Biomedical subjects

Daniel Lundin

Publications and source records attributed to Daniel Lundin.

3 recordsLinked to original sources

PubMed2026

Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.

SUMMARY: nf-core/mag is a reproducible Nextflow pipeline for best-practice metagenomic de novo assembly and binning within the nf-core framework. Here we present a major update that adds support for long-read-only assembly and bin refinement, includes five new binning tools, expands taxonomic classification to viruses and eukaryotes, and improves bin quality evaluation with new tools and latest databases. Through sustained community-driven development spanning seven years and four primary curator teams, nf-core/mag remains actively developed as an open source workflow for metagenomic analysis, benefiting from contributions from across the broader metagenomics, nf-core, and Nextflow ecosystem. AVAILABILITY AND IMPLEMENTATION: The source code of nf-core/mag v5 is available on GitHub (https://github.com/nf-core/mag) under the open source MIT license, with v5.5.0 source code archived on Zenodo (https://zenodo.org/records/21735731). Documentation is viewable on the nf-core website (https://nf-co.re/mag).

Metagenomics↗

PubMed2026

nf-core/magmap: Map metatranscriptomes to large collections of genomes.

SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes. AVAILABILITY AND IMPLEMENTATION: The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

Software↗

PubMed2025

NrdR in Streptococcus and Listeria spp.: DNA Helix Phase Dependence of the Bacterial Ribonucleotide Reductase Repressor.

NrdR is a universal transcriptional repressor of bacterial genes coding for ribonucleotide reductases (RNRs), essential enzymes that provide DNA building blocks in all living cells. Despite its bacterial prevalence, the NrdR mechanism has been scarcely studied. We report the biochemical, biophysical, and bioinformatical characterization of NrdR and its binding sites from two major bacterial pathogens of the phylum Bacillota Listeria monocytogenes and Streptococcus pneumoniae. NrdR consists of a Zn-ribbon domain followed by an ATP-cone domain. We show that it forms tetramers that bind to DNA when loaded with ATP and dATP, but if loaded with only ATP, NrdR forms various oligomeric complexes unable to bind DNA. The DNA-binding site in L. monocytogenes is a pair of NrdR boxes separated by 15-16 bp, whereas in S. pneumoniae, the NrdR boxes are separated by unusually long spacers of 25-26 bp. This observation triggered a comprehensive binding study of four NrdRs from L. monocytogenes, S. pneumoniae, Escherichia coli, and Streptomyces coelicolor to a series of dsDNA fragments where the NrdR boxes were separated by 12-27 bp. The in vitro results were confirmed in vivo in E. coli and revealed that NrdR binds most efficiently when there is an integer number of DNA turns between the center of the two NrdR boxes. The study facilitates the prediction of NrdR binding sites in bacterial genomes and suggests that the NrdR mechanism is conserved throughout the bacterial domain. It sheds light on RNR regulation in Listeria and Streptococcus, and since NrdR does not occur in eukaryotes, opens a way to the development of novel antibiotics.

Ribonucleotide Reductases↗