Synthetic Metabolic Pathways Methods and Protocols

Parts characterization for tunable protein expression.- Enzyme nicotinamide cofactor specificity reversal guided by automated structural analysis and library design.- Bacterial genome editing strategy for control of transcription and protein stability.- An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.- Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design.- Extended Metabolic Space Modeling.- Computational Methods to Assess the Production.- Designing and Implementing Algorithmic DNA Assembly Pipelines for Multi-gene Systems.- An adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism.- CRISPR-Cas9 toolkit for Actinomycete Genome Editing.- Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast using CasEMBLR.- A modified Gibson assembly method for cloning large DNA fragments with high GC contents.- Coupling Yeast Golden Gate and VEGAS for efficient assembly of the violacein pathway in Saccharomyces cerevisiae.- Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites For Phenotyping Of Microorganisms.- Selection of Highly Expressed Gene Variants in Escherichia coli using Translationally-coupled Antibiotic Selection Markers.- Design, Engineering, and Characterization Of Prokaryotic Ligand-binding Transcriptional Activators as Biosensors in Yeast.- A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers against Small Molecules.- High-throughput Microfluidics for the Screening Of Yeast Libraries.- Growth-Coupled Carotenoids Production Using Adaptive Laboratory Evolution.- Two scale 13C Metabolic Flux Analysis for Metabolic Engineering.