Publications associées à Shifting Fitness Landscapes In Response To Altered Environments

The role of LRRK2 in lung adenocarcinoma

Lung cancer is the leading cause of cancer-related deaths worldwide and the most common lung cancer subtype is lung adenocarcinoma (LUAD). Frequently mutated genes involve activating mutations in KRAS and loss of function mutations in TP53. LUADs primarily ...

EPFL2024

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Ana Marija Jaksic

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

BMC2024

Multiscale Spatiotemporal Characterization of Embodied Environmental Performance of Building Structures in Geneva from 1850 to 2018

Corentin Jean Dominique Fivet, Catherine Elvire L. De Wolf, Serena Vanbutsele

Load-bearing systems in buildings, significant in material use and embodied greenhouse gas emissions (EGHGE), have lacked detailed analysis on their environmental and functional relationships over time and space. This study evaluates the environmental impa ...

2024

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Christian Iseli, Nicolas Jean Philippe Guex, Giovanna Ambrosini

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

BMC2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Massimo Bourquin

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Florence Pojer, Sergey Nazarov, Kelvin Ka Ching Lau, Dongchun Ni, Alexander Myasnikov, Emiko Uchikawa

nvestigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported to be transmitted from humans to various animals after req ...

2023

Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Sebastian Martin Waszak

Background: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatri ...

2023

The role of the NF-kappaB pathway in Amyotrophic lateral sclerosis pathogenesis

Emma Charlotta Källstig

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative motor disorder, which results in death within a few years of diagnosis. While the cause of most cases of ALS is unknown, 10% of cases are familial (fALS), and associated with mutations in one of ov ...

EPFL2023

Roadmap on Optical Sensors

Luc Thévenaz, Lei Zhang

Optical sensors and sensing technologies are playing a more and more important role in our modern world. From micro-probes to large devices used in such diverse areas like medical diagnosis, defense, monitoring of industrial and environmental conditions, o ...

2023

Computational Studies for the Design of Metalloenzyme Mimics

Guido Frisari

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

EPFL2023

Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

Sebastian Maerkl, Michael Andrew Crone, Hon Ming Andrew Yip, Evan James Olson, Shiyu Cheng

Cells cope with and adapt to ever-changing environmental conditions. Sophisticated regulatory networks allow cells to adjust to these fluctuating environments. One such archetypal system is the Saccharomyces cerevisiae Pho regulon. When external inorganic ...

National Academy of Sciences2023

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive

Konstantin Popadin

The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells ...

Elsevier Sci Ltd2023

Optimization of elastic wave propagation in a reconfigurable medium by genetic algorithms with adaptive mutation probability

Romain Christophe Rémy Fleury, Janez Rus

We introduce a reconfigurable medium for the manipulation of elastic propagation properties of Lamb waves. It is based on a shape memory polymer (SMP) with temperature-dependent Young's modulus. Waves are excited by a laser pulse and detected by a laser vi ...

IOP Publishing Ltd2023

Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline

Konstantin Popadin

The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age c ...

Oxford University Press2022

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Aline Sondra Adler, Christof Holliger, Julien Maillard, Marco Pagni, Simon Marius Jean Poirier

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...

WILEY2022

Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals

Omaya Pierre Dudin

Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. How ...

PUBLIC LIBRARY SCIENCE2022

Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools

Henning Paul-Julius Stahlberg, Dongchun Ni

Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme Cas3 is then recruited in trans for processive DNA degrad ...

CELL PRESS2022