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ProteomicsExpanding the scope of redox balance growth coupling techniques with a carbon co-feeding strategy
Metabolic engineering to produce molecules not naturally synthesized by the host often requires directed evolution to improve pathway enzyme performance. Growth-coupled selection can dramatically increase directed-evolution throughput, and manipulation of redox balance has proven effective for tying...
ORGANISM(S): Escherichia coli 
2026-10-15 | PXD075294 | Pride
Hmg-coa reductase (hmgr) Cofactor specificity Directed evolution 3-hydroxybutyrate Growth-coupled selection Redox balance Jbei Mevalonate pathway 
ProteomicsProteomic analysis reveals global iron starvation response to metal mixture exposure in a Bacillus cereus strain native to a heavy metal contaminated site
Globally, multiple heavy metal contamination is an increasingly common problem. As heavy metals have the potential to disrupt microbially-mediated biogeochemical cycling, it is critical to understand their impact on microbial physiology. However, systems-level studies on the effects of a combination...
ORGANISM(S): Bacillus cereus group 
2022-09-19 | PXD035730 | Pride
Cadmium Cobalt Manganese Uranium Nickel Iron Aluminum Copper 
ProteomicsA rapid methods development workflow for high-throughput quantitative proteomic applications
we developed a workflow using data acquired from discovery proteomic experiments, retention time prediction, and standard-flow chromatography to rapidly develop targeted proteomic assays
ORGANISM(S): Escherichia coli 
2019-06-27 | PXD011212 | Pride
Workflow Proteomics High-throughput 
ProteomicsDiscovery and Characterization of a Novel Carbohydrate-Active Enzyme from the Anaerobic Fungus Piromyces finnis
Dwelling in the gut of herbivores, anaerobic gut fungi (AGF) have evolved several strategies to efficiently degrade unpretreated biomass. Their genomes encode a diverse array of carbohydrate-active enzymes (CAZymes), yet exceedingly few of these enzymes have been validated. Here, we developed a pred...
ORGANISM(S): Escherichia coli 
2025-07-31 | PXD061558 | Pride
Cazymes Jbei Proteomics High-throughput screen Heterologous expression 
ProteomicsAutomation of a CRISPRi platform for enhanced isoprenol production in Pseudomonas putida [DBTL6]
Recent advances in genome engineering technologies have significantly enhanced the ability to perturb microbial metabolic networks. Despite this progress, many bioproduction efforts struggle to parse complex metabolic datasets (e.g., -omics) within the constraints of the traditional design-build-tes...
ORGANISM(S): Pseudomonas putida KT2440 
2025-09-19 | PXD063746 | Pride
Machine learning Saf Isoprenol Jbei Laboratory automation Crispri 
ProteomicsAutomation of a CRISPRi platform for enhanced isoprenol production in Pseudomonas putida [DBTL3]
Recent advances in genome engineering technologies have significantly enhanced the ability to perturb microbial metabolic networks. Despite this progress, many bioproduction efforts struggle to parse complex metabolic datasets (e.g., -omics) within the constraints of the traditional design-build-tes...
ORGANISM(S): Pseudomonas putida KT2440 
2025-09-19 | PXD063740 | Pride
Machine learning Saf Isoprenol Jbei Laboratory automation Crispri 
ProteomicsAutomation of a CRISPRi platform for enhanced isoprenol production in Pseudomonas putida [DBTL5]
Recent advances in genome engineering technologies have significantly enhanced the ability to perturb microbial metabolic networks. Despite this progress, many bioproduction efforts struggle to parse complex metabolic datasets (e.g., -omics) within the constraints of the traditional design-build-tes...
ORGANISM(S): Pseudomonas putida KT2440 
2025-09-19 | PXD063744 | Pride
Machine learning Saf Isoprenol Jbei Laboratory automation Crispri 
ProteomicsAutomation of a CRISPRi platform for enhanced isoprenol production in Pseudomonas putida [DBTL4]
Recent advances in genome engineering technologies have significantly enhanced the ability to perturb microbial metabolic networks. Despite this progress, many bioproduction efforts struggle to parse complex metabolic datasets (e.g., -omics) within the constraints of the traditional design-build-tes...
ORGANISM(S): Pseudomonas putida KT2440 
2025-09-19 | PXD063743 | Pride
Machine learning Saf Isoprenol Jbei Laboratory automation Crispri 
ProteomicsAutomation of a CRISPRi platform for enhanced isoprenol production in Pseudomonas putida [DBTL2]
Recent advances in genome engineering technologies have significantly enhanced the ability to perturb microbial metabolic networks. Despite this progress, many bioproduction efforts struggle to parse complex metabolic datasets (e.g., -omics) within the constraints of the traditional design-build-tes...
ORGANISM(S): Pseudomonas putida KT2440 
2025-09-19 | PXD063738 | Pride
Machine learning Saf Isoprenol Jbei Laboratory automation Crispri 
ProteomicsAutomation of a CRISPRi platform for enhanced isoprenol production in Pseudomonas putida [DBTL1]
Recent advances in genome engineering technologies have significantly enhanced the ability to perturb microbial metabolic networks. Despite this progress, many bioproduction efforts struggle to parse complex metabolic datasets (e.g., -omics) within the constraints of the traditional design-build-tes...
ORGANISM(S): Pseudomonas putida KT2440 
2025-09-19 | PXD063737 | Pride
Machine learning Saf Isoprenol Jbei Laboratory automation Crispri 
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