Publications associées à Genomic Characterization of Mycobacterium lepraeto Explore Transmission Patterns Identifies New Subtype in Bangladesh

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Bart Deplancke, Daniel Migliozzi, Hüseyin Baris Atakan, Mustafa Demir, Riccardo Dainese, Daniel Alpern, Dariia Gudkova, Gilles Weder

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

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

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Melanie Blokesch, Sandrine Stutzmann, Natalia Carolina Drebes Dorr, Alexandre Lemopoulos

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

2024

Single-cell analysis of the interactions between Mycobacterium tuberculosis and macrophages

Ophélie Rutschmann

Mycobacterium Tuberculosis is a highly effective pathogen infecting nearly a third of the world's population. An M. tuberculosis infection starts when droplets containing bacteria enter an individual's lungs. The first host cells to contact the bacteria ar ...

EPFL2024

Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria

Tamar Kohn, Htet Kyi Wynn, Céline Terrettaz, Aline Laetitia Schaub, Athanasios Nenes, Kalliopi Violaki, Marta Augugliaro, Shannon Christa David, Ghislain Gilles Jean-Michel Motos, Walter Hugentobler, Laura José Costa Henriques, Daniel Scott Nolan

Aerosol transmission remains a major challenge for control of respiratory viruses, particularly those causing recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorgan ...

American Society for Microbiology2024

Microfluidic systems for infectious disease diagnostics

Thomas Lehnert, Martinus Gijs

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, i ...

Royal Soc Chemistry2024

Inactivation of influenza A virus in expiratory droplets and aerosol particles and the associated physicochemical drivers

Aline Laetitia Schaub

Influenza is an infectious respiratory illness caused by influenza viruses. Every year, it causes up to one billion cases of disease worldwide. Despite its high disease burden, the transmission pathway of influenza remains subject to debate. There is incre ...

EPFL2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

Jacques Fellay, Zhi Ming Xu

The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aim ...

Nature Portfolio2024

Accessible and highly observable gastrointestinal organoid model systems for studying host-pathogen interactions

Moritz Hofer

Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inabi ...

EPFL2024

Human alveolar lining fl uid from the elderly promotes Mycobacterium tuberculosis intracellular growth and translocation into the cytosol of alveolar epithelial cells

Vivek Vijay Thacker, Richa Mishra

The elderly population is highly susceptible to developing respiratory diseases, including tuberculosis, a devastating disease caused by the airborne pathogen Mycobacterium tuberculosis ( M.tb ) that kills one person every 18 seconds. Once M.tb reaches the ...

Elsevier Science Inc2024

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

S-acylation and lipid exchange at the ER-Golgi membrane contact sites regulate pathogen entry in human cells

Muhammad Umair Anwar

Cells have evolved endocytic pathways to internalize different molecules, to regulate intra-cellular communication and their interaction with external environment. Pathogens have co-evolved with cells to exploit these processes for infections. In particula ...

EPFL2024

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Riccardo Dainese, Daniel Alpern, Vincent Roland Julien Gardeux

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

2023

Systematic benchmarking of single-cell ATAC-sequencing protocols

Bart Deplancke, Jörn Pezoldt, Camille Lucie Germaine Lambert

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

NATURE PORTFOLIO2023

Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E

Jacques Fellay

Background and Aims:The clinical spectrum of human infection by HEV ranges from asymptomatic to severe acute hepatitis. Furthermore, HEV can cause diverse neurological manifestations, especially Parsonage-Turner syndrome. Here, we used a large-scale human ...

Lippincott Williams & Wilkins2023

Electronic readout of DNA amplification in nanoliter chambers. Strategies towards highly parallel semiconductor-based nucleic acid amplification testing

Saurabh Tomar

Polymerase chain reaction (PCR) has been the most significant driver in the field of nucleic acid testing (NAT) since its invention. Popularized as an abbreviation by the Covid-19 pandemic, PCR-based methods are the gold standard in the field of diagnostic ...

EPFL2023

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

Time-Resolved Scanning Ion Conductance Microscopy and Single-Molecule Spectroscopy

Samuel Mendes Leitão

The evolution of the 3D morphology is at the center of many relevant biological processes ranging from cellular differentiation to cancer invasion and metastasis. Microscopy techniques, such as electron microscopy (EM), super-resolution (SR) optical micros ...

EPFL2023