ABSTRACT
Follicular atresia is an energy-saving oocyte resorption process that can allow the survival of female fish when environmental conditions are unfavourable and at the expense of fecundity. This study investigated the transcription levels of apoptosis and autophagy-related genes during atresia in the European hake that can show episodes of increased follicular atresia throughout the reproductive cycle. 169 female individuals were collected from the Bay of Biscay, and the ovaries were analysed using histological and molecular methods. Different levels of atresia were histologically detected in 73.7% of the ovaries analysed and the TUNEL assay identified apoptotic nuclei in follicles from both previtellogenic and vitellogenic stages. Transcripts of beclin-1 and ptenb were up-regulated in the ovaries containing atretic follicles, whereas p53, caspase-3, cathepsin D and dapk1 were up-regulated only in ovaries presenting vitellogenic atretic follicles. Our results indicate different implications of apoptotic vs autophagic processes leading to atresia during oocyte development, vitellogenesis being the moment of maximal apoptotic and autophagic activity in atretic hakes. The analysed genes could provide early warning biomarkers to identify follicular atresia in fish and evaluate fecundity in fish stocks.
Subject(s)
Gadiformes , Perciformes , Animals , Female , Ovary , Follicular Atresia , Apoptosis , Fishes , Transcription, Genetic , AutophagyABSTRACT
The use of whole-genome sequencing (WGS) for bacterial characterisation has increased substantially in the last decade. Its high throughput and decreasing cost have led to significant changes in outbreak investigations and surveillance of a wide variety of microbial pathogens. Despite the innumerable advantages of WGS, several drawbacks concerning data analysis and management, as well as a general lack of standardisation, hinder its integration in routine use. In this work, a bioinformatics workflow for (Illumina) WGS data is presented for bacterial characterisation including genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, core-genome-based or single nucleotide polymorphism (SNP)-based phylogenetic clustering and sequence typing. Workflow was tested using a collection of 22 in-house sequences of Salmonella enterica isolates belonging to a local outbreak, coupled with a collection of 182 Salmonella genomes publicly available. No errors were reported during the execution period, and all genomes were analysed. The bioinformatics workflow can be tailored to other pathogens of interest and is freely available for academic and non-profit use as an uploadable file to the Galaxy platform.
ABSTRACT
After Salmonella Enteritidis and S. Typhimurium, S. 4,[5],12:i:- is the most reported serovar in human clinical cases. During the past 20 years, many tools have been used for its typing and second-phase flagellar deletion characterization. Currently, whole genome sequencing (WGS) and different bioinformatic programs have shown the potential to be more accurate than earlier tools. To assess this potential, we analyzed by WGS and in silico typing a selection of 42 isolates of S. 4,[5],12:i:- and S. Typhimurium with different in vitro characteristics. Comparative analysis showed that SeqSero2 does not differentiate fljB-positive S. 4,[5],12:i:- strains from those of serovar Typhimurium. Our results proved that the strains selected for this work were non-clonal S. 4,[5],12:i:- strains circulating in Spain. Using WGS data, we identified 13 different deletion types of the second-phase flagellar genomic region. Most of the deletions were generated by IS26 insertions, showing orientation-dependent conserved deletion ends. In addition, we detected S. 4,[5],12:i:- strains of the American clonal line that would give rise to the Southern European clone in Spain. Our results suggest that new S. 4,[5],12:i:- strains are continuously emerging from different S. Typhimurium strains via different genetic events, at least in swine products.
