Publications associées à How reliable are thermodynamic feasibility statements of biochemical pathways?

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

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Evangelia Vagena

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

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

Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms

Christof Holliger, Julien Maillard, Florence Armand, Romain Hamelin, Mathilde Stéphanie Willemin

IntroductionDesulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy meta ...

Frontiers Media SA2023

Metabolic Performance and Fate of Electrons during Nitrate-Reducing Fe(II) Oxidation by the Autotrophic Enrichment Culture KS Grown at Different Initial Fe/N Ratios

Natalia Jakus

Autotrophic nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms fix CO2 and oxidize Fe(II) coupled to denitrification, influencing carbon, iron, and nitrogen cycles in pH-neutral, anoxic environments. However, the distribution of electrons from Fe(II ...

AMER SOC MICROBIOLOGY2023

Engineering extracellular electron transfer for enhanced energy harvesting in microbial electrochemical devices

Mohammed Mouhib

Microorganisms known as exoelectrogens evolved the ability of transporting electrons across insulating biological membranes. In a physiological context, this enables respiration on extracellular electron acceptors and electron transfer to other organisms. ...

EPFL2023

Early Neuroprotective Effects of Bovine Lactoferrin Associated with Hypothermia after Neonatal Brain Hypoxia-Ischemia in Rats

Yohan Van de Looij

Neonatal hypoxic-ischemic (HI) encephalopathy (HIE) in term newborns is a leading cause of mortality and chronic disability. Hypothermia (HT) is the only clinically available therapeutic intervention; however, its neuroprotective effects are limited. Lacto ...

MDPI2023

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

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Vassily Hatzimanikatis, Jasmin Maria Hafner, Victor Luc Etienne Viterbo, Anastasia Sveshnikova

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

Nature Portfolio2022

Characterization of the electron-accepting part of the organohalide respiration chain of Dehalobacter and Desulfitobacterium

Lorenzo Cimmino

Organohalide respiration (OHR) is a bacterial anaerobic process that use halogenated compounds, e.g. tetrachloroethene (PCE), as terminal electron acceptors. D. restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and D. hafniense strain TCE1, a ba ...

EPFL2022

Metabolic regulation of cytokinesis in Schizosaccharomyces pombe

Özge Uysal Özdemir

All cells need to be able to sense their environment, and adapt their metabolism, growth and cell division appropriately. In this study, I examined the response of Schizosaccharomyces pombe to a change in the carbon source and how that affects cytokinesis. ...

EPFL2022

Acetate, a metabolic product of Heligmosomoides polygyrus, facilitates intestinal epithelial barrier breakdown in a FFAR2-dependent manner

Luc Xavier Marie Lebon, Nicola Harris, Mario Michael Zaiss, Julia Esser-von Bieren, Lalit Kumar Dubey

Approximately 2 billion people worldwide and a significant part of the domestic livestock are infected with soil-transmitted helminths, of which many establish chronic infections causing substantial eco-nomic and welfare burdens. Beside intensive research ...

2022

Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"

Vassily Hatzimanikatis, Homa Mohammadi Peyhani, Anastasia Sveshnikova

Supplementary datasets accompanying the manuscript "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" published in the Metabolic Engineering Journal (https://doi.org/10.1016/j.ymben.2022.03.013). In line w ...

Zenodo2022

Primary data for EPFL thesis "Metabolic regulation of cytokinesis in Schizosaccharomyces pombe"

Özge Uysal Özdemir

All cells need to be able to sense their environment, and adapt their metabolism, growth and cell division appropriately. In this study, I examined the response of Schizosaccharomyces pombe to a change in the carbon source and how that affects cytokinesis. ...

EPFL Infoscience2022

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Vassily Hatzimanikatis, Jasmin Maria Hafner

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

OXFORD UNIV PRESS2021

Genetic, metabolic, and molecular insights into the diverse outcomes of diet-induced obesity in mouse

Alexis Maximilien Bachmann

Overweight and obesity are increasingly common public health issues worldwide, leading to a wide range of diseases from metabolic syndrome to steatohepatitis and cardiovascular diseases. While the increase in the prevalence of obesity is partly attributabl ...

EPFL2021

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Vassily Hatzimanikatis, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Diauxie, or the sequential consumption of carbohydrates in bacteria such as Escherichia coli, has been hypothesized to be an evolutionary strategy which allows the organism to maximize its instantaneous specific growth-giving the bacterium a competitive ad ...

National Academy of Sciences2021