Publications related to Antagonism as a Foraging Strategy in Microbial Communities

Related publications (23)

Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

2025

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

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Clement Helsens

Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address thes ...

LIFE SCIENCE ALLIANCE LLC2023

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, 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

Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL

Christelle Dubey, Freddy Radtke, Ute Koch, Nadine Fournier, Mateusz Waldemar Antoszewski, Marianne Nkosi, Tara Kimberly Sugrue

NOTCH1 is a well-established lineage specifier for T cells and among the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape du ...

AMER SOC HEMATOLOGY2022

Host genomics of SARS-CoV-2 infection

Jacques Fellay, Christian Axel Wandall Thorball

SARS-CoV-2 infected a large fraction of humans in the past 2 years. The clinical presentation of acute infection varies greatly between individuals, ranging from asymptomatic or mild to life-threatening COVID-19 pneumonia with multi-organ complications. De ...

SPRINGERNATURE2022

Photodynamic treatment of multidrug-resistant bacterial infection using indium phosphide quantum dots

Francesco Stellacci

Infections caused by multidrug-resistant (MDR) bacteria pose an impending threat to humanity, as the evolution of MDR bacteria outpaces the development of effective antibiotics. In this work, we use indium phosphide (InP) quantum dots (QDs) to treat infect ...

ROYAL SOC CHEMISTRY2022

Pilus production in Acinetobacter baumannii is growth phase dependent and essential for natural transformation

Melanie Blokesch, Nina Vesel

Acinetobacter baumannii is a severe threat to human health as a frequently multidrug-resistant hospital-acquired pathogen. Part of the danger from this bacterium comes from its genome plasticity and ability to evolve quickly by taking up and recombining ex ...

American Society for Microbiology2021

A complex regulatory landscape involved in the development of mammalian external genitals

Denis Duboule, Lucille Delisle, Christopher Chase Bolt

Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. ...

2020

Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells

Petr Leiman, Sergey Nazarov, Mikhail Shneyder, Ricardo Cesar Guerrero Ferreira, Nicholas Michael Ian Taylor

Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteri ...

WILEY2019

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

Whole Genome Sequencing is a process in the field of bioinformatics that transforms biological samples of DNA into an electronic dataset of genetic bases. The process consists of two sequential components. First, the laboratory process of sequencing transf ...

EPFL2019

Genome-to-genome analysis of Epstein-Barr virus infection

Jacques Fellay, Christian Hammer

NATURE PUBLISHING GROUP2019

A Tale of Two Tumors: Unraveling the Complexities of Epigenetic Dysregulation in Cancer

Maria Christine Donaldson

Epigenetics plays an important role in cancer development and progression. Cancer cells hijack the epigenome by modifying the histone protein units responsible for packaging DNA, or by modifying the DNA itself, resulting in changes to chromatin topology an ...

EPFL2019

Calorie restriction slows age-related microbiota changes in an Alzheimer's disease model in female mice

Julia Chiara Vincentini

Alzheimer's disease (AD) affects an estimated 5.8 million Americans, and advanced age is the greatest risk factor. AD patients have altered intestinal microbiota. Accordingly, depleting intestinal microbiota in AD animal models reduces amyloid-beta (A beta ...

Springer Nature2019

Two Nimrod receptors, NimC1 and Eater, synergistically contribute to bacterial phagocytosis in Drosophila melanogaster

Bruno Lemaitre, Jan Paul Dudzic, Elodie Julie Virginie Ramond, Claudia Melcarne

Eater and NimC1 are transmembrane receptors of the Drosophila Nimrod family, specifically expressed in haemocytes, the insect blood cells. Previous ex vivo and in vivoRNAi studies have pointed to their role in the phagocytosis of bacteria. Here, we have cr ...

2019

Relationship Between Inactivation and Genome Damage of Human Enteroviruses Upon Treatment by UV254, Free Chlorine, and Ozone

Tamar Kohn, Virginie Bachmann, Jason Robert Torrey, Suzanne Marie Young

Quantitative PCR (qPCR) is a convenient tool for monitoring virus concentrations in water and wastewater treatment trains, though it only informs about virus presence, but not infectivity. This limitation can be overcome if the relationship between infecti ...

2019

Nanostructured surface topographies have an effect on bactericidal activity

Jürgen Brugger, Songmei Wu

Background Due to the increased emergence of antimicrobial resistance, alternatives to minimize the usage of antibiotics become attractive solutions. Biophysical manipulation of material surface topography to prevent bacterial adhesion is one promising app ...

2018

Trypanosoma brucei UMSBP2 is a single-stranded telomeric DNA binding protein essential for chromosome end protection

Galina Glousker

Universal minicircle sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind a single-stranded G-rich sequence, UMS, conserved at the replication origins of the mitochondrial (kinetoplast) DNA of trypanosomatids. Here, we report tha ...

OXFORD UNIV PRESS2018

Identification of the inactivating factors and mechanisms exerted on MS2 coliphage in concentrated synthetic urine

Tamar Kohn, Loïc Decrey

Volume reduction (condensation) is a key for the practical usage of human urine as a fertilizer because it enables the saving of storage space and the reduction of transportation cost. However, concentrated urine may carry infectious disease risks resultin ...

Elsevier2017

Genomic targets and molecular partners of the chromatin regulator KAP1

Annamaria Kauzlaric

KAP1 is an enigmatic regulatory protein, first described some twenty years ago, shown to be involved in multiple and diverse cellular functions. Specifically, it mediates tasks critical to cell growth and differentiation, pluripotency, apoptosis, gene sile ...

EPFL2017