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

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

Ljubisa Miskovic, Vassily Hatzimanikatis, 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

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

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

Laura Sigg, Kristin Schirmer, 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

Enzyme inhibition by metal complexes: concepts, strategies and applications

Paul Joseph Dyson, Kelly Joan Kilpin

Metal complexes are increasingly being used to inhibit enzymes. The reasons for this increased interest arise from the special features that metal complexes offer, e.g. the facile construction of 3D architectures that tightly fill enzyme active sites incre ...

2013

Comparative study of three lactate oxidases from Aerococcus viridans for biosensing applications

Giovanni De Micheli, Sandro Carrara, Irene Taurino

A comparison between engineered and commercially available L-lactate oxidases from Aerococcus viridans was conducted for biosensing applications. Enzymes were adsorbed onto the surfaces of graphite electrodes modified with multi-walled carbon nanotubes. Th ...

Elsevier2013

Functional Genotyping of Sulfurospirillum spp. in Mixed Cultures Allowed the Identification of a New Tetrachloroethene Reductive Dehalogenase

Christof Holliger, Julien Maillard, Géraldine Florence Buttet

Reductive dehalogenases are the key enzymes involved in the anaerobic respiration of organohalides such as the widespread groundwater pollutant tetrachloroethene. The increasing number of available bacterial genomes and metagenomes gives access to hundreds ...

Amer Soc Microbiology2013

Studies of Glutathione Transferase P1-1 Bound to a Platinum(IV)-Based Anticancer Compound Reveal the Molecular Basis of Its Activation

Paul Joseph Dyson, Ursula Röthlisberger, Wee Han Ang, Pablo Campomanes Ramos

Platinum-based cancer drugs, such as cisplatin, are highly effective chemotherapeutic agents used extensively for the treatment of solid tumors. However, their effectiveness is limited by drug resistance, which, in some cancers, has been associated with an ...

Wiley-Blackwell2011

Development of Bimetallic Titanocene-Ruthenium-Arene Complexes As Anticancer Agents: Relationships between Structural and Biological Properties

Philippe Richard, Olivier Pierre Zava, Fabio Edafe

A series of bimetallic titanium-ruthenium complexes of general formula (η5-C5H5)(μ-η5:κ1-C5H4(CR12)nPR2R3)TiCl2RuCl2 (n = 0, 1, 2 or 4; R1 = H or Me; R2 = H, Ph, or Cy; R3 = Ph or Cy) have been synthesized, including two novel compds. as wel ...

American Chemical Society2010

Identification and characterization of proteins supporting dehalorespiration in Desulfitobacterium hafniense strain TCE1

Laure Prat

Respiration is a fundamental catalytic process in the aerobic and anaerobic energy metabolism of many prokaryotic and most eukaryotic organisms. The major difference between these organisms is that various organic and inorganic substrates can be used to do ...

EPFL2009

A novel reactive perstraction system based on liquid-core microcapsules applied to lipase-catalyzed biotransformations

Ian William Marison, Urs von Stockar

A novel reactive perstraction system has been developed based on liq.-core capsules, involving an enzyme-catalyzed reaction coupled with simultaneous in situ product recovery. Lipase-catalyzed reactions, hydrolysis of triprionin and nitrophenyl laurate, we ...

2006

Optimized methods for the enzymatic ligation of oligoribonucleotides and analogues

Frédéric David Meylan

The preparation of oligoribonucleotides is of great interest for structural and functional investigations in biomolecular chemistry and biology. Relevant RNAs are relatively long and contain often modifications. Two methods for their preparation are curren ...

EPFL2006