PENGUINN : precise exploration of nuclear G-quadruplexes using interpretable neural networks

G-quadruplexes (G4s) are a class of stable structural nucleic acid secondary structures that are known to play a role in a wide spectrum of genomic functions, such as DNA replication and transcription. The classical understanding of G4 structure points to four variable length guanine strands joined by variable length nucleotide stretches. Experiments using G4 immunoprecipitation and sequencing experiments have produced a high number of highly probable G4 forming genomic sequences. The expense and technical difficulty of experimental techniques highlights the need for computational approaches of G4 identification. Here, we present PENGUINN, a machine learning method based on Convolutional neural networks, that learns the characteristics of G4 sequences and accurately predicts G4s outperforming state-of-the-art methods. We provide both a standalone implementation of the trained model, and a web application that can be used to evaluate sequences for their G4 potential.peer-reviewe

Controls on δ26Mg variability in three Central European headwater catchments characterized by contrasting bedrock chemistry and contrasting inputs of atmospheric pollutants.

Magnesium isotope ratios (26Mg/24Mg) can provide insights into the origin of Mg pools and fluxes in catchments where Mg sources have distinct isotope compositions, and the direction and magnitude of Mg isotope fractionations are known. Variability in Mg isotope compositions was investigated in three small, spruce-forested catchments in the Czech Republic (Central Europe) situated along an industrial pollution gradient. The following combinations of catchment characteristics were selected for the study: low-Mg bedrock + low Mg deposition (site LYS, underlain by leucogranite); high-Mg bedrock + low Mg deposition (site PLB, underlain by serpentinite), and low-Mg bedrock + high Mg deposition (site UDL, underlain by orthogneiss). UDL, affected by spruce die-back due to acid rain, was the only investigated site where dolomite was applied to mitigate forest decline. The δ26Mg values of 10 catchment compartments were determined on pooled subsamples. At LYS, a wide range of δ26Mg values was observed across the compartments, from -3.38 ‰ (bedrock) to -2.88 ‰ (soil), -1.48% (open-area precipitation), -1.34 ‰ (throughfall), -1.19 ‰ (soil water), -0.99 ‰ (xylem), -0.95 ‰ (needles), -0.82 ‰ (bark), -0.76 ‰ (fine roots), and -0.76 ‰ (runoff). The δ26Mg values at UDL spanned 1.32 ‰ and were thus less variable, compared to LYS. Magnesium at PLB was isotopically relatively homogeneous. The δ26Mg systematics was consistent with geogenic control of runoff Mg at PLB. Mainly atmospheric/biological control of runoff Mg was indicated at UDL, and possibly also at LYS. Our sites did not exhibit the combination of low-δ26Mg runoff and high-δ26Mg weathering products (secondary clay minerals) reported from several previously studied sites. Six years after the end of liming at UDL, Mg derived from dolomite was isotopically undetectable in runoff