Stockholm University

About: Stockholm University is a education organization based out in Stockholm, Sweden. It is known for research contribution in the topics: Population & Context (language use). The organization has 21052 authors who have published 62567 publications receiving 2725859 citations. The organization is also known as: University of Stockholm & Stockholms universitet.

Detecting sequence signals in targeting peptides using deep learning.

Abstract: In bioinformatics, machine learning methods have been used to predict features embedded in the sequences. In contrast to what is generally assumed, machine learning approaches can also provide new insights into the underlying biology. Here, we demonstrate this by presenting TargetP 2.0, a novel state-of-the-art method to identify N-terminal sorting signals, which direct proteins to the secretory pathway, mitochondria, and chloroplasts or other plastids. By examining the strongest signals from the attention layer in the network, we find that the second residue in the protein, that is, the one following the initial methionine, has a strong influence on the classification. We observe that two-thirds of chloroplast and thylakoid transit peptides have an alanine in position 2, compared with 20% in other plant proteins. We also note that in fungi and single-celled eukaryotes, less than 30% of the targeting peptides have an amino acid that allows the removal of the N-terminal methionine compared with 60% for the proteins without targeting peptide. The importance of this feature for predictions has not been highlighted before.

No supernovae associated with two long-duration gamma ray bursts

Abstract: The tidy classification system that divided γ-ray bursts (GRBs) into long-duration busts (lasting more than two seconds) and short may have had its day. The final nail in its coffin may be GRB 060614. Discovered on 14 June 2006 by the Burst Alert Telescope on-board the Swift satellite, this burst was long, at 102 seconds, but as reported in a clutch of papers in this issue, it has a number of properties, including the absence of an accompanying supernova, that were previously considered diagnostic of a 'short' GRB. The hunt is now on for a classification system to take account of the diversity now apparent in GRBs. In the accompanying News & Views, Bing Zhang suggests that the answer may be to adopt a Type I/Type II classification similar to that used for supernovae. GRB 060505 and GRB 060614 were not accompanied by supernova emission down to limits hundreds of times fainter than the archetypal SN 1998bw that accompanied GRB 980425, and fainter than any type Ic supernova ever observed. It is now accepted that long-duration γ-ray bursts (GRBs) are produced during the collapse of a massive star1,2. The standard ‘collapsar’ model3 predicts that a broad-lined and luminous type Ic core-collapse supernova accompanies every long-duration GRB4. This association has been confirmed in observations of several nearby GRBs5–9. Here we report that GRB 060505 (ref. 10) and GRB 060614 (ref. 11) were not accompanied by supernova emission down to limits hundreds of times fainter than the archetypal supernova SN 1998bw that accompanied GRB 980425, and fainter than any type Ic supernova ever observed12. Multi-band observations of the early afterglows, as well as spectroscopy of the host galaxies, exclude the possibility of significant dust obscuration and show that the bursts originated in actively star-forming regions. The absence of a supernova to such deep limits is qualitatively different from all previous nearby long-duration GRBs and suggests a new phenomenological type of massive stellar death.