Publications associées à Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Portfolio2024

Statistical physics of periodic biological processes

Lorenzo Talamanca

Earth rotation around its axis imposes a 24-hour rhythmicity to all life on the planet. Rather than passively responding to these periodic changes, nature has given us an internal timekeeper, the circadian clock, to anticipate to our advantage the fluctuat ...

EPFL2023

Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans

Felix Naef, Cédric Gobet, Lorenzo Talamanca

The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an a ...

American Association for the Advancement of Science2023

Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior

Cédric Gobet, Sylviane Métairon, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

The synchronization of circadian clock depends on a central pacemaker located in the suprachiasmatic nuclei. However, the potential feedback of peripheral signals on the central clock remains poorly characterized. To explore whether peripheral organ circad ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Uncovering personalized glucose responses and circadian rhythms from multiple wearable biosensors with Bayesian dynamical modeling

Felix Naef, Nicholas Edward Phillips

Wearable biosensors and smartphone applications can measure physiological variables over multiple days in free-living conditions. We measure food and drink ingestion, glucose dynamics, physical activity, heart rate (HR), and heart rate variability (HRV) in ...

CELL PRESS2023

The circadian clock time tunes axonal regeneration

Thomas Haynes Hutson

Nerve injuries cause permanent neurological disability due to limited axonal regeneration. Injury-dependent and-independent mechanisms have provided important insight into neuronal regeneration, however, common denominators underpinning regeneration remain ...

Cell Press2023

Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution

Maria Brbic, Sandy Lee

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We c ...

American Association for the Advancement of Science2023

Reduced order models for coupled systems

Niccolo' Discacciati

Efficient numerical simulations of coupled multi-component systems can be particularly challenging. This is mostly due to the complexity of their solutions, as mutual interactions may cause emergent behaviors, including synchronization and instabilities. V ...

EPFL2023

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Judith Franziska Kribelbauer, Guido Van Mierlo

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP

Didier Trono, Julien Léonard Duc, Christina Ernst

RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challengin ...

2023

Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

Felix Naef, Cédric Gobet, Clémence Yumie Syloun Hurni, Benjamin Dieter Weger

In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of ...

PUBLIC LIBRARY SCIENCE2022

Preliminary evidence that daily light exposure enhances the antibody response to influenza vaccination in patients with dementia

Jean-Louis Scartezzini

Enhancing lighting conditions in institutions for individuals with dementia improves their sleep, circadian rhythms and well-being. Here, we report first findings that exposure to brighter light during daytime may support the immune response to the annual ...

ELSEVIER2022

A simulation tool for building and lighting design considering ipRGC-influenced light responses

Marilyne Andersen, Clotilde Marie A Pierson, Myrta Gkaintatzi-Masouti

The ipRGCs in the human eye mediate several effects on people, such as alertness and circadian rhythms. The spectral, temporal and spatial characteristics of light influence the magnitude of these effects. To facilitate the anticipation of the ipRGC-influe ...

2022

Optimized office lighting advances melatonin phase and peripheral heat loss prior bedtime

Jean-Louis Scartezzini, Mirjam Münch, Lenka Maierova, Marta Benedetti

Improving indoor lighting conditions at the workplace has the potential to support proper circadian entrainment of hormonal rhythms, sleep, and well-being. We tested the effects of optimized dynamic daylight and electric lighting on circadian phase of mela ...

Nature Research2022

Type 2 diabetes disrupts circadian orchestration of lipid metabolism and membrane fluidity in human pancreatic islets

Howard Riezman, Jonathan Paz Montoya

Recent evidence suggests that circadian clocks ensure temporal orchestration of lipid homeostasis and play a role in pathophysiology of metabolic diseases in humans, including type 2 diabetes (T2D). Nevertheless, circadian regulation of lipid metabolism in ...

PUBLIC LIBRARY SCIENCE2022

A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes

Linlin Cao

The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing ...

American Association of Immunologists ; Oxford University Press2022

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Felix Naef, Cédric Gobet

Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained dif ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

Bart Deplancke, Sandy Lee

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs condi ...

Nature Portfolio2022

Integrative transcriptome analyses of Transposable Elements (TEs) and genes contribute to a better understanding of colorectal cancer

Eunji Shin

Cancer is the second leading cause of death worldwide. Cancer develops through multiple hallmark functions including apoptosis evasion, unlimited replicative potential, metastasis, and immune avoidance. Over the past few decades, researchers have reported ...

EPFL2022

Natural competence of the pathogen Acinetobacter baumannii: an elusive phenomenon

Nina Vesel

Natural competence for transformation is an important driver of horizontal DNA exchange between different organisms. This can result in accumulation of dangerous genetic features, such as antibiotic resistance genes, in a single organism. One example of an ...

EPFL2022