Robo-Therm, a pipeline to RNA thermometer discovery and validation.

RNA thermometers are highly structured noncoding RNAs located in the 5'-untranslated regions (UTRs) of genes that regulate expression by undergoing conformational changes in response to temperature. The discovery of RNA thermometers through bioinformatics is difficult because there is little sequence conservation among their structural elements. Thus, the abundance of these thermosensitive regulatory structures remains unclear. Herein, to advance the discovery and validation of RNA thermometers, we developed Robo-Therm, a pipeline that combines an adaptive and user-friendly in silico motif search with a well-established reporter system. Through our application of Robo-Therm, we discovered two novel RNA thermometers in bacterial and bacteriophage genomes found in the human gut. One of these thermometers is present in the 5'-UTR of a gene that codes for σ 70 RNA polymerase subunit in the bacteria Mediterraneibacter gnavus and Bacteroides pectinophilus, and in the bacteriophage Caudoviricetes, which infects B. pectinophilus The other thermometer is in the 5'-UTR of a tetracycline resistance gene (tetR) in the intestinal bacteria Escherichia coli and Shigella flexneri Our Robo-Therm pipeline can be applied to discover multiple RNA thermometers across various genomes.

A long-term field study on the effects of dietary exposure of clothianidin to varroosis-weakened honey bee colonies.

Clothianidin is a commonly used systemic insecticide in seed treatments. Residues of clothianidin can occur in nectar and pollen as a result of within-plant-translocation. Foraging bees can collect contaminated nectar or pollen. Concerns have been brought forward that exposure to pesticide residues might affect colonies especially if they are weakened by varroosis. However, there are few scientific studies investigating such multiple-stressor scenarios in the context of the entire colony. To close this gapa field trial with 24 colonies was set up. The study design comprised four groups of six colonies each fed with uncontaminated sugar syrup ('C0'), or syrup spiked with 10 µg L-1 clothianidin ('C10'), 50 µg L-1 clothianidin ('C50') or 200 µg L-1 clothianidin ('C200'). C10 represented a residue concentration that may exceptionally occur and therefore a worst-case scenario, the higher dietary concentrations exceed and do not reflect fieldrealistic levels. A substantial load of 8 mites of Varroa destructor per ten gram bees in autumn was adjusted. The colonies were followed up for 328 days. The amount of brood and the strength of each colony were regularly assessed. Colony health, bee mortality, overwintering success, hive weights, and levels of in-hive residues were determined. Varroosis turned out to be the significant key factor for the endpoint colony strength. Clothianidin did not have a statistically significant impact on C0, C10 and C50 colonies. No statistical evidence was found for an interaction between varroosis andexposure to clothianidin.