Description
Engineering Multicellular Systems: Methods and Protocols, focuses on laboratory procedures used in recent efforts for constructing synthetic multicellular systems and their applications. In particular, constructing multicellular systems to form various microbial ecosystems has been extensively explored to examine evolution and interactions of microbial ecosystems, while co-cultures have emerged as an efficient tool to produce some complex chemical molecules. 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 key tips on troubleshooting and avoiding known pitfalls. Engineering Multicellular Systems: Methods and Protocols provide a comprehensive laboratory protocol reference for constructing multicellular systems for various applications. Part I: Constructing Multicellular Systems 1. Recent Progress in Engineering Human-associated Microbiomes Stephanie J. Yaung, George M. Church, Harris H. Wang 2. Constructing Synthetic Microbial Communities to Explore the Ecology and Evolution of Symbiosis Adam James Waite and Wenying Shou 3. Combining Engineering and Evolution to Create Novel Metabolic Mutualisms Between Species Lon Chubiz, Sarah Douglas, and William Harcombe 4. Design, Construction, and Characterization Methodologies for Synthetic Microbial Consortia Hans C. Bernstein and Ross P. Carlson 5. An Observation Method for Autonomous Signaling-mediated Synthetic Diversification in Escherichia coli Ryoji Sekine, Shotaro Ayukawa, and Daisuke Kiga 6. Integration-free Reprogramming of Somatic Cells to Induced Pluripotent Stem Cells (iPSCs) without Viral Vectors, Recombinant DNA and Genetic Modification Boon Chin HENG and Martin FUSSENEGGER 7. Transformation of Bacillus subtilis Xiao-Zhou Zhang, Chun You and Y.-H. Percival Zhang 8. Culturing Anaerobes to use as a Model System for Studying the Evolution of Syntrophic Mutualism Sujung Lim, Sergey Syolyar, Kristina Hillesland 9. Therapeutic Microbes for Infectious Disease Choon Kit Wong, Mui Hua Tan, Bahareh Haji Rasouliha, In Young Hwang, Hua Ling, Chueh Loo Poh, and Matthew Wook Chang Part II: Analyzing and Modeling Multicellular Systems 10. Quantitative Measurement and Analysis in a Synthetic Pattern Formation Multicellular System Xiongfei Fu and Wei Huang 11. Transcriptome Analysis of a Microbial Coculture in which the Cell Populations are Separated by a Membrane Kazufumi Hosoda, Naoaki Ono, Shingo Suzuki, and Tetsuya Yomo 12. Identification of Mutations in Laboratory Evolved Microbes from Next-generation Sequencing data using breseq Daniel E. Deatherage and Jeffrey E. Barrick 13. 3D-Fluorescence in situ Hybridization of Intact, Anaerobic Biofilm Kristen A. Brileya, Laura B. Camilleri, and Matthew W. Fields 14. The Characterization of Living Bacterial Colonies Using Nanospray Desorption Electrospray Ionization Mass Spectrometry Brandi S. Heath, Matthew J. Marshall, Julia Laskin 15. Modeling Community Population Dynamics with the Open-Source Language R Robin Green and Wenying Shou 16. Simulating Microbial Community Patterning using Biocellion Seunghwa Kang, Simon Kahan, Babak Momeni
