed-accuracy behaviour than to increase the energy cost. Moreover, we identified another accuracy-speed trade-off under fixed metabolic cost, but this time the trade-off is controlled by the position of the switching threshold of the gene. In particular, there are two optimal configurations, one for speed and another one for accuracy, and all configurations in between lie on an optimal trade-off curve. Finally, we showed that a negatively auto-regulated gene can display better trade-offs between speed and accuracy compared with a simple one (a gene without feedback) when the two systems have equal metabolic cost. This optimality of the negative auto-regulation is controlled by the leak rate of the gene, in the sense that higher leak rates lead to faster systems and lower leak rates to more accurate ones. This in conjunction with the fact that many genes display low but non-vanishing leak rates can indicate the reason why negative auto-regulation is a network motif (has high occurrence in genetic networks). These trade-offs that we identified in this thesis indicate that there are some physical limits which constrain the computations performed by genes and further enhancement usually comes at the cost of impairing at least one property.

Download or read book Generating Synthetic Noncoding RNAs for Programmable and Tunable Gene Control written by Andrew L. Chang and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The engineering of biological systems offers significant promise for advances in areas including health and medicine, scalable manufacturing, and environmental sustainability. Realizing this potential requires tools that enable design of sophisticated genetic systems. The functional diversity of RNA makes it an attractive and versatile substrate for genetically encoding molecular sensing, catalysis, data storage, information processing, and gene regulatory capabilities. We describe the development and application of methods for generating and characterizing functional noncoding RNA sequences, including novel biological sensing capabilities and regulatory switches in microbial and mammalian hosts. We developed a surface plasmon resonance-based platform for the rapid characterization of kinetic and equilibrium binding properties of aptamers to small molecules and a high-throughput, quantitative, cell-based screening strategy to support rapid generation of ribozyme-based RNA switches with user-specified regulatory activities. We applied these screening and characterization strategies to construct synthetic RNA regulatory switches to the pharmaceutical drug folinic acid in both microbial and mammalian cells in response to drug administration.

Download or read book A Systems Theoretic Approach to Systems and Synthetic Biology II Analysis and Design of Cellular Systems written by Vishwesh V. Kulkarni and published by Springer. This book was released on 2014-07-03 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume II contains chapters contributed by leading researchers in the field of systems and synthetic biology that concern modeling physiological processes and bottom-up constructions of scalable biological systems. The modeling problems include characterisation and synthesis of memory, understanding how homoeostasis is maintained in the face of shocks and relatively gradual perturbations, understanding the functioning and robustness of biological clocks such as those at the core of circadian rhythms, and understanding how the cell cycles can be regulated, among others. Some of the bottom-up construction problems investigated in Volume II are as follows: How should biomacromolecules, platforms, and scalable architectures be chosen and synthesised in order to build programmable de novo biological systems? What are the types of constrained optimisation problems encountered in this process and how can these be solved efficiently? As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.

Download or read book Regulation of Gene Expression by Small RNAs written by Rajesh K. Gaur and published by CRC Press. This book was released on 2009-04-27 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p

Download or read book The Metabolic Pathway Engineering Handbook written by Christina Smolke and published by CRC Press. This book was released on 2009-07-28 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second volume of the Metabolic Pathway Engineering Handbook delves into evolutionary tools and gene expression tools for metabolic pathway engineering. It covers applications of emerging technologies including recent research genome-wide technologies, DNA and phenotypic microarrays, and proteomics tools for experimentally determining flux thro

Download or read book Biomolecular Feedback Systems written by Domitilla Del Vecchio and published by Princeton University Press. This book was released on 2014-10-26 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu

Download or read book Biomolecular and Computational Frameworks for Genetic Circuit Design written by Alec A. K. Nielsen and published by . This book was released on 2017 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living cells naturally use gene regulatory networks termed "genetic circuits" to exhibit complex behaviors such as signal processing, decision-making, and spatial organization. The ability to rationally engineer genetic circuits has applications in several biotechnology areas including therapeutics, agriculture, and materials. However, genetic circuit construction has traditionally been time- and labor-intensive; tuning regulator expression often requires manual trial-and-error, and the results frequently function incorrectly. To improve the reliability and pace of genetic circuit engineering, we have developed biomolecular and computational frameworks for designing genetic circuits. A scalable biomolecular platform is a prerequisite for genetic circuits design. In this thesis, we explore TetR-family repressors and the CRISPRi system as candidates. First, we applied 'part mining' to build a library of TetR-family repressors gleaned from prokaryotic genomes. A subset were used to build synthetic 'NOT gates' for use in genetic circuits. Second, we tested catalytically-inactive dCas9, which employs small guide RNAs (sgRNAs) to repress genetic loci via the programmability of RNA:DNA base pairing. To this end, we use dCas9 and synthetic sgRNAs to build transcriptional logic gates with high on-target repression and negligible cross-talk, and connected them to perform computation in living cells. We further demonstrate that a synthetic circuit can directly interface a native E. coli regulatory network. To accelerate the design of circuits that employ these biomolecular platforms, we created a software design tool called Cello, in which a user writes a high-level functional specification that is automatically compiled to a DNA sequence. Algorithms first construct a circuit diagram, then assign and connect genetic "gates", and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design the largest library of genetic circuits to date, where each DNA sequence was built as predicted by the software with no additional tuning. Across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decisionmaking, control, sensing, or spatial organization.

Download or read book Preparing for Future Products of Biotechnology written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-07-28 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Between 1973 and 2016, the ways to manipulate DNA to endow new characteristics in an organism (that is, biotechnology) have advanced, enabling the development of products that were not previously possible. What will the likely future products of biotechnology be over the next 5â€"10 years? What scientific capabilities, tools, and/or expertise may be needed by the regulatory agencies to ensure they make efficient and sound evaluations of the likely future products of biotechnology? Preparing for Future Products of Biotechnology analyzes the future landscape of biotechnology products and seeks to inform forthcoming policy making. This report identifies potential new risks and frameworks for risk assessment and areas in which the risks or lack of risks relating to the products of biotechnology are well understood.