Preface

Understanding complex biological systems and their relation to biological function is a current challenge in biological sciences. During the last two decades, the field of synthetic biology has allowed the design and construction of synthetic biological systems at different scales of complexity. The first level of complexity to be explored was related to the design of BioBricks (e.g., promoters, coding sequences, terminators, reporters, and regulatory sequences), which are the essential building blocks for pathway engineering. Over the last decade, an astonishing improvement in sequencing technologies has resulted in millions of bits of information in public databases. This is a valuable mine of data for identifying novel BioBricks so far not elucidated, many of them attributed to novel biological functions.

Moreover, the development of low-cost DNA synthesis technologies has boosted the rational design of these BioBricks and their subsequent integration into synthetic gene networks. Many methodological approaches have been designed to simplify cloning and BioBricks' assembly into networks. This represents the second level of complexity, where synthetic metabolic networks can be designed, constructed, and studied as a modular part of a more complex biological system. Recently, different attempts to integrate these modules into complex systems have opened the possibility to engineer and construct entire synthetic genomes, representing a tremendous advance in Synthetic Biology. Accordingly, a new research field has emerged called synthetic genomics. The general goal of this novel area of synthetic biology is to engineer synthetic genomes from scratch using a set of pre-designed building blocks coupled in a hierarchical and modular way.

This book discusses the state of the art in synthetic genomics by presenting relevant examples in this emerging area. The introductory chapter, "From BioBricks to Synthetic Genomes," describes the evolution of synthetic genomics, starting from BioBricks design and ending with the construction of complete viral and bacterial synthetic genomes. "Multi-*Omics* Data Mining: A Novel Tool for BioBrick Design" provides a deeper explanation of the principles of BioBricks design. "Applications of CRISPR/Cas Technology to Research the Synthetic Genomics of Yeast" and "CRISPR-Cas9: Role in Processing of Modular Metabolic Engineered Bio-Based Products" present examples of technologies employed to engineering genomes using CRISPR-based approaches. The final chapter, "Synthetic Gene Circuits for Antimicrobial Resistance and Cancer Research," describes the use of mathematical modeling for genome engineering. This book is a valuable tool for students and scientists who would like to become familiar with this new research area.

We would like to thank the researchers from the Group of Product and Process Design at Universidad de Los Andes, Colombia, and the Group of Biotechnology at the Leibniz Institute of Plant Biochemistry, Germany, for their contributions, correct observations, and excellent knowledge that improved this work. We would like to especially thank Dr. Prof. Ludger Wessjohann, Dr. Prof. Luis H. Reyes,

and Dr. Martin Dippe for their valuable contributions and fruitful discussions. We would also like to thank Author Service Managers Iva Ribic and Marijana Francetic at IntechOpen for their support and contributions during the editorial process.

#### **Miguel Fernández-Niño**

Researcher at the Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle, Germany

#### **Luis Humberto Reyes**

Associate Professor at the Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia Section 1
