Synthetic Metabolic Pathways

Part I: Parts and Models for Designing Synthetic Metabolic Pathways 1. Parts characterization for tunable protein expression Michael S. Klausen and Morten O. A. Sommer 2. Enzyme Nicotinamide Cofactor Specificity Reversal Guided by Automated Structural Analysis and Library Design Jackson K.B. Cahn, Sabine Brinkmann-Chen, and Frances H. Arnold 3. Bacterial Genome Editing Strategy for Control of Transcription and Protein Stability Ida Lauritsen, Virginia Martínez, Carlotta Ronda, Alex Toftgaard Nielsen, and Morten H. H. Nørholm 4. An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization Sean M. Halper, Daniel P. Cetnar, and Howard M. Salis 5. Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design Mohammad Mazharul Islam and Rajib Saha 6. Extended Metabolic Space Modeling Pablo Carbonell, Baudoin Delépine, and Jean-Loup Faulon 7. Computational Methods to Assess the Production Potential of Bio-based Chemicals Miguel A. Campodonico, Sumesh Sukumara, Adam M. Feist, and Markus J. Herrgård Part II: Building and Refactoring Synthetic Metabolic Pathways 8. Multiplex Genome Editing in Escherichia coli Sheila Ingemann Jensen and Alex Toftgaard Nielsen 9. Designing and Implementing Algorithmic DNA Assembly Pipelines for Multi-gene Systems Szu-Yi Hsu and Michael J. Smanski 10. An adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism Tian Zhang and Pier-Luc Tremblay 11. CRISPR-Cas9 toolkit for Actinomycete Genome Editing Yaojun Tong, Helene Lunde Robertsen, Kai Blin, Tilmann Weber, and Sang Yup Lee 12. Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast using CasEMBLR Tadas Jakociunas, Emil D. Jensen, Michael K. Jensen, and Jay D. Keasling 13 A modified Gibson assembly method for cloning large DNA fragments with high GC contents Lei Li, Weihong Jiang, and Yinhua Lu 14 Coupling Yeast Golden Gate and VEGAS for efficient assembly of the violacein pathway in Saccharomyces cerevisiae James Chuang, Jef D. Boeke, and Leslie A. Mitchell Part III: Screening and Selection of Synthetic Metabolic Pathways 15 Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites For Phenotyping Of Microorganisms Christoph Halbfeld, Jörg Ingo Baumbach, Lars M. Blank, and Birgitta E. Ebert 16 Selection of Highly Expressed Gene Variants in Escherichia coli using Translationally-coupled Antibiotic Selection Markers Maja Rennig, Daniel O. Daley, and Morten H. H. Nørholm 17. Design, Engineering, and Characterization Of Prokaryotic Ligand-binding Transcriptional Activators as Biosensors in Yeast Francesca Ambri, Tim Snoek, Mette L. Skjoedt, Michael K. Jensen, and Jay D. Keasling 18. A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers against Small Molecules Lasse H. Lauridsen, Holger B. Doessing, Katherine S. Long, and Alex T. Nielsen 19. High-throughput Microfluidics for the Screening Of Yeast Libraries Mingtao Huang, Haakan N. Joensson, and Jens Nielsen 20. Growth-Coupled Carotenoids Production Using Adaptive Laboratory Evolution Luis H. Reyes and Katy C. Kao Part IV: Learnings from Design-Build-Test-based Projects 21. Two scale 13C Metabolic Flux Analysis for Metabolic Engineering David Ando and Hector Garcia Martin... Mehr