Engineering and Analyzing Multicellular Systems

1. Front Matter

   Pages i-xi

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2. Constructing Multicellular Systems

   1. Front Matter

      Pages 1-1

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   2. Recent Progress in Engineering Human-Associated Microbiomes

      • Stephanie J. Yaung, George M. Church, Harris H. Wang

      Pages 3-25

   3. Constructing Synthetic Microbial Communities to Explore the Ecology and Evolution of Symbiosis

      • Adam James Waite, Wenying Shou

      Pages 27-38

   4. Combining Engineering and Evolution to Create Novel Metabolic Mutualisms Between Species

      • Lon Chubiz, Sarah Douglas, William Harcombe

      Pages 39-47

   5. Design, Construction, and Characterization Methodologies for Synthetic Microbial Consortia

      • Hans C. Bernstein, Ross P. Carlson

      Pages 49-68

   6. An Observation Method for Autonomous Signaling-Mediated Synthetic Diversification in Escherichia coli

      • Ryoji Sekine, Shotaro Ayukawa, Daisuke Kiga

      Pages 69-74

   7. Integration-Free Reprogramming of Human Somatic Cells to Induced Pluripotent Stem Cells (iPSCs) Without Viral Vectors, Recombinant DNA, and Genetic Modification

      • Boon Chin Heng, Martin Fussenegger

      Pages 75-94

   8. Transformation of Bacillus subtilis

      • Xiao-Zhou Zhang, Chun You, Yi-Heng Percival Zhang

      Pages 95-101

   9. Culturing Anaerobes to Use as a Model System for Studying the Evolution of Syntrophic Mutualism

      • Sujung Lim, Sergey Stolyar, Kristina Hillesland

      Pages 103-115

   10. Therapeutic Microbes for Infectious Disease

       • Choon Kit Wong, Mui Hua Tan, Bahareh Haji Rasouliha, In Young Hwang, Hua Ling, Chueh Loo Poh et al.

       Pages 117-133

3. Analyzing and Modeling Multicellular Systems

   1. Front Matter

      Pages 135-135

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   2. Quantitative Measurement and Analysis in a Synthetic Pattern Formation Multicellular System

      • Xiongfei Fu, Wei Huang

      Pages 137-149

   3. Transcriptome Analysis of a Microbial Coculture in which the Cell Populations Are Separated by a Membrane

      • Kazufumi Hosoda, Naoaki Ono, Shingo Suzuki, Tetsuya Yomo

      Pages 151-164

   4. Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq

      • Daniel E. Deatherage, Jeffrey E. Barrick

      Pages 165-188

   5. 3D-Fluorescence In Situ Hybridization of Intact, Anaerobic Biofilm

      • Kristen A. Brileya, Laura B. Camilleri, Matthew W. Fields

      Pages 189-197

   6. The Characterization of Living Bacterial Colonies Using Nanospray Desorption Electrospray Ionization Mass Spectrometry

      • Brandi S. Heath, Matthew J. Marshall, Julia Laskin

      Pages 199-208

   7. Modeling Community Population Dynamics with the Open-Source Language R

      • Robin Green, Wenying Shou

      Pages 209-231

   8. Simulating Microbial Community Patterning Using Biocellion

      • Seunghwa Kang, Simon Kahan, Babak Momeni

      Pages 233-253

4. Back Matter

   Pages 255-256

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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.

• Microbial ecosystems
• cell-cell interactions
• engineering genetic
• microbial communities
• microbial species
• predictive mathematical models
• synthetic communities
• biochemical engineering

• School of Life Sciences, University of Science & Technology of China,, Hefei, China

  Lianhong Sun

• Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, USA

  Wenying Shou

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