Rainbow Trout Research Articles

The application of plasmid DNA constructs encoding antiviral proteins as potential therapeutics against viral infections in salmonid aquaculture

Treatments to control infectious diseases in aquacultured fish commonly focus on the use of antibiotics (which are ineffective against viruses) and inorganic disinfectants. Currently, antiviral treatments are not available for use in aquaculture. The use of plasmid vectors to overexpress antiviral proteins in fish has been reported, with positive results against viral infections. The aim of this work was to overexpress the antiviral proteins interferon-induced protein with tetratricopeptide repeats 5 (IFIT5) and natural killer enhancing factor (NKEF) using plasmid vectors (pIFIT5 and pNKEF) as novel therapeutic agents against viral infections. The antiviral activity of pIFIT5 against viral hemorrhagic septicemia virus (VHSV) and infectious pancreatic necrosis virus (IPNV) was evaluated in vitro in epithelioma papulosum cyprinid and Chinook salmon embryo cell lines. Moreover, pNKEF antiviral activity against IPNV was also evaluated. Results showed that pIFIT5 had antiviral activity against both viruses, but pNKEF did not protect against IPNV. In addition, we evaluated the use of pIFIT5 and pNKEF constructs as therapeutics in rainbow trout. Biodistribution assays demonstrated systemic distribution of the IFIT5-TFP1 and NKEF-TFP1 proteins in rainbow trout injected with the plasmids, and pIFIT5 and pNKEF triggered an immune response in the injected fish. In a pilot study, we evaluated the level of protection conferred by pIFIT5 and pNKEF against VHSV in rainbow trout, and we observed 10 % percent survival for pIFIT5 compared to pTFP. Together, these results suggest the potential of pIFIT5 as therapeutic agent in aquaculture.

Comparison of the Effects of Hesperidin Over 30- and 60-Day Intervals on Rainbow Trout: A Potential Biostimulant to Promote Growth, Immunological and Antioxidant Responses, and Disease Resistance

Abstract The current research evaluated the effects of dietary hesperidin (HSP) on growth parameters, digestive enzyme activities, innate immune markers, and antioxidant responses in rainbow trout, Oncorhynchus mykiss after the 30- and 60-day feeding trial. Then, specimens were subjected to Yersinia ruckeri infection for 14 days. For this, six hundred rainbow trout juveniles (initial weight; 25.49±0.40 g) were fed with different levels of HSP including 0 (HSP0; control), 50 (HSP50), 100 (HSP100), 150 (HSP150), and 200 (HSP200) mg/kg feed. After 60 days, dietary HSP100 supplementation significantly improved growth and feed efficiency indices. The optimal dose of HSP based on the regression test for WG and FCR detected 122 and 131 mg/kg, respectively. At the end of the 30th day, dietary HSP150 supplementation markedly boosted serum lysozyme (LYZ), myeloperoxidase (MPO), complement component C3, and immunoglobulin (Ig) levels, but decreased malondialdehyde (MDA) content. In the same period, dietary administration of HSP at the different concentrations markedly increased complement component C4 (HSP150 and HSP200), superoxide dismutase (SOD), skin mucus alkaline phosphatase (ALP) (HSP100–HSP200), skin mucus LYZ and catalase (CAT) (HSP100 and HSP 150), and skin mucus Ig level (HSP50–HSP200). After 60 days, all dietary HSP supplementation significantly improved lipase, serum C3, glutathione peroxidase (GPX), and skin mucus ALP, LYZ, and Ig levels, but decreased MDA, aspartate aminotransferase (AST), and alanine aminotransferase (ALT) values. After 60 days, dietary administration of HSP150 induced a significant discrepancy in the activity of serum LYZ, MPO, respiratory burst (RB), and lactate dehydrogenase (LDH) compared to the control group. In the same period, dietary HSP supplementation at different levels induced a remarkable increase in digestive protease activity (HSP100), serum ACH50 and CAT activities (HSP100 and HSP150), skin mucus peroxidase and serum SOD levels (HSP100–HSP200), and serum C4 value (HSP50, HSP150, and HSP200), but markedly decreased ALP activity (HSP150 and HSP200). In addition, dietary HSP supplementation, especially HSP150, markedly boosted disease resistance against Y. ruckeri infection. The current data demonstrated that the oral administration of 100–150 mg/kg HSP has a high potential to promote growth performance, disease resistance, and faster induction of immune and antioxidant responses.

Using Genetic Data to Determine Origin for Out-Migrating Smolt and Returning Adult Steelhead Trout (Oncorhynchus mykiss) in a Southeast Alaska Drainage.

Oncorhynchus mykiss is a partially migratory salmonid species, and many migratory populations (known as steelhead) have declined in recent decades in the western United States and Canada. Closely related resident populations (known as rainbow trout) may be an effective resource in the recovery of these declining migratory populations. However, the extent to which different populations of resident rainbow trout produce migratory individuals and how likely these individuals are to return as adults to spawn remains unknown. One limitation to answering these questions is the identification of loci that accurately segregate between migratory and resident populations. To address this limitation, we used existing genomic data from a well-studied population of O. mykiss from Southeastern Alaska (Sashin Creek) to identify loci that segregate between phenotypes. We then utilized Double Mismatch Allele-Specific qPCR (DMAS-qPCR) to genotype 233 smolts out-migrating from Sashin Creek and 99 returning adult steelhead trout across a five-year period to determine (a) the origin of out-migrating smolts and returning adults and (b) to quantify the extent to which the resident population contributes to the migratory population. Our results show that 37.3% of out-migrating smolts were produced from resident parents, whereas 19.3% of returning adults had resident parents. Ultimately, these results demonstrate that resident populations of rainbow trout produce migrant offspring that successfully complete their migration and return to spawn, increasing population sizes and likely improving genetic diversity. Therefore, conservation efforts should consider landlocked resident populations for producing smolts when developing recovery plans for migratory steelhead populations.

Determination of per- and polyfluoroalkyl substances (PFAS) in six different fish species from Swiss lakes

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants with bioaccumulation potential, particularly affecting aquatic ecosystems and human health also via fish consumption. There is therefore a need for reliable extraction methods and studies to accurately assess PFAS levels in fish, crucial for understanding bioaccumulation and potential toxicological effects on both fish and humans through consumption. This study investigated PFAS levels in freshwater fish from Swiss lakes, focusing on six common species: Coregonus wartmanni, Cyprinus carpio, Oncorhynchus mykiss, Perca fluviatilis, Salmo trutta, and Squalius cephalus. Utilizing an optimized QuEChERS extraction method, 15 PFAS were analyzed in 218 fish fillet samples using liquid chromatography-mass spectrometry (LC–MS/MS). The results were compared to EU regulations and EFSA guidelines for tolerable weekly intake (TWI), with a specific focus on correlations between fish size and PFAS concentration. Our findings reveal significant PFAS contamination, particularly in Perca fluviatilis with perfluorooctane sulfonic acid (PFOS) and perfluorohexane sulfonic acid (PFHxS) levels often exceeding EU safety limits. TWI, calculated for a person of 70 kg body weight and an intake of 200 g of fish fillet, is exceeded in 95% of Coregonus wartmanni, 100% of Squalius cephalus, and in 55%, 50%, and 36% of the specimens Oncorhynchus mykiss, Salmo trutta, and Perca fluviatilis respectively. Correlation analysis between PFAS concentration and fish size in 121 Salmo trutta specimens revealed significant positive correlations for perfluorobutane sulfonic acid (PFBS), perfluorodecanoic acid (PFDA), and perfluorohexane sulfonic acid (PFHxS), and a negative correlation for perfluoropentanoic acid (PFPeA). These results underscore the critical need for continuous monitoring and regulatory efforts to mitigate PFAS exposure risks to both ecosystems and human health.

Growth and Depuration of Off‐Flavors in Rainbow Trout Oncorhynchus Mykiss in a Partial Recirculating Aquaculture System (PRAS)

ABSTRACTIn recirculating aquaculture systems (RAS), off‐flavours accumulated in fish muscle tissue can be problematic in terms of consumer acceptance and the reputation of farmed fish products. Off‐flavours often give fish earthy, muddy, or other undesirable flavours. Typically, off‐flavours are removed during a depuration period in which fish are fasted and held in clean water. Unfortunately, this causes additional costs and delayed sales, while fish lose weight and show a decrease in lipid content. First, we studied fish growth in a partial RAS (PRAS) where the conditions are very similar to those in depuration with a water exchange rate of 4000 L kg−1 feed, compared to RAS with a 650‐L water kg−1 feed. Rainbow trout (Oncorhynchus mykiss) was reared in both systems. Our aim was to combine the benefits of a higher water exchange rate: the lack of need for biofilters and a lower accumulation of off‐flavours while obtaining stable rearing conditions. Additionally, we studied the effects of moderate feeding and H2O2 addition during depuration. The fish grew faster in a PRAS than in a RAS when fed ad libitum. Thirteen off‐flavour compounds were found in the fish flesh and 11 in the circulating water. The H2O2 addition led to decreased levels of off‐flavours in the tank water and in fish muscle. The results showed no significant differences in off‐flavours between the fed and not‐fed systems, showing that moderate feeding did not prevent a good depuration result. However, the lipid content and the overall fish weight were higher in the fed systems, which suggests more effective depuration. Increased depuration efficiency can be an important tool when considering ways to improve the profitability of production.

Enhancing the Quality of Ready‐to‐Eat Trout Burger Patties: Investigating the Combination of Modified Atmosphere Packaging and Microbial Transglutaminase Enzyme

ABSTRACTIn this study, rainbow trout patties (Oncorhynchus mykiss Walbaum, 1792) were treated under a modified atmosphere (MA) (60/40:CO2/N2) packed with microbial transglutaminase enzyme (MTGase) at varying concentrations (0.5% and 1%) and kept for a full day at 2°C ± 2°C. Denser and more complex intermolecular cross‐linking formations between peptides and gel network structures were observed in the first and last scanning electron microscope images of MTGase‐containing groups. MTGase increased the springiness, hardness, shear force, and work‐of‐shear parameters during the storage period in uncooked and cooked patties compared to the control group. The protein, energy, moisture, and amino acid contents were maintained in the MTGase‐containing groups, but using MTGase at higher concentrations was ineffective. Microbiological analyses have shown that MTGase is partially effective on microbial fauna, and the most significant inhibitory effect was determined on total mesophilic aerobic bacteria (TMAB). In all groups, the total amounts of saturated, monosaturated, and polyunsaturated fatty acids remained unchanged on both production and expiration days (p > 0.05). After mixing the burger patty additives into the ground meat, the amounts of sodium, calcium, potassium, and magnesium increased in all groups (p < 0.05); however, a decrease in calcium was observed in the MTGase‐containing groups (p < 0.05) compared to the control group. The higher proportion of the MTGase‐contained group did not exhibit significant differences compared to the lower proportion of the MTGase‐contained group, except for textural characteristics and the TMAB inhibition effect.

Effect of Vermicompost Supplement on Rainbow Trout Performance

Vermicompost is the product of organic waste digestion by earthworms besides aerobic decomposition at ambient temperature. It is a rich composition containing plant nutrients and beneficial microorganisms. Some fishes, especially predatory species such as rainbow trout, need nutritive feed so that they can be healthy; a useful and cheaper additive such as vermicompost can supply this aim. In this study, the effect of different percentages of vermicompost in the diet of rainbow trout was investigated. For this purpose, 100 rainbow trout with an average weight of 120±3 g were distributed in 5 groups in concrete tanks. Their nutrition and physical and chemical water parameters were determined according to the standard. Vermicompost with confirmable analysis was added to their daily feed (2, 4, 6, and 10%). After 2 months, the feed conversion ratio and survival rate were examined. The results showed that there was a significant relationship between the performance of the control group and the treatment groups (p

Performance Evaluation of Hydroponic Grow-Outs in An Innovative Coldwater Aquaponic System Featuring Rainbow Trout and Lettuce

A 45-day trial was carried out to assess the production performance of different hydroponic media in a novel do-it-yourself (DIY) low-tech re-circulating aquaponic system for temperate regions with rainbow trout (Oncorhynchus mykiss) and lettuce (Lactuca sativa). Rainbow trout juveniles (average weight of 35.59 g) were stocked in the experimental units at 2.8 kg.m-3 and fed with commercial floating pelleted feed at 8 % of their body weight in three treatments and a control. The lettuce saplings were randomly planted in the river stone bed (T1), crushed stone bed (T2), raft/deep water culture (DWC) unit (T3) and control (C) soil bed (fortified with NPK fertiliser) with equivalent planting intervals of 42 saplings.m-2. The system, designed with low-tech simplicity, was managed without alkalinity correction and depended entirely on plant growth and metabolism for biofiltration. The water quality parameters such as temperature, pH, dissolved oxygen (DO), dissolved free CO2, hardness, total alkalinity, ammonium, nitrite, and nitrate varied significantly (P < 0.05) among the treatments compared to the control. The final individual weight, biomass gain, specific growth rate (SGR), and feed conversion ratio (FCR) of rainbow trout were significantly better (P < 0.05) in media beds (crushed stone and river stone) compared to control and DWC systems. The final mean weights of rainbow trout in river stone (12.33 ± 0.002 g and crushed stone (12.39 ± 0.054 g) treatments were significantly higher (P < 0.05) than in DWC (12.1 ± 0.023 g) and control (12.09 ± 0.002 g) treatments. The production of lettuce was significantly greater (P < 0.05) in all three treatments (river stone: 4.33 ± 0.123 g, crushed stone: 4.53 ± 0.09 g and DWC: 4.31 ± 0.163 g) compared to the control (3.31 ± 0.172 g). The DWC including the media bed systems facilitates the improved performance of lettuce saplings in terms of final height and leaf number. These results show that a low-tech media bed system without a supplementary biofiltration unit can achieve sustainable production of both fish and vegetables in temperate hilly terrains.

AI-Driven Realtime Monitoring of Early Indicators for Ichthyophthirius multifiliis Infection of Rainbow Trout.

A novel video-based real-time system based on AI (artificial intelligence) was developed to detect clinical signs in fish exposed to pathogens. We selected a White Spot Disease model involving rainbow trout as the experimental animal and the parasitic ciliate Ichthyophthirius multifiliis as a pathogen. We compared two identical fish tank systems: one tank was infected by co-habitation, whereas the other tank was kept non-infected (sham infection). The two fish tanks were separately video monitored (full top and side view) during the course of infection, during which fish were removed whenever they developed clinical signs (direct visual inspection by the observer). Image analysis (object detection, classification and tracking) was used to track behavioural changes in fish (in every recorded video frame), focusing on movement patterns and spatial localisation. Initially, the two fish groups (infected and non-infected) exhibited similar behaviour and non-infected fish did not change behaviour during the 15 d observation period (from 5 d before infection until 10 dpi). At 4, 7, 8, 9 and 10 dpi some infected fish showed clinical signs (equilibrium disturbance, gasping and lethargy) and were removed from the experiment. Anorexia occurred from 5 dpi and a gradual progression of gasping behaviour was noted, whereas the frequency of fish flashing (rubbing/scratching against objects) was low. Equilibrium disturbances and the development of white spots in the skin appeared to be a much later (8-10 dpi at this temperature) indicator of infection. The video analysis showed a general distribution of non-infected fish in all parts of the fish tank during the entire experiment, whereas infected fish already at 4-5 dpi moved towards higher water currents in the top and bottom positions. This change of fish positioning within the tank appeared as a promising early indicator of infection. The study suggests that continuous monitoring of fish behaviour using AI can potentially optimise the timing of humane endpoints, indicate disease signs earlier and thereby improve animal welfare in both animal experimentation and in aquaculture settings.

Event-based wave statistics for the Baltic Sea

Abstract. Typical statistics, such as mean or percentiles, provide an excellent baseline for studying variations and changes in physical variables that have socioeconomic relevance. Nonetheless, they lack information on how often, and for how long, a certain wave height is exceeded, which might be needed for practical applications, such as planning marine operations. Using a 29-year wave hindcast, we determined the individual events where the significant wave height exceeded warning thresholds for Baltic Sea marine traffic (2.5, 4, and 7 m). During the summer months (JJA), the significant wave height exceeded 2.5 m less than twice a month. During the winter months (DJF), a significant wave height of 2.5 m was exceeded on average once a week in the larger Baltic Proper and Bothnian Sea sub-basins. Events with wave heights of over 7 m occurred roughly once every other year in the larger sub-basins. Our case study for fish-farm-related operations compared two sites that are located 10 and 30 km from the coast in the Bothnian Sea, where we determined wave events that could affect operations at the cage – meaning a significant wave height over 1 m. During the growth period of rainbow trout (May–October) there were roughly twice as many possibly disruptive events at the location further offshore than at the location closer to the coast. Even at the less-exposed location half of the wave events lasted more than 12 h, with a few events in September and October lasting around a week.

Effect of Starvation and Refeeding on Gamete Quality and Fertilization in Rainbow Trout (Oncorhynchus mykiss) Broodstock

In this study, the impact of starvation and refeeding on broodstocks was observed by examining quality parameters of gametes and fertilization. While the control group fish were fed every day, the male and female members of the group were fed one week apart and placed in starvation after a week of feeding. Weight gain in the control group was the highest. The feed conversion ratio was normal in all groups (0.9-1.3%). Relative fecundity was (935±62 eggs/kg) in control group females; it was found to be (1317±241 eggs/kg) in starving females and statistically different in the groups (p < .05). The egg diameter of the group receiving intermittent feeding for a week (3.36±0.2 mm) was found to be the lowest. All spermatological parameters were similar between groups, except for sperm volume. The most sperm count was seen in the group that received one-week intermittent feeding (46.9± 20 ml). The results of fertilization with the control female in the fertilization study based on male individuals showed similarity for the male individuals of the trial group, the highest fertilization rate was seen in fertilization using the control female and control male.

Risk assessment of heavy metals (Zn, Cu, Pb, and Ni) in the edible tissue of Oncorhynchus mykiss trout in the rivers of the southern Caspian Sea and the northern and southeast coast of Iran

The study aims to monitor and compare the concentration of heavy metals viz., zinc, copper, lead and nickel in the edible tissue of Oncorhynchus mykiss trout in the southern coast of Caspian Sea and the rivers of Khash city in the north-southeast coast of Iran. The average concentrations of zinc, copper, lead and nickel for the Stations in the north of Iran and the southeast of Iran were found 10.1, 8.1, 5.9, 4.7 and 6.5, 6.1, 3.5, 3.2 μg/g dry weight, respectively. Lead exceeded was the recommended standard limits by WHO, FAO, NHMRC, EC and UKMAFF. Based on the results, the average nickel metal was higher than the allowed concentration of international standards in all the studied stations, which indicates that more control should be done on the sources producing this metal around the target areas. furthermore, the daily intake (EDI) of the studied metals in all age groups were lower than the reference dose determined by the EPA organization and the tolerable intake (TI) provided by the FAO/WHO organization. The lowest frequency of daily consumption of Oncorhynchus mykiss was reported for the group of adult males and based on nickel metal (1.67 μg/g) and lead metal (1.14 μg/g) in the rivers located in the south of the Caspian Sea and the rivers of Khash city located in the southeast of Iran, respectively. The risk potential and risk index for non-cancerous diseases for all age groups in the muscle tissue of this fish was less than one, which shows that the consumption of this type of fish for human consumption will not cause a problem from the point of view of health and public health. However, management measures are necessary to prevent and control pollutants, especially in the southern shores of the Caspian Sea.

Unpredictable Repeated Stress in Rainbow Trout (Oncorhynchus mykiss) Shifted the Immune Response against a Fish Parasite.

Farmed fish are regularly subjected to various stressors due to farming practices, and their effect in the context of a disease outbreak is uncertain. This research evaluated the effects of unpredictable repeated stress in rainbow trout challenged with the ciliate Ichthyophthirius multifiliis, known to cause white spot disease in freshwater fish. Before and after the pathogen exposure, fish were handled with a random rotation of three procedures. At 7 days post-infection (dpi), the parasite burden was evaluated in fish and in the tank's water, and the local and systemic immune responses were investigated in the gill and spleen, respectively. The fish mortality was recorded until 12 dpi, when all the fish from the infected groups died. There was no statistical difference in parasite burden (fish and tank's water) and infection severity between the two infected fish groups. The immune gene expression analysis suggested a differential immune response between the gill and the spleen. In gills, a T helper cell type 2 immune response was initiated, whereas in spleen, a T helper cell type 1 immune response was observed. The stress has induced mainly upregulations of immune genes in the gill (cat-1, hep, il-10) and downregulations in the spleen (il-2, il-4/13a, il-8). Our results suggested that the unpredictable repeated stress protocol employed did not impair the fish immune system.

Molecular mechanism of infectious hematopoietic necrosis G protein N-glycosylation escaping from rainbow trout immunity

Infectious Hematopoietic Necrosis (IHN) is a viral disease that causes great economic losses in salmonid fish farming industry. It is known that the N-glycosylation site on the G protein affects the immune evasion and pathogenicity of the Infectious Hematopoietic Necrosis Virus (IHNV). In this study, a mutation in the N-glycosylation site of the G protein (438 amino acids) of IHNV resulted in an increased the survival rate of rainbow trout from 17.1 % to 75.3 %, and a decreased serum antibody IgM level after virus infection. In addition, this mutation decreased the expression of CD83 and CD209 on dendritic cells and enhanced the binding of G protein to TCR. This suggests that the activation of CD4+ T-cells was enhanced. We hypothesize that IHNV evades the host's immune system by impairing antigen presentation and T-cell responses through the N-glycosylation of G protein. This finding could provide new insights for developing live attenuated vaccines.

Comparative study of influence of Cu, CuO nanoparticles and Cu2+ on rainbow trout (Oncorhynchus mykiss W.) spermatozoa.

The same elements can yield disparate nanoproducts that may elicit different harmful effects in cells and organisms. This study aimed to compare the effects of copper (Cu NPs) and copper oxide (CuO NPs) nanoparticles and Cu2+ (from CuSO4) on the physico-biochemical variables of rainbow trout spermatozoa. The cell death assay, along with the activation of caspases 8 and 9, the level of reactive oxygen species (ROS), and the percentage of cells exhibiting a high mitochondrial membrane potential (MMP) were quantified over 24-hour incubation. Interestingly, during exposure, all copper products induced cell apoptosis. However, Cu NPs had a stronger effect than CuO NPs, while the impact of the Cu in ionic form was found to be between the other two compounds. The extrinsic and intrinsic apoptotic pathways were activated, as evidenced by the activation of caspases 8 and 9. Initially, caspase activation increased without a corresponding decrease in MMPs but prolonged exposure resulted in a significant decrease in MMP levels. In all treated cells, the ROS levels increased over time. Further studies are needed to confirm the lower CuO NPs' toxicity compared to Cu NPs because their effect on cells also depends on many other parameters such as size or shape.

Immunostimulant In Fish Hatchery- A Tool In Pharmacological Research

Fish is an aquatic animal that is used as food and presently they are used in scientific research. They provide a simple system for biomedical research and hence there is an increase in demand for fish production due to its dynamic purposes. The fish are less sentient and they have a high potency with the homology of mammals hence they are used as a model in pharmacological research. The various fish that are used are zebra fish, rainbow trout fish, medaka fish, etc. Various husbandry techniques were introduced to increase the production of fish. Their intensification led to poor-quality of fish production. Immunostimulants are drugs that enhance the innate immunity of fish and increase their resistance to the disease. They are biological and synthetic compounds that increase phagocytic, lysosomal, and bactericidal activity by directly activating the immune cells and NK cells and helping in the control of disease. They are used in the pharmacological research of toxicology, genetics, cancer research, biomedicine, neurobiology, endocrinology, ecology, and gerontology, and also in the development of biology and act as a model to provide elemental knowledge on biological science.

Reduced Streamflow From Water Diversion Alters Stream Ecology and Fish Behavior

ABSTRACTUnderstanding invertebrate and fish responses to altered streamflows is important for water management that balances ecological function and societal needs. We studied the impacts of a significant water diversion on a stream food web, including benthic biofilms, benthic macroinvertebrates (BMI), and drifting macroinvertebrates. In the dry season, drift flux (number of aquatic individuals or biomass/s) and drift concentration (individual/m3) were lower below the diversion than above. Drift concentration (biomass/m3) was slightly higher below the diversion, due to the presence of large Trichopterans. All measures of drift dropped to nearly zero at the end of the dry season below the diversion, when streamflows were reduced by > 90% below the diversion relative to above, representing a significant loss of food resources for trout. Simultaneously, native Rainbow Trout (Oncorhynchus mykiss) switched from drift to benthic foraging 1 month earlier below the diversion as drift and water velocities declined. The ecology of the benthos was not as impacted by the diversion: BMI densities were higher below the diversion, while benthic biofilm densities were similar at the two sites. The taxonomic composition of BMI was also similar between the sites, but fewer Ephemeroptera entered the drift below the diversion. Overall, the late season decrease in drift below the diversion despite the similar or higher benthic production suggests that streamflows influence food availability for trout even in the absence of benthic responses. Reduced streamflows, due to water diversions as studied here, or due to climate change, will likely reduce food resources and growth opportunities for fishes.

GenoTriplo: A SNP genotype calling method for triploids.

Triploidy is very useful in both aquaculture and some cultivated plants as the induced sterility helps to enhance growth and product quality, as well as acting as a barrier against the contamination of wild populations by escapees. To use genetic information from triploids for academic or breeding purposes, an efficient and robust method to genotype triploids is needed. We developed such a method for genotype calling from SNP arrays, and we implemented it in the R package named GenoTriplo. Our method requires no prior information on cluster positions and remains unaffected by shifted luminescence signals. The method relies on starting the clustering algorithm with an initial higher number of groups than expected from the ploidy level of the samples, followed by merging groups that are too close to each other to be considered as distinct genotypes. Accurate classification of SNPs is achieved through multiple thresholds of quality controls. We compared the performance of GenoTriplo with that of fitPoly, the only published method for triploid SNP genotyping with a free software access. This was assessed by comparing the genotypes generated by both methods for a dataset of 1232 triploid rainbow trout genotyped for 38,033 SNPs. The two methods were consistent for 89% of the genotypes, but for 26% of the SNPs, they exhibited a discrepancy in the number of different genotypes identified. For these SNPs, GenoTriplo had >95% concordance with fitPoly when fitPoly genotyped better. On the contrary, when GenoTriplo genotyped better, fitPoly had less than 50% concordance with GenoTriplo. GenoTriplo was more robust with less genotyping errors. It is also efficient at identifying low-frequency genotypes in the sample set. Finally, we assessed parentage assignment based on GenoTriplo genotyping and observed significant differences in mismatch rates between the best and second-best couples, indicating high confidence in the results. GenoTriplo could also be used to genotype diploids as well as individuals with higher ploidy level by adjusting a few input parameters.

Environmental Implications of Ionic Liquid and Deep Eutectic Solvent in Geothermal Application: Comparing Traditional and New Approach Methods.

The significant surge of ionic liquids (ILs) research over the past decade has led to the formation of various novel ionic liquid compounds and their diverse applications. Enhanced geothermal systems (EGS) for geothermal power generation are an emerging IL application as a heat extraction fluid. The once widely held belief in the environmentally friendly characteristics of ionic liquids, mainly due to their insignificant vapor pressure, is now being scrutinized. It has become apparent that while ILs do not readily evaporate into the atmosphere, they are not guaranteed to remain entirely isolated from the environment. Recent attention has been directed toward toxicological studies, including ecotoxicity impacts, with the long-accepted assumption of ILs having low toxicity being invalid. This paper aims to shed light on the toxicity of hexylepyradinium bromide (HPyBr) IL and a deep eutectic solvent (DES) comprising choline chloride with magnesium chloride hexahydrate (ChCl:MgCl2·6H2O) to five test species, an algal species (Raphidocelis subcapitata), the water flea (Ceriodaphnia dubia and Daphina magna), the fathead minnow (Pimephales promelas), and the earthworm (Eisenia fetida), to measure acute and chronic toxicity. Additionally, new approach methods (NAMs) are presented using the fathead minnow embryo and the rainbow trout (Oncorhynchus mykiss) gill cell line and the RTgill-W1 assay to compare sensitivity across species. Overall, ChCl:MgCl2·6H2O displayed lower toxicity, while HPyBr demonstrated higher toxicity, highlighting the need for caution in handling it to prevent harm to aquatic ecosystems. Comparative analysis underscored the potential threat of ChCl:MgCl2·6H2O to aquatic life, highlighting the cumulative effects of the environmental components.

Environmentally Relevant Concentrations of S-6PPD-Quinone Caused More Serious Hepatotoxicity Than R-Enantiomer and Racemate in Oncorhynchus mykiss.

6PPD-quinone (6PPD-Q) is frequently detected in various environmental media, and the environmentally relevant concentrations can be fatal to Oncorhynchus mykiss. Notably, 6PPD-Q has two enantiomers (S-6PPD-Q and R-6PPD-Q). In this study, O. mykiss was separately exposed to each enantiomer and racemate of 6PPD-Q for 96 h at environmentally relevant concentrations, and livers were collected. Effects on the biochemical, pathological, and ultrastructural changes were assessed, and metabolomics was conducted to elucidate the potential hepatotoxicity mechanism. Compared with the control treatment, the levels of catalase (CAT, all treatments except for 0.1 μg/L rac-6PPD-Q), and glutathione-S-transferase (GST, all treatments) significantly declined. Hepatocyte space became smaller, nuclear morphology changed, and nucleolysis occurred. Mitochondrial malformation and vesicle-like structure dilation of the endoplasmic reticulum (ER) were observed in the hepatocytes, which was most serious after S-6PPD-Q exposure. Some amino acid metabolism, folate biosynthesis, taurine and hypotaurine metabolism and purine metabolism were disturbed, consistent with mitochondrial dysfunction and ER stress. The differential metabolites were in the order of S-6PPD-Q (216) > rac-6PPD-Q (88) > R-6PPD-Q (56). Thus, 6PPD-Q-induced hepatic mitochondrial dysfunction and ER stress, causing metabolic disturbance and oxidative stress might be the toxic mechanism of 6PPD-Q in O. mykiss liver, and S-6PPD-Q effects were the most serious.