Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features.

Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function.

A critical analysis of the current state of virus taxonomy.

Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and . Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification.

Dendrimer nanosystems for adaptive tumor-assisted drug delivery via extracellular vesicle hijacking.

Drug delivery systems (DDSs) that can overcome tumor heterogeneity and achieve deep tumor penetration are challenging to develop yet in high demand for cancer treatment. We report here a DDS based on self-assembling dendrimer nanomicelles for effective and deep tumor penetration via in situ tumor-secreted extracellular vesicles (EVs), an endogenous transport system that evolves with tumor microenvironment. Upon arrival at a tumor, these dendrimer nanomicelles had their payload repackaged by the cells into EVs, which were further transported and internalized by other cells for delivery "in relay.

Local pH Modulation during Electro-Enzymatic O Reduction: Characterization of the Influence of Ionic Strength by Fluorescence Microscopy.

Understanding how environmental factors affect the bioelectrode efficiency and stability is of uttermost importance to develop high-performance bioelectrochemical devices. By coupling fluorescence confocal microscopy to electrochemistry, this work focuses on the influence of the ionic strength on electro-enzymatic catalysis. In this context, the 4 e/4 H reduction of O into water by the bilirubin oxidase from (BOD) is considered as a model.

Investigating the Concept and Origin of Viruses.

The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread acceptance of new views and insights.

Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses.

The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which a description encompassing all their diversity remains not available.

A Putative Role of de-Mono-ADP-Ribosylation of STAT1 by the SARS-CoV-2 Nsp3 Protein in the Cytokine Storm Syndrome of COVID-19.

As more cases of COVID-19 are studied and treated worldwide, it had become apparent that the lethal and most severe cases of pneumonia are due to an out-of-control inflammatory response to the SARS-CoV-2 virus. I explored the putative causes of this specific feature through a detailed genomic comparison with the closest SARS-CoV-2 relatives isolated from bats, as well as previous coronavirus strains responsible for the previous epidemics (SARS-CoV and MERS-CoV). The high variability region of the nsp3 protein was confirmed to exhibit the most variations between closest strains.

[A scenario to safely ease the covid-19 lockdown while allowing economic recovery].

If they work as expected, the strict containment measures enforced to stop the French Covid-19 epidemic will leave a large proportion of the population "naive" about the SARS-CoV-2 virus. In these conditions, how can we prevent the epidemic from rebounding, at a time when this restrictive policy will soon become untenable economically and socially? Based on the figures, now well known, of the lethality of covid-19 according to age classes, I suggest that a gradual release of the containment be instituted, which will keep retirees in isolation (the 65+ age class), whose risk is maximal and the impact on economic production the lowest. This scenario might be applicable to most European countries that enforce mandatory retirement ages for most of workers.

In Situ Fluorescence Tomography Enables a 3D Mapping of Enzymatic O Reduction at the Electrochemical Interface.

Getting information about the fate of immobilized enzymes and the evolution of their environment during turnover is a mandatory step toward bioelectrode optimization for effective use in biodevices. We demonstrate here the proof-of-principle visual characterization of the reactivity at an enzymatic electrode thanks to fluorescence confocal laser scanning microscopy (FCLSM) implemented in situ during the electrochemical experiment. The enzymatic O reduction involves proton-coupled electron transfers.

Draft genome of a macrolide resistant XDR Salmonella enterica serovar Paratyphi A strain using a shotgun sequencing approach.

Objectives: Salmonella enterica serovar Paratyphi A, the causative pathogen of enteric fever, is a major public-health concern affecting millions of people around the world. We conducted whole-genome sequencing and analysis of a novel macrolide-resistant Salmonella Paratyphi A strain isolated from Karachi, Pakistan.

Methods: Genomic DNA of Salmonella Paratyphi A strain JRCGR-AK14 was sequenced on a MiSeq platform.

Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Genomes.

With genomes of up to 2.7 Mb propagated in μm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution.

Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins.

Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp.

: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes.

Since 1998, when Jim van Etten's team initiated its characterization, Chlorella virus 1 (PBCV-1) had been the largest known DNA virus, both in terms of particle size and genome complexity. In 2003, the -infecting Mimivirus unexpectedly superseded PBCV-1, opening the era of giant viruses, i.e.

New genomic data and analyses challenge the traditional vision of animal epithelium evolution.

Background: The emergence of epithelia was the foundation of metazoan expansion. Epithelial tissues are a hallmark of metazoans deeply rooted in the evolution of their complex developmental morphogenesis processes. However, studies on the epithelial features of non-bilaterians are still sparse and it remains unclear whether the last common metazoan ancestor possessed a fully functional epithelial toolkit or if it was acquired later during metazoan evolution.

CRISPR-Cas-like system in giant viruses: why MIMIVIRE is not likely to be an adaptive immune system.

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Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes.

High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution.

Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.

Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E.

Giant virus in the sea: Extending the realm of Megaviridae to Viridiplantae.

The viral nature of the first "giant virus," Mimivirus, was realized in 2003, 10 y after its initial isolation from the water of a cooling tower in Bradford, UK. Soon after its genome was sequenced, the mining of the Global Ocean Sampling environmental sequence database revealed that the closest relatives of Mimivirus, only known to infect Acanthamoeba, were to be found in the sea. These predicted marine Mimivirus relatives remained elusive until 2010, with the first genomic characterization of a virus infecting a heterotrophic unicellular eukaryote, the microflagellate grazer Cafeteria roenbergensis.

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.

Background: Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced.

Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.

Background: The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.

Results: Our bioinformatics analysis revealed that R555 protein sequence is constituted from the fusion of an N-terminal Mre11-like domain with a C-terminal Rad50-like domain.