Hidde de Jong

Fluorescent proteins misreport ribosome abundance under translation inhibition

The paper shows that fluorescent proteins misreport ribosome abundance under translation inhibition, as fluorescence intensity does not track ribosome abundance during chloramphenicol treatment.

Pareto Suboptimal Resource Allocation and Microbial Growth

The paper examines Pareto suboptimal resource allocation in microbial growth, showing that suboptimal phenotypes can arise from various resource allocation strategies and testing this with models and experimental data on E. coli and Tisochrysis lutea.

Multi-Species, Genome-Wide Metabolic Network Reconstructions Reveal the Basis for Metabolic Versatility in Mycobacteria

The paper develops genome-scale metabolic models for five Mycobacterium species to test if metabolic versatility stems from nutrient uptake capabilities, finding that transporters and substrate availability are key.

Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data

The paper develops a pipeline called Tabigecy to predict metabolic functions from metabarcoding data and integrate them into biogeochemical cycle representations.

Single-cell data reveal heterogeneity of resource allocation across a bacterial population

The paper uses single-cell data to show variability in ribosome concentrations and growth rates in Escherichia coli, challenging the population-level growth law.

Optimal protein production by a synthetic microbial consortium: Coexistence, distribution of labor, and syntrophy

This paper studies a synthetic microbial consortium of E. coli strains to optimize protein production by analyzing coexistence, labor distribution, and syntrophy in a chemostat model.

Resource allocation accounts for the large variabilityof rate-yield phenotypes across bacterial strains

The paper develops a model showing resource allocation strategies explain growth rate and yield variability in E. coli strains, supported by experimental data.

Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs

This study investigates a synthetic microbial consortium to enhance heterologous protein production, finding that productivity increases but yield decreases due to resource allocation trade-offs.