Publication

Engineering of ecological niches to create stable artificial consortia for complex biotransformations

Publications associées (18)

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification

Daniel Probst

Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed a ...

2023

Model-based scale-up of a continuously operated consolidated bioprocess based on a microbial consortium for the production of ethanol

David Beat Dempfle

This work demonstrated that consolidated bioprocessing is a promising concept for conversion of lignocellulose to ethanol at industrial scale. CBP offers great cost saving potential, is feasible to be operated continuously and may be scaled up due to exten ...

EPFL2022

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

Vassily Hatzimanikatis, Liliana Angeles Martinez

The metabolic capabilities of the species and the local environment shape the microbial interactions in a community either through the exchange of metabolic products or the competition for the resources. Cells are often arranged in close proximity to each ...

2021

Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time

Alexandre Buttler, Luca Bragazza, Constant Signarbieux, Vincent Eric Jules Jassey, Bjorn Jozef Maria Robroek, Samuel Thomas Gabriel Hamard

Plant specialized metabolites play an important role in soil carbon (C) and nutrient fluxes. Through anti-microbial effects, they can modulate microbial assemblages and associated microbial-driven processes, such as nutrient cycling, so to positively or ne ...

Frontiers Media SA2019

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Stefano Andreozzi

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-base ...

Academic Press Inc Elsevier Science2016

Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene

Klaus Kern, Kannan Balasubramanian

Mono layer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enz ...

Amer Chemical Soc2015

Tetrahydrobiopterin Biosynthesis as a Potential Target of the Kynurenine Pathway Metabolite Xanthurenic Acid

Kai Johnsson, Rudolf Hovius, Hirohito Haruki, Miriam Grønlund Pedersen

Tryptophan metabolites in the kynurenine pathway are up-regulated by pro-inflammatory cytokines or glucocorticoids, and are linked to anti-inflammatory and immunosuppressive activities. In addition, they are up-regulated in pathologies such as cancer, auto ...

Amer Soc Biochemistry Molecular Biology Inc2015

Light availability affects stream biofilm bacterial community composition and function, but not diversity

Tom Ian Battin

Changes in riparian vegetation or water turbidity and browning in streams alter the local light regime with potential implications for stream biofilms and ecosystem functioning. We experimented with biofilms in microcosms grown under a gradient of light in ...

Wiley-Blackwell2015

Effect of TiO2 Nanoparticles and UV Radiation on Extracellular Enzyme Activity of Intact Heterotrophic Biofilms

Kristin Schirmer, Laura Sigg, Hannah Inka Schug

When introduced into the aquatic environment, TiO2 NP are likely to settle from the water column, which results in increased exposure of benthic communities. Here, we show that the activity of two extracellular enzymes of intact heterotrophic biofilms, bet ...

Amer Chemical Soc2014