Publications associées à Model Organisms Proteomics-From Holobionts to Human Nutrition

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

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

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Yimon Aye

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Wiley-V C H Verlag Gmbh2024

Industrial Biotechnology Conservation Processes: Similarities with Natural Long-Term Preservation of Biological Organisms

Nathalie Hirt-Burri, Philippe Abdel Sayed, Corinne Scaletta, Lee Ann Laurent-Applegate, Laurent Alexis Clément Vannay, Alexis Laurent

Cryopreservation and lyophilization processes are widely used for conservation purposes in the pharmaceutical, biotechnological, and food industries or in medical transplantation. Such processes deal with extremely low temperatures (e.g., -196 degrees C) a ...

MDPI2023

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Omaya Pierre Dudin

Many eukaryotes form multinucleated cells during their devel-opment. Some cells persist as such during their lifetime, others choose to cleave each nucleus individually using a specialized cytokinetic process known as cellularization. What is cellula-rizat ...

CURRENT BIOLOGY LTD2023

Centromere structure and function: lessons from Drosophila

Eftychia Kyriacou

The fruit fly Drosophila melanogaster serves as a powerful model organism for advancing our understanding of biological processes, not just by studying its similarities with other organisms including ourselves but also by investigating its differences to u ...

Genetics Society America2023

Label-free plasmonic microarray for multiplexed analysis of cells and tumor organoids

Yen-Cheng Liu

Investigating the dynamic activities of protein expression and signaling in living organisms is a crucial focus of intense research aimed at elucidating the processes that underlie disease progression and improving treatments and drug development. Resolvin ...

EPFL2023

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

Microfluidic culture platforms for C. elegans bacterial interaction and digestion studies at single-organism resolution

Vittorio Viri

Increasing interest in understanding fundamental biological processes, among which aging and nutrition, has led to the study of simple and powerful model organisms, as the round-worm Caenorhabditis elegans (C. elegans). The nematode, selected by Sydney Bre ...

EPFL2021

New and improved methods for integrated models of metabolism and gene expression

Pierre Guy Rémy Salvy

The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...

EPFL2021

Approaches to Test the Neurotoxicity of Environmental Contaminants in the Zebrafish Model: From Behavior to Molecular Mechanisms

Anze Zupanic, Sarah-Katharina Könemann, Colette vom Berg

The occurrence of neuroactive chemicals in the aquatic environment is on the rise and poses a potential threat to aquatic biota of currently unpredictable outcome. In particular, subtle changes caused by these chemicals to an organism's sensation or behavi ...

2021

Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities

Guido Van Mierlo

Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emer ...

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2021

Biotechnology Applications of Nanocarbons in Plant and Algal Systems

Ardemis Anoush Boghossian, Alessandra Antonucci, Alice Judith Gillen

The unique combination of structural, optical, and electronic properties of nanocarbons (NCs) has made these materials particularly attractive for various applications in biotechnology and biomedicine, ranging from sensing, gene-delivery, bioimaging and th ...

Royal Society of Chemistry2021

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Florence Mehl, Noushin Hadadi, Merten Morales, Anush Chiappino-Pepe, Vikash Kumar Pandey

Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation re ...

NATURE PUBLISHING GROUP2020

Biogeography and biochemistry of bile acid 7-dehydroxylation in the mammalian gut

Solenne Anne Marie Marion

Bile acids (BAs) are small molecules synthesized by the host and chemically modified by the microorganisms inhabiting the intestinal tract. The microbial transformation of BAs in the gut is critical to BA-mediated signaling as it modifies their amount and ...

EPFL2020

A perspective view on the nanomotion detection of living organisms and its features

Giovanni Dietler, Sandor Kasas, Anne-Céline Verenna Kohler, Giovanni Longo, Massimiliano Bertacchi, Petar Stupar, María Inés Villalba, Leonardo Venturelli

The insurgence of newly arising, rapidly developing health threats, such as drug-resistant bacteria and cancers, is one of the most urgent public-health issues of modern times. This menace calls for the development of sensitive and reliable diagnostic tool ...

WILEY2020

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Vassily Hatzimanikatis, Sofia Tsouka

Metabolism is a network of biotransformations that sustain life in cells. Over the past decades, metabolism has been studied in multiple contexts, ranging from medicine to industrial manufacturing. In particular, lipid metabolism has been linked to various ...

EPFL2020

Do chance encounters between heterogeneous cells shape the outcome of tuberculosis infections?

John McKinney, Ophélie Rutschmann, Chiara Toniolo

The sum of all of the interactions between single bacteria and host cells determines if an infection is cleared, controlled, or progresses at the whole host-organism level. These individual interactions have independent trajectories defined by diverse and ...

2020

The social nature of mitochondria: Implications for human health

Maria del Carmen Sandi Perez

Sociality has profound evolutionary roots and is observed from unicellular organisms to multicellular animals. In line with the view that social principles apply across levels of biological complexity, a growing body of data highlights the remarkable socia ...

2021

Interaction of Fluorescent Single-Walled Carbon Nanotubes with Photosynthetic Microbes

Alessandra Antonucci

The discovery of carbon-based nanomaterials has impacted a variety of research areas in ways that could not be imagined three decades ago. Their unique combination of structural, optical, and electronic properties has made these nano-sized materials partic ...

EPFL2020

Development of novel tools for imaging of metabolic fluxes in vivo

Tamara Maric

Bioluminescent imaging is a powerful technique that enables imaging in living organisms with high sensitivity, low background signal, low cost and without the need for radioactivity. The emitted photons are produced in the oxidation reaction of luciferin c ...

EPFL2020