Monthly Archives: August 2018

Targeted Proteomics

Overview: Targeted proteomics assays are applied to specific hypotheses via selected-reaction monitoring (SRM) mass spectrometry methods that accurately quantify a select group of proteins. This approach has been applied to determine pathway bottlenecks, compare enzyme homologs for a specific enzymatic step, and to track dynamic regulation of protein levels engineered microbes. For instance, application of […]

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Targeted Metabolomics

Overview:  Targeted metabolomic analyses at the pathway and organism level provide functional information for both pathway and host-engineering research. Tools for strain improvement, such as metabolic flux analysis rely heavily on accurate metabolite data and carbon-flux measurements to restrict parameters for model predictions. Monitoring metabolites that are part the engineered pathway as well as central […]

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Riboregulators for Precise Control of Gene Expression

Overview:  Riboregulators of various classes have been developed to allow for the tuning of gene expression. The two classes we have designed are: cis-repressor/trans-activator pairs, and tuned standalone cis-repressors. The constructs have been designed to be universal irrespective of gene sequence. Cis-repressing riboregulators can be placed in front of genes in the genome of a […]

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Microfluidic Screening

Overview:  Droplet-based microfluidics is used to survey cell-based or cell-free expression libraries of the 1×104 – 1×106 size in picoliter aqueous droplets to identify rare events. The system can identify enzymes with promiscuous activities and can be used for protein engineering. The droplet-based microfluidics complements FACS-based methods, and supports high-throughput protein engineering. A fluorescent-based reporter […]

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Global Metabolomics and Isotopically-Labeled Metabolomics for Metabolic Flux Analysis

Overview:  Metabolomics is another key aspect of an integrated systems biology approach to understanding engineered and basal strains under different conditions to enable learning that leads to the next set of Designs for DBTL. Global metabolomics is the derivatization GC-MS analysis of the intracellular metabolome. The extracellular metabolites can be analyzed separately to assess substrate […]

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FRET Biosensors

Overview: FRET-based biosensors couple ligand-dependent protein conformational changes to a fluorescent signal response. Such biosensors can be used intra- or extracellularly to provide rapid, real-time responses to ligands or metabolites of interest. Unlike typical reporter systems, signals from FRET biosensors are reversible, permitting detection of anabolic and catabolic (conversion) processes and variations in metabolite fluxes. […]

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Experimental Data Depot

Overview: EDD is an online tool designed as a repository of experimental data and metadata. EDD can uptake experimental data, provide visualization of these data, and produce downloadable data in several standard output formats. The input of data to EDD is performed through automated data streams: each of these input streams automatically parses the standard […]

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High throughput screening platform for enzymes, pathways and strains using ‘Smart’ Microbial Cell Technology

Overview: While ‘Design’ and ‘Build’ steps of DBTL cycle for bio-based products show high throughput, the ‘Test’ step remains a bottleneck due to low efficiency of the current screening technologies. We have developed Smart Microbial Cell technology that utilizes a custom-design sensor-reporter system for a given small molecule of interest (value-added chemical, industrial precursor) in […]

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Biolector and Robolector automated fermentation and sampling platform

Overview: The Biolector is a microbioreactor for high-throughput fermentations with the online monitoring of biomass, pH, DO, and fluorescence. The RoboLector combines the high-throughput fermentation and online monitoring capability of the BioLector with the precise and accurate liquid handling of a robotic system. The RoboLector autonomously prepares media compositions, among others, from the design of experiments […]

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Biocatalyst Optimization

Overview: A microfluidic platform is utilized for rapid enzyme engineering relevant to identify improved and/or missing catalysts in production pathways.  This approach is compatible with aerobic/anaerobic enzyme screening (in vivo or cell-free).  The system is capable of utilizing TF-sensors or FRET and enzyme-linked sensors.  Once candidate genes have been identified, variants are synthesized using rational design/directed […]

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