Publications related to VAX1 Mutation Associated with Microphthalmia, Corpus Callosum Agenesis, and Orofacial Clefting: The First Description of a VAX1 Phenotype in Humans

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

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

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

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

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

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

The functional characterization of callosal connections

Giorgio Innocenti, Muhamed Barakovic

The brain operates through the synaptic interaction of distant neurons within flexible, often heterogeneous, distributed systems. Histological studies have detailed the connections between distant neurons, but their functional characterization deserves fur ...

PERGAMON-ELSEVIER SCIENCE LTD2022

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

Jacques Fellay, Stepan Denisov, Konstantin Popadin, Dmitrii Iliushchenko

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are ...

OXFORD UNIV PRESS2022

Premature Vertebral Mineralization in hmx1-Mutant Zebrafish

H6 family homeobox 1 (HMX1) regulates multiple aspects of craniofacial development, and mutations in HMX1 are linked to an ocular defect termed oculoauricular syndrome of Schorderet-Munier-Franceschetti (OAS) (MIM #612109). Recently, additional altered oro ...

2022

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

A highly virulent variant of HIV-1 circulating in the Netherlands

Jacques Fellay, Luca Ferretti

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log(10) increase (i.e., a similar to 3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited ...

American Association for the Advancement of Science2022

Assessing Experiences and Visual Perception in Train Station Environments with a Mobile Application and Eye Tracking

Andrea Regula Schneider

The Customer Experience Management at the Swiss Federal Railways (SBB) experiments with new technologies and methods to capture experiences and perceptions of passengers to design safe and customer friendly environments. First, a new methodological approac ...

2022

A new rat model of creatine transporter deficiency reveals behavioral disorder and altered brain metabolism

Maria del Carmen Sandi Perez, Cristina Ramona Cudalbu, Jocelin Grosse, Dunja Simicic

Creatine is an organic compound used as fast phosphate energy buffer to recycle ATP, important in tissues with high energy demand such as muscle or brain. Creatine is taken from the diet or endogenously synthetized by the enzymes AGAT and GAMT, and specifi ...

Nature Research2021

Interferon Lambda Delays the Emergence of Influenza Virus Resistance to Oseltamivir

Francesco Stellacci, Paulo Henrique Jacob Silva, Chiara Medaglia

Influenza viruses are a leading cause of morbidity and mortality worldwide. These air-borne pathogens are able to cross the species barrier, leading to regular seasonal epidemics and sporadic pandemics. Influenza viruses also possess a high genetic variabi ...

2021

Revisiting brain rewiring and plasticity in children born without corpus callosum

Dimitri Nestor Alice Van De Ville, Maria Giulia Preti, Silvia Obertino, Vanessa Siffredi

The corpus callosum is the largest white matter pathway connecting homologous structures of the two cerebral hemispheres. Remarkably, children and adults with developmental absence of the corpus callosum (callosal dysgenesis, CD) show typical interhemisphe ...

WILEY2021

The role and transcriptional regulation of FAM46A in adipocyte differentiation

Ann-Kristin Hov

Obesity is currently a leading global health concern. Treatments include undergoing a weight-loss regimen. However, successful weight-loss is variable, where the heritability of obesity is considered part of the cause. This patient variability to weight-lo ...

EPFL2021

Large-scale functional network dynamics in human callosal agenesis: Increased subcortical involvement and preserved laterality

Dimitri Nestor Alice Van De Ville, Anjali Bagunu Tarun, Younes Farouj, Vanessa Siffredi

In the human brain, the corpus callosum is the major white-matter commissural tract enabling the transmission of sensory-motor, and higher level cognitive information between homotopic regions of the two cerebral hemispheres. Despite developmental absence ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2021

OCT-angiography assessing quiescent and active choroidal neovascularization in retinitis pigmentosa associated with PRPH2 pathogenic variant

Imen Habibi

Purpose: To report multimodal imaging findings including optical coherence tomography angiography (OCT-A) of a patient presenting with a quiescent choroidal neovascularization (CNV) in one eye and an active CNV in the fellow eye, complicating retinitis pig ...

2021