bims-micpro 2021-05-02 papers

Issue of 2021‒05‒02
two papers selected by
Thomas Martinez
Salk Institute for Biological Studies

Nat Commun. 2021 04 27. 12(1): 2453

Sight of parasitoid wasps accelerates sexual behavior and upregulates a micropeptide gene in Drosophila.

Shimaa A M Ebrahim, Gaëlle J S Talross, John R Carlson.

Parasitoid wasps inflict widespread death upon the insect world. Hundreds of thousands of parasitoid wasp species kill a vast range of insect species. Insects have evolved defensive responses to the threat of wasps, some cellular and some behavioral. Here we find an unexpected response of adult Drosophila to the presence of certain parasitoid wasps: accelerated mating behavior. Flies exposed to certain wasp species begin mating more quickly. The effect is mediated via changes in the behavior of the female fly and depends on visual perception. The sight of wasps induces the dramatic upregulation in the fly nervous system of a gene that encodes a 41-amino acid micropeptide. Mutational analysis reveals that the gene is essential to the behavioral response of the fly. Our work provides a foundation for further exploration of how the activation of visual circuits by the sight of a wasp alters both sexual behavior and gene expression.

DOI: https://doi.org/10.1038/s41467-021-22712-0

Biology (Basel). 2021 Apr 26. pii: 371. [Epub ahead of print]10(5):

Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish.

Shital Kumar Mishra, Han Wang.

Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify 2730-6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted by all the six bioinformatic tools. We also compared the sensitivity and specificity of these six bioinformatic tools for identifying lncRNAs with coding potentials and summarized their strengths and weaknesses. These predicted zebrafish coding lncRNAs set the stage for further experimental studies.

Keywords: bioinformatics; coding probabilities; lncRNAs; zebrafish

DOI: https://doi.org/10.3390/biology10050371