Publications associées à Dual Valorization of Lignin as a Versatile and Renewable Matrix for Enzyme Immobilization and (Flow) Bioprocess Engineering

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

Organ-specific biotransformation in salmonids: Insight into intrinsic enzyme activity and biotransformation of three micropollutants

Kristin Schirmer, Juliane Hollender

Aquatic ecosystems continue to be threatened by chemical pollution. To what extent organisms are able to cope with chemical exposure depends on their ability to display mechanisms of defense across different organs. Among these mechanisms, biotransformatio ...

Elsevier2024

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

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Vassily Hatzimanikatis, Daniel Robert Weilandt, Asli Sahin

One of the main challenges hampering the development of kinetic models is the lack of kinetic parameters for many enzymatic reactions. Here, the authors introduce a framework to explore the catalytically optimal operating conditions of any complex enzyme m ...

Nature Portfolio2023

Hypervalent Iodine: New Reagents and Functionalization of Peptides

Eliott Hugo Joran Le Du

Alkynes are found in a multitude of natural or synthetic bioactive compounds. In addition to the capacity of these chemical motifs to impact the physicochemical properties of a molecule of interest, the well-established reactivity of alkynes makes them ide ...

EPFL2023

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

Investigation of Carboxylic Acid Isosteres and Prodrugs for Inhibition of the Human SIRT5 Lysine Deacylase Enzyme

Alexander Lund Nielsen

Sirtuin 5 (SIRT5) is a protein lysine deacylase enzyme that regulates diverse biology by hydrolyzing epsilon-N-carboxyacyllysine posttranslational modifications in the cell. Inhibition of SIRT5 has been linked to potential treatment of several cancers but ...

Wiley-VCH Verlag GmbH2022

Dissecting the role of the asparagine synthesis in acute liver injury

Yu Sun

Amino acids are some of the main building stones of life used in a variety of biological processes, such as protein synthesis, energy metabolism or even as precursors for hormone synthesis. How-ever, some of them also participate and coordinate certain cel ...

EPFL2022

Probiotics and gut microbiome-Prospects and challenges in remediating heavy metal toxicity

Edgard Gnansounou, Ranjna Sirohi

The gut microbiome, often referred to as "super organ", comprises up to a hundred trillion microorganisms, and the species diversity may vary from person to person. They perform a decisive role in diverse biological functions related to metabolism, immunit ...

ELSEVIER2021

Organohalide respiration in Firmicutes: energy metabolism and transcription regulation

Mathilde Stéphanie Willemin

Organohalides are a class of compounds often considered as persistent pollutants and harmful to environmental and human health. Some bacteria, among which are representatives from the Firmicutes phylum, are capable of using these compounds as terminal acce ...

EPFL2021

Microfluidics and cell-free synthetic biology in the development of new diagnostic and therapeutic platforms

Grégoire Michielin

In phenylketonuria, absence or malfunction of the phenylalanine hydroxylase enzyme results in toxic accumulation of phenylalanine in the body. An injectable recombinant enzyme therapy was recently approved and has the potential to improve the quality of li ...

EPFL2021

Cluster Catalysis with Lattice Oxygen: Tracing Oxygen Transport from a Magnetite (001) Support onto Small Pt Clusters

Wolfgang Harbich, Giulia Elisabetta Pacchioni, Ke Zhang

Oxidation catalysis on reducible oxide-supported small metal clusters often involves lattice oxygen. The present work aims at differentiating whether the reaction takes place at the cluster/support interface or on the cluster. To that purpose, we trace the ...

AMER CHEMICAL SOC2021

Asymmetric azide-alkyne Huisgen cycloaddition on chiral metal surfaces

Harald Brune, Roland Widmer, Roland Hany, Michael Bauer, Samuel Thomas Stolz

Achieving fundamental understanding of enantioselective heterogeneous synthesis is marred by the permanent presence of multitudinous arrangements of catalytically active sites in real catalysts. In this study, we address this issue by using structurally co ...

NATURE RESEARCH2021

Modeling, predicting and mining metabolism at atom-level resolution

Jasmin Maria Hafner

Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understa ...

EPFL2020

Algorithms and flowchart for the design of synthetic biochemical networks

Homa Mohammadi Peyhani

New drugs are needed to assure effective therapies for previously untreated diseases, emerging diseases, and personalized medicine, but the process of drug development is complex, costly, and time-consuming. This is especially problematic considering that ...

EPFL2020

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

Yimon Aye, Alexandra Krina Van Hall-Beauvais

Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of `omics', we discuss what makes the larger subunit o ...

ELSEVIER SCI LTD2020

Evaluation of the NAD(+) biosynthetic pathway in ALS patients and effect of modulating NAD(+) levels in hSOD1-linked ALS mouse models

Johan Auwerx

Amyotrophic lateral sclerosis (ALS) is characterized by progressive degeneration of motor neurons. Astrocytes from diverse ALS models induce motor neuron death in co-culture. Enhancing NAD(+) availability, or increasing the expression of the NAD(+)-depende ...

2020

New Approach to Synthesis of Tetralin via Naphthalene Hydrogenation in Supercritical Conditions Using Polymer-Stabilized Pt Nanoparticles

Lioubov Kiwi

Supercritical (SC) fluid technologies are well-established methods in modern green chemical synthesis. Using SC fluids as solvents instead of traditional liquids gives benefits of higher diffusivity and lower viscosity, which allows mass transfer intensifi ...

2020

LC-APCI(-)-MS Determination of 1-Chloro-2,4-dinitrobenzene, a Model Substrate for Glutathione S-Transferases

Kristin Schirmer, Alena Tierbach

1-Chloro-2,4-dinitrobenzene (CDNB) is widely used as a model substrate for measuring the enzyme activity of glutathione S-transferases in toxicity studies and in studies focusing on the metabolic capacity of different test systems. To allow the quantificat ...

AMER CHEMICAL SOC2020

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

Nature Research2020