Frank J. Bruggeman

Emergent metabolic cooperation in communities of microbes that maximise growth rate by optimal protein expression

This paper develops a mathematical framework to model microbial communities optimizing growth rates through metabolic cooperation and resource allocation.

Comprehensive calculation of product and ATP yields for glucose fermentation

The paper calculates product and ATP yields for glucose fermentation by analyzing a pan-catabolic network of anaerobic digestion, revealing many novel conversions and varying ATP yields.

Net conversion calculations of catabolic pathways

This paper introduces a computational framework to calculate net conversions in metabolic networks using elementary flux modes and thermodynamic parameters, with applications in microbial ecology and metabolic engineering.

Flux balance analysis of microbial communities from metabolic strategies: composition, cross-feeding and ecological service

The paper introduces a simplified cFBA method to predict microbial community composition, growth rates, and metabolic interactions by reducing species metabolism to macrochemical equations.

A rapid HPLC-based method to determine NAD(P)(H) and NMN redox cofactor concentrations and ratios in microbes

This paper introduces a rapid HPLC-based method to measure NAD(P)(H) and NMN redox cofactor concentrations and ratios in microbes, validated against a classical assay and applied to engineered E. coli and Pseudomonas putida.

On the conditions for shifts in metabolic strategies

The paper derives conditions under which microorganisms shift to an inefficient overflow metabolism above a critical growth rate, using a core metabolic model and validating it with yeast data.

Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR

The paper develops a method to track G-protein and ERK activities in single cells using biosensors but finds challenges in obtaining robust FRET measurements.

Stoichiometric analysis of microbial communities: interrelating community function, structure and biomass carrying capacity

The paper develops a theoretical framework to analyze microbial community dynamics by linking metabolic stoichiometry, growth rates, and biomass carrying capacity.

Entangled stoichiometric objectives shape microbial catabolism

The paper analyzes microbial catabolism using genome-scale stoichiometric models to show how energy and biosynthetic objectives shape metabolic pathways and precursor usage across species.

Thermodynamics of unicellular life: Entropy production rate as function of the balanced growth rate

The paper investigates whether microbial cells can reduce entropy production rate by shifting to less thermodynamically driven metabolism at faster growth rates, using yeast models and experimental data.

Mitochondrial efficiency determines Crabtree effect across yeasts

This study identifies mitochondrial efficiency as the key factor determining the Crabtree effect in yeasts by comparing Pichia kluyveri and Saccharomyces cerevisiae.

Sensing cellular growth rate facilitates its robust optimal adaptation to changing conditions

The paper shows that cells can sense their growth rate and optimize it through gene regulatory circuits, supported by analysis of E. coli's use of ppGpp.

Biosensor imaging of G protein mediated Signaling Pathways Activated Immediately Downstream of CaSR

The paper uses biosensors to study CaSR-mediated signaling pathways in HEK-293 cells, showing activation of Gq and Gi proteins and their effects on intracellular calcium and cAMP levels.

Escherichia coli robustly expresses ATP synthase at growth rate maximizing concentrations

This study shows that Escherichia coli expresses ATP synthase at concentrations that maximize immediate growth rate across 27 nutrient conditions.

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

The paper develops a whole-cell metabolic model for yeast to predict compartment-specific proteome constraints that explain metabolic strategies under different growth conditions.

Unlocking Elementary Conversion Modes: ecmtool unveils all capabilities of metabolic networks

This paper introduces ecmtool, a tool that enumerates elementary conversion modes to fully characterize metabolic capabilities from genome-scale networks.

Elementary Growth Modes provide a molecular description of cellular self-fabrication

The paper develops a theory to describe all possible molecular states of cellular self-fabrication, identifying Elementary Growth Modes as the fundamental building blocks of cellular phenotype.

The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints

The paper shows that overflow metabolism arises from two growth-limiting constraints across different metabolic models.

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

The paper shows that maximizing microbial growth rate limits the number of active metabolic pathways to the number of enzyme expression constraints, explaining simple metabolic behaviors through evolutionary optimization.

Maintaining maximal metabolic flux by gene expression control

The paper develops a theoretical framework for optimal metabolic flux maintenance through gene expression control in bacteria, showing that it requires a minimum number of metabolite-regulated transcription factors.

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

The paper uses EFCM to show growth rate/yield trade-offs in E. coli depend on metabolic kinetics and environmental conditions, with oxygen limitation favoring faster but less efficient growth.

Bifurcation analysis of metabolic pathways: an illustration from yeast glycolysis

The paper develops new methods for bifurcation analysis of metabolic pathways, applying them to yeast glycolysis to explore steady-state behavior and bistability.

Glucose limitation in Lactococcus shapes a single-peaked fitness landscape exposing membrane occupancy as a constraint

The paper shows a mutation in CcpA improves fitness in Lactococcus lactis by reprogramming transporters, revealing membrane occupancy as a constraint.