Publications related to Influence of Uncertainties in pH, pMg, Activity Coefficients, Metabolite Concentrations, and Other Factors on the Analysis of the Thermodynamic Feasibility of Metabolic 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

Unique corrosion behavior of an archaeological Roman iron ring: Microchemical characterization and thermodynamic considerations

Stefano Mischler, Laura Brambilla

The corrosion mechanisms of a Roman iron bezel ring were investigated by in-depth characterization of its uncommon corrosion pattern and thermodynamic modelling. A silver foil and altered glass remnants were identified, covered with thick strata of magneti ...

2024

HaloTag-Based Tools for Live-Cell Imaging and Elucidation of Organellar Redox Biology

Sarah Emmert

Redox homeostasis is a key factor in maintaining cellular function and health. The main determinant of the intracellular redox potential is ubiquitous glutathione (GSH) together with its oxidized dimer (GSSG). Importantly, both redox equilibrium and GSH ho ...

EPFL2024

In situ architecture of Opa1-dependent mitochondrial cristae remodeling

Juan Cruz Landoni Martin

Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Op ...

Springernature2024

Rational combination platform trial design for children and young adults with Diffuse Midline Glioma: a report from PNOC

Sebastian Martin Waszak

Diffuse midline glioma (DMG) is a devastating pediatric brain tumor unresponsive to hundreds of clinical trials. Approximately 80% of DMGs harbor H3K27M oncohistones, which reprogram the epigenome to increase the metabolic profile of the tumor cells. We ha ...

2023

Mitochondrial matrix protein LETMD1 maintains thermogenic capacity of brown adipose tissue in male mice

Johan Auwerx, Maroun Bou Sleiman, Jun Yong Kim, Xiaoxu Li

Brown adipose tissue (BAT) has abundant mitochondria with the unique capability of generating heat via uncoupled respiration. Here, Park et al. identify LETMD1 as a mitochondrial matrix protein enriched in brown adipose tissue (BAT) and reveal a crucial ro ...

Nature Portfolio2023

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

SLC25A46 promotes mitochondrial fission and mediates resistance to lipotoxic stress in INS-1E insulin-secreting cells

Loïc Dayon, Andreas Wiederkehr

Glucose sensing in pancreatic D-cells depends on oxidative phosphorylation and mitochondria-derived signals that promote insulin secretion. Using mass spectrometry-based phosphoproteo-mics to search for downstream effectors of glucose-dependent signal tran ...

COMPANY BIOLOGISTS LTD2023

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria

Marek Elias, Shweta Vinodrai Pipaliya

The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how th ...

Public Library Science2023

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

Transcriptomic analysis reveals mitochondrial pathways associated with distinct adolescent behavioral phenotypes and stress response

Maria del Carmen Sandi Perez, Dogukan Hazar Ülgen, Thamyris Silva

Adolescent individuals exhibit great variability in cortical dynamics and behavioral outcomes. The developing adolescent brain is highly sensitive to social experiences and environmental insults, influencing how personality traits emerge. A distinct patter ...

2023

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Christof Holliger, Julien Maillard, Junxiong Wang

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirill ...

2023

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

The mitochondrial calcium uniporter (MCU) activates mitochondrial respiration and enhances mobility by regulating mitochondrial redox state

Umberto De Marchi, Sonia Karaz, Federico Sizzano, Vincenzo Sorrentino

Regulation of mitochondrial redox balance is emerging as a key event for cell signaling in both physiological and pathological conditions. However, the link between the mitochondrial redox state and the modulation of these conditions remains poorly defined ...

ELSEVIER2023

Countering T cell exhaustion and senescence for enhanced adoptive T cell therapies against solid tumors

Yang Zhao

CAR-T cell therapy has shown remarkable success in treating hematopoietic malignancies, but its efficacy in solid tumors is limited by T cell dysfunction, including exhaustion and senescence. In this study, we designed metabolically armored CAR-T cells to ...

EPFL2023

Machine-learning the electronic density of states: electronic properties without quantum mechanics

Chiheb Ben Mahmoud

The electronic density of states (DOS) quantifies the distribution of the energy levels that can be occupied by electrons in a quasiparticle picture and is central to modern electronic structure theory. It also underpins the computation and interpretation ...

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

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

Role of the cystathionine beta-synthase / H2S pathway in the development of cellular metabolic dysfunction and pseudohypoxia in down syndrome

Theodora Panagaki

Background: Overexpression of the transsulfuration enzyme cystathionine-beta-synthase (CBS), and overproduction of its product, hydrogen sulfide (H2S) are recognized as potential pathogenetic factors in Down syndrome (DS). The purpose of the study was to d ...

ELSEVIER2022