Biology subjects

Papadopoulou, A.

Publications and source records attributed to Papadopoulou, A..

4 recordsLinked to original sources

bioRxiv2022

Understanding host response to infectious salmon anaemia virus in an Atlantic salmon cell line using single-cell RNA sequencing

BackgroundInfectious Salmon Anaemia Virus (ISAV) is an Orthomixovirus that currently represents a large problem for salmonid aquaculture worldwide. Prevention and treatment methods are only partially effective. Genetic selection and genome engineering strategies have potential to develop ISAV resistant salmon stocks. However, this requires a detailed understanding of the genomic regulation of ISAV pathogenesis. Here, we used single cell RNA sequencing on a salmonid cell line to provide a high dimensional insight into the transcriptional landscape that underpin host-virus interactions during ISAV infection at the single cell level. ResultsSalmon head kidney 1 (SHK-1) cells were single-cell RNA sequenced before challenge, and at 24h, 48h, and 96h post-ISAV challenge. The results revealed marked changes in the host transcriptome at 48h and 96h post-infection, even in uninfected cells, potentially suggesting paracrine signalling. This paracrine activation of uninfected cells seemed to be unspecific, involving pathways such as mRNA sensing, ubiquitination or proteasome, and also the up-regulation of the mitochondrial ribosome genes. At 24h post infection, cells showed expression signatures consistent with viral entry, with up-regulation of genes such as PI3K, FAK or JNK. At 48h and 96h, infected cells showed a clear anti-viral response, characterised by the expression of IFNA2 or IRF2. ConclusionsThis study has increased our understanding of the cellular response of Atlantic salmon during ISAV infection, and revealed potential host-virus interactions at the cellular level. The results highlight the value of single-cell sequencing to characterise cell culture models of viral infection, and the results can be exploited in future functional studies to increase the resistance of Atlantic salmon to ISAV.

genomics↗

bioRxiv2021

Image-based taxonomic classification of bulk biodiversity samples using deep learning and domain adaptation

Complex bulk samples of invertebrates from biodiversity surveys present a great challenge for taxonomic identification, especially if obtained from unexplored ecosystems. High-throughput imaging combined with machine learning for rapid classification could overcome this bottleneck. Developing such procedures requires that taxonomic labels from an existing source data set are used for model training and prediction of an unknown target sample. Yet the feasibility of transfer learning for the classification of unknown samples remains to be tested. Here, we assess the efficiency of deep learning and domain transfer algorithms for family-level classification of below-ground bulk samples of Coleoptera from understudied forests of Cyprus. We trained neural network models with images from local surveys versus global databases of above-ground samples from tropical forests and evaluated how prediction accuracy was affected by: (a) the quality and resolution of images, (b) the size and complexity of the training set and (c) the transferability of identifications across very disparate source-target pairs that do not share any species or genera. Within-dataset classification accuracy reached 98% and depended on the number and quality of training images and on dataset complexity. The accuracy of between-datasets predictions was reduced to a maximum of 82% and depended greatly on the standardisation of the imaging procedure. When the source and target images were of similar quality and resolution, albeit from different faunas, the reduction of accuracy was minimal. Application of algorithms for domain adaptation significantly improved the prediction performance of models trained by non-standardised, low-quality images. Our findings demonstrate that existing databases can be used to train models and successfully classify images from unexplored biota, when the imaging conditions and classification algorithms are carefully considered. Also, our results provide guidelines for data acquisition and algorithmic development for high-throughput image-based biodiversity surveys.

zoology↗

bioRxiv2020

Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing

Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon breeders and producers worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV in commercial strains of Atlantic salmon is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing. A total of 2,833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1,353 animals were genotyped using a 55K SNP array, and the estimate of heritability for the trait of binary survival was 0.33 ({+/-}0.04). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome 13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4,927 and 2,437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated, while several metabolic pathways were up-regulated in infected fish compared to controls. The interferon pathway was mildly activated at 7 days and showed no sign of up-regulation at 14 days post infection, implying a crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance (4 high resistance and 4 low resistance animals per time point) highlighted TRIM25 as being up-regulated in resistant fish, suggesting it may be a key antiviral gene involved in the functional genetic basis of resistance to ISAV.

genetics↗

bioRxiv2020

A commercial autogenous injection vaccine protects ballan wrasse (Labrus bergylta, Ascanius) against Aeromonas salmonicida vapA type V

Atypical Aeromonas salmonicida (aAs) and Vibrionaceae related species are bacteria routinely recovered from diseased ballan wrasse used as cleaner fish in Atlantic salmon farming. Autogenous multivalent vaccines formulated from these microorganisms are widely used by the industry to protect farmed wrasse despite limited experimental proof that they are primary pathogens. In this study, the components of a commercial multivalent injection wrasse vaccine were tested for infectivity, pathogenicity and virulence via intra peritoneal injection at pre-deployment size (25-50g) and the efficacy of the vaccine for protection against aAs assessed. Injection with 3.5x109, 8x109 1.8x109 and 5x109 cfu/fish of Vibrio splendidus, V. ichthyoenteri, Aliivibrio logeii and A. salmonicida, respectively, did not cause significant mortalities, lesions or clinical signs after a period of 14 days. IP injection with both aAs and Photobacterium indicum successfully reproduced the clinical signs and internal lesions observed during natural outbreaks of the disease. Differences in virulence (LD50 at day 8-post infection of 3.6x106 cfu/fish and 1.6x107 cfu/fish) were observed for two aAs vapA type V isolates. In addition, the LD50 for Photobacterium indicum was 2.2x107 cfu/fish. The autogenous vaccine was highly protective against the two aAs vapA type V isolates after 700-degree days of immunisation. The RPSFINAL values for the first isolate were 95 and 91% at 1x106 cfu/fish and 1x107 cfu/fish, respectively, and 79% at 1x107 cfu/fish for the second isolate tested. In addition, significantly higher anti aAs seral antibodies (IgM), were detected by ELISA in vaccinated fish in contrast with control (mock vaccinated) fish. These results suggest wrasse can be effectively immunised and protected against aAs infection by injection with oil adjuvanted vaccines prepared with inactivated homologous isolates. Further work should assess the efficacy of vaccination against other isolates that have proven to be pathogenic such as aAs type VI and Photobacterium indicum and explore the feasibility of immersion vaccination. In addition, a full characterisation of aAs isolates within the same vapA types should be performed as differences in virulence between vapA type V isolates were observed and partial genome analysis indicated small but potentially important genomic differences in these isolates.

pathology↗