Sequence-to-Signal Learning for CLIP-Seq Data
RNA-binding proteins (RBPs) are a family of over 2,000 proteins that bind to coding and RNA-binding proteins (RBPs) are key actors in post-transcriptional regulation which recognize and bind distinct sub-sequences (so called motifs) on coding and non-coding RNAs. A common experimental protocol to identify RBP binding sites in vivo is CLIP-seq, which yields a (sparse) signal over the transcriptome. We present a novel deep-learning-based approach to model RBP-binding by learning the raw CLIP-seq signal as a function of RNA sequence. Subsequent model interrogation enables the identification of highly predictive sub-sequences, which correspond to RBP binding motifs.
SignalP 6.0 achieves signal peptide prediction across all types using protein language models
Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects the presence and structure of all five SP types and that is applicable to metagenomic data.
SATC: Sex Assignment Through Coverage
Non-model organisms often have genome assemblies at scaffold-level and lack characterization of sex-linked scaffolds.
Here, we present ‘Sex Assignment Through Coverage’ (SATC), a method to assign sex to samples and identify sex-linked scaffolds from next generation sequencing (NGS) data.
The method works for species with a homogametic/heterogametic sex determination system and only requires a scaffold-level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data.
The enzyme that plankton uses to scare off fish
The copepod Gaussia princeps has a fascinating strategy for escaping predators in the twilight zone of the ocean. When it feels a disturbance in the water, it secretes a liquid that makes a flash of light, allowing it to swim away safely while the predator is distracted. The compounds in the liquid that are responsible for the flash are the enzyme Gaussia luciferase and its substrate coelenterazine. A light-producing enzyme (a luciferase) like this is extremely useful as a reporter to visualize biomolecular processes in model systems. Compared to luciferases from other organisms, Gaussia luciferase is very small and produces very bright light, which means that its light is easy to measure and it interferes little with the system in which it is used. We study the properties of Gaussia luciferase by producing it in E. coli cells and purified it in the lab. We explore its reaction with coelenterazine, its light emission and its three-dimensional structure.
Drying-rewetting frequency rather than intensity affects Soil CO2 emission and priming effect under nitrogen addition condition
We used 13C-labeled litter to investigate effects of four drying-rewetting patterns (two drying-rewetting intensities crossed with two drying-rewetting frequencies) and N addition on soil CO2 emission and priming effect in the Zoigê alpine wetland soil (China). N addition significantly reduced soil CO2 emission by 10% and priming effect by 21%; litter addition increased CO2 emission by 176%. Drying-rewetting intensity had no effect on soil CO2 emission overall, but low frequency significantly promoted CO2 emission as compared to higher frequency of drying-rewetting, and this effect was regulated by N addition. Priming effect decreased at low frequency of drying-rewetting and the reduction was inhibited by N addition.
Jacopo Di Clemente
Same needs, different pressure: Bryde’s whales foraging ecology in different ecosystems
Bryde’s whales are one of the least studied top predator cetaceans, almost nothing is known about their foraging behaviour and whether this is affected by anthropogenic pressure. By deploying non-invasive multi-sensor camera tags on individual whales of two populations living in different ecosystems, this project aims to shed light on underwater feeding techniques and the energetic costs associated therewith of this elusive species. This comparison of two geographically distinct populations will further provide insights on the intrinsic and extrinsic drivers of foraging and migratory behaviours in baleen whales