Real-time RT-qPCR assay to detect sequences in the Piscine orthoreovirus-1 genome segment S1 associated with heart and skeletal muscle inflammation in Atlantic salmon

During the last decade, Piscine orthoreovirus was identified as the main causative agent of heart and skeletal muscle inflammation (HSMI) in Atlantic Salmon, Norway. A recent study showed that PRV-1 sequences from salmonid collected in North Atlantic Pacific Coast (NAPC) grouped separately from the Norwegian sequences found in Atlantic Salmon diagnosed with HSMI. Currently, the routine assay used to screen for PRV-1 in NAPC water and worldwide cannot differentiate between the two groups of PRV-1. Therefore, this study aimed at developing a real-time polymerase chain reaction (RT-qPCR) assay to target the PRV-1 genome segments specific for variants associated with HSMI. The assay was optimized and tested against 71 tissue samples collected from different regions including Norway, Chile and both coast of Canada and different hosts farmed Atlantic Salmon, wild Coho Salmon and escaped Atlantic Salmon collected in British Columbia, West Coast of Canada. This assay has the potential to be used for screening salmonids and non-salmonids that may carry PRV-1 potentially causing HSMI.     

What can we learn by studying dead fish fry?

This study investigated the influence of temperature (4, 8 and 12°C) on development and survival of brown trout (Salmo trutta) fry. The three aims of this study were: (a) to propose a typology of malformations; (b) to compare malformation types between live and dead fry and (c) to establish relationships between temperature and malformation occurrences. It was found 20 single malformations and 39 combinations of two or more malformations. Comparison between dead and live fry at different development stages (hatching, emergence and first food intake) showed that malformations of yolk sac were predominant at hatching and then decreased, while malformations of skeleton or multiple malformations were higher thereafter. All dead fry, and only 14% of live fry were malformed. Dead fry were mainly characterized by yolk sac malformations and multiple malformations whatever the temperature. Live fry showed a higher rate of skeleton malformations at 12°C, and the different types of malformations were equally represented at two other temperatures (4 and 8°C). To conclude, it is suggested that some malformations (yolk sac at hatching, yolk sac associated with skeleton malformations at emergence and skeleton at first food intake or combinations of malformations at all stages)might be lethal as they were founding dead fry and that temperature influences differently the occurrence of malformations.     

Parental participation in progeny and effective population sizes in experimental seed orchards of wild cherry Prunus avium L. (Batsch)

Parents and progenies genetic diversity, and male and female contributions to the seed crop were assessed in three experimental Prunus avium seed orchards. Collected data were used to compare different effective population sizes, based on phenological, seed crop and paternity analysis. Our results did not show any difference of genetic diversity between parents and progenies. A limited pollen pollution was detected. We showed that distance and coflowering among clones had a significant effect on effective pollination, and a significant effect of the production of flowers was revealed in one of the seed orchards. Our study also revealed a quite low number of effective size of fathers per mother, but high effective sizes of mothers, fathers and parents at the level of the seed orchard. Finally, the calculation of effective size of mothers, fathers and parents was not highly modified when having the complete information based on the paternity analysis.     

Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia,Canada (1985–94)

In response to concerns that novel infectious agents were introduced through the movement of eggs as Atlantic salmon aquaculture developed in British Columbia (BC), Canada, we estimated the prevalence of infectious agents in archived return‐migrating Sockeye salmon, from before and during aquaculture expansion in BC (1985–94). Of 45 infectious agents assessed through molecular assays in 652 samples, 23 (7 bacterial, 2 viral and 14 parasitic) were detected in liver tissue from six regions in BC. Prevalence ranged from 0.005 to 0.83 and varied significantly by region and year. Agent diversity ranged from 0 to 12 per fish (median 4), with the lowest diversity observed in fish from the Trans‐Boundary and Central Coast regions. Agents known to be endemic in Sockeye salmon in BC, including Flavobacterium psychrophilum, Infectious haematopoietic necrosis virus, Ceratonova shasta and Parvicapsula minibicornis, were commonly observed. Others, such as Kudoa thyrsites and Piscirikettsia salmonis, were also detected. Surprisingly, infectious agents described only recently in BC salmon, Ca. Branchiomonas cysticola, Parvicapsula pseudobranchicola and Paranucleospora theridion, were also detected, indicating their potential presence prior to the expansion of the aquaculture industry. In general, our data suggest that agent distributions may not have substantially changed because of the salmon aquaculture industry.     

To pool or not to pool? Guidelines for pooling samples for use in surveillance testing of infectious diseases in aquatic animals

Samples from multiple animals may be pooled and tested to reduce costs of surveillance for infectious agents in aquatic animal populations. The primary advantage of pooling is increased population‐level coverage when prevalence is low (<10%) and the number of tests is fixed, because of increased likelihood of including target analyte from at least one infected animal in a tested pool. Important questions and a priori design considerations need to be addressed. Unfortunately, pooling recommendations in disease‐specific chapters of the 2018 OIE Aquatic Manual are incomplete and, except for amphibian chytrid fungus, are not supported by peer‐reviewed research. A systematic review identified only 12 peer‐reviewed aquatic diagnostic accuracy and surveillance studies using pooled samples. No clear patterns for pooling methods and characteristics were evident across reviewed studies, although most authors agreed there is a negative effect on detection. Therefore, our purpose was to review pooling procedures used in published aquatic infectious disease research, present evidence‐based guidelines, and provide simulated data examples for white spot syndrome virus in shrimp. A decision tree of pooling guidelines was developed for use by peer‐reviewed journals and research institutions for the design, statistical analysis and reporting of comparative accuracy studies of individual and pooled tests for surveillance purposes.     

Water sensitivity, antimicrobial, and physicochemical analyses of edible films based on HPMC and/or chitosan

Several properties of chitosan films associated or not with hydroxypropylmethylcellulose polymer (HPMC) and HPMC films incorporating or not nisin and/or milk fat were studied. Nisin addition at a level of 250 microg mL-1 and likewise chitosan at 1% (w/v) concentration were efficient for total inhibiting Aspergillus niger and Kocuria rhizophila food deterioration microorganisms. HPMC and chitosan films were transparent, whereas nisin and/or fat incorporation induced a 2-fold lightness parameter increase and, consequently, involved more white films. Measurements of tensile strength, as well as ultimate elongation, showed that chitosan and HPMC initial films were elastic and flexible. High thermal treatments and additive incorporation induced less elastic and more plastic films. Water vapor transmission as far as total water desorption rates suggested that chitosan films were slightly sensitive to water. Water transfer was decreased by <60% as compared with other biopolymer films. Regarding its hydrophobic property, the capacity of fat to improve film water barrier was very limited.     

Egg and larval quality,and egg fatty acid composition of Eurasian perch breeders (Perca fluviatilis) fed different dietary DHA/EPA/AA ratios

In Eurasian perch (Perca fluviatilis), the variability in spawning quality is a major limiting factor for successful production, especially when breeders are fed with an artificial diet. The influence of the dietary DHA/EPA/AA ratio on the egg and larval quality and on the fatty acid and lipid class composition of eggs has been investigated in perch broodstock. Two experimental diets (16% lipids) with two different DHA/EPA/AA ratios, D1 (3/2/2) and D2 (23/9/1), were compared with a natural diet consisting of cultured carp juveniles, CC (10/10/1) and with a commercial diet for salmonids, CDS (14/16/1). Percentages of fertilization and hatching were comparable between fish fed D1, D2 and CC, with the highest hatching rate observed for D1 (63.5 ± 3.8%). These diets supported better values than the CDS. Larval survival and TL50 observed after osmotic stress were higher for the D1 group, followed by larvae produced by fish fed D2 and CC. Larvae from fish fed D1, D2 and CC were significantly more robust than larvae from the CDS group. Differences were observed regarding the fatty acid (FA) profile in the eggs, which was related to the dietary FA composition. The results indicate that a ratio of 3/2/2 seemed to be effective for obtaining eggs and larvae of good quality.     

Historical processes and landscape context influence genetic structure in peripheral populations of the collared lizard (<Emphasis Type="Italic">Crotaphytus collaris</Emphasis>)

Populations at the periphery of a species’ range often show reduced genetic variability within populations and increased genetic divergence among populations compared to those at the core, but the mechanisms that give rise to this core-periphery pattern in genetic structure can be multifaceted. Peripheral population characteristics may be a product of historical processes, such as founder effects or population expansion, or due to the contemporary influence of landscape context on gene flow. We sampled collared lizards (Crotaphytus collaris) at four locations within the northern Flint Hills of Kansas, which is at the northern periphery of their range, to determine the genetic variability and extent of genetic divergence among populations for ten microsatellite loci (n = 229). We found low genetic variability (average allelic richness = 3.37 ± 0.23 SE; average heterozygosity = 0.54 ± 0.05 SE) and moderate population divergence (average F_ST = 0.08 ± 0.01 SE) among our sample sites relative to estimates reported in the literature at the core of the species’ range in Texas. We also identified differences in dispersal rates among sampling locations. Gene flow within the Flint Hills was thus greater than for other peripheral populations of collared lizards, such as the Missouri glade system where most of the mesic grasslands have been converted to forest since the last glacial retreat, which appears to have greatly impeded gene flow among populations. Our findings signify the importance of considering landscape context when evaluating core-peripheral trends in genetic diversity and population structure.