The Peculiar Characteristics of Fish Type I Interferons

Acknowledgments This work was supported by INRA, by Institut Pasteur, and by the “Projet TEFOR—Investissement d’avenir”—ANR-II-INBS-0014.Peer reviewedPublisher PD

Oral Vaccination of Baculovirus-Expressed VP28 Displays Enhanced Protection against White Spot Syndrome Virus in Penaeus monodon

White Spot Syndrome Virus (WSSV) is an infectious pathogen of shrimp and other crustaceans, and neither effective vaccines nor adequate treatments are currently available. WSSV is an enveloped dsDNA virus, and one of its major envelope proteins, VP28, plays a pivotal role in WSSV infection. In an attempt to develop a vaccine against WSSV, we inserted the VP28 gene into a baculovirus vector tailored to express VP28 on the baculovirus surface under the WSSV ie1 promoter (Bac-VP28). The Bac-VP28 incorporated abundant quantity (65.3 µg/ml) of VP28. Shrimp were treated by oral and immersion vaccination with either Bac-VP28 or wild-type baculovirus (Bac-wt). The treatment was followed by challenge with WSSV after 3 and 15 days. Bac-VP28 vaccinated shrimp showed significantly higher survival rates (oral: 81.7% and 76.7%; immersion: 75% and 68.4%) than Bac-wt or non-treated shrimp (100% mortality). To verify the protective effects of Bac-VP28, we examined in vivo expression of VP28 by immunohistochemistry and quantified the WSSV copy number by qPCR. In addition to that, we quantified the expression levels shrimp genes LGBP and STAT by real-time RT-PCR from the samples obtained from Bac-VP28 vaccinated shrimp at different duration of vaccine regime. Our findings indicate that oral vaccination of shrimp with Bac-VP28 is an attractive preventative measure against WSSV infection that can be used in the field

Fish responses to viruses : From interferon to T-cells

Viruses affecting farmed fish species, such as the rainbow trout, have been studied extensively because they cause significant economic losses. Studies on vaccines developed against Viral Hemorrhagic Septicemia (VHS) have provided evidence of an effective and specific response based on neutralizing antibodies, as well as of an immune memory. Various techniques of differential transcript analysis were used to investigate the non-specific leukocyte response to the VHS virus in trout. As in mammals, this response was dependent on interferon-responsive genes. A VDJ junction spectratyping approach of transcripts of the specific T-cell antigen receptor (TCR) was also developed to examine the specific cellular response in rainbow trout. This approach was used to show the existence of complex antiviral T-cell responses in fish.Les virus des poissons d'intérêt agronomique, comme la truite arc-en-ciel, ont été bien étudiés parce qu'ils causent des dommages significatifs dans les élevages. Ainsi, des vaccins ont été développés contre la Septicémie Hémorragique Virale (SHV), montrant l'existence d'une réponse efficace et spécifique basée sur les anticorps neutralisants et celle d'une mémoire immunitaire. La réponse non spécifique des leucocytes de truite induite par le virus de la SHV a pu être explorée par différentes techniques d'analyse différentielle des transcrits. Il a ainsi été démontré que les gènes induits par l'interféron orchestrent cette réponse, comme c'est aussi le cas chez les mammifères. Enfin, une stratégie de spectratypage des longueurs de jonctions VDJ des transcrits du récepteur spécifique de l'antigène des lymphocytes T (TCR) a été développée pour l'étude de la réponse cellulaire spécifique chez la truite arc-en-ciel. Cette approche a permis de démontrer l'existence de réponses T antivirales complexes chez les poissons

Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods

BACKGROUND: Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. RESULTS: We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed “advanced” phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. CONCLUSIONS: We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of probability of the tree topologies) of the evolutionary affinities between double-stranded RNA and positive strand RNA viruses. In particular, we were able to show that there exists a good statistical support for the claims that dsRNA viruses are not monophyletic and that viruses with permuted RdRps belong to a common evolution lineage as previously proposed by other groups. We also propose a tree topology with a good statistical support describing the evolutionary relationships between the Picornaviridae, Caliciviridae, Flaviviridae families and a group including the Alphatetraviridae, Nodaviridae, Permutotretraviridae, Birnaviridae, and Cystoviridae families

Phylogeny and expression of tetraspanin CD9 paralogues in rainbow trout (Oncorhynchus mykiss)

Open Access via the Elsevier Agreement Acknowledgements This work was funded by BBSRC project BB/R008973/1 and European Union’s Horizon 2020 research and innovation program under grant agreement 817923 (AQUA-FAANG).Peer reviewedPublisher PD

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line

This project was carried out during CD’s BBSRC Eastbio PIPS placement at Marine Scotland. The authors are grateful to Dr Milena Monte (University of Aberdeen) for help with the FACS analysis. The authors wish to thank Dr Filippo Del Bene (Neuronal Circuit Development, Institut Curie) and Dr Wenbiao Chen (School of Medicine, Vanderbilt University) for the Addgene plasmids, #61051 and #47929, respectively, and Prof. Nancy C. Reich Marshall (Department of Molecular Genetics and Microbiology, Stony Brooks University) for the plasmid pmEGFP-N1.Peer reviewedPublisher PD

High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions

Predicting protein binding affinities from structural data has remained elusive, adifficulty owing to the variety of protein binding modes. Using the structure-affinity-benchmark(SAB, 144 cases with bound/unbound crystal structures and experimental affinity measurements),prediction has been undertaken either by fitting a model using a handfull of pre-defined variables,or by training a complex model from a large pool of parameters (typically hundreds). The formerroute unnecessarily restricts the model space, while the latter is prone to overfitting.We design models in a third tier, using twelve variables describing enthalpic and entropic variationsupon binding, and a model selection procedure identifying the best sparse model built from a subsetof these variables. Using these models, we report three main results. First, we present modelsyielding a marked improvement of affinity predictions. For the whole dataset, we present a modelpredicting Kd within one and two orders of magnitude for 48% and 79% of cases, respectively.These statistics jump to 62% and 89% respectively, for the subset of the SAB consisting of highresolution structures. Second, we show that these performances owe to a new parameter encodinginterface morphology and packing properties of interface atoms. Third, we argue that interfaceflexibility and prediction hardness do not correlate, and that for flexible cases, a performancematching that of the whole SAB can be achieved. Overall, our work suggests that the affinityprediction problem could be partly solved using databases of high resolution complexes whoseaffinity is known