Organic synthesis is essential to creating new materials. While synthetic design has reached a high level of sophistication, many details remain unplannable. To become proficient in organic synthesis, one must study case histories in the same way as a lawyer does. Attention must be paid to overcoming stumbling blocks as one prepares himself to meet future challenges of similar kinds. This book discusses many important syntheses, with emphasis on the need for detours and ways leading back to the main pathways. It thus focuses on one of the most important aspects of organic synthesis, which virtually none of the synoptic literature addresses.

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.

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.

This volume outlines key steps associated with the design, building, and testing of synthetic metabolic pathways for optimal cell factory performance and robustness, and illustrates how data-driven learning from these steps can be used for rational cost-effective engineering of cell factories with improved performance. Chapters are divided into four sections focusing on the four steps of the iterative design-build-test-learn cycle related to modern cell factory engineering. 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 practical, Synthetic Metabolic Pathways: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This textbook presents solid tools for in silico engineering biology, offering students a step-by-step guide to mastering the smart design of metabolic pathways. The first part explains the Design-Build-Test-Learn-cycle engineering approach to biology, discussing the basic tools to model biological and chemistry-based systems. Using these basic tools, the second part focuses on various computational protocols for metabolic pathway design, from enzyme selection to pathway discovery and enumeration. In the context of industrial biotechnology, the final part helps readers understand the challenges of scaling up and optimisation. By working with the free programming language Scientific Python, this book provides easily accessible tools for studying and learning the principles of modern in silico metabolic pathway design. Intended for advanced undergraduates and master’s students in biotechnology, biomedical engineering, bioinformatics and systems biology students, the introductory sections make it also useful for beginners wanting to learn the basics of scientific coding and find real-world, hands-on examples.

Molecular evolutionary analyses commonly focus on individual genes and their products without considering functional interactions necessary for organismal fitness. There is a need to understand how evolutionary forces act on multiple interacting genes together that function as components of molecular pathways and networks. A question that emerges is how stable rate-limiting steps are over evolutionary time? Although the biochemistry community has generally assumed that metabolic pathways have evolutionarily stable rate limiting steps, the idea has not been rigorously tested. Glycolysis is an essential metabolic pathway that involves a breakdown of one glucose molecule to two pyruvate molecules. Common thought is that control in glycolysis is governed by reaction free energy and pathway position. The prevailing view is that the rates of individual enzymes in glycolysis are controlled by reaction free energy and their relative positions in the pathway. Here we performed a sensitivity analysis in all available glycolysis kinetic models and discovered that rate-limiting steps varied between different species. Another approach to evaluate evolutionary instability of rate-limiting steps is to use an evolutionary computational simulation of a glycolysis-like synthetic pathway with mutation and various selective schemes. The simulations performed used combinations of selection for steady state flux. That were compared against the cost of synthesizing mRNA and proteins, and against the accumulation of high concentrations of a deleterious intermediate. Results from this study suggest that rate-limiting steps in metabolic pathways are generally not evolutionarily stable and are subject to co-evolutionary mutation-selection balance. We further hypothesized that when the system is out of equilibrium due to fluctuating selection, population size or due to positive directional selection, the evolutionary stability of rate limiting steps will have a different evolutionary dynamic. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result suggests that differences in patterns of evolution when systems are in and out of equilibrium, may lead to predictable differences in observed patterns for divergent evolutionary scenarios.