Publications associées à Marqueur de séquence exprimée

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

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

Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring

Ianina Altshuler

Background Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (similar to 7 degrees C), hypersaline (7-8% salinity), anoxic (similar ...

BMC2023

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Bart Deplancke, Riccardo Dainese, Daniel Alpern, Mustafa Demir

The invention relates to methods for the preparation of method of preparation of cDNA library based on one or many RNA samples useful for efficient RNA sequencing and uses thereof. The invention further relates to related tools and kits useful in said meth ...

2022

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Rizlan Bernier-Latmani, Karin Lederballe Meibom, Karen Elda Viacava Romo, Nicolas Louis Maurice Jacquemin, Matthew Charles Reid, Jiangtao Qiao

Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype ...

2022

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

Christof Holliger, Julien Maillard, Aline Sondra Adler, 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

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

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

Overexpression of transcription factor Foxa1 and target genes remediate therapeutic protein production bottlenecks in Chinese hamster ovary cells

Nicolas Mermod, Iris Bodenmann

Despite extensive research conducted to increase protein production from Chinese hamster ovary (CHO) cells, cellular bottlenecks often remain, hindering high yields. In this study, a transcriptomic analysis led to the identification of 32 genes that are co ...

WILEY2020

The functional proteome landscape of Escherichia coli

Camille Véronique Bernadette Goemans

Recent developments in high-throughput reverse genetics1,2 have revolutionized our ability to map gene function and interactions3,4,5,6. The power of these approaches depends on their ability to identify functionally associated genes, which elicit similar ...

2020

Hybrid Transcriptional Regulators for the Screening of Target DNA Motifs in Organohalide-Respiring Bacteria

Christof Holliger, Julien Maillard, Mathilde Stéphanie Willemin, Marie Vingerhoets

The bioremediation of persistent organohalide molecules under anoxic conditions mostly relies on the bacterial process called organohalide respiration (OHR). Organohalide-respiring bacteria (OHRB) are phylogenetically diverse anaerobic bacteria that share ...

Frontiers Media SA2020

Methylation of arsenic by single-species and soil-derived microbial cultures

Karen Elda Viacava Romo

Arsenic (As) is simultaneously a ubiquitous and a toxic element. Arsenic is subject to bio-transformations catalyzed by microorganisms constituting the As biogeochemical cycle. The primordial Earth was devoid of oxygen, exposing life to the highly mobile a ...

EPFL2020

A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex

Henry Markram, Olivier Burri, Romain Guiet, Julie Meystre, Felix Schürmann, Daniel Keller, Rahul Valiya Veettil

Obtaining a catalog of cell types is a fundamental building block for understanding the brain. The ideal classification of cell-types is based on the profile of molecules expressed by a cell, in particular, the profile of genes expressed. One strategy is, ...

2019

Benchmarking protocols for the metagenomic analysis of stream biofilm viromes

Tom Ian Battin, Hannes Markus Peter, Jade Brandani, Massimo Bourquin, Meriem Bekliz

Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. ...

PeerJ2019

Promoter mutagenesis for fine-tuning expression of essential genes in Mycobacterium tuberculosis

Stewart Cole, Claudia Sala, Gaëlle Séraphine Kolly

A range of regulated gene expression systems has been developed for mycobacteria in the last few years to facilitate the study of essential genes, validate novel drug targets and evaluate their vulnerability. Among these, the TetR/Pip-OFF repressible promo ...

Wiley2018

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Giovanna Ambrosini, Philipp Bucher, Romain Fernand Pietro Groux, René Dreos, Rouayda Cavin Perier

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next gene ...

2017

Scanning tunneling microscopy on large bio-molecular systems on surfaces

Sebastian Koslowski

The ever growing demand for the development of new technologies and materials has led to extensive studies inspired by biological functional complexes. Peptides with their outstanding ability to efficiently self-assemble can express a broad spectrum of int ...

EPFL2017

A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics

Douglas Hanahan, Anguraj Sadanandam, Stephan Wullschleger, Ismaël Wafy

Seeking to assess the representative and instructive value of an engineered mouse model of pancreatic neuroendocrine tumors (PanNET) for its cognate human cancer, we profiled and compared mRNA and miRNA transcriptomes of tumors from both. Mouse PanNET tumo ...

Amer Assoc Cancer Research2015

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Jacques Fellay, Amalio Telenti, Istvan Bartha, Nimisha Chaturvedi, Paul Jack Mc Laren

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We a ...

Public Library Science2015

Evolutionary dynamics of coding and non-coding transcriptomes

Anamaria Necsulea

Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive a ...

Nature Publishing Group2014