Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp nov

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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 ...

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical opti ...

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

In this thesis, we investigate the inverse problem of trees and barcodes from a combinatorial, geometric, probabilistic and statistical point of view. Computing the persistent homology of a merge tree yields a barcode B. Reconstructing a tree from B invol ...

The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we ...

Antimicrobial peptides (AMPs) are host-encoded antibiotics that combat invading microbes. These short immune effectors are conserved in plants, animals, and fungi. Early work showed that AMPs killed bacteria in generalist fashions in vitro: i.e. AMPs that ...

Background As trans women are disproportionately affected by the HIV epidemic, and are still understudied, we aimed to identify and characterize the trans women in the Swiss HIV Cohort Study (SHCS). Methods A combination of criteria from pre-existing cohor ...

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to- ...

Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have docume ...

The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900) originating from North America has been mentioned for several decades in Europe, the Middle East and Russia. Its distribution and abundance in Europe is still unknown but it ca ...

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

One of the most conserved traits in the evolution of biomineralizing organisms is the taxon-specific selection of skeletal minerals. All modern scleractinian corals are thought to produce skeletons exclusively of the calcium-carbonate polymorph aragonite. ...

Spiroplasma poulsonii is a vertically transmitted endosymbiont of Drosophila melanogaster that causes male-killing, that is the death of infected male embryos during embryogenesis. Here, we report a natural variant of S. poulsonii that is efficiently verti ...

Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembl ...

It was argued that, in contrast to all known modern scleractinian corals that form aragonite skeletons, the original mineralogy of the Cretaceous "Coelosmilia" (ca. 70-65 Ma) was calcite during a period when the Mg2+/Ca2+ ratio of the seawater was presumab ...

High-throughput sequencing of DNA molecules has revolutionized biomedical research by enabling the quantitative analysis of the genome to study its function, structure and dynamics. It is driving sequencing-based experiments in life sciences as evidenced b ...

Interpretation of biomineralization processes based solely on the end product - the skeleton - may seem abreakneck task. This is because the biologically controlled mineralization involves cascades of intermediatephases and the activity of a myriad of orga ...

Work on Drosophila melanogaster paved the way to our current understanding of modern genetics. Since then, this model organism has contributed greatly to various fields such as neurobiology, development, and immunology. The discovery and analysis of the va ...

RNA interference (RNAi) related pathways are essential for germline development and fertility in metazoa and can contribute to inter- and trans-generational inheritance. In the nematode Caenorhabditis elegans, environmental double-stranded RNA provided by ...

Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp nov

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The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Impact of phylogeny on structural contact inference from protein sequence data

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

From Trees to Barcodes and Back Again: A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

A systematic CRISPR approach to understanding the role of Drosophila antimicrobial peptides in immunity in vivo

Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

The foreign oligochaete species Quistadrilus multisetosus (Smith, 1900) in Lake Geneva: morphological and molecular characterization and environmental influences on its distribution

MPGM: Scalable and Accurate Multiple Network Alignment

A modern scleractinian coral with a two-component calcite–aragonite skeleton

Blind killing of both male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

The modern analogue of a Cretaceous coral with a calcitic skeleton

On the relevance of quality score metadata in genomic sequence data for omics applications

From the product to the process: Fine-scale skeletal structures of scleractinian corals and their relevance to biomineralization models, geochemical sampling strategies, and phylogenetic reconstructions

Elucidating regulatory mechanisms shaping the transcriptome and proteome of the gut immune response in Drosophila melanogaster

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment