An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbiotic interactions.

Background Whole blood samples are often used to generate whole genome sequences, which provide valuable insights into the genetic make-up of viruses. However, the collection and management present si...

Scheme for the labeling of the cell membrane. The scattering tags, gold nanoparticles of two different diameters (Ø20 nm and Ø40 nm), target the biotinylated lipids inserted in the cellular membrane,...

Background Ebolavirus and related filoviruses are feared pathogens due to high mortality rates, and cases are confirmed using reverse transcription-polymerase chain reaction (RT-PCR) testing. Compared...

The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...

High-fidelity Nanopore sequencing offers a cost-effective, portable path to uncovering viral dark matter in complex environments—but suffers from severe read-length bias, low throughput, and limited ...

Insight into the rigidity or flexibility of molecular structures is integral for a series of common research questions in molecular biology, including the identification of functional regions, simulated protein unfolding, or tracking and prediction of conformational changes in proteins over time. Determining rigidity in 3-dimensional space is a difficult problem in general. For a well-defined subclass of frameworks, however, this task can be solved in polynomial time with the help of constraint counting algorithms known as pebble games. Although this approach is well established, no easy-to-use implementation of the pebble game algorithm in the context of general graph analysis and molecular rigidity is currently available to researchers. To close this gap, we developed TRAMbio, a Python-based software tool for Topological Rigidity Analysis in Molecular Biology. We summarize and discuss the theoretical foundation of the pebble game and how it can be applied to molecular rigidity. TRAMbio performs well even on large molecules and on discrete time series of protein movement. Results are accessible for both bioinformaticians and biologists, as rigid components can be rendered using standard molecular visualization platforms.

imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...

Background Aquatic plants play key roles in ecosystems, serving as primary producers and providing habitat for other aquatic life. While many are ecologically important, some invasive species, often i...

Scientific Reports - Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures

In the virus-encoded CRISPR-based direct readout system, single-guide RNA libraries are expressed directly from the genomes of viruses so that single-guide RNA abundance at distinct stages of the vira...

Human host-associated cellular products may act as induction agents for bacteriophages.

Background Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window of several months, and cannot assess the cumulative impact of an intervention. Results We developed a Random Forest Regression model, HIV-phyloTSI, which combines measures of within-host diversity and divergence to generate continuous TSI estimates directly from viral deep-sequencing data, with no need for additional variables. HIV-phyloTSI provides a continuous measure of TSI up to 9 years, with a mean absolute error of less than 12 months overall and less than 5 months for infections with a TSI of up to a year. It performs equally well for all major HIV subtypes based on data from African and European cohorts. Conclusions We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.