Meet the editors

Dr. Miguel Fernández-Niño is a biologist from The National University of Colombia with a master's degree in Biochemistry from the same institution and a Ph.D. in Biochemical Engineering from Jacobs University, Bremen, Germany. He is currently working as a researcher at the Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany. Dr. Fernández-Niño has extensive experience in synthetic biology, metabolic engineering, genome

mining/editing, and molecular biotechnology, which can be applied to engineer and improve microorganisms with biotechnological applications.

Dr. Luis H. Reyes is a highly skilled and forward-thinking chemical engineer with a Ph.D. in Chemical Engineering and broad knowledge and experience in several fields of molecular and synthetic biology, genetics, evolutionary and protein engineering, and bioprocess engineering, using diverse microorganisms including *Escherichia coli*, *Saccharomyces cerevisiae*, *Pichia pastoris*, *Clostridium thermocellum*, *Kluyveromyces lactis,* and *Lactoba-*

*cillus brevis*. Currently, he is an associate professor in the Department of Chemical and Food Engineering, Universidad de Los Andes, Bogota, Colombia.

Contents

**Section 1**

**Section 2**

Genomics of Yeast

Bio-Based Products

*Preeti Nain and Manish Biyani*

*and Daniel A. Charlebois*

**Preface XI**

Rational Design of BioBricks for Genome Assembly **1**

**Chapter 1 3**

**Chapter 2 11**

and Mathematical Modelling **35**

**Chapter 3 37**

**Chapter 4 55**

**Chapter 5 71**

Synthetic Gene Circuits for Antimicrobial Resistance and Cancer Research

Introductory Chapter: From BioBricks to Synthetic Genomes

Multi-*Omics* Data Mining: A Novel Tool for BioBrick Design

Engineering Genomes through CRISPR-Based Technologies

Applications of CRISPR/Cas Technology to Research the Synthetic

*by Huafeng Lin, Haizhen Wang, Aimin Deng, Minjing Rong, Lei Ye,* 

CRISPR-Cas9: Role in Processing of Modular Metabolic Engineered

*by Vishnu Sharma, Tarun Kumar Kumawat, Anjali Pandit, Bhoomika Sharma, Pooja Agarwal, Bhawana Sharma,* 

*by Kevin S. Farquhar, Michael Tyler Guinn, Gábor Balázsi* 

*Ludger Aloisius Wessjohann and Miguel Fernández-Niño*

*Lei Shi, Tuanmei Wang and Xiangwen Peng*

*by Angie Burgos-Toro, Martin Dippe, Andres Felipe Vásquez, Eric Pierschel,* 

*by Luis Humberto Reyes and Miguel Fernández-Niño*

## Contents


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

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

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,

elucidated, many of them attributed to novel biological functions.

building blocks coupled in a hierarchical and modular way.
