Publications related to Baltimore classification

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

Peptide-based virucidal drugs

Francesca Olgiati

Before the COVID-19 pandemic, viruses were not a major priority for the scientific community. Today, many events have changed the world and the importance of studying viruses, vaccines, and antiviral drugs is fully appreciated. The development of effective ...

EPFL2024

Simultaneous membrane and RNA binding by Tick-Borne Encephalitis Virus capsid protein

Sarah Victoria Barrass

Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family Flaviviridae, genus Flavivirus. Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the end ...

PUBLIC LIBRARY SCIENCE2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Lignin, from biomass waste to sustainable materials for food packaging, antiviral coatings and agriculture

Alice Boarino

Our planet has been challenged for years by our reckless use of fossil fuels, which has led to the ongoing climate change and energy crisis. The transition to the use of renewable alternative sources has now became urgent and inevitable. The valorization o ...

EPFL2023

Viral diversity is linked to bacterial community composition in alpine stream biofilms

Tom Ian Battin, Hannes Markus Peter, Paraskevi Pramateftaki, Meriem Bekliz

Biofilms play pivotal roles in fluvial ecosystems, yet virtually nothing is known about viruses in these communities. Leveraging an optimized sample-to-sequence pipeline, we studied the spatiotemporal turnover of dsDNA viruses associated with stream biofil ...

Springer2022

Antiviral Screen against Canine Distemper Virus-Induced Membrane Fusion Activity

Gerardo Turcatti, Marc Chambon, Jonathan Patrice Vesin

Canine distemper virus (CDV), a close relative of the human pathogen measles virus (MeV), is an enveloped, negative sense RNA virus that belongs to the genus Morbillivirus and causes severe diseases in dogs and other carnivores. Although the vaccination is ...

2021

Towards an artificial cell: Development of a system which self-regenerates the protein components of the PURE system in microfluidic reactors

Barbora Lavickova

Thanks to recent advancements in synthetic biology, the dream of creating a synthetic cell has become feasible. However, due to its inherent complexity, one of the fundamental functions of all living systems, i.e., self-replication, remains to be introduce ...

EPFL2021

Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features

Michaël Unser, Cathrin Brisken, Daniel Sage, Olivier Burri, Quentin Juppet, Fabio De Martino, Martin Weigert

Patient-Derived Xenografts (PDXs) are the preclinical models which best recapitulate inter- and intra-patient complexity of human breast malignancies, and are also emerging as useful tools to study the normal breast epithelium. However, data analysis gener ...

2021

Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases

Kristina Makasheva

Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) st ...

2020

Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere

Meriem Bekliz

The history of giant viruses began in 2003 with the identification of Acanthamoeba polyphaga mimivirus. Since then, giant viruses of amoeba enlightened an unknown part of the viral world, and every discovery and characterization of a new giant virus modifi ...

MDPI2019

Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

David Lyndon Emsley, Marc Anthony Caporini

We report dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their life cycles and infectivity through modulation of their structures and dynamics. W ...

2019

Differences in viral disinfection mechanisms as revealed by quantitative transfection of Echovirus 11 genomes

Urs von Gunten, Tamar Kohn, Jason Robert Torrey

Virus inactivation mechanisms can be elucidated by methods which measure the loss of specific virus functionality (e.g., host attachment, genome internalization, genome replication). Genome functionality is frequently assessed by PCR-based methods, which a ...

2019

Role of Condensing Particles in Polymer Confinement: A Model for Virus-Packed "Minichromosomes"

Sanjin Marion

Confined mixtures of a polymer and nonspecifically binding particles (condensers) are studied as models for viruses containing double-stranded DNA (polymer) and condensing proteins (particles). We explore a model in which all interactions between the packe ...

Cell Press2017

Solar disinfection (SODIS) of viruses in PET bottles

Tamar Kohn, Anna Carratala Ripolles, Michael Jon Mattle, Alex Dionisio Calado

Solar disinfection of drinking water in PET bottles (SODIS) is a simple point-of-use technique efficient for the inactivation of many bacterial pathogens. In contrast, the efficiency of SODIS toward viruses is not well known. In this work, we studied the i ...

American Society for Microbiology2016

Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins

Matteo Dal Peraro, Luciano Andres Abriata, Albert Sanghoon Song

Parainfluenza virus 5 (PIV5) is an enveloped, single-stranded, negative-sense RNA virus of the Paramyxoviridae family. PIV5 fusion and entry are mediated by the coordinated action of the receptor-binding protein, hemagglutinin-neuraminidase (HN), and the f ...

National Academy of Sciences2016

Ammonia as an in-situ sanitizer: influence of virus genome type on inactivation

Tamar Kohn, Loïc Decrey, Shinobu Kazama

Treatment of human excreta and animal manure (HEAM) is key in controlling the spread of persistent enteric pathogens such as viruses. The extent of virus inactivation during HEAM storage and treatment appeared to vary with virus genome type, though the rea ...

American Society for Microbiology2016

Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies

Paul Joseph Dyson, Ursula Röthlisberger, Tina Riedel, Giulia Palermo, Thibaud Edouard Alistair von Erlach

Many transition metal complexes have unique physicochemical properties that can be efficiently exploited in medicinal chemistry for cancer treatment. Traditionally, double-stranded DNA has been assumed to be the main binding target; however, recent studies ...

2016

Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment

Jeffrey David Jensen, Matthieu Foll

Influenza A virus (IAV) has a segmented genome that allows for the exchange of genome segments between different strains. This reassortment accelerates evolution by breaking linkage, helping IAV cross species barriers to potentially create highly virulent ...

Oxford University Press2015

UVC inactivation of dsDNA and ssRNA viruses in water: UV fluences and a qPCR-based approach to evaluate decay on viral infectivity

Tamar Kohn, Anna Carratala Ripolles

Disinfection by low-pressure monochromatic ultraviolet (UVC) radiation (253.7 nm) became an important technique to sanitize drinking water and also wastewater in tertiary treatments. In order to prevent the transmission of waterborne viral diseases, the an ...

Springer2014